tag:blogger.com,1999:blog-68915330724402192762024-03-05T13:10:57.715-08:00RNA BioinformaticsPaul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.comBlogger22125tag:blogger.com,1999:blog-6891533072440219276.post-54971549733712286352017-07-24T15:04:00.001-07:002017-07-24T15:12:29.186-07:00On the importance of controls, even when the tools are computational<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">NB. this content is reposted from an article I wrote for the <a href="https://nzsbmb.science.org.nz/">NZSBMB</a> "Southern Blot" newsletter. </span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> I thought I’d talk about something else, something I find particularly interesting: Negative Controls</span><a href="https://paperpile.com/c/TIIjLE/8opM" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 6.6pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">4</span></a><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">! I have worked with researchers who proudly talk about how many lanes of their gels are dedicated to their negative controls, and I’m sure all researchers spend a lot of time and effort on developing appropriate negative controls. Which is great. Yet, some researchers when they move from the wet-lab to sitting in front of a computer will forget about running negative controls on their bioinformatic experiments too. I did mention this issue in my talk in the context of our investigation into the interplay behind the speed and accuracy of bioinformatic tools</span><a href="https://paperpile.com/c/TIIjLE/XDwJ" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 6.6pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">3</span></a><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. </span></div>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Negative Controls are a backbone of research, and an important component of the definition of P-values that are frequently used to report the significance of findings </span><a href="https://paperpile.com/c/TIIjLE/byij" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 6.6pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">5</span></a><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (the “null” distribution/hypothesis is of course a form of negative control). </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></div>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">But how many researchers run a negative control when they conduct a homology search (e.g. BLAST), or build a multiple sequence alignment (Clustal, MUSCLE, MAFFT), assemble a genome, map reads to a genome or predict the structure of a biomolecule of interest? </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">What is a reasonable negative control for these tasks? Randomised, reversed or circularly permuted sequences are popular instruments (this requires care too, as randomisation can be surprisingly difficult</span><a href="https://paperpile.com/c/TIIjLE/wuHW" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 6.6pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">6</span></a><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). Biological controls may include approaches like trying to map </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">E. coli </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">reads onto a human genome as a control for a human RNA-seq experiment. There are a myriad number of possible controls, and it can sometimes take a lot of imagination and thought to find good ones. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">These are very worthwhile, as the results of negative controls can be surprisingly informative. They can not only allow us to reject null hypotheses and compute P-values, but can help identify false positives, contamination, biases or even identify unanticipated signals in our data. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b id="docs-internal-guid-1a4cc7f0-7689-ac71-7e41-677d0f226f74" style="font-weight: normal;"><br /></b></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Some bioinformatic tools will try to give an idea of the significance of different results. E-values are a popular measure of significance, these are the expected number of matches of a score as good or better, for a known query and database size. Most variants of BLAST, for example, will report an E-value for each match</span><a href="https://paperpile.com/c/TIIjLE/NGAF" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 6.6pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">7</span></a><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. These E-values are estimated using the following formula: </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 12pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">E = </span><span style="background-color: white; color: #222222; font-family: "arial"; font-size: 12pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Κmn e</span><span style="background-color: white; color: #222222; font-family: "arial"; font-size: 7.199999999999999pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">-λx </span></div>
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<span style="background-color: white; color: #222222; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Where ‘x’ is the alignment bitscore, ‘m’ and ‘n’ are the size of your search database, and ‘Κ’ and ‘λ’ are generic fitting parameters to model the distribution of scores expected between non-homologous sequences. BLAST attains much of it’s speed by using pre-computed values of ‘Κ’ and ‘λ’ for typical selections of search parameters. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b style="font-weight: normal;"><br /></b></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">As widely used as these E-values are, they can be misused and misleading in a number of ways. Two of which I’ll discuss below. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">How many times do we conduct multiple searches in a single experiment? Now, how often do we correct E-values for the multiple searches that we have run? I’ve got to admit, I have never done this. Many of us know about the statistical sin of uncorrected multiple-testing</span><a href="https://paperpile.com/c/TIIjLE/Csbu" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 6.6pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">8</span></a><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, where multiple comparisons may be made but the P-values are computed assuming a single comparison. For example, we may wish to test if there is a correlation between the expression of a particular gene and the expression of other genes. If we use a P-value threshold of 0.05, then 5% of the time we expect to falsely reject the null (i.e. report a significant finding), if we run 10,000 tests assuming each time that a single test is being run (e.g. ‘</span><span style="background-color: transparent; color: black; font-family: "courier new"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">cor.test()</span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">’ in R), then we can expect to report 500 falsely significant results. Since there is a straightforward correspondence between E-values and P-values</span><span style="color: black; font-family: "arial"; font-size: 6.6pt; vertical-align: super; white-space: pre-wrap;"><a href="https://paperpile.com/c/TIIjLE/NGAF" style="text-decoration-line: none;">7</a></span><span style="font-family: "arial"; font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;"> (P = 1-e</span><span style="font-family: "arial"; font-size: 6.6pt; vertical-align: super; white-space: pre-wrap;">-E</span><span style="font-family: "arial"; font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;">)</span><span style="font-family: "arial"; font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;">, then we really should be correcting our E-values as well as our P-values.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">A common practice is to compare the entire proteome of one organism against that of another organism (e.g. </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">E. coli </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">and</span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> Salmonella </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">typhi) or it is more common these days to compare hundreds or thousands of bacterial proteomes at a time. If we’re using E-values to evaluate the significance of results, then a correction of the E- or P-values should be made. Commonly used methods may include Bonferroni or the Benjamini–Hochberg, each of which may provide a better estimate of the true significance of your results. Alternatively, another strategy that may be more informative, yet uses a lot more computational resources, is to run the same queries with randomized sequences and use these results to evaluate the significance of one’s results. The distribution of (bit) scores resulting from these searches will help establish the significance of the “real” matches. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b id="docs-internal-guid-1a4cc7f0-768a-1680-434f-0e574b6d6de4" style="font-weight: normal;"><br /></b></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Another common mistake than can compound errors when working with E-values is to use ‘-log(E)’ values as a summary statistic. This value is used by the popular orthoMCL tool for finding homologous clusters resulting from all-vs-all comparisons of proteomes</span><a href="https://paperpile.com/c/TIIjLE/5LJl+8sSM" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 6.6pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">9,10</span></a><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. Computationally, the all-vs-all comparison is an extremely costly procedure. It is therefore surprising to me that ‘-log(E)’ is used for assessing the relationships between proteins. If you take the ‘-log’ of the above definition of ‘E’ and use a little algebra, you will hopefully see that that ‘-log(E)’ is a conversion back to a bitscore with some other terms that may accentuate, rather than correct problems due to database and query size (i.e. the larger the database or query, the larger a chance bitscore is likely to be). In fact, it was recently shown empirically that ‘-log(E)’ values perform worse than unadulterated bitscores for sequence clustering</span><a href="https://paperpile.com/c/TIIjLE/Dqtz" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 6.6pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">11</span></a><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /><span style="font-size: 11pt; vertical-align: baseline;">In order to illustrate how it is possible to find matches between randomised sequences and large sequence databases I have selected sigma factors from </span><span style="font-size: 11pt; font-style: italic; vertical-align: baseline;">E. coli</span><span style="font-size: 11pt; vertical-align: baseline;"> and used randomised versions of these as queries for the NCBI BLAST and EBI HMMER webservices. Each method reported matches to my queries, the E-values associated with these are not meaningful (due to multiple testing, as described above), therefore I have only reported the bit scores (Figure 1). </span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><b id="docs-internal-guid-1a4cc7f0-768a-6eed-49fc-133e8717e5ad" style="font-weight: normal;"><br /></b></span></span></div>
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<table style="border-collapse: collapse; border: none;"><colgroup><col width="645"></col></colgroup><tbody>
<tr style="height: 0pt;"><td style="border-bottom: solid #000000 1pt; border-left: solid #000000 1pt; border-right: solid #000000 1pt; border-top: solid #000000 1pt; padding: 5pt 5pt 5pt 5pt; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-style: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">BLASTP:</span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">38.0 bits</span></span></div>
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<span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;"><span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Query 301 GEVETSIPRVDVQENNSNNQLRQLLALSLLIELPLDNVQQLGSMPPISYSAFDLGEMNLT </span><span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> G E ++R+D ++ + + L+++ + ++ +++++G++P + ++ L + + </span><span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Sbjct 22 GRAEVMLARLDAGTLDAAQLRKGLVSIREMTRDAIVQLERMGPLPRATEAP--LPAVLVV</span></span></div>
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<span style="background-color: white; color: #222222; font-style: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">PHMMER:</span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">18.5 bits</span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">QUERY yeap.rtvhhq.dqtksdlealesnhlesqtkmsspivgvllldgrtttsvdlategaietkdvqq</span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">MATCH y p r +h q d + d e e+ hl++ + +++v+ +d+rt +v+l+ + +ietkd q </span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">PP 55553678877255589**********8765..56789*************************875</span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">TARGET YATPeRQLHLQtDTDRCDSETSENQHLQNIE--NQAMINVVAIDNRTPQNVNLSKDHSIETKDQQS</span></span></div>
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<span style="background-color: transparent; color: black; font-family: "courier new"; font-style: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: xx-small;">JACKHMMER:</span></span></div>
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<span style="background-color: transparent; color: black; font-family: "courier new"; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><img alt="jackhmmer-logo-iteration4-crop.png" height="158" src="https://lh4.googleusercontent.com/BHiXmBFjfgUOOYIdOnzfZqoRDWxpi1Aut8eVEl_wjfttf4op6iJmID4Kpl7WzHsZTQA5iUtWpu6LxCwwZTHOR8ThIeBQZD73VlAkbqrUButyOBanJ86bZhGqVZ7x6YWIdaE9cn4b" style="border: none; transform: rotate(0rad);" width="640" /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><br /><span style="font-size: 11pt; vertical-align: baseline;"><b>Figure 1: </b>Alignments resulting from homology searches with randomised </span><span style="font-size: 11pt; font-style: italic; font-weight: 400; vertical-align: baseline;">E. coli</span><span style="font-size: 11pt; font-weight: 400; vertical-align: baseline;"> sigma </span><span style="background-color: white; color: #222222; font-size: 11pt; font-weight: 400; vertical-align: baseline;">54 (RpoN) sequences using the NCBI webservice for BLASTP and the “nr” database (April 2017), the EBI webservice for PHMMER (</span><span style="font-size: 11pt; font-weight: 400; vertical-align: baseline;">v3.1b2)</span><span style="background-color: white; color: #222222; font-size: 11pt; font-weight: 400; vertical-align: baseline;"> and the “reference proteome” database, and a fragment of a sequence logo generated after four iterations of the EBI’s JACKHMMER (</span><span style="font-size: 11pt; font-weight: 400; vertical-align: baseline;">v3.1b2)</span><span style="background-color: white; color: #222222; font-size: 11pt; font-weight: 400; vertical-align: baseline;"> webservice. </span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><br /></span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span id="docs-internal-guid-1a4cc7f0-768b-8f40-90d4-3f68e1426c26"><br /><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;">Should I only pick on BLAST and other homology search tools? BLAST is one of the work-horses of bioinformatics, a popular tool for many pipelines, and it’s original description is one of the world’s most cited papers. Unlike homology searches, multiple sequence alignment is almost entirely free of any sort of significance assessment. Therefore we have some reports of terrifying statistics regarding multiple sequence alignment </span><a href="https://paperpile.com/c/TIIjLE/JzHH" style="text-decoration-line: none;"><span style="background-color: transparent; color: black; font-size: 6.6pt; vertical-align: super;">12</span></a><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;">. Bradley </span><span style="background-color: transparent; color: black; font-size: 11pt; font-style: italic; vertical-align: baseline;">et al.</span><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"> conclude from a randomized sequence alignment test that “for most alignment programs, aligned sequences are not necessarily homologous”. In fact, popular alignment tools like ClustalW will align 95 to 97% of randomised (non-homologous) sequences that are given as input. This is worrying as multiple sequence alignment is the first step before many phylogenetic, genomic, evolutionary and structural analyses. Most of the popular tools for this assume that the input sequences are in fact homologous, this can result in superficially robust results that are indistinguishable from randomly generated results (Figure 2). </span></span></span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><b id="docs-internal-guid-1a4cc7f0-768b-c676-36df-21eaa14aafb6" style="font-weight: normal;"><br /></b></span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><img alt="RAxML_bootstrap-T7-consensus.png" height="308" src="https://lh4.googleusercontent.com/Vn_1G1I758C7LDLOyA-lw2JID21k3ZIIvt9-ruomJaiWGRkc_uyeDcqPOk1Cxz_SRUb7OlNM-WbIiqFttBOdIKCgtCk1adtGt46-tY1nhI_dd4zjQw0JJ04vmq4knc1Dw_vzxlnI" style="-webkit-transform: rotate(0.00rad); border: none; transform: rotate(0.00rad);" width="279" /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><br /><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"><b>Figure 2: </b>Randomised sigma factor sequences from </span><span style="background-color: transparent; color: black; font-size: 11pt; font-style: italic; font-weight: 400; vertical-align: baseline;">E. coli</span><span style="background-color: transparent; color: black; font-size: 11pt; font-weight: 400; vertical-align: baseline;"> were clustered using MAFFT (v7.271) alignments and distances from “protdist” (PHYLIP v3.696). A “clade” of sequences was extracted (left) and a phylogenetic tree for these was inferred using RaxML with the “PROTGAMMAWAG” model, 100 bootstrap replicates were used to establish the robustness of tree edges, a consensus tree was built using “consense” from PHYLIP (right). </span></span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"><br /></span></span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">We can run similar experiments and show similar issues with falsely significant findings with all the sequence assembly, read mapping, expression analysis, metagenomics, proteomics and bioinformatic tools we use to analyse bioinformatic data. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"><b id="docs-internal-guid-1a4cc7f0-768c-8aba-a315-3525da330408" style="font-weight: normal;"><br /></b></span></span></span></span></div>
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<span style="background-color: white; color: #222222; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Closing statements</span></div>
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<span style="background-color: white; color: #222222; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">As our ability to generate larger datasets, our databases, and our computational resources continue to grow exponentially, it is a good idea to question the likelihood of results, using genuine and realistic negative controls. This is because, </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">as sequence space grows, the number of false positives increase, meaning that calibrations that worked decades ago are increasingly irrelevant. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"><b style="font-weight: normal;"><br /></b></span></span></span></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: white; color: #222222; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Some of our other assumptions regarding genomics are also worth revisiting. How biologically meaningful are the data from the sequences we assemble, the comparisons we make, the RNA-seq reads, the protein-nucleotide interactions and the myriad other datasets we collect on a daily basis? Sean Eddy proposed a fascinating experiment, the “</span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Random Genome Project”</span><span style="background-color: white; color: #222222; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><a href="https://paperpile.com/c/TIIjLE/WNzd" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 6.6pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: super; white-space: pre-wrap;">13</span></a><span style="background-color: white; color: #222222; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. This project acknowledges that cells are noisy environments, packed full of biomolecules that jostle together, and random, non-functional interactions and events constantly occur. In this context a useful control to have, is a synthetic “random” chromosome that has been inserted into your organism of interest. Then all outputs, RNA, protein and interactions that map to your random chromosome serve the invaluable, yet missing null distribution for genomics projects. I’ve not seen a project that has taken on Sean’s challenge yet, but I’m very much looking forward to seeing the results. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"><b style="font-weight: normal;"><br /></b></span></span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"><b>Note added:</b></span></span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="vertical-align: baseline;"><span style="background-color: white; color: #222222; vertical-align: baseline;"><span style="background-color: transparent; color: black; vertical-align: baseline;"><b style="font-weight: normal;">This paper comes close to the "random genome project" idea:</b></span></span></span></span></div>
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<span style="background-color: transparent; vertical-align: baseline;"><span style="vertical-align: baseline;"><span style="background-color: white; vertical-align: baseline;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: "arial";">Neme et al. (2017) </span></span></span></span></span><span style="background-color: white; color: #222222; font-family: "lora" , "palatino" , "times" , "times new roman" , serif; letter-spacing: 0.17px;"><a href="https://www.nature.com/articles/s41559-017-0127">Random sequences are an abundant source of bioactive RNAs or peptides.</a></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"><b style="font-weight: normal;"><br /></b></span></span></span></span></div>
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<span style="background-color: white; color: #222222; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Acknowledgements </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"><b style="font-weight: normal;"><br /></b></span></span></span></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: white; color: #222222; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Thanks to Bethany Jose and Nicole Wheeler for proofreading the draft and lively research discussions. A huge thanks to the clever, fun and inspiring community of students and collaborators that I get to work with.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"><b style="font-weight: normal;"><br /></b></span></span></span></span></div>
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<span style="background-color: white; color: #222222; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">References </span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">1.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/Q16E" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Gardner, P. Random RNA interactions control protein expression in prokaryotes. (2016). Available at: </span></a><a href="https://www.slideshare.net/ppgardne/random-rna-interactions-control-protein-expression-in-prokaryotes." style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">https://www.slideshare.net/ppgardne/random-rna-interactions-control-protein-expression-in-prokaryotes.</span></a><a href="http://paperpile.com/b/TIIjLE/Q16E" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (Accessed: 2nd April 2017)</span></a></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">2.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/glJt" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Umu, S. U., Poole, A. M., Dobson, R. C. J., Gardner, P. P. & Adelman, K. Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">eLife Sciences</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">5,</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> e13479 (2016).</span></a></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">3.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/XDwJ" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Gardner, P. P. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">et al.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> A meta-analysis of bioinformatics software benchmarks reveals that publication-bias unduly influences software accuracy. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">bioRxiv</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> 092205 (2017). doi:</span></a><a href="http://dx.doi.org/10.1101/092205" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">10.1101/092205</span></a></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">4.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/8opM" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Wikipedia contributors. Scientific control. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Wikipedia, The Free Encyclopedia</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (2017). Available at: </span></a><a href="https://en.wikipedia.org/w/index.php?title=Scientific_control&oldid=768804853." style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">https://en.wikipedia.org/w/index.php?title=Scientific_control&oldid=768804853.</span></a><a href="http://paperpile.com/b/TIIjLE/8opM" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (Accessed: 1st April 2017)</span></a></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">5.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/byij" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Wikipedia contributors. p-value. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Wikipedia, The Free Encyclopedia</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (2017). Available at: </span></a><a href="https://en.wikipedia.org/w/index.php?title=P-value&oldid=771502462." style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">https://en.wikipedia.org/w/index.php?title=P-value&oldid=771502462.</span></a><a href="http://paperpile.com/b/TIIjLE/byij" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (Accessed: 1st April 2017)</span></a></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">6.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/wuHW" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Wikipedia contributors. Fisher–Yates shuffle. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Wikipedia, The Free Encyclopedia</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (2017). Available at: </span></a><a href="https://en.wikipedia.org/w/index.php?title=Fisher%E2%80%93Yates_shuffle&oldid=771535751." style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">https://en.wikipedia.org/w/index.php?title=Fisher%E2%80%93Yates_shuffle&oldid=771535751.</span></a><a href="http://paperpile.com/b/TIIjLE/wuHW" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (Accessed: 1st April 2017)</span></a></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">7.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/NGAF" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The Statistics of Sequence Similarity Scores. Available at: </span></a><a href="https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html." style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html.</span></a><a href="http://paperpile.com/b/TIIjLE/NGAF" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (Accessed: 1st April 2017)</span></a></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">8.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/Csbu" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Wikipedia contributors. Multiple comparisons problem. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Wikipedia, The Free Encyclopedia</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (2017). Available at: </span></a><a href="https://en.wikipedia.org/w/index.php?title=Multiple_comparisons_problem&oldid=770714321." style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">https://en.wikipedia.org/w/index.php?title=Multiple_comparisons_problem&oldid=770714321.</span></a><a href="http://paperpile.com/b/TIIjLE/Csbu" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (Accessed: 1st April 2017)</span></a></div>
<div dir="ltr" style="line-height: 2.4; margin-bottom: 0pt; margin-top: 0pt; padding: 0pt 0pt 0pt 22pt; text-indent: -22pt;">
<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">9.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/5LJl" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Li, L., Stoeckert, C. J., Jr & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Genome Res.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">13,</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> 2178–2189 (2003).</span></a></div>
<div dir="ltr" style="line-height: 2.4; margin-bottom: 0pt; margin-top: 0pt; padding: 0pt 0pt 0pt 22pt; text-indent: -22pt;">
<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">10.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/8sSM" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Enright, A. J., Van Dongen, S. & Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Nucleic Acids Res.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">30,</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> 1575–1584 (2002).</span></a></div>
<div dir="ltr" style="line-height: 2.4; margin-bottom: 0pt; margin-top: 0pt; padding: 0pt 0pt 0pt 22pt; text-indent: -22pt;">
<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">11.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/Dqtz" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Genome Biol.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">16,</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> 157 (2015).</span></a></div>
<div dir="ltr" style="line-height: 2.4; margin-bottom: 0pt; margin-top: 0pt; padding: 0pt 0pt 0pt 22pt; text-indent: -22pt;">
<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">12.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/JzHH" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Bradley, R. K. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">et al.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> Fast statistical alignment. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">PLoS Comput. Biol.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">5,</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> e1000392 (2009).</span></a></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 11pt; vertical-align: baseline;"><span style="background-color: white; color: #222222; font-size: 11pt; vertical-align: baseline;"><span style="background-color: transparent; color: black; font-size: 11pt; vertical-align: baseline;"></span></span></span></span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">13.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/TIIjLE/WNzd" style="text-decoration: none;"><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Eddy, S. R. The ENCODE project: missteps overshadowing a success. </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: italic; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Curr. Biol.</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">23,</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 11pt; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> R259–61 (2013).</span></a></div>
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Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-88528587572775665612015-04-13T19:41:00.001-07:002015-04-13T19:41:29.830-07:00NZ's hottest researchers from 2012-2014.Roughly two years ago I blogged "<a href="http://rnainformation.blogspot.co.nz/2012/08/nzs-hottest-researchers-from-2010-2012.html">NZ's hottest researchers from 2010-2012</a>" (<a href="http://rnainformation.blogspot.co.nz/2012/11/updated-hottest-researcher-figure.html">updated figure</a>), this was a list of NZ-based researchers that had published several papers that had been cited 10 or more times between 2010 and 2012.<br />
<br />
I thought it was about time to update this listing and I had some spare time over the Xmas holidays to work on this (hayfever at my in-law's place in Taranaki laid me out for a day or two). I'm now finishing this up during the Easter holidays. Has anything changed in the past two years? I was also curious to find out which funding agencies were funding these researchers and whether the researchers they published was open access or not.<br />
<br />
<br />
<a name='more'></a>The HRC were very excited about the 2010-2012 results [<a href="http://www.hrc.govt.nz/news-and-media/news/new-zealands-hottest-researchers-revealed">1</a>]. Are they still funding the hottest research in NZ.<br />
<br />
The rules of the game are the same as last time. Briefly, use Scopus "affiliation search" to find articles with a NZ address listed, select only articles published between 2012 and 2014, sort these on the number of citations and remove any with fewer than 10 citations. I then exported the results to a text file and wrote a little script that would remove articles with more than 20 authors, parse author names and count the number of times each name appeared and the total citation count.<br />
<br />
I had to do some manual curation of the data too. <a href="http://www.mang.canterbury.ac.nz/people/hall.shtml">C. Michael Hall</a>, a professor of marketing at University of Canterbury and <a href="https://unidirectory.auckland.ac.nz/profile/c-hall">Christopher J. Hall</a>, a senior research fellow at the University of Auckland were counted as the same person. I only checked the 50 most prolific authors, so some homonyms and other errors may have still slipped through.<br />
<br />
At the same time I identified the host institution of the top 50 authors and I checked the top three most cited articles for each author. If the articles were open-access (OA), I recorded this and I checked the "Acknowledgements" section of the OA articles to see which NZ-based funding agencies were listed.<br />
<br />
All of the results are listed in this GoogleDocs <a href="https://docs.google.com/spreadsheets/d/1hmdYdFLccDBWW4GNKcUV_FN-mT6lFz6_NUmVdxm0wuI/edit?usp=sharing">spreadsheet</a>. There are 288 authors listed, further data is only available for the top 50 authors though. Feel free to play find your and your friend's names on the list. <br />
<br />
In the top 10 researchers were Ian Reid, Christian Hartinger, Michael W. Taylor and John A. Windsor from the University of Auckland; Shinichi Nakagawa, Richard Beasley and Christine Winterbourn from the University of Otago; Edward J Gane and Harvey D White from Auckland City Hospital; and Philip W Boyd from NIWA.<br />
<br />
Once again Ian Reid, professor of medicine and endocrinology,<span style="background-color: white; color: #667788; font-family: proxima-nova, sans-serif; font-size: 15px; line-height: 24px;"> </span>has topped the table. Just beating Christian Hartinger, an associate professor in the School of Chemical Sciences by 32 citations.<br />
<b id="docs-internal-guid-5c3f0922-b597-77a1-c29c-3925b4e170ad" style="font-weight: normal;"><br /></b>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Institution</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">13</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">334</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Ian_Reid</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">UOA</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">13</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">302</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Christian_Hartinger</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">UOA</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">12</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">659</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Edward_J_Gane</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Auckland_City_Hospital</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">11</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">479</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Michael_W_Taylor</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">UOA</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">11</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">379</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Shinichi_Nakagawa</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">UOO</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">11</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">190</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Richard_Beasley</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">UOO/Wellington_Regional_Hospital</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">11</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">145</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Philip_W_Boyd</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">NIWA</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">10</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">260</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Christine_Winterbourn</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">UOO</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">10</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">248</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">John_A_Windsor</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">UOA</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">10</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">232</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Harvey_D_White</span></div>
</td><td style="border-bottom: solid #cccccc 1px; border-left: solid #cccccc 1px; border-right: solid #cccccc 1px; border-top: solid #cccccc 1px; padding: 3px 3px 3px 3px; vertical-align: bottom;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: right;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Auckland_City_Hospital</span></div>
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</tbody></table>
</div>
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How much of this high-profile research is being made available to the public that is largely funding it? I found that 26% of the researchers were exclusively publishing their research behind paywalls (at least the few articles I had time to check). This isn't as bad as I thought it would be. 40% of researchers had published at least some of their research with OA models (possibly because this was required by the funding agencies of co-authors). 32% appeared to publishing all of their research with OA models. I only spotted one researcher, Miro Erkintalo , a physicist at the University of Auckland, using green OA publishing (i.e. depositing preprints in <a href="http://arxiv.org/find/physics/1/au:+Erkintalo_M/0/1/0/all/0/1">arxiv.org</a> or similar). Obviously NZ researchers could do far more to make their research available but the uptake amongst this group is respectable, proving that OA publishing certainly doesn't do your profile any harm.<br />
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What about the funding agencies? Unfortunately I was unable to check who was funding the research that was exclusively published with closed-access models (i.e. locked behind paywalls). For those three articles that I checked for each author in the top 50 I recorded the NZ-based funding agencies listed in the Acknowledgements. Nearly 60% of the authors either listed no funding agencies, or their work was inaccessible. Of the remainder, 13% of authors were funded by the HRC (or collaborating with HRC funded researchers). Likewise, 12% were supported by the Marsden Fund, 7% were supported by Rutherford Discovery Fellowships and 8% were supported by MSI or FRST funding. 10% were supported by other agencies, these were the Otago Research Fund, LactoPharma, NZ Breast Cancer Research Trust, Cancer Society of NZ, NZ Ministry of Health and the National Heart Foundation of NZ. </div>
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It was very pleasing to see so many Rutherford Discovery Fellows in the top 50 of NZ's hottest researchers. This is a comparatively new funding scheme that aims to "attract and retain New Zealand’s most talented early- to mid-career researchers". In a short time it is already, demonstrably, having an impact on the NZ research scene. -- Disclaimer: I was one of the <a href="http://www.royalsociety.org.nz/programmes/funds/rutherford-discovery/awardees/2010-awardees/gardner/">inaugural recipients</a> of the fellowship. </div>
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Now, I'd better get back to grading assignments and think about what I'm going to cook for my little horrors' dinner. </div>
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<br />Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-65922980423034507702014-08-22T03:37:00.004-07:002014-08-22T03:41:18.085-07:00A response to the New Zealand Government's National Statement of Science Investment from the Rutherford Discovery FellowsThe New Zealand Government recently requested feedback on their "<a href="http://www.msi.govt.nz/update-me/major-projects/national-statement-of-science-investment/">National Statement of Science Investment</a>". New Zealand is a wonderful place to live and work. However, research and development in this country is chronically underfunded (e.g. <a href="http://www.sciencemag.org/content/342/6160/817.long">What's So Special About Science (And How Much Should We Spend on It?)</a>. Consequently, our response is fairly predictable. Feel free to read it on <a href="http://dx.doi.org/10.6084/m9.figshare.1148891">figshare</a>.<br />
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Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-83626811555029551062014-04-16T16:18:00.001-07:002014-04-16T16:18:38.280-07:00Opening up research proposalsI'm involved with a submission to the Knight News Challenge called "<a href="https://www.newschallenge.org/challenge/2014/submissions/opening-up-research-proposals">opening up research proposals</a>". The basic idea is to make more funding applications publicly accessible. In the hope that this will increase collaboration, <a href="http://www.nature.com/nature/journal/v493/n7434/full/493599a.html">reduce unethical application recycling</a> and generally make the world a happier and more productive place.<br />
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I think I have to practise what I'm preaching. Therefore I have made my Rutherford Discovery Fellowship Application available via <a href="http://figshare.com/articles/Bioinformatic_approaches_to_functionally_characterise_RNAs/1000785">figshare</a>.<br />
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<br />Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-22426449485102104382014-04-16T15:12:00.000-07:002014-04-16T18:28:50.087-07:00Ten suggestions for selecting a research topic<span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%; orphans: 0; widows: 0;">Paul
P. Gardner</span><sup style="font-family: Arial, Helvetica, sans-serif; line-height: 115%; orphans: 0; widows: 0;">1</sup><span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%; orphans: 0; widows: 0;"> and Venkateswarlu Pulakanam</span><sup style="font-family: Arial, Helvetica, sans-serif; line-height: 115%; orphans: 0; widows: 0;">2</sup><br />
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; orphans: 0; widows: 0;">
<span style="color: black;"><span style="font-family: Arial, Helvetica, sans-serif;"><sup><br /></sup></span></span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; orphans: 0; widows: 0;">
<span style="color: black;"><span style="font-family: Arial, Helvetica, sans-serif;">1.
Biomolecular Interactions Centre and School of Biological Sciences,
University of Canterbury, Christchurch, New Zealand</span></span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; orphans: 0; widows: 0;">
<span style="color: black;"><span style="font-family: Arial, Helvetica, sans-serif;">2.
College of Business and Law, University of Canterbury, Christchurch,
New Zealand</span></span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; orphans: 0; widows: 0;">
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<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; orphans: 0; widows: 0;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;">Selecting
a research project is one of the most important decisions researchers<span style="color: red;">
</span>at any stage of their career<span style="color: red;"> </span>can
make <span style="color: navy;"><span lang="en-US"><u><a href="https://paperpile.com/c/vztpAP/Qqhw">[1]</a><a href="https://paperpile.com/c/vztpAP/ebGY">[2]</a><a href="https://paperpile.com/c/vztpAP/OmBU">[3]</a></u></span></span>.
This is of particular importance for early-career academics. An early
selection of the wrong project can have a negative impact on later
career options. We believe it is very important to invest time
mulling over which of the infinitude of projects we can investigate.
In the following we present a number of ideas that will mitigate the
risk of failure before embarking on a project. We target our
suggestions for younger scientists, however, more experienced
researchers may also benefit from these ideas. We hope that this will
further your career goals, rather than sap your will to live. </span>
</span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; orphans: 0; widows: 0;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;">The
project management literature contains a number of useful tools for
identifying good projects. Tools
like <a href="http://en.wikipedia.org/wiki/SMART_criteria">
SMART criteria
</a>
<a href="https://paperpile.com/c/vztpAP/C7AV">[4]</a>
for identifying sensible objectives and <a href="http://en.wikipedia.org/wiki/SWOT_analysis">SWOT
analyses</a>
<a href="https://paperpile.com/c/vztpAP/Qbtp">[5]</a>
for selecting good projects are handy additions to include in your
strategic approach to research. </span>
</span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; orphans: 0; widows: 0;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;"><span style="color: red;"> </span>We
have identified 10 key tools that we believe are of particular
benefit to early-career scientists. </span>
</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;"></span></span><br />
<a name='more'></a><span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;"><br /></span></span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; margin-left: 0.64cm; orphans: 0; widows: 0;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;"><span style="font-size: small;">1. </span><span style="font-size: small;"><b>What
are your research and career objectives and goals?</b></span><span style="color: green;"><span style="font-size: small;"><b>
</b></span></span><span style="font-size: small;">Ask yourself, where you want to be
five or ten years from now? E.g. Marketing, Consultancy, Government,
Education, Research, … Try to be pragmatic and strategic about your
goals. Then identify institutions, supervisors, collaborators and
projects that are a good fit between your abilities and goals. </span></span>
</span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; margin-left: 0.64cm; orphans: 0; widows: 0;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;"><span style="font-size: small;">2. </span><span style="font-size: small;"><b>Brainstorm
to find ideas, questions and hypotheses. </b></span>Identify where
your ideas come from e.g. <span style="font-size: small;">literature, conferences,
seminars, discussions with colleagues, at the gym, in the shower or
on a mountainside. Use these areas and activities wisely to gain a
good mix of exciting and realistic research questions. There is some
wonderful research being performed on the origins of good ideas that
is worth exploring e.g. </span><span style="color: navy;"><span lang="en-US"><u><a href="https://paperpile.com/c/vztpAP/a1Qh"><span style="font-size: small;">[6]</span></a></u></span></span><span style="font-size: small;">.
</span></span>
</span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; margin-left: 0.64cm; orphans: 0; widows: 0;">
<span style="color: black;"><span style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: small;">3. </span><span style="font-size: small;"><b>Is
it a worthwhile research project?</b></span><span style="font-size: small;"> Is it the
‘right research’? Will it lead to other research? Is this of
interest to you? Are you competent or will you need further training?
Is someone you can collaborate with competent?</span>
Is it SMART <span style="color: navy;"><span lang="en-US"><u><a href="https://paperpile.com/c/vztpAP/C7AV">[4]</a></u></span></span>?</span></span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; margin-left: 0.64cm; orphans: 0; widows: 0;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;"><span style="font-size: small;">4. </span><span style="font-size: small;"><b>Undertake
a preliminary assessment of your research topic.</b></span><span style="font-size: small;">
Read general background information. Is this a novel area or merely a
minor extension of existing research? If possible,</span>
<span style="font-size: small;">run a preliminary analysis. Is the problem
solvable? Try to work in an agile fashion </span><span style="color: navy;"><span lang="en-US"><u><a href="https://paperpile.com/c/vztpAP/gz0S"><span style="font-size: small;">[7]</span></a></u></span></span><span style="font-size: small;">.
Successful research groups don’t necessarily have better ideas,
they test more ideas in a shorter amount of time. Quickly test
hypotheses on small (public) datasets. If there is no support for
your idea then it is probably not worth pursuing (except as an
under-published negative result). If there is support, then develop
more stringent tests and independent datasets. Take any opportunities
to discuss your project with your peers, collaborators, supervisors.
Act on their feedback and criticisms. </span></span>
</span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; margin-left: 0.64cm; orphans: 0; widows: 0;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;"><span style="font-size: small;">5. </span><span style="font-size: small;"><b>Narrow
your topic to a manageable size.</b></span><span style="font-size: small;"> Can you
define your topic as a focused research question? What are the
essential elements that require testing? What are the non-essential
or nice-to-have elements? </span></span>
</span></div>
<div lang="en-US" style="line-height: 115%; margin-bottom: 0cm; margin-left: 0.64cm; orphans: 0; widows: 0;">
<span style="color: black;"><span style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: small;">6. </span><span style="font-size: small;"><b>Be
open, flexible and opportunistic.</b></span><span style="font-size: small;"> You may
need to modify your project during the research process. Science is a
non-linear process. We </span><span style="color: #00000a;"><span style="font-size: small;">endeavour</span></span><span style="font-size: small;">
to circle around a hypothesis, testing from multiple angles and
perspectives. Try to collaborate as much as possible. We all have
different talents and perspectives. By collaborating we can test more
and identify solutions faster. Take the opportunity to talk over
ideas with your colleagues. We find that giving seminars presenting
preliminary results can be particularly helpful. This forces you to
collate and present your results, which the audience can give you
valuable pre-submission feedback on.</span></span></span></div>
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<span style="color: black;"><span style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: small;">7. </span><span style="font-size: small;"><b>Research
and read more about your topic. </b></span><span style="font-size: small;">Most PhD
programs require a detailed literature review. The literature review
process is an invaluable skill. It allows you to read widely and
deeply,</span><span style="color: red;"><span style="font-size: small;"> </span></span><span style="font-size: small;">increasing
your familiarity with your chosen subject area. This time will help
you formulate a research question and strategy as well as hone your
writing and presentation skills </span><span style="color: navy;"><span lang="en-US"><u><a href="https://paperpile.com/c/vztpAP/s5wb"><span style="font-size: small;">[8]</span></a></u></span></span><span style="font-size: small;">.</span></span></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;"><span style="font-size: small;">8. </span><span style="font-size: small;"><b>Formulate
a thesis statement. </b></span><span style="font-size: small;">What will the title of
your thesis be? Can you write a short abstract about it? Is this a
well-defined thesis statement? This will help define the boundaries
of your project and focus your attention on the important areas. </span></span>
</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: black;"><span style="font-size: small;">9. </span><span style="font-size: small;"><b>Keep
a positive attitude.</b></span><span style="font-size: small;"> In research you should
hope for the best, but plan for the worst. It is very rare that a
research project</span><span style="color: red;"><span style="font-size: small;"> </span></span><span style="font-size: small;">is
completely trouble-free. Try to run a risk analysis. Endeavor to be
optimistic and enthusiastic about your work. If you aren’t then it
is unlikely that your peers and collaborators will be. </span></span>
</span></div>
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<span style="color: black;"><span style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: small;">10.
</span><span style="font-size: small;"><b>Keep a portfolio of project ideas. </b></span><span style="font-size: small;">You
never know when you will need a new research project. A new student
joins your group or you need to write a research grant. A portfolio
will provide a helpful reminder of those brilliant 3 am ideas. If
possible try to annotate your projects as either low-risk and a small-contributions to current knowledge (a.k.a. “oysters” or “bread
and butter”) or as high-risk and the potential to be major-contributions to your field (a.k.a. “pearls” or “jam and
cream”). Allocate</span><span style="color: red;"><span style="font-size: small;"> </span></span><span style="font-size: small;">your
research-time wisely. Something like an 80-85% time allotment for
low-risk projects and 15-20% for high-risk projects will mitigate
your risks of failure. Regularly consult colleagues with “black
hat” or “referee three” skills and present your work to them.
Let them expose the most significant flaws in your work and respond
as best you can.</span></span></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></div>
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References</span></h2>
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<br />
<div dir="ltr" style="line-height: 1; margin-bottom: 11pt; margin-left: 22pt; margin-top: 11pt; text-indent: -22pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">1. <span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/vztpAP/Qqhw" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Alter S, Dennis A (2002) Selecting Research Topics: Personal experiences and speculations for the future. Communications of the AIS. Available: </span></a><a href="http://www.researchgate.net/publication/228883408_Selecting_Research_Topics_Personal_experiences_and_speculations_for_the_future/file/72e7e524ad2b630968.pdf" style="text-decoration: none;"><span style="background-color: transparent; color: #000099; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://www.researchgate.net/publication/228883408_Selecting_Research_Topics_Personal_experiences_and_speculations_for_the_future/file/72e7e524ad2b630968.pdf</span></a><a href="http://paperpile.com/b/vztpAP/Qqhw" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">.</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></div>
<div dir="ltr" style="line-height: 1; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">2. <span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/vztpAP/ebGY" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Bhatti JA, Akhtar U, Raza SA, Ejaz K (2012) Selecting a research topic. J Pak Med Assoc 62: 184–186.</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></div>
<div dir="ltr" style="line-height: 1; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">3. <span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/vztpAP/OmBU" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Lubbe S (2004) From PostGrad to Professional: Useful tips for choosing and executing a doctoral thesis. Electronic Journal of Business Research Methods.</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></div>
<div dir="ltr" style="line-height: 1; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">4. <span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/vztpAP/C7AV" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Meyer PJ (2003) Attitude Is Everything: If You Want to Succeed Above and Beyond. Paul J. Meyer Resources. Available: </span></a><a href="http://books.google.co.nz/books/about/Attitude_Is_Everything.html?hl=&id=C2V0OwAACAAJ" style="text-decoration: none;"><span style="background-color: transparent; color: #000099; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://books.google.co.nz/books/about/Attitude_Is_Everything.html?hl=&id=C2V0OwAACAAJ</span></a><a href="http://paperpile.com/b/vztpAP/C7AV" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">.</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></div>
<div dir="ltr" style="line-height: 1; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">5. <span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/vztpAP/Qbtp" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Humphrey A (2005) SWOT analysis for management consulting. SRI Alumni Newsletter (SRI International).</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></div>
<div dir="ltr" style="line-height: 1; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">6. <span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/vztpAP/a1Qh" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Björk J, Magnusson M (2009) Where Do Good Innovation Ideas Come From? Exploring the Influence of Network Connectivity on Innovation Idea Quality. Journal of Product Innovation Management 26: 662–670.</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></div>
<div dir="ltr" style="line-height: 1; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">7. <span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/vztpAP/gz0S" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Beck K, Beedle M, Van A, Cockburn A (2001) Manifesto for agile software development. Available: </span></a><a href="http://academic.brooklyn.cuny.edu/cis/sfleisher/Chapter_03_sim.pdf" style="text-decoration: none;"><span style="background-color: transparent; color: #000099; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://academic.brooklyn.cuny.edu/cis/sfleisher/Chapter_03_sim.pdf</span></a><a href="http://paperpile.com/b/vztpAP/gz0S" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">.</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></div>
<span id="docs-internal-guid-2c15a3a8-6c97-a725-01b1-e106d0edbe13"></span><br />
<div dir="ltr" style="line-height: 1; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">8. <span class="Apple-tab-span" style="white-space: pre;"> </span></span><a href="http://paperpile.com/b/vztpAP/s5wb" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Hart C (1998) Doing a Literature Review: Releasing the Social Science Research Imagination. SAGE Publications. Available: </span></a><a href="http://books.google.co.nz/books?id=tc8LS6qa_KIC" style="text-decoration: none;"><span style="background-color: transparent; color: #000099; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://books.google.co.nz/books?id=tc8LS6qa_KIC</span></a><a href="http://paperpile.com/b/vztpAP/s5wb" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">.</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></div>
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Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-1106162717783112042013-05-30T17:59:00.000-07:002013-05-30T21:57:12.944-07:00Which country is the best at converting research spending into Nobel Prizes? The short answer is "probably Switzerland".<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsK2jlbtDGevJsb5w9-qC5Ls23MEQg7Wmol4yZwY0lnAlGhNfhV7sQVXbr_rW6-n2Ymrkh57PsdTQOEmlrFCoGtg7XH3pqspWbMGCOibsDT6-h0JeG26lVmgcCB-5viQ5k7CCu_JOjuEGz/s1600/nobelsPerDollar.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsK2jlbtDGevJsb5w9-qC5Ls23MEQg7Wmol4yZwY0lnAlGhNfhV7sQVXbr_rW6-n2Ymrkh57PsdTQOEmlrFCoGtg7XH3pqspWbMGCOibsDT6-h0JeG26lVmgcCB-5viQ5k7CCu_JOjuEGz/s400/nobelsPerDollar.png" width="400" /></a></div>
First, some background. Before I moved back to NZ from the UK, I became very curious about how NZ was performing internationally on the research front. I have put together several different measures of research productivity and have extracted data on research spending from OECD datasets. This was one of the more interesting results, IMHO.<br />
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Now, NZ has produced a total of 3 Nobel Prize winners. Ernest Rutherford, Maurice Wilkins and Alan MacDiarmid (<a href="http://en.wikipedia.org/wiki/List_of_Nobel_laureates_by_country">http://en.wikipedia.org/wiki/List_of_Nobel_laureates_by_country</a>), each of whom NZ educated and then shipped off to either the UK or US where they performed their magnificent research. Therefore I split the Nobel Prize counts into "employing country" and raw totals from the Wikipedia entry.<br />
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Hungary, UK, Switzerland, NZ and Denmark are very efficient countries in terms of producing Nobel Prize winners.<br />
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Switzerland, UK, Denmark, Hungary and the Netherlands are very efficient at employing and investing in Nobel Prize winning research. These countries have been doing something right!<br />
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Wouldn't it be nice if one day a NZer was awarded a Nobel for research they actually conducted in NZ?<br />
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Raw data and higher quality images are available here:<br />
<a href="https://github.com/ppgardne/misc-projects/tree/master/research_performance">https://github.com/ppgardne/misc-projects/tree/master/research_performance</a><br />
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<br />Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-27698796246874415612013-04-03T18:06:00.005-07:002013-04-03T18:06:45.831-07:00A PhD position is available in my group! I have one exciting opportunity for a lucky applicant. If you're interested in RNA, Bioinformatics and living in our little village on the underside of the planet then please follow the instructions in my <a href="http://www.biol.canterbury.ac.nz/phd-opportunity-bioinformatics.shtml">advertisement</a>.<br />
<br />Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-45261082648949393392013-01-20T17:23:00.000-08:002013-01-20T18:07:29.900-08:00Kiwis, what will you die from? Sometimes exciting results come from chance interactions. Twitter, The Facebook, Blogs and even the occasional Conference and ensuing <a href="http://en.wikipedia.org/wiki/Real_life">IRL</a> discussions appear to be accelerating research and certainly the discussion of research. For example, <a href="http://sciblogs.co.nz/infectious-thoughts/">Siousxie Wiles</a> and I have discussed the "<a href="http://www.thegreatnzscienceproject.co.nz/fighting-disease">Fighting Disease</a>" component of The Great NZ Science Project in multiple forums. We were both frustrated by the lack of real-data that claims have been based upon, in the associated website and Facebook groups. Then at the annual <a href="http://www.nzms2012.org.nz/">NZ Microbial Society Meeting</a> we decided to do something about it.<br />
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It turns out that mortality data for NZers in 2009 is freely accessible from <a href="http://www.health.govt.nz/publication/mortality-and-demographic-data-2009">Statistics NZ</a>. There is a useful ontology, classifying the causes of each 2009 death. We can parse snippets of information from this data and use it to ask questions. Initially we wanted to know, "What is killing New Zealanders?".<br />
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<a href="http://www.adzebill.com/">Dr Mike Dickison</a> has subsequently generated a gorgeous <a href="http://www.numberpix.com/how-to-show-how-we-die/">graphic</a> illustrating the leading causes of Kiwi deaths. Siousxie has now <a href="http://sciblogs.co.nz/infectious-thoughts/2013/01/18/what-do-kiwis-die-of/">blogged</a> about the result and compared it to the result of a quick online survey she conducted.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhFHJZ9PsZFAGRHfqlVmzOJWNZOsZjiHObemf5kmxWhw2J0pT-Mqi145STgc6QuhalluinSW9wcKjSorlsxVRo-5rb669vB89Yw8bdDP3xbZbRMBzBnA25TAO6vxn-IXeY7O7nX6nvhzrbv/s320/Final%C2%B7v1%C2%B7NZDI1.png" style="margin-left: auto; margin-right: auto;" width="195" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="http://www.numberpix.com/how-to-show-how-we-die/">http://www.numberpix.com/how-to-show-how-we-die/</a></td></tr>
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This is great. Mike's graphic now tells us that Circulatory Disease and Cancer are our biggest killers. Now we have a tonne of other questions to address.<br />
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<li>What are the main contributors to these killers? </li>
<li>Is prevention really better than cure? </li>
<li>How well does my sedentary lifestyle predict my risk of any of these diseases? What if I take up smoking and drinking?</li>
<li>If obesity & lack of exercise predicts circulatory disease &/or disease, and traffic accident deaths are comparatively low, then should I drop the kids of at kindergarten on my bike instead of by car?</li>
<li>Cause of Death is a very clear metric, but are there better ones? E.g. dollars spent, hospital visits, ...</li>
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Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-45164225799075399972012-11-29T16:22:00.000-08:002012-11-29T16:22:10.432-08:00Evolving an NZ home into a European one<div class="separator" style="clear: both; text-align: left;">
I've been meaning to share this for ages. </div>
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I recently bought a house in New Zealand after living in Europe for nearly a decade. This caused a slight shock to my system. European homes are warm, New Zealand homes are not. My house is a fairly typical 1950s bungalow, it had no insulation in the ceiling, walls or underfloor, no double glazing and no central heating. There is a heatpump attached to the wall but without insulation one is trying to warm the environment as well as ones house when it is on. Since I'm a miser, this makes me mad. So I've tried to do something about this. </div>
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Consequently, we added insulation to the ceiling (<a href="http://www.terralana.co.nz/">Terra Lana</a>), underfloor (<a href="http://autexindustries.com/nz/">Autex</a>) and a moisture vapour barrier was laid on the ground under the house. A week later the single-glazed windows in the house were removed and replaced with double-glazed windows by <a href="http://www.thermoglaz.co.nz/">Thermoglaz</a>. Their method allowed us to retain the character of the original wooden frames. The timing also allowed me to collect temperature recordings in our house as uninsulated, insulated and insulated+double-glazing. We also changed the way we used the heat-pump this last winter (2012). We now leave the door open from the living room and the heatpump on low over night. So, I included some of this data too. </div>
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The data plotted here was collected in my bedroom using a "weather forecast multi-channel in-out thermometer with cable free sensor and radio controlled clock" (model TTN302). The data was chiefly gathered over the winter of 2011 in Christchurch, NZ. </div>
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As you can see, insulating the house made a significant improvement to the internal room temperatures. Prior to adding insulation I had been putting my children to bed in a room that was 5<b style="background-color: white; font-family: sans-serif; font-size: 13px; line-height: 19px;">°</b>C or less. Roughly the same temperature as your refrigerator! No wonder illnesses are so prevalent in NZ. The insulated house temperature improved markedly, but still only by +3<b style="background-color: white; font-family: sans-serif; font-size: 13px; line-height: 19px;">°</b>C or so.<br />
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Flushed with this success we hoped that double-glazing all of our windows would make a similar improvement. Unfortunately, double-glazing our house made no apparent difference. Since the cost of double-glazing is more than twice as much as insulation, this was a bit irritating (says the miser in me). Double-glazing did appear to reduce the amount of condensation inside -- but I haven't been measuring that -- also, I've been running a dehumidifier which has probably helped too. Next time I think we'll just buy some very good drapes and a dehumidifier instead of double-glazing, saving a huge amount of money.<br />
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Finally, changing our heatpump behaviour made a major improvement too. While our bedrooms were rarely at an ideal room-temperature of 20<b style="background-color: white; font-family: sans-serif; font-size: 13px; line-height: 19px;">°</b>C they were vastly more comfortable than when we first took over the property. </div>
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I hope these notes will help inform other home improvers, saving a lot of money and increasing the health of NZ families. </div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgt__oQWA-cHXEuSbK_ubRxEXjTOOc3YEv0HcWnL6x_DQlN6X-WEOzhrN_oh1wEaUf4_cwhpbh0vX9IApuzYK2XlPBs6gXWzTXZ52lEaPlLdMDVQ2PhT8g_bahFfJ2IvngLqf0mO7bDVlko/s1600/roomTemperatures.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="576" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgt__oQWA-cHXEuSbK_ubRxEXjTOOc3YEv0HcWnL6x_DQlN6X-WEOzhrN_oh1wEaUf4_cwhpbh0vX9IApuzYK2XlPBs6gXWzTXZ52lEaPlLdMDVQ2PhT8g_bahFfJ2IvngLqf0mO7bDVlko/s640/roomTemperatures.png" width="640" /></a></div>
<br />Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com3tag:blogger.com,1999:blog-6891533072440219276.post-82678597330390536192012-11-28T18:35:00.000-08:002012-11-28T18:35:17.844-08:00Updated hottest researcher figure<div class="separator" style="clear: both; text-align: center;">
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I realise the previous version of this figure was not the prettiest thing to look at. I was divorced from the internet in my Dunedin hotel room last night, so I dedicated a bit of time to making it look more palatable. Enjoy!</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSzvYD-8kxbVvYkiHsyrprAKTr3SiWEeyWqnnFceAyn027K07G8ALCwJYkOVjzlDD8kHyq33KH6jL9ykEEyLT0RpeLL89piHqa6j6bz-Q-8P5uJf8OTMf_8FeNFSiibJem5RWQjVOQBAIs/s1600/nz_most_cited_articles_2010-2012-4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="392" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSzvYD-8kxbVvYkiHsyrprAKTr3SiWEeyWqnnFceAyn027K07G8ALCwJYkOVjzlDD8kHyq33KH6jL9ykEEyLT0RpeLL89piHqa6j6bz-Q-8P5uJf8OTMf_8FeNFSiibJem5RWQjVOQBAIs/s400/nz_most_cited_articles_2010-2012-4.png" width="400" /></a></div>
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Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-11198348793960113792012-10-22T19:52:00.002-07:002012-10-22T20:01:19.143-07:00Is Open Access for Free Too Much to Ask?<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><br /></span>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><span style="color: #555555;"><span style="line-height: 21px;">Google is now the </span></span><a href="http://www.creativecommons.org.nz/2012/10/is-open-access-for-free-too-much-to-ask/www.telegraph.co.uk/finance/newsbysector/mediatechnologyandtelecoms/digital-media/9580422/Google-passes-Microsoft-to-become-second-richest-tech-firm-behind-Apple.html" style="background-color: transparent; border: 0px; color: #c63f00; line-height: 21px; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">second most valuable IT company</a><span style="color: #555555;"><span style="line-height: 21px;">. They made the bulk of their fortune by providing fast and accurate internet searches for </span></span><b style="color: #555555; line-height: 21px;">free</b><span style="color: #555555;"><span style="line-height: 21px;"> and are funded almost entirely by advertising. If you had told me this would happen a decade or two ago I would’ve thought it was ludicrous! Similarly, the </span></span><a href="http://www.alexa.com/siteinfo/wikipedia.org" style="background-color: transparent; border: 0px; color: #c63f00; line-height: 21px; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">6th most visited website on the internet</a><span style="color: #555555;"><span style="line-height: 21px;"> is an encyclopedia, called Wikipedia. Wikipedia is written </span></span><span style="color: #555555; line-height: 21px;">entirely by amateurs and volunteers and is funded entirely by donations. This would have also seemed </span><span style="color: #555555; line-height: 21px;">crazy a decade ago. Wikipedia is supported by a non-profit organisation called the Wikimedia Foundation </span><span style="color: #555555; line-height: 21px;">that employs just 50 people.</span></span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><span style="color: #555555;"><span style="line-height: 21px;">Yet this </span></span><b style="color: #555555; line-height: 21px;">IS</b><span style="color: #555555;"><span style="line-height: 21px;"> the world we live in. Google and the Wikimedia Foundation are remarkably successful and influential businesses. They show that unusual business models can be remarkably successful. However, the major academic publishing houses have languished. Large publishing houses continue to lock vital medical, basic science and engineering literature behind paywalls. </span></span><a href="http://www.biomedcentral.com/about/apccomparison/" style="background-color: transparent; border: 0px; color: #c63f00; line-height: 21px; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">A few, major publishers</a><span style="color: #555555;"><span style="line-height: 21px;"> provide a variety of </span></span><span style="color: #555555; line-height: 21px;">author-pays open access (OA) models. The costs of which range from $300 to $5000 USD, even with a strong NZ dollar, the average cost is equivalent to a few Summer Scholarships (to test wild research ideas), a new computer or 60GB of next-gen sequencing data, at current costs (this is roughly 20 human genomes-worth of sequence data).</span><span style="color: #555555; line-height: 21px;"> </span><a href="http://www.landesbioscience.com/journals/rnabiology/guidelines/" style="background-color: transparent; border: 0px; color: #c63f00; line-height: 21px; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">Some, rare, publishers</a><span style="color: #555555; line-height: 21px;"> </span><span style="color: #555555; line-height: 21px;">make all their articles open access (with the author’s permission) after 1-2 years.</span></span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><span style="color: #555555;"><span style="line-height: 21px;">A few new publishing models have been proposed. One of particular interest is the child of major German, </span></span><span style="color: #555555;"><span style="line-height: 21px;">UK and US funding agencies. These are The Max Planck Society (a publicly funded NGO named after </span></span><span style="color: #555555;"><span style="line-height: 21px;">theoretical physicist, Max Planck), The Wellcome Trust (founded by pharmaceutical magnate, Sir Henry </span></span><span style="color: #555555;"><span style="line-height: 21px;">Wellcome in 1936) and The Howard Hughes Medical Institute (founded by businessman, Howard Hughes in </span></span><span style="color: #555555;"><span style="line-height: 21px;">1953). One can only assume that these charities have become tired of their donations being used to line the </span></span><span style="color: #555555; line-height: 21px;">pockets of publishers. Therefore, in a cost cutting exercise, they have launched their own journal, <a href="http://www.elifesciences.org/the-journal/publishing-fees/">eLife</a>. A </span><span style="color: #555555; line-height: 21px;">new open access journal, that initially is experimenting with free OA publishing. The first edition of the journal was</span><span style="color: #555555; line-height: 21px;"> </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467772/" style="background-color: transparent; border: 0px; color: #c63f00; line-height: 21px; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">released this week</a><span style="color: #555555; line-height: 21px;">!