MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with '#plos one'. Tue, 04 May 2010 18:39:40 +0100 http://www.medworm.com/index.php?rid=3208426&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FxlDVrp72_j0%2Fcool-paper-winner-of-worst-new-omics.html And the bad new omics words keep streaming in. Today's winner of the "Worst New Omics Word Award" is going to Carey Lambert, Chien-Yi Chang, Michael J. Capeness and R. Elizabeth Sockett from Nottingham for their use/ invention of "Predatosome". They use this term in the title of their new PLoS One paper: The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio. Here is the very long sentence where the define it:The gene products required for the initial invasive predatory processes have not been extensively studied but the genome sequencing of B. bacteriovorus HD100 [1] revealed a genome of 3.85Mb, including a core genome similar to that of non-predatory bacteria and some 40% of the genome comprising a potential predicted “predatosome” of genes, encoding both ... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3208426 Tue, 26 Jan 2010 16:50:48 +0100 3208426 http://www.medworm.com/index.php?rid=3208427&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FXtZQoZfDerk%2Fisi-late-to-index-plos-one-but-now.html Well, just a mini post here. In case you did not know - PLoS One is now being indexed by ISI (see their announcement: PLoS ONE and see the PLOS blog post here and see Erik Svensson's blog post for an interesting take) and will get an impact factor and be in their Citation Index and all such things. Now mind you, I think "Impact Factor" is a silly thing overall in that we should evaluate papers not journals per se.So why am I writing this - because I find it pretty funny that despite being slow to recognize PLoS One ISI is now promoting the fact that they are indexing PLoS One on their home page. See the screen capture above. -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For shor... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3208427 Tue, 26 Jan 2010 03:49:26 +0100 3208427 http://www.medworm.com/index.php?rid=3146009&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2FM0eLJgCnwRA%2Fplosone-paper-keywords-revealing-penis.html This study is the first molecular assessment of the bacterial diversity in the male genital mucosa. The observed decrease in anaerobic bacteria after circumcision may be related to the elimination of anoxic microenvironments under the foreskin. Detection of these anaerobic genera in other human infectious and inflammatory pathologies suggests that they may mediate genital mucosal inflammation or co-infections in the uncircumcised state. Hence, the decrease in these anaerobic bacteria after circumcision may complement the loss of the foreskin inner mucosa to reduce the number of activated Langerhans cells near the genital mucosal surface and possibly the risk of HIV acquisition in circumcised men." And this all sounds interesting and the work seems solid.  I note that some friends / co... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3146009 Wed, 06 Jan 2010 01:49:16 +0100 3146009 http://www.medworm.com/index.php?rid=2670862&cid=t_321732_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fplos-one-impact-factor-and-page-rank.html Discussion Expert for PLoS. Everyone and their grandmother knows that Impact Factor is a crude, unreliable and just wrong metric to use in evaluating individuals for career-making (or career-breaking) purposes. He adds that despite this, many institutions (or rather, their bureaucrats – scientists would abandon it if their bosses would) cling to impact factor anyway. Alternatives to impact factor are being attempted, and in today’s online world of social bookmarking, forums and preprint archives it is not without irony that the Google pagerank model may offer a new approach. A version of PageRank has recently been proposed as a replacement for the traditional Institute for Scientific Information (ISI) impact factor. It has been implemented at eigenfactor.org. Instead of simply ... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=2670862 Wed, 05 Aug 2009 12:00:47 +0100 2670862 http://www.medworm.com/index.php?rid=2156536&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2009%2F02%2Fplease-bash-my-latest-paper-for-benefit.html We report what I think are some very interesting things in the paper. Among them:We report the first example of a plasmid that encodes all the genes needed for chemotaxis including all the genes for making a flagellum. Given that they are on a plasmid this suggests that motility could be easily transfered between species.We report experimental work and genome analysis that helps understand the novel membrane and cell wall structure in this species.This is the first thermophile known to oxidize carbon monoxideBut I am not writing per se about the things I like about our paper. I am instead asking people out there to find things wrong with our paper. Why am I doing this? Because this paper is part of a broader experiment in publishing in that it is in PLoS One. And one of the main benefits o... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=2156536 Tue, 03 Feb 2009 04:04:00 +0100 2156536 http://www.medworm.com/index.php?rid=2046785&cid=t_321732_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fone-way-for-rdf-to-help-a-bioinformatician-build-a-database-s3db.html%3F_c%3Dfeed-rss This post is part of the PLoS One syncroblogging day, as part of the PLoS ONE @ Two birthday celebrations. Happy Synchroblogging! Here's a link to the paper on the PLoS One website. Biological data: vitally important, determinedly unruly. This... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=2046785 Thu, 18 Dec 2008 08:34:11 +0100 2046785 http://www.medworm.com/index.php?rid=1825493&cid=t_321732_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F09%2F25%2Fgenomic-analysis-of-pseudoalteromonas-tunicata%2F Some years ago, I provided advice and a little analysis for a group at UNSW studying marine bacteria. It’s nice to see that they remembered me: Thomas, T., Evans, F.F., Schleheck, D., Mai-Prochnow, A., Burke, C., Penesyan, A., Dalisay, D.S., Stelzer-Braid, S., Saunders, N., Johnson, J., Ferriera, S., Kjelleberg, S. and Egan, S. (2008). Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment. PLoS ONE 3:e3252. If correlating genomic features with microbial physiology is your thing, go and check it out. The article is open access, for your pleasure - as are five of my last six efforts, I just noticed. Posted in bioinformatics, genomics, publications, research diary   Tagged: plos one, pseudoalter... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1825493 Thu, 25 Sep 2008 06:31:41 +0100 1825493 http://www.medworm.com/index.php?rid=1625670&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2008%2F07%2Fi-see-plos-in-everything.html Seen recently at the California Railroad Museum. I guess the people from Nature were right - PLoS One is leaving its mark everywhere.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist at the University of California, Davis. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1625670 Tue, 15 Jul 2008 21:45:00 +0100 1625670 http://www.medworm.com/index.php?rid=1563964&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2008%2F07%2Fonly-nature-could-turn-success-of-plos.html Now, mind, you I like Nature as a publishing unit. They publish some very fine journals. Now, most of them are not Open Access, so I choose not to publish there if I can avoid it. But I still like them. And many of the editors and reporters there are excellent - smart, creative, insightful and such. But Nature the publisher can also be completely inane when it comes to writing about Open Access and PLoS. In a new article by Declan Butler, Nature takes another crack at the PLoS "publishing model"The problem with PLoS now is ... wait for this ... the success of PLoS One.  PLoS One it turns out is publishing a lot of papers (including one by me, today).  And bringing in a decent amount of money to PLoS apparently (note for full disclosure - I am involved in PLoS Biology as "Academic Editor ... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1563964 Wed, 02 Jul 2008 22:03:00 +0100 1563964 http://www.medworm.com/index.php?rid=1563965&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2008%2F07%2Fmy-first-plos-one-paper-yay.html Well, I have truly entered the modern world. My first PLoS One paper has just come out. It is entitled "An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)" and well, it describes automated software for analyzing rRNA sequences that are generated as part of microbial diversity studies. The main goal behind this was to keep up with the massive amounts of rRNA sequences we and others could generate in the lab and to develop a tool that would remove the need for "manual" work in analyzing rRNAs. The work was done primarily by Dongying Wu, a Project Scientist in my lab with assistance from a Amber Hartman, who is a PhD student in my lab. Naomi Ward, who was on the faculty at TIGR and is now at Wyoming, and I helped guide the development and testing of... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1563965 Wed, 02 Jul 2008 15:45:00 +0100 1563965 http://www.medworm.com/index.php?rid=1143482&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2008%2F01%2Foakley-keeping-his-eye-on-evolution.html I saw an interesting talk today and thought I would post on it. I was not expecting to be able to go to the talk as I was supposed to be at a workshop in San Francisco but had to bail on it because my kids have been sick. But I did go in to Davis for a brief spell to go to a seminar by Todd Oakley who is a candidate for a faculty position here at Davis in the Evolution and Ecology department.It was a generally insightful phylogenomic tour of the evolution of opsins and eyes in animals. He also mentioned a paper he had recently in PLoS One on Animal Opsin evolution. This is from the work of his graduate student David Plachetzki and it does a nice job of doing "phylogenomic" analysis in the way I think of phylogenomics -- that is -- a integration of evolutionary and genomic analyses. (NOTE -... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1143482 Fri, 11 Jan 2008 04:12:00 +0100 1143482 http://www.medworm.com/index.php?rid=1030170&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2007%2F11%2Fopen-access-dinosaurs-and-way-to-go.html Well, I met Paul Sereno, the dinosaur hunter, for the first time at SciFoo camp (for more about that see here). I confess I was skeptical when he said he was committed to Open Access. But now he has really proven his OA chops. He has a new paper in PLoS One on some friggin cool dinosaur fossils.The paper is "Structural Extremes in a Cretaceous Dinosaur" by Paul C. Sereno1*, Jeffrey A. Wilson2, Lawrence M. Witmer3, John A. Whitlock2, Abdoulaye Maga4, Oumarