tag:blogger.com,1999:blog-36768584.post9051727053361981021..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: A Fatally Flawed PaperKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-36768584.post-36844503915775146572009-02-22T13:21:00.000-05:002009-02-22T13:21:00.000-05:00@AnonymousReviewer - one of my great frustrations ...@AnonymousReviewer - one of my great frustrations with peer review is spending a non-trivial amount of time constructively criticising a manuscript, only to see it resurface in all its flawed glory at some other journal. Gah!Chris Cotsapashttps://www.blogger.com/profile/02256985652919023996noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-3196105732225546392009-02-04T17:04:00.000-05:002009-02-04T17:04:00.000-05:00I meant to plant the idea that this paper could be...I meant to plant the idea that this paper could be a useful starting point for a bioinformatics course exercise. My grad school professors loved to require us to read seriously flawed papers (in one case, a complete fraud) to see what we would pick up on (none of us figured out the fraudulent paper was such, a good exercise in instilling humility!)Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-60226703999976644772009-02-04T14:56:00.000-05:002009-02-04T14:56:00.000-05:00Can I use your example to craft a bioinformatics l...Can I use your example to craft a bioinformatics laboratory for a class?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-82211553311701299962009-02-04T13:12:00.000-05:002009-02-04T13:12:00.000-05:00This is hilarious. I remember slaugthering an earl...This is hilarious. I remember slaugthering an earlier version of this manuscript when it was in review at a different journal. I guess you can get anything published if you just shop it around long enough...Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-45404313408843126222009-02-04T12:35:00.000-05:002009-02-04T12:35:00.000-05:00Good catch, Keith. Unfortunately everyone is now a...Good catch, Keith. Unfortunately everyone is now an expert and uses published information rather than revalidating what are in actuality tentative results. <BR/><BR/>I do a lot of reanalysis of genomics projects as a consultant. Guess it's true that there's always time (and money) to do something twice, but never time to do it once properly. <BR/><BR/>- Brian Moldover (and hi!)BrianRunsPhillyhttps://www.blogger.com/profile/02625118688530242167noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-12099178313180146582009-02-03T13:07:00.000-05:002009-02-03T13:07:00.000-05:00DUH!!! Thanks for catching that missing "NOT". I ...DUH!!! Thanks for catching that missing "NOT". I probably would, on thinking about it, write something different, such as "If you haven't explicitly rooted your tree, then don't treat it as a rooted tree".Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-21112304041261690952009-02-03T11:04:00.000-05:002009-02-03T11:04:00.000-05:00You wrote: Always try to root your phylogenetic tr...You wrote: <EM>Always try to root your phylogenetic trees, unless you have a really good reason to do so. And, if your tree is rooted, you must explain how you rooted it</EM><BR/><BR/>Are you trying to say:<BR/>1) Always try to root your phylogenetic trees, unless you have a really good reason not to do so.<BR/> <BR/>or<BR/><BR/>2) Never root your phylogenetic trees, unless you have a really good reason to do so.<BR/><BR/>There are arguments for rooting and not rooting, so I'm not just being picky about grammar; I really don't know which side you are supporting.Jonathan Badgerhttps://www.blogger.com/profile/04921990886076027719noreply@blogger.com