</span></span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Other models include a hybrid of traditional publishing and preprint archiving pioneered by <a href="https://peerj.com/" style="background-color: transparent; border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">PeerJ</a>, with a very reasonably priced Lifetime Subscription model. While on the subject of preprints, there is also the free (physics) preprint archive epitomised by<a href="http://arxiv.org/" style="background-color: transparent; border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank"> arXiv.org</a>. I’ve recently converted to using <a href="http://arxiv.org/" style="background-color: transparent; border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">arXiv.org</a> and have been very impressed by the near instantaneous indexing by<a href="http://scholar.google.co.nz/citations?hl=en&user=yag55pAAAAAJ&view_op=list_works&pagesize=100" style="background-color: transparent; border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank"> GoogleScholar</a>. Also, arXiv.org is ranked very well by <a href="http://scholar.google.com/citations?view_op=top_venues" style="background-color: transparent; border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">GoogleScholar’s H5-index</a>. This appears to be a great option for freeing your research, if your field is eligible (thank you qBIO).</span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">As a follower of Impact Factors and other (better) measures of journal quality I’m not a fan of new journals. Personally I think there are already too many journals. However, the eLife model is so novel and has the backing three of the most powerful funding agencies in the world, therefore they may have the traction to build a successful new journal.</span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">So, what about the other publishing groups? What fees do they charge for OA? Are any providing good value for money? To investigate this I have obtained OA fee ranges from a probably biased <a href="http://www.biomedcentral.com/about/apccomparison/">table</a> prepared by BMC. Then for each of these publishers I have used the ISI Web of Science(TM) database to look up the range of impact factors for each publisher’s top 5 journals. See figure 1 for a visualisation of this data.</span><br />
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<tr><td class="tr-caption" style="text-align: center;"><span style="background-color: rgba(255, 255, 255, 0.699219); color: #555555; font-family: Arial, Helvetica, sans-serif; font-size: 11px; line-height: 22px;">Figure 1: The figure on the left shows the range of OA costs charged by each publishing house. The fi gure on the right shows the Impact Factor range for each publishing house’s top 5 journals.</span></td></tr>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Then I became curious: Which publishers are providing the best OA deals in terms of dollars per impact factor point? (figure 2). Ignoring eLife for now, Wiley-Blackwell (W-B) may be charging $18.18USD/IF if one can really publish in the insanely high-impact (101.78) journal, “<a href="http://www.creativecommons.org.nz/2012/10/is-open-access-for-free-too-much-to-ask/onlinelibrary.wiley.com/journal/10.3322/(ISSN)1542-4863" style="border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">CA: A Cancer Journal for Clinicians</a>” for $1850USD. However, <a href="http://onlinelibrary.wiley.com/journal/10.3322/%28ISSN%291542-4863/homepage/FundedAccess.html" style="border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">checking the guidelines</a> for this journal, I found that the only OA option costs $3000USD. This drops W-B to 5th place. Next is the American Chemical Society (ACS), with a potential charge of $24.88USD/IF if one can publish in Chemical Reviews (IF:40.197) for $1000USD. This option is <a href="http://pubs.acs.org/page/policy/authorchoice/index.html" style="border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">available to ACS Members and Affliated Subscribers</a>. Dues are $148.00 per year. This is surprisingly reasonable deal for a publisher with a history of a <a href="http://en.wikipedia.org/w/index.php?title=American_Chemical_Society&oldid=510751997#Stance_against_open_access" style="border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">strong anti-OA stance</a>.</span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFafcr8NrOkNLnvBHcIflCSCosTgLk8k5fexXcFg8GPhXoVGINywQZo8t0BkbShaCeslxSyvfg7OUt_4IeO4EUxZTs5ZCF8GkrwuY38Jy2_0V44EBJpZf1o8EfYSjxzyFLPt1zcJZy3jpU/s1600/dollar_per_IF.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="304" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFafcr8NrOkNLnvBHcIflCSCosTgLk8k5fexXcFg8GPhXoVGINywQZo8t0BkbShaCeslxSyvfg7OUt_4IeO4EUxZTs5ZCF8GkrwuY38Jy2_0V44EBJpZf1o8EfYSjxzyFLPt1zcJZy3jpU/s320/dollar_per_IF.png" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="background-color: rgba(255, 255, 255, 0.699219); color: #555555; font-family: Arial, Helvetica, sans-serif; font-size: 11px; line-height: 22px;">Figure 2: This figure shows the potential range of cost/IF-point for each publisher’s top 5 journals.</span></td></tr>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><span style="color: #555555;"><span style="line-height: 21px;">Now, the other end of the spectrum. Who is providing the worst deal? This is a difficult question to answer: almost all the publishers support journals with impact factors near zero that charge for OA. Consequently, any monetary value divided by a small IF results in a large value. However, let’s look at the worst deals in the data I have. The list is topped by America’s National Academy of Science (which only publishes 3 journals indexed by ISI). “Transportation Research Record” (IF:0.471), as far as I can tell from </span></span><a href="http://www.trb.org/Publications/PubsTRRJournalOnline.aspx#copyrightrules" style="background-color: transparent; border: 0px; color: #c63f00; line-height: 21px; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">their website</a><span style="color: #555555;"><span style="line-height: 21px;">, has no open access policy at all. That is no OA deal at all. Next down the list is “mBio” (IF:5.3) which, according to BMC’s table, may be charging $3285USD for OA publishing. Checking </span></span><a href="http://mbio.asm.org/site/misc/authors.xhtml" style="background-color: transparent; border: 0px; color: #c63f00; line-height: 21px; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">their website</a><span style="color: #555555;"><span style="line-height: 21px;"> ASM members can publish for $2000USD, non-members for $3000USD. ASM membership costs $50, this is probably a worthwhile investment. $2050/5.3 drops mBio to 7th worst OA deal on my list. Next on my hitlist is Hindawi–a bunch of academic spammers if my inbox is anything to go by. Hindawi are potentially charging $1500USD to publish in “Journal of Biomedicine and Biotechnology” (IF:2.436). A quick</span></span><a href="http://www.hindawi.com/journals/jbb/apc/" style="background-color: transparent; border: 0px; color: #c63f00; line-height: 21px; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank"> trip to their website</a><span style="color: #555555;"><span style="line-height: 21px;"> confirms this is the case. We finally have a winner for the worst deal award! Next down the list is, surprisingly, PLoS. PLoS’ 5-th </span></span><span style="color: #555555;"><span style="line-height: 21px;">ranked journal is “PLoS Computational Biology” (IF:5.215). According to their <a href="http://www.plos.org/publish/pricing-policy/publication-fees/?__utma=54900660.891545091.1349392616.1350381163.1350621226.6&__utmb=54900660.6.10.1350621226&__utmc=54900660&__utmx=-&__utmz=54900660.1350621226.6.6.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided)&__utmv=-&__utmk=62362280">fee</a> page, publication for </span></span><span style="color: #555555;"><span style="line-height: 21px;">research in middle to high income country incurs a fee of $2250USD. This is cheaper than anticipated so </span></span><span style="color: #555555;"><span style="line-height: 21px;">PLoS moves down to 8th worst slot. Phew! Anthony Poole and I have just had an article accepted in PLoS </span></span><span style="color: #555555; line-height: 21px;">CB. I think I’ll finish this tiresome game there.</span></span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">I have been terribly unfair to the publishers I have mentioned here (and probably the ones I haven’t). The rules of my game have been rather arbitrary. If I was to do this fairly I would survey a large number of academics from a number of disciplines to find out what OA fees they are really paying in which journals. I haven’t the time to do this, however, this is something that could be added to the next <a href="http://project-soap.eu/" style="background-color: transparent; border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">SOAP initiative</a>.</span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Another issue I haven’t discussed is copyright. Some of the publishers still retain the copyright on OA articles, others do not. This topic is covered by <a href="http://www.creativecommons.org.nz/open_access_2012/" style="background-color: transparent; border: 0px; color: #c63f00; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;">other blogposts in the series</a>. </span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><span style="color: #555555;"><span style="line-height: 21px;">In summary, open access is great but can be extremely expensive. Not all publishers are equal, therefore, it </span></span><span style="color: #555555;"><span style="line-height: 21px;">is worth shopping around. Preprint archives can provide a nice intermediate solution. Finally, please buy </span></span><span style="color: #555555; line-height: 21px;">Paul’s Patented Cognitive Enhancement Vitamin Formula, produced in association with Placeboceuticals.</span></span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Conflicts of interest:</span></div>
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<span style="color: #555555;"><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif; line-height: 21px;">1. I am an Assistant Editor in Chief for the Landes Bioscience journal, RNA Biology. I regularly invite</span></span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><span style="color: #555555;"><span style="line-height: 21px;">contributions and referee articles for the journal. I receive no salary for this position. They did send me an </span></span><span style="color: #555555;"><span style="line-height: 21px;">iPad nearly 2 years ago after I cheekily asked for one when they advertised their new iPad App. This was </span></span><span style="color: #555555; line-height: 21px;">very nice, my kids regularly use it for watching YouTube clips about ”Lego” and ”Thomas the Tank </span><span style="color: #555555; line-height: 21px;">Engine”. I’m sometimes permitted to use it for email, Facebook, Twitter and as a Kindle.</span></span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><span style="color: #555555;"><span style="line-height: 21px;">2. I was funded by the Wellcome Trust for 4 years. They were wonderful, my contract specified that all my </span></span><span style="color: #555555;"><span style="line-height: 21px;">articles must be deposited in UKPMC within 6 months of publication. They happily paid the OA fees </span></span><span style="color: #555555; line-height: 21px;">when I managed to publish my work.</span></span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Abbreviations used in the above figures: T&F=Taylor & Francis, ACS=American Chemical Society, NAS=National Academy of Science, PLoS-Public Library of Science, BMC=BioMed Central, W-B=Wiley-Blackwell, BMJ=British Medical Journal, CUP=Cambridge University Press, OUP=Oxford University Press, NPG=Nature Publishing Group.</span></div>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">A version of this article is cross posted on the <a href="http://www.creativecommons.org.nz/2012/10/is-open-access-for-free-too-much-to-ask/">NZ Creative Commons Blog</a>. </span></div>
Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-12614969541980687442012-10-22T19:32:00.001-07:002012-10-22T19:32:14.556-07:00Open Access Week, 2012<br />
Together with a number of other open access advocates, I have written a blog post for Open Access week, 2012. To read it and some other fantastic posts from my colleagues visit the <a href="http://www.creativecommons.org.nz/open_access_2012/">NZ Creative Commons</a> website.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFafcr8NrOkNLnvBHcIflCSCosTgLk8k5fexXcFg8GPhXoVGINywQZo8t0BkbShaCeslxSyvfg7OUt_4IeO4EUxZTs5ZCF8GkrwuY38Jy2_0V44EBJpZf1o8EfYSjxzyFLPt1zcJZy3jpU/s1600/dollar_per_IF.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="304" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFafcr8NrOkNLnvBHcIflCSCosTgLk8k5fexXcFg8GPhXoVGINywQZo8t0BkbShaCeslxSyvfg7OUt_4IeO4EUxZTs5ZCF8GkrwuY38Jy2_0V44EBJpZf1o8EfYSjxzyFLPt1zcJZy3jpU/s320/dollar_per_IF.png" width="320" /></a></div>
<br />Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-50550388932240924492012-08-24T06:07:00.000-07:002012-08-24T18:26:11.536-07:00NZ's hottest researchers from 2010-2012.<br />
In response to the recently released "The Hottest Research of 2011" report from <a href="http://sciencewatch.com/newsletter/2012/201203/hottest_research_2012/">ScienceWatch</a> (where several of my former colleagues at the <a href="http://www.blogger.com/goog_1864735127">Wellcome Trust Sanger</a> <a href="http://sangerinstitute.wordpress.com/2012/06/21/64/">Institute</a> feature) I thought I'd take a look at NZ's hottest research and researchers.<br />
<br />
<br />
<h3>
<a name='more'></a>The rules of the game:</h3>
<ol>
<li>Using <a href="http://www.scopus.com/home.url">Scopus</a> find institutes with New Zealand affiliations. I took the 19 most prolific institutes, which ranged from "University of Auckland" to "Manaaki Whenua - Landcare Research".</li>
<li>Filter the documents from these institutes by publication date (2010-2012) and sort the list by number of citations.</li>
<li>Select those articles with 10 or more citations. </li>
<li>Remove articles with 20 or more authors. This step excludes e.g. the <a href="http://arxiv.org/find/hep-ex/1/au:+Collaboration_CMS/0/1/0/all/0/1">LHC</a> and <a href="http://www.ncbi.nlm.nih.gov/pubmed/21833088">genome</a> papers which cause problems for the later analyses.</li>
<li>Write a simple bit of Perl that will parse the author names and count number of articles and total citations for each. Remove the high-ranked authors from outside NZ.</li>
<li>Make a scatter plot of number of hot articles vs number of citations to hot article.</li>
<li>Peruse the results and Google-stalk the successful authors. </li>
</ol>
<h3>
The Results</h3>
<br />
First the graph:<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjA94atKxYkSL9TYXzdYFg-jfV-lq1SBD87DDnXuc8QxQWbtdO6zOVZGYyojSq1RmVsY1zdjVC8-1KlR1s_5sSeHYckxscXoyK-Ihw7_V1obomdwaYd5b2pBneu6LEiHd7rMnHlu9BahvQB/s1600/nz_most_cited_articles_2010-2012.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjA94atKxYkSL9TYXzdYFg-jfV-lq1SBD87DDnXuc8QxQWbtdO6zOVZGYyojSq1RmVsY1zdjVC8-1KlR1s_5sSeHYckxscXoyK-Ihw7_V1obomdwaYd5b2pBneu6LEiHd7rMnHlu9BahvQB/s640/nz_most_cited_articles_2010-2012.png" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">These people are doing amazing work! </td></tr>
</tbody></table>
<br />
<ul>
<li><span style="font-family: inherit;">There is one very prolific group of authors in the <a href="http://www.ncbi.nlm.nih.gov/pubmed/21833088">Bone Density Group</a> at The University of Auckland's Department of Medicine [1-20]. These include Professor Ian Reid, Greg Gamble, <span style="text-align: left;">Associate Professor Andrew Grey and </span><span style="line-height: 16px; text-align: left; text-indent: -38px;">Mark Bolland. As a team they have published 20 hot articles! Predominantly on the effects of a variety of minerals and vitamins (e.g. calcium and vitamin D) on a variety of health outcomes (e.g. osteoporosis and <span style="line-height: normal; text-align: -webkit-auto; text-indent: 0px;">cardiovascular events</span>). Keep up the good work folks!</span></span></li>
<li style="text-align: -webkit-auto;"><div style="text-align: -webkit-auto;">
<span style="color: black;"><a href="http://www.des.auckland.ac.nz/uoa/don-nield" style="font-family: inherit;"><span style="line-height: 18px; text-align: left;">Honorary Associate Professor Don</span><span style="font-weight: bold; line-height: 18px; text-align: left;"> </span>Nield</a><span style="font-family: inherit;"> from the </span>Department of Engineering Science, University of Auckland <span style="font-family: inherit;">has had a very productive few years [21-30]. Together with his </span>colleague<span style="font-family: inherit;"> </span><a href="http://www.blogger.com/goog_1864735164" style="font-family: inherit;">Professor Andrey </a><em style="font-family: inherit; font-style: normal;"><a href="http://www.mae.ncsu.edu/faculty-staff/profile/andrey-kuznetsov/">Kuznetsov</a> at the</em><em style="font-family: inherit; font-style: normal; font-weight: bold;"> </em><span style="font-family: inherit; line-height: 20px;">Department of Mechanical and Aerospace Engineering, North Carolina State University. They have produced 10 hot articles on fluids flowing under an array of conditions. </span></span></div>
</li>
<li style="text-align: -webkit-auto;"><a href="http://phsl.otago.ac.nz/peoplelab.php?lab=14" style="font-family: inherit; line-height: 20px;">Professor Allan Herbison</a><span style="font-family: inherit; line-height: 20px;"> from the </span><span style="font-family: inherit; line-height: 20px;">Department of Physiology,</span><span style="font-family: inherit; line-height: 20px;"> University of Otago has been involved in publishing 11 hot articles [31-41]. Their work inspects the interplay between gene expression, hormone levels and neurobiology. </span></li>
<li><span style="line-height: 20px;">My favourite group is the computational biologists. NZ produces some inspirational comp. bio. researchers for someone like me. Our hot researchers are <a href="http://www.blogger.com/goog_1864735174">Associate Professor Christopher </a></span><a href="http://www.otago.ac.nz/christchurch/departments/psychmed/ourpeople/otago011211.html">Frampton</a> from the Department of Medicine, Christchurch School of Medicine and Health Sciences who has contributed statistical analyses for 9 hot papers [42-53]. <a href="http://compevol.auckland.ac.nz/dr-alexei-drummond/">Associate Professor Alexei Drummond</a> from the Department of Computer Science at the University of Auckland has contributed 3 hot articles on Bayesian approaches to phylogenetic analysis [54-56]. <a href="http://compevol.auckland.ac.nz/stephane-guindon/">Stéphane Guindon</a> from the Department of Statistics, University of Auckland has published 2 hot papers on maximum-likelihood approaches to phylogenetic analysis and an update to the sequence alignment viewer, Sea view[57-58].</li>
<li><a href="http://www.lincoln.ac.nz/staff-profile?staffId=Philip.Hulme">Professor Philip Hulme</a> from down the road at the Bio-Protection Research Centre, Lincoln University has published 10 hot articles on ecosystems under pressure from invasive species [59-68].</li>
<li><a href="http://oneocean.cbc.ca/series/experts/malcolm-clark">Malcolm Clark</a>, Principle Scientist at the National Institute of Water and Atmospheric Research (NIWA), Wellington has published 7 hot articles exploring the ecology, fisheries, human impacts and biomass of seamounts and submarine canyons [69-75]. </li>
<li>Professor Robert Poulin from the Department of Zoology, University of Otago has published 8 hot articles on the ecology of host-parasite interactions [76-83].</li>
<li>There is a very productive group of marine natural products researchers that curate novel chemicals found in marine life, this work has resulted in 8 hot articles [84-91]. The group includes <a href="http://www.victoria.ac.nz/scps/about/staff/peter-northcote">Associate Professor Peter Northcote</a> from the Centre for Biodiscovery, Victoria University of Wellington; <a href="http://www.chem.canterbury.ac.nz/people/munro.shtml">Emeritus Professor Murray Munro</a> and <a href="http://www.chem.canterbury.ac.nz/people/blunt.shtml">Emeritus Professor John Blunt</a> Department of Chemistry, University of Canterbury; <a href="http://sci.waikato.ac.nz/about-us/people/michele">Michele Prinsep</a> from the Department of Chemistry, University of Waikato and <a href="http://web.chemistry.auckland.ac.nz/staff-profile-jahia.aspx?staffid=12">Associate Professor Brent Copp</a> from the Department of Chemistry, University of Auckland. </li>
</ul>
<br />
######################################################################<br />
<h3>
References </h3>
[1] Bolland, M.J., Grey, A., Avenell, A., Gamble, G.D., Reid, I.R.<br />
Calcium supplements with or without vitamin D and risk of cardiovascular events: reanalysis of the Women's Health Initiative limited access dataset and meta-analysis.<br />
(2011) BMJ (Clinical research ed.), 342, . Cited 72 times.<br />
<br />
[2] Bolland, M.J., Grey, A.B., Gamble, G.D., Reid, I.R.<br />
Effect of osteoporosis treatment on mortality: A meta-analysis<br />
(2010) Journal of Clinical Endocrinology and Metabolism, 95 (3), pp. 1174-1181. Cited 48 times.<br />
<br />
[3] Reid, I.R., Miller, P.D., Brown, J.P., Kendler, D.L., Fahrleitner-Pammer, A., Valter, I., Maasalu, K., Bolognese, M.A., Woodson, G., Bone, H., Ding, B., Wagman, R.B., San Martin, J., Ominsky, M.S., Dempster, D.W.<br />
Effects of denosumab on bone histomorphometry: The FREEDOM and STAND studies<br />
(2010) Journal of Bone and Mineral Research, 25 (10), pp. 2256-2265. Cited 45 times.<br />
<br />
[4] Eisman, J.A., Bone, H.G., Hosking, D.J., McClung, M.R., Reid, I.R., Rizzoli, R., Resch, H., Verbruggen, N., Hustad, C.M., Dasilva, C., Petrovic, R., Santora, A.C., Ince, B.A., Lombardi, A.<br />
Odanacatib in the treatment of postmenopausal women with low bone mineral density: Three-year continued therapy and resolution of effect<br />
(2011) Journal of Bone and Mineral Research, 26 (2), pp. 242-251. Cited 43 times.<br />
<br />
[5] Bolland, M.J., Avenell, A., Baron, J.A., Grey, A., MacLennan, G.S., Gamble, G.D., Reid, I.R.<br />
Effect of calcium supplements on risk of myocardial infarction and cardiovascular events: Meta-analysis<br />
(2010) BMJ (Online), 341 (7767), art. no. c3691, p. 289. Cited 41 times.<br />
<br />
[6] Bolland, M.J., Bacon, C.J., Horne, A.M., Mason, B.H., Ames, R.W., Wang, T.K.M., Grey, A.B., Gamble, G.D., Reid, I.R.<br />
Vitamin D insufficiency and health outcomes over 5 y in older women<br />
(2010) American Journal of Clinical Nutrition, 91 (1), pp. 82-89. Cited 32 times.<br />
<br />
[7] Reid, I.R., Gamble, G.D., Mesenbrink, P., Lakatos, P., Black, D.M.<br />
Characterization of and risk factors for the acute-phase response after zoledronic acid<br />
(2010) Journal of Clinical Endocrinology and Metabolism, 95 (9), pp. 4380-4387. Cited 21 times.<br />
<br />
[8] Young, R.P., Whittington, C.F., Hopkins, R.J., Hay, B.A., Epton, M.J., Black, P.N., Gamble, G.D.<br />
Chromosome 4q31 locus in COPD is also associated with lung cancer<br />
(2010) European Respiratory Journal, 36 (6), pp. 1375-1382. Cited 19 times.<br />
<br />
[9] Grey, A., Bolland, M., Wattie, D., Horne, A., Gamble, G., Reid, I.R.<br />
Prolonged antiresorptive activity of zoledronate: A randomized, controlled trial<br />
(2010) Journal of Bone and Mineral Research, 25 (10), pp. 2251-2255. Cited 19 times.<br />
<br />
[10] Reid, I.R., Bolland, M.J., Avenell, A., Grey, A.<br />
Cardiovascular effects of calcium supplementation<br />
(2011) Osteoporosis International, 22 (6), pp. 1649-1658. Cited 17 times.<br />
<br />
[11] Young, R.P., Hopkins, R.J., Whittington, C.F., Hay, B.A., Epton, M.J., Gamble, G.D.<br />
Individual and cumulative effects of GWAS susceptibility loci in lung cancer: Associations after sub-phenotyping for COPD<br />
(2011) PLoS ONE, 6 (2), art. no. e16476, . Cited 16 times.<br />
<br />
[12] Bolland, M.J., Grey, A., Avenell, A., Gamble, G.D., Reid, I.R.<br />
Calcium supplements with or without vitamin D and risk of cardiovascular events: Reanalysis of the Women's Health Initiative limited access dataset and meta-analysis<br />
(2011) BMJ, 342 (7804), art. no. d2040, . Cited 14 times.<br />
<br />
[13] Williams, G.A., Callon, K.E., Watson, M., Costa, J.L., Ding, Y., Dickinson, M., Wang, Y., Naot, D., Reid, I.R., Cornish, J.<br />
Skeletal phenotype of the leptin receptor-deficient db/db mouse<br />
(2011) Journal of Bone and Mineral Research, 26 (8), pp. 1698-1709. Cited 13 times.<br />
<br />
[14] Bolland, M.J., Grey, A., Gamble, G.D., Reid, I.R.<br />
Calcium and vitamin D supplements and health outcomes: A reanalysis of the Women's Health Initiative (WHI) limited-access data set<br />
(2011) American Journal of Clinical Nutrition, 94 (4), pp. 1144-1149. Cited 12 times.<br />
<br />
[15] Reid, I.R., Avenell, A.<br />
Evidence-based policy on dietary calcium and vitamin D<br />
(2011) Journal of Bone and Mineral Research, 26 (3), pp. 452-454. Cited 12 times.<br />
<br />
[16] Eastell, R., Christiansen, C., Grauer, A., Kutilek, S., Libanati, C., McClung, M.R., Reid, I.R., Resch, H., Siris, E., Uebelhart, D., Wang, A., Weryha, G., Cummings, S.R.<br />
Effects of denosumab on bone turnover markers in postmenopausal osteoporosis<br />
(2011) Journal of Bone and Mineral Research, 26 (3), pp. 530-537. Cited 12 times.<br />
<br />
[17] Dalbeth, N., Wong, S., Gamble, G.D., Horne, A., Mason, B., Pool, B., Fairbanks, L., McQueen, F.M., Cornish, J., Reid, I.R., Palmano, K.<br />
Acute effect of milk on serum urate concentrations: A randomised controlled crossover trial<br />
(2010) Annals of the Rheumatic Diseases, 69 (9), pp. 1677-1682. Cited 12 times.<br />
<br />
[18] Grey, A., Bolland, M.<br />
Vitamin D: A place in the sun?<br />
(2010) Archives of Internal Medicine, 170 (13), pp. 1099-1100. Cited 12 times.<br />
<br />
[19] Sankaran, S., Gamble, G., Bolland, M., Reid, I.R., Grey, A.<br />
Skeletal effects of interventions in mild primary hyperparathyroidism: A meta-analysis<br />
(2010) Journal of Clinical Endocrinology and Metabolism, 95 (4), pp. 1653-1662. Cited 12 times.<br />
<br />
[20] Black, D.M., Reid, I.R., Boonen, S., Bucci-Rechtweg, C., Cauley, J.A., Cosman, F., Cummings, S.R., Hue, T.F., Lippuner, K., Lakatos, P., Leung, P.C., Man, Z., Martinez, R.L.M., Tan, M., Ruzycky, M.E., Su, G., Eastell, R.<br />
The effect of 3 versus 6 years of Zoledronic acid treatment of osteoporosis: A randomized extension to the HORIZON-Pivotal Fracture Trial (PFT)<br />
(2012) Journal of Bone and Mineral Research, 27 (2), pp. 243-254. Cited 11 times.<br />
<br />
###################################<br />
<br />
[21] Kuznetsov, A.V., Nield, D.A.<br />
Natural convective boundary-layer flow of a nanofluid past a vertical plate<br />
(2010) International Journal of Thermal Sciences, 49 (2), pp. 243-247. Cited 68 times.<br />
<br />
[22] Kuznetsov, A.V., Nield, D.A.<br />
Thermal instability in a porous medium layer saturated by a nanofluid: Brinkman model<br />
(2010) Transport in Porous Media, 81 (3), pp. 409-422. Cited 30 times.<br />
<br />
[23] Kuznetsov, A.V., Nield, D.A.<br />
Effect of local thermal non-equilibrium on the onset of convection in a porous medium layer saturated by a nanofluid<br />
(2010) Transport in Porous Media, 83 (2), pp. 425-436. Cited 29 times.<br />
<br />
[24] Nield, D.A., Kuznetsov, A.V.<br />
The onset of convection in a horizontal nanofluid layer of finite depth<br />
(2010) European Journal of Mechanics, B/Fluids, 29 (3), pp. 217-223. Cited 28 times.<br />
<br />
[25] Kuznetsov, A.V., Nield, D.A.<br />
The Onset of Double-Diffusive Nanofluid Convection in a Layer of a Saturated Porous Medium<br />
(2010) Transport in Porous Media, 85 (3), pp. 941-951. Cited 18 times.<br />
<br />
[26] Nield, D.A., Kuznetsov, A.V.<br />
The Cheng-Minkowycz problem for the double-diffusive natural convective boundary layer flow in a porous medium saturated by a nanofluid<br />
(2011) International Journal of Heat and Mass Transfer, 54 (1-3), pp. 374-378. Cited 15 times.<br />
<br />
[27] Nield, D.A., Kuznetsov, A.V.<br />
The effect of local thermal nonequilibrium on the onset of convection in a nanofluid<br />
(2010) Journal of Heat Transfer, 132 (5), pp. 1-7. Cited 15 times.<br />
<br />
[28] Kuznetsov, A.V., Nield, D.A.<br />
Double-diffusive natural convective boundary-layer flow of a nanofluid past a vertical plate<br />
(2011) International Journal of Thermal Sciences, 50 (5), pp. 712-717. Cited 11 times.<br />
<br />
[29] Kuznetsov, A.V., Nield, D.A., Simmons, C.T.<br />
The effect of strong heterogeneity on the onset of convection in a porous medium: Periodic and localized variation<br />
(2010) Transport in Porous Media, 81 (1), pp. 123-139. Cited 11 times.<br />
<br />
[30] Nield, D.A., Kuznetsov, A.V., Simmons, C.T.<br />
The effect of strong heterogeneity on the onset of convection in a porous medium: 2d/3d localization and spatially correlated random permeability fields<br />
(2010) Transport in Porous Media, 83 (3), pp. 465-477. Cited 10 times.<br />
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###################################<br />
<br />
[31] Herbison, A.E., De Tassigny, X.D., Doran, J., Colledge, W.H.<br />
Distribution and postnatal development of Gpr54 gene expression in mouse brain and gonadotropin-releasing hormone neurons<br />
(2010) Endocrinology, 151 (1), pp. 312-321. Cited 38 times.<br />
<br />
[32] Clarkson, J., Han, S.-K., Liu, X., Lee, K., Herbison, A.E.<br />
Neurobiological mechanisms underlying kisspeptin activation of gonadotropin-releasing hormone (GnRH) neurons at puberty<br />
(2010) Molecular and Cellular Endocrinology, 324 (1-2), pp. 45-50. Cited 19 times.<br />
<br />
[33] Lee, K., Duan, W., Sneyd, J., Herbison, A.E.<br />
Two slow calcium-activated afterhyperpolarization currents control burst firing dynamics in gonadotropin-releasing hormone neurons<br />
(2010) Journal of Neuroscience, 30 (18), pp. 6214-6224. Cited 19 times.<br />
<br />
[34] Constantin, S., Jasoni, C.L., Wadas, B., Herbison, A.E.<br />
γ-aminobutyric acid and glutamate differentially regulate intracellular calcium concentrations in mouse gonadotropin-releasing hormone neurons<br />
(2010) Endocrinology, 151 (1), pp. 262-270. Cited 18 times.<br />
<br />
[35] Ducret, E., Gaidamaka, G., Herbison, A.E.<br />
Electrical and morphological characteristics of anteroventral periventricular nucleus kisspeptin and other neurons in the female mouse<br />
(2010) Endocrinology, 151 (5), pp. 2223-2232. Cited 16 times.<br />
<br />
[36] Brown, R.S.E., Kokay, I.C., Herbison, A.E., Grattan, D.R.<br />
Distribution of prolactin-responsive neurons in the mouse forebrain<br />
(2010) Journal of Comparative Neurology, 518 (1), pp. 92-102. Cited 14 times.<br />
<br />
[37] Liu, X., Porteous, R., D'Anglemont De Tassigny, X., Colledge, W.H., Millar, R., Petersen, S.L., Herbison, A.E.<br />
Frequency-dependent recruitment of fast amino acid and slow neuropeptide neurotransmitter release controls gonadotropin-releasing hormone neuron excitability<br />
(2011) Journal of Neuroscience, 31 (7), pp. 2421-2430. Cited 12 times.<br />
<br />
[38] Herbison, A.E., Moenter, S.M.<br />
Depolarising and Hyperpolarising Actions of GABAA Receptor Activation on Gonadotrophin-Releasing Hormone Neurones: Towards an Emerging Consensus<br />
(2011) Journal of Neuroendocrinology, 23 (7), pp. 557-569. Cited 11 times.<br />
<br />
[39] Yeo, S.-H., Herbison, A.E.<br />
Projections of arcuate nucleus and rostral periventricular kisspeptin neurons in the adult female mouse brain<br />
(2011) Endocrinology, 152 (6), pp. 2387-2399. Cited 11 times.<br />
<br />
[40] Iremonger, K.J., Constantin, S., Liu, X., Herbison, A.E.<br />
Glutamate regulation of GnRH neuron excitability<br />
(2010) Brain Research, 1364, pp. 35-43. Cited 11 times.<br />
<br />
[41] Herde, M.K., Geist, K., Campbell, R.E., Herbison, A.E.<br />
Gonadotropin-releasing hormone neurons extend complex highly branched dendritic trees outside the blood-brain barrier<br />
(2011) Endocrinology, 152 (10), pp. 3832-3841. Cited 10 times.<br />
<br />
###################################<br />
<br />
[42] Endre, Z.H., Walker, R.J., Pickering, J.W., Shaw, G.M., Frampton, C.M., Henderson, S.J., Hutchison, R., Mehrtens, J.E., Robinson, J.M., Schollum, J.B.W., Westhuyzen, J., Celi, L.A., McGinley, R.J., Campbell, I.J., George, P.M.<br />
Early intervention with erythropoietin does not affect the outcome of acute kidney injury (the EARLYARF trial)<br />
(2010) Kidney International, 77 (11), pp. 1020-1030. Cited 47 times.<br />
<br />
[43] Ritzema, J., Troughton, R., Melton, I., Crozier, I., Doughty, R., Krum, H., Walton, A., Adamson, P., Kar, S., Shah, P.K., Richards, M., Eigler, N.L., Whiting, J.S., Haas, G.J., Heywood, J.T., Frampton, C.M., Abraham, W.T.<br />
Physician-directed patient self-management of left atrial pressure in advanced chronic heart failure<br />
(2010) Circulation, 121 (9), pp. 1086-1095. Cited 42 times.<br />
<br />
[44] Snow, B.J., Rolfe, F.L., Lockhart, M.M., Frampton, C.M., O'Sullivan, J.D., Fung, V., Smith, R.A.J., Murphy, M.P., Taylor, K.M.<br />
A double-blind, placebo-controlled study to assess the mitochondria- targeted antioxidant MitoQ as a disease-modifying therapy in Parkinson's disease<br />
(2010) Movement Disorders, 25 (11), pp. 1670-1674. Cited 31 times.<br />
<br />
[45] Stamp, L.K., O'Donnell, J.L., Zhang, M., James, J., Frampton, C., Barclay, M.L., Chapman, P.T.<br />
Using allopurinol above the dose based on creatinine clearance is effective and safe in patients with chronic gout, including those with renal impairment<br />
(2011) Arthritis and Rheumatism, 63 (2), pp. 412-421. Cited 28 times.<br />
<br />
[46] Gane, E.J., Weilert, F., Orr, D.W., Keogh, G.F., Gibson, M., Lockhart, M.M., Frampton, C.M., Taylor, K.M., Smith, R.A.J., Murphy, M.P.<br />
The mitochondria-targeted anti-oxidant mitoquinone decreases liver damage in a phase II study of hepatitis C patients<br />
(2010) Liver International, 30 (7), pp. 1019-1026. Cited 27 times.<br />
<br />
[47] Nejat, M., Pickering, J.W., Walker, R.J., Westhuyzen, J., Shaw, G.M., Frampton, C.M., Endre, Z.H.<br />
Urinary cystatin C is diagnostic of acute kidney injury and sepsis, and predicts mortality in the intensive care unit<br />
(2010) Critical Care, 14 (3), art. no. R85, . Cited 27 times.<br />
<br />
[48] Endre, Z.H., Pickering, J.W., Walker, R.J., Devarajan, P., Edelstein, C.L., Bonventre, J.V., Frampton, C.M., Bennett, M.R., Ma, Q., Sabbisetti, V.S., Vaidya, V.S., Walcher, A.M., Shaw, G.M., Henderson, S.J., Nejat, M., Schollum, J.B.W., George, P.M.<br />
Improved performance of urinary biomarkers of acute kidney injury in the critically ill by stratification for injury duration and baseline renal function<br />
(2011) Kidney International, 79 (10), pp. 1119-1130. Cited 24 times.<br />
<br />
[49] Stamp, L.K., O'Donnell, J.L., Chapman, P.T., Zhang, M., James, J., Frampton, C., Barclay, M.L.<br />
Methotrexate polyglutamate concentrations are not associated with disease control in rheumatoid arthritis patients receiving long-term methotrexate therapy<br />
(2010) Arthritis and Rheumatism, 62 (2), pp. 359-368. Cited 22 times.<br />
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[50] Gearry, R.B., Richardson, A.K., Frampton, C.M., Dodgshun, A.J., Barclay, M.L.<br />
Population-based cases control study of inflammatory bowel disease risk factors<br />
(2010) Journal of Gastroenterology and Hepatology, 25 (2), pp. 325-333. Cited 22 times.<br />
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[51] Hickford, J.G.H., Forrest, R.H., Zhou, H., Fang, Q., Han, J., Frampton, C.M., Horrell, A.L.<br />
Polymorphisms in the ovine myostatin gene (MSTN) and their association with growth and carcass traits in New Zealand Romney sheep<br />
(2010) Animal Genetics, 41 (1), pp. 64-72. Cited 16 times.<br />
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[52] Pearse, A.J., Hooper, G.J., Rothwell, A., Frampton, C.<br />
Survival and functional outcome after revision of a unicompartmental to a total knee replacement: The New Zealand National Joint Registry<br />
(2010) Journal of Bone and Joint Surgery - Series B, 92 (4), pp. 508-512. Cited 13 times.<br />
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[53] Rothwell, A.G., Hooper, G.J., Hobbs, A., Frampton, C.M.<br />
An analysis of the Oxford hip and knee scores and their relationship to early joint revision in the New Zealand Joint Registry<br />
(2010) Journal of Bone and Joint Surgery - Series B, 92 (3), pp. 413-418. Cited 10 times.<br />
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Bayesian Inference of Species Trees from Multilocus Data<br />
(2010) Molecular Biology and Evolution, 27 (3), pp. 570-580. Cited 171 times.<br />
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Bayesian random local clocks, or one rate to rule them all<br />
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Epidemic dynamics revealed in dengue evolution<br />
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New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0<br />
(2010) Systematic Biology, 59 (3), pp. 307-321. Cited 347 times.<br />
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Sea view version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building<br />
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<br />
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[59] Vilà, M., Basnou, C., Pyšek, P., Josefsson, M., Genovesi, P., Gollasch, S., Nentwig, W., Olenin, S., Roques, A., Roy, D., Hulme, P.E.<br />
How well do we understand the impacts of alien species on ecosystem services? A pan-European, cross-taxa assessment<br />
(2010) Frontiers in Ecology and the Environment, 8 (3), pp. 135-144. Cited 73 times.<br />
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Disentangling the role of environmental and human pressures on biological invasions across Europe<br />
(2010) Proceedings of the National Academy of Sciences of the United States of America, 107 (27), pp. 12157-12162. Cited 46 times.<br />
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[61] Essl, F., Dullinger, S., Rabitsch, W., Hulme, P.E., Hülber, K., Jarošík, V., Kleinbauer, I., Krausmann, F., Kühn, I., Nentwig, W., Vilà, M., Genovesi, P., Gherardi, F., Desprez-Loustau, M.-L., Roques, A., Pyšek, P.<br />
Socioeconomic legacy yields an invasion debt<br />
(2011) Proceedings of the National Academy of Sciences of the United States of America, 108 (1), pp. 203-207. Cited 27 times.<br />
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[62] Vilà, M., Espinar, J.L., Hejda, M., Hulme, P.E., Jarošík, V., Maron, J.L., Pergl, J., Schaffner, U., Sun, Y., Pyšek, P.<br />
Ecological impacts of invasive alien plants: A meta-analysis of their effects on species, communities and ecosystems<br />
(2011) Ecology Letters, 14 (7), pp. 702-708. Cited 25 times.<br />
<br />
[63] Schweiger, O., Biesmeijer, J.C., Bommarco, R., Hickler, T., Hulme, P.E., Klotz, S., Kühn, I., Moora, M., Nielsen, A., Ohlemüller, R., Petanidou, T., Potts, S.G., Pyšek, P., Stout, J.C., Sykes, M.T., Tscheulin, T., Vilà, M., Walther, G.-R., Westphal, C., Winter, M., Zobel, M., Settele, J.<br />
Multiple stressors on biotic interactions: How climate change and alien species interact to affect pollination<br />
(2010) Biological Reviews, 85 (4), pp. 777-795. Cited 25 times.<br />
<br />
[64] Pyšek, P., Bacher, S., Chytrý, M., Jarošík, V., Wild, J., Celesti-Grapow, L., Gassó, N., Kenis, M., Lambdon, P.W., Nentwig, W., Pergl, J., Roques, A., Sádlo, J., Solarz, W., Vilà, M., Hulme, P.E.<br />
Contrasting patterns in the invasions of European terrestrial and freshwater habitats by alien plants, insects and vertebrates<br />
(2010) Global Ecology and Biogeography, 19 (3), pp. 317-331. Cited 21 times.<br />
<br />
[65] Aikio, S., Duncan, R.P., Hulme, P.E.<br />
Lag-phases in alien plant invasions: Separating the facts from the artefacts<br />
(2010) Oikos, 119 (2), pp. 370-378. Cited 17 times.<br />
<br />
[66] Hulme, P.E.<br />
Addressing the threat to biodiversity from botanic gardens<br />
(2011) Trends in Ecology and Evolution, 26 (4), pp. 168-174. Cited 12 times.<br />
<br />
[67] Memmott, J., Cadotte, M., Hulme, P.E., Kerby, G., Milner-Gulland, E.J., Whittingham, M.J.<br />
Putting applied ecology into practice<br />
(2010) Journal of Applied Ecology, 47 (1), pp. 1-4. Cited 12 times.<br />
<br />
[68] Diez, J.M., Dickie, I., Edwards, G., Hulme, P.E., Sullivan, J.J., Duncan, R.P.<br />
Negative soil feedbacks accumulate over time for non-native plant species<br />
(2010) Ecology Letters, 13 (7), pp. 803-809. Cited 10 times.<br />
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<br />
[69] Clark, M.R., Rowden, A.A., Schlacher, T., Williams, A., Consalvey, M., Stocks, K.I., Rogers, A.D., O'Hara, T.D., White, M., Shank, T.M., Hall-Spencer, J.M.<br />
The ecology of seamounts: Structure, function, and human impacts<br />
(2010) Annual Review of Marine Science, 2 (1), pp. 253-278. Cited 38 times.<br />
<br />
[70] McMillan, H., Freer, J., Pappenberger, F., Krueger, T., Clark, M.<br />
Impacts of uncertain river flow data on rainfall-runoff model calibration and discharge predictions<br />
(2010) Hydrological Processes, 24 (10), pp. 1270-1284. Cited 24 times.<br />
<br />
[71] De Leo, F.C., Smith, C.R., Rowden, A.A., Bowden, D.A., Clark, M.R.<br />
Submarine canyons: Hotspots of benthic biomass and productivity in the deep sea<br />
(2010) Proceedings of the Royal Society B: Biological Sciences, 277 (1695), pp. 2783-2792. Cited 22 times.<br />
<br />
[72] Pitcher, T.J., Clark, M.R., Morato, T., Watson, R.<br />
Seamount fisheries: Do they have a future?<br />
(2010) Oceanography, 23 (1), pp. 134-144. Cited 18 times.<br />
<br />
[73] Williams, A., Schlacher, T.A., Rowden, A.A., Althaus, F., Clark, M.R., Bowden, D.A., Stewart, R., Bax, N.J., Consalvey, M., Kloser, R.J.<br />
Seamount megabenthic assemblages fail to recover from trawling impacts<br />
(2010) Marine Ecology, 31 (SUPPL. 1), pp. 183-199. Cited 15 times.<br />
<br />
[74] Rowden, A.A., Schlacher, T.A., Williams, A., Clark, M.R., Stewart, R., Althaus, F., Bowden, D.A., Consalvey, M., Robinson, W., Dowdney, J.<br />
A test of the seamount oasis hypothesis: Seamounts support higher epibenthic megafaunal biomass than adjacent slopes<br />
(2010) Marine Ecology, 31 (SUPPL. 1), pp. 95-106. Cited 13 times.<br />
<br />
[75] Ramirez-Llodra, E., Tyler, P.A., Baker, M.C., Bergstad, O.A., Clark, M.R., Escobar, E., Levin, L.A., Menot, L., Rowden, A.A., Smith, C.R., van Dover, C.L.<br />
Man and the last great wilderness: Human impact on the deep sea<br />
(2011) PLoS ONE, 6 (8), art. no. e22588, . Cited 10 times.<br />
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<br />
[76] Fortuna, M.A., Stouffer, D.B., Olesen, J.M., Jordano, P., Mouillot, D., Krasnov, B.R., Poulin, R., Bascompte, J.<br />
Nestedness versus modularity in ecological networks: Two sides of the same coin?<br />
(2010) Journal of Animal Ecology, 79 (4), pp. 811-817. Cited 22 times.<br />
<br />
[77] Johnson, P.T.J., Dobson, A., Lafferty, K.D., Marcogliese, D.J., Memmott, J., Orlofske, S.A., Poulin, R., Thieltges, D.W.<br />
When parasites become prey: Ecological and epidemiological significance of eating parasites<br />
(2010) Trends in Ecology and Evolution, 25 (6), pp. 362-371. Cited 20 times.<br />
<br />
[78] Vidal-Martínez, V.M., Pech, D., Sures, B., Purucker, S.T., Poulin, R.<br />
Can parasites really reveal environmental impact?<br />
(2010) Trends in Parasitology, 26 (1), pp. 44-51. Cited 16 times.<br />
<br />
[79] Koehler, A.V., Poulin, R.<br />
Host partitioning by parasites in an intertidal crustacean community<br />
(2010) Journal of Parasitology, 96 (5), pp. 862-868. Cited 14 times.<br />
<br />
[80] Studer, A., Thieltges, D.W., Poulin, R.<br />
Parasites and global warming: Net effects of temperature on an intertidal host-parasite system<br />
(2010) Marine Ecology Progress Series, 415, pp. 11-22. Cited 11 times.<br />
<br />
[81] Poulin, R.<br />
Network analysis shining light on parasite ecology and diversity<br />
(2010) Trends in Parasitology, 26 (10), pp. 492-498. Cited 10 times.<br />
<br />
[82] Thomas, F., Poulin, R., Brodeur, J.<br />
Host manipulation by parasites: A multidimensional phenomenon<br />
(2010) Oikos, 119 (8), pp. 1217-1223. Cited 10 times.<br />
<br />
[83] Kelly, D.W., Thomas, H., Thieltges, D.W., Poulin, R., Tompkins, D.M.<br />
Trematode infection causes malformations and population effects in a declining New Zealand fish<br />
(2010) Journal of Animal Ecology, 79 (2), pp. 445-452. Cited 10 times.<br />
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<br />
[84] Blunt, J.W., Copp, B.R., Munro, M.H.G., Northcote, P.T., Prinsep, M.R.<br />
Marine natural products<br />
(2010) Natural Product Reports, 27 (2), pp. 165-237. Cited 139 times.<br />
<br />
[85] Blunt, J.W., Copp, B.R., Munro, M.H.G., Northcote, P.T., Prinsep, M.R.<br />
Marine natural products<br />
(2011) Natural Product Reports, 28 (2), pp. 196-268. Cited 102 times.<br />
<br />
[86] Shiohara, A., Hanada, S., Prabakar, S., Fujioka, K., Lim, T.H., Yamamoto, K., Northcote, P.T., Tilley, R.D.<br />
Chemical reactions on surface molecules attached to silicon quantum dots<br />
(2010) Journal of the American Chemical Society, 132 (1), pp. 248-253. Cited 34 times.<br />
<br />
[87] Blunt, J.W., Copp, B.R., Keyzers, R.A., Munro, M.H.G., Prinsep, M.R.<br />
Marine natural products<br />
(2012) Natural Product Reports, 29 (2), pp. 144-222. Cited 16 times.<br />
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[88] Singh, A.J., Xu, C.-X., Xu, X., West, L.M., Wilmes, A., Chan, A., Hamel, E., Miller, J.H., Northcote, P.T., Ghosh, A.K.<br />
Peloruside B, a potent antitumor macrolide from the New Zealand marine sponge Mycale hentscheli: Isolation, structure, total synthesis, and bioactivity<br />
(2010) Journal of Organic Chemistry, 75 (1), pp. 2-10. Cited 15 times.<br />
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[89] Månsson, M., Phipps, R.K., Gram, L., Munro, M.H.G., Larsen, T.O., Nielsen, K.F.<br />
Explorative solid-phase extraction (E-SPE) for accelerated microbial natural product discovery, dereplication, and purification<br />
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Lagunamides A and B: Cytotoxic and antimalarial cyclodepsipeptides from the marine cyanobacterium Lyngbya majuscula<br />
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Microtubule-stabilizing drugs from marine sponges: Focus on peloruside A and zampanolide<br />
(2010) Marine Drugs, 8 (4), pp. 1059-1079. Cited 10 times.<br />
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<br />Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com1tag:blogger.com,1999:blog-6891533072440219276.post-52502422589221383802012-08-14T16:37:00.001-07:002012-08-14T16:37:08.696-07:00Re-blogging: Rfam 11.0 is out!<br />
<br /><br />The really BIG news for this release is the <a href="http://xfam-biomart.sanger.ac.uk/martwizard/#!/default?mart=Rfam+11.0&step=2">Xfam-Biomart</a>. Which finally allows researchers to easily fetch all the sequences in Rfam from their favourite organism. For example, lets pretend I was really interested in <i>Helicobacter pylori</i> 35A. I go to the <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi">NCBI Taxonomy</a>, look the species up there and record the taxid (585535). Back at the Biomart I enter the taxid beside "NCBI Taxonomy ID:", hit "Next", then select a number of handy looking features, hit "Results" and suddenly I have ALL the sequences from <i>Helicobacter pylori</i> 35A. This is an extraordinarily useful feature that has, until now, been missing from the Xfam arsenal. I'll be making heavy use of it in future. <br /><br /><div class="separator" style="clear: both;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZO5gLuS94kciJKFCMUYovMiwVXWI-bw-5qCsAVMW1yRVWfJPblrJutEHM2pNj5El9yAs6_LGHEk-OkhVljsHupi3vpFsdAxlSmn7h9qkaa537Yu-3ew-X3ZTOFDYkRZp0qt81vCK_99T8/s1600/Selection_008.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="268" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZO5gLuS94kciJKFCMUYovMiwVXWI-bw-5qCsAVMW1yRVWfJPblrJutEHM2pNj5El9yAs6_LGHEk-OkhVljsHupi3vpFsdAxlSmn7h9qkaa537Yu-3ew-X3ZTOFDYkRZp0qt81vCK_99T8/s640/Selection_008.jpeg" width="640" /></a></div>
<br />
See the <a href="http://xfam.wordpress.com/2012/08/14/rfam-11-0-is-out/">Xfam blog</a> for more details.<br />
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<div>
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Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com1tag:blogger.com,1999:blog-6891533072440219276.post-38650837552172161822012-04-10T18:58:00.000-07:002012-04-10T18:58:12.969-07:00LaTeX fun with periodic tablesFor a while now I've wanted to generate a simple <a href="http://en.wikipedia.org/wiki/Periodic_table_of_elements">periodic table of elements</a> in <a href="http://en.wikipedia.org/wiki/LaTeX">LaTeX</a>. I've <a href="https://www.google.co.nz/search?q=%22Periodic+table+of+elements%22+latex">googled</a> around a bit without too much joy. So I've made a simple one myself.<br />
<br />
Here is the code:<br />
<br />
<span style="font-family: 'Courier New', Courier, monospace;">\documentclass[a4paper,12pt]{article}</span><br />
<span style="font-family: 'Courier New', Courier, monospace;">\pagestyle{empty}</span><br />
<div><div><span style="font-family: 'Courier New', Courier, monospace;">\usepackage{rotating}</span></div></div><div><div><span style="font-family: 'Courier New', Courier, monospace;">\linespread{1.2}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;"><br />
</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\begin{document}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;"><br />
</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\begin{sidewaystable}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;"> {</span></div><div><span style="font-family: 'Courier New', Courier, monospace;"> \renewcommand{\arraystretch}{1.5}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;"> \bfseries</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\centering</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\begin{tabular}{|c|c|c|c|c|c|c|c|c|c|c|c|c|c|c|c|c|c|}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\cline{1-1} \cline{18-18}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">H & \multicolumn{16}{|c|}{} & He \\</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\cline{1-2} \cline{13-18}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">Li & Be & \multicolumn{10}{|c|}{} & Bo & C & N & O & Fl & Ne \\</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\cline{1-2} \cline{13-18}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">Na & Mg & \multicolumn{10}{|c|}{} & Al & Si & P & S & Cl & Ar \\</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\hline</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">K & Ca & Sc & Ti & V & Cr & Mn & Fe & Co & Ni & Cu & Zn & Ga & Ge & As & Se & Br & Kr \\</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\hline</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">Rb & Sr & Y & Zr & Nb & Mo & Tc & Ru & Rh & Pd & Ag & Cd & In & Sn & Sb & Te & I & Xe \\</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\hline</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">Cs & Ba & * & Hf & Ta & W & Re & Os & Ir & Pt & Au & Hg & Tl & Pb & Bi & Po & At & Rn \\</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\hline</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">Fr & Ra & ** & Rf & Db & Sg & Bh & Hs & Mt & Ds & Rg & Cn & Uut & Uuq & Uup & Uuh & Uus & Uuo \\</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\hline</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\end{tabular}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\end{sidewaystable}</span></div><div><span style="font-family: 'Courier New', Courier, monospace;"><br />
</span></div><div><span style="font-family: 'Courier New', Courier, monospace;">\end{document}</span></div></div><div>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div><div><br />
</div><br />
And here is the resulting table:<br />
<br />
<div class="separator" style="clear: both; text-align: center;"></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6EWXg58F4dCdVaHZEpp8GqybB3D2GGy__BJLQbb4TjfNni3qmT5J9HerQhq6cR3JBC-cA2b_SW0aSJvMmUw96H6EZti4vZ4Gr5_Hp2Q0kvoZaiS39_KfFHNnPeQJTrQ-FOg0Zco4VhO33/s1600/periodic_table.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="128" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6EWXg58F4dCdVaHZEpp8GqybB3D2GGy__BJLQbb4TjfNni3qmT5J9HerQhq6cR3JBC-cA2b_SW0aSJvMmUw96H6EZti4vZ4Gr5_Hp2Q0kvoZaiS39_KfFHNnPeQJTrQ-FOg0Zco4VhO33/s400/periodic_table.png" width="400" /></a></div>Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com1tag:blogger.com,1999:blog-6891533072440219276.post-53000474853475186052012-03-15T02:13:00.000-07:002012-03-15T02:13:03.397-07:00Two Lecturer positions in Bioinformatics/Genomics : Auckland / Palmerston North, New ZealandLecturer positions in NZ are as rare as <a href="http://en.wikipedia.org/wiki/Moa">Moa</a> teeth. If you are interested read more at <a href="http://www.unijobs.co.nz/show.php?title=lecturer_in_bioinformatics_genomics_11981">UniJobs</a>, <a href="http://jobs.newscientist.com/job/1401343973/lecturer-in-bioinformatics-genomics/">NewScientist</a> and <a href="http://www.nature.com/naturejobs/science/jobs/251749-Two-Lecturer-positions-in-Bioinformatics-Genomics">NatureJobs</a>.Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-76822609734705065732012-03-08T19:05:00.000-08:002012-03-08T19:05:36.396-08:00PhD position in the evolution and bioinformatics of RNA in New Zealand<div style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;"><span style="font-family: verdana, sans-serif;"><a href="http://www.biol.canterbury.ac.nz/people/poole.shtml">Anthony Poole</a> and I are<span style="line-height: 18px;"> seeking a talented PhD candidate to explore the evolution and bioinformatics of</span><strong style="line-height: 18px;"> </strong><span style="line-height: 18px;">RNA. Tell your friends!</span></span></div><div style="background-color: rgba(255, 255, 255, 0.917969); color: #222222; font-family: arial, sans-serif; font-size: 13px;"><span style="font-family: verdana, sans-serif;"><span style="line-height: 18px;">Closing Date: 30 March 2012</span><br style="line-height: 18px;" />For more, see the i<a href="http://www.bic.canterbury.ac.nz/documents/BIC-PhD2012.pdf" style="border-bottom-color: rgb(187, 153, 255); border-bottom-style: initial; border-bottom-width: 0px; border-left-color: rgb(187, 153, 255); border-right-color: rgb(187, 153, 255); border-top-color: rgb(187, 153, 255); color: #660099; line-height: 18px;" target="_blank">nformation sheet</a>. </span></div>Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com2University Dr, Ilam, Christchurch 8041, New Zealand-43.525652400000013 172.58292619999997-43.527191400000014 172.57883219999997 -43.524113400000012 172.58702019999998tag:blogger.com,1999:blog-6891533072440219276.post-51449785375114840302012-02-23T13:16:00.000-08:002012-02-23T13:16:21.693-08:00RNA Biology provides incentives to reviewThe full text of the email from Renee Schroeder and Eva Riedmann from <a href="http://www.landesbioscience.com/journals/rnabiology/">RNA Biology</a> is below. The gist of it is that researchers get free subscriptions and discounts on publication costs in exchange for reviewing. This is a clever move by them (in my completely biased opinion). The journal, <a href="http://nar.oxfordjournals.org/content/early/2011/12/04/nar.gkr1195.full">Nucleic Acids Research</a>, is the only other journal I know of that offers incentives for reviews. They offer a few pounds towards <a href="http://www.oup.co.uk/">books</a> or <a href="http://www.chandos.net/">CDs</a> from their preferred suppliers in exchange for reviewing. This is nice, but frankly the selection from those sources is very limited. I'd much rather have full access to the journals I review for (actually, I'd rather everyone had full access, that's another battle). All too often I've wanted to look at the published version of a manuscript that I've reviewed and not had access to it. This is ridiculous.<br />
<br />
<br />
<br />
Dear Research Community –<br />
<br />
We are writing to you now because you have either served as a reviewer or have submitted a manuscript to the journal RNA Biology in the past.<br />
<br />
RNA Biology will be instituting a reviewer incentive program offering free subscriptions and discounts on publication costs in exchange for timely reviews. To guarantee the success of this program we need to update our database and are requesting a few moments of your time.<br />
<br />
Please login to the RNA Biology submission and peer-review website here:<br />
<br />
http://rnabiol.msubmit.net/<br />
<br />
and click on the link “Modify Profile/Password.”<br />
<br />
If you could please ensure that your institutional affiliation, address, and email address are up to date AND please select up to five ‘Areas of Expertise’, we would greatly appreciate this. (For your convenience, we have listed the areas of expertise below.)<br />
<br />
This will ensure that we are able to notify you of new developments with the journal. Additionally, this information will help ensure that we have a robust database from which to quickly identify appropriate peer-reviewers.<br />
<br />
If you have any questions or concern please contact us at rna@landesbioscience.com<br />
<br />
Thank you very much for your help.<br />
<br />
Sincerely,<br />
<br />
Renee Schroeder<br />
Editor-in-Chief<br />
University of Vienna<br />
<br />
Eva Riedmann, Ph.D.<br />
Acquisitions Editor<br />
Landes Bioscience<br />
<br />
Areas of Expertise<br />
<br />
Apatamers<br />
biogenesis<br />
bioinformatics<br />
cancer<br />
cell biology<br />
chromatin<br />
developmental biology<br />
epigenetics<br />
mechanism of translation<br />
methods<br />
miRNA<br />
mRNA transport/localization<br />
natural antisense<br />
neurobiology/neurological disease<br />
prokaryotes<br />
protein-RNA interactions<br />
regulation of stability/degradation<br />
regulation of translation<br />
ribonucleases<br />
ribosome<br />
riboswitches<br />
ribozymes<br />
RNA binding proteins<br />
RNA damage/repair<br />
RNA in disease<br />
RNA stability/degradation<br />
RNA viruses<br />
RNomics<br />
siRNA<br />
small and large non-coding RNAs<br />
splicing/pre-mRNA processing<br />
therapeutics<br />
transcriptome<br />
TRNA<br />
<div><br />
</div>Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-76042361495076568592012-02-22T12:44:00.000-08:002013-05-28T02:06:57.495-07:00Fetching sequences from EMBL/ENA using wget/curlEvery time I want to download several EMBL files (eg. all the bacterial genomes) I spend at least an hour trying to find the right URL syntax. This post is a public note to self that will help me next time and perhaps help others who are also receiving a few lines of HTML when all they want is a verdammt plain-text EMBL formatted file.<br />
<br />
There is actual documentation on the right syntax <a href="http://www.ebi.ac.uk/Tools/webservices/services/dbfetch_rest">here</a>, which again takes a while to find, searching for wget, curl, EMBL and various related combinations doesn't get you there quickly. However, the main issue I have is, if I go to the recommended sequence record eg. <a href="http://www.ebi.ac.uk/ena/data/view/CP000362">here</a>, none of the links work with a simple "wget URL" or "curl -G URL".<br />
<br />
So, if I want to fetch the <i>Roseobacter denitrificans</i> genome sequence with EMBL accession CP000362. I use:<br />
<span class="Apple-style-span" style="font-family: 'Courier New', Courier, monospace;">wget http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/CP000362</span><br />
or if you're into curl:<br />
<span class="Apple-style-span" style="font-family: 'Courier New', Courier, monospace;">curl -G http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/CP000362 > CP000362.embl</span><br />
<br />
Simple!Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com5tag:blogger.com,1999:blog-6891533072440219276.post-77258374394862112012-02-12T19:52:00.001-08:002012-02-12T19:52:41.806-08:00Excited about eQTLsDuring my time at the Sanger Institute I heard many talks from people in Manolis Dermitzakis' group on <a href="http://en.wikipedia.org/wiki/Expression_quantitative_trait_loci">expressed quantitative trait loci</a> (eQTLs). For practical purposes these eQTLs are <a href="http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism">SNPs</a> that are strongly correlated with expression level eg. a population's genotypes at one site might be <b>AA</b>, <b>AG</b> and <b>GG</b>, a nearby gene might have corresponding median expression levels of <b>2</b>, <b>4</b> and <b>6</b> (arbitrary units) across multiple genotyped individuals. Something I've always thought would be very interesting to look at was the functional characterisation of the sites these SNPs lie in. A recent paper by Gaffney <i>et al</i> entitled "<a href="http://genomebiology.com/2012/13/1/R7/abstract">Dissecting the regulatory architecture of gene expression QTLs</a>" has made some inroads into this problem. It looks like they've focussed on the promoter regions and found that ~40% are in open chromatin structures and are enriched in transcription factor binding sites. My interests are of course more on the putative cis-regulatory elements such as structured UTR elements (eg. IREs) and microRNA binding sites that the eQTLs can presumably influence. So it looks like there are still many fun projects that these datasets can spawn.Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0tag:blogger.com,1999:blog-6891533072440219276.post-13878645848298332402011-08-04T16:40:00.000-07:002011-08-04T16:40:03.695-07:00Interesting articlesThis week I've been setting up a new laptop. Shifting from a MacBook back to my beloved Lenovo ThinkPad running Ubuntu. Things have really moved along in the last 4 years (glipper/klipper - how I've missed you!).<br />
<br />
Consequently I haven't done anything terribly useful this week other than give a brief talk for the monthly <a href="https://biocoop.biocommons.org.nz/homepage">NZ Bioinformatics VC</a> (I don't know what VC stands for yet - must find out). Also, later today I'll give a talk at the <a href="http://www.bic.canterbury.ac.nz/">BIC Symposium</a>. Fortunately I can reuse one or two slides.<br />
<br />
In the absence of anything really useful to say I've spotted a couple of articles this week that have made it to my "I really must read these on the bus to work one day" pile. The first [1] describes some experimental work that shows that <a href="http://en.wikipedia.org/wiki/Hfq_protein">Hfq</a> binds to the rho independent terminator of the sRNA SgrS. Since I've recently developed quite an <a href="http://nar.oxfordjournals.org/content/early/2011/04/07/nar.gkr168.abstract">interest in terminators</a> I think I'd better take a look at this result. The second [2] is pulled from Sean Eddy's <a href="http://selab.janelia.org/publications.html">preprint server</a>. This describes some of his and Diana Kolbe's work on applying HMMER3-like speedups to covariance models. The results appear to be both promising and disappointing. They definitely speed up CMs but to come at a cost to sensitivity, however merging the accelerated CM results with an HMM-filter appears to bring the sensitivity back up to the level of a raw CM, the combined filters appear to be much faster than running a raw CM. So all in all a very promising result. Hopefully this work will be added to the main trunk of <a href="http://infernal.janelia.org/">Infernal</a> soon. <br />
<br />
[1] <span style="color: black; font-size: small;">Otaka H<span style="font-family: inherit;">, </span>Ishikawa H<span style="font-family: inherit;">, </span>Morita T<span style="font-family: inherit;">, </span>Aiba H<span style="font-family: inherit;">. </span></span>(2011)<span style="font-size: small;"> <a href="http://www.pnas.org/content/early/2011/07/18/1107050108.abstract">PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action.</a> Proc Natl Acad Sci U S A.</span><br />
<br />
[2] D. L. Kolbe, S. R. Eddy. (2011) <a href="ftp://selab.janelia.org/pub/publications/KolbeEddy11/KolbeEddy11-preprint.pdf">Fast Filtering for RNA Homology Search</a>. <i>In press.</i>Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com3tag:blogger.com,1999:blog-6891533072440219276.post-11334671000095106072011-07-22T21:08:00.000-07:002011-07-22T21:08:57.883-07:00First postI hope to make this a fairly active blog. Including a weekly roundup of links and articles in the RNA bioinformatics field, an edited diary of my research activities, comments on other research areas, thoughts on bioinformatics and research in New Zealand and anything else roughly professional that seems blog-worthy.Paul Gardnerhttp://www.blogger.com/profile/06986200606814928944noreply@blogger.com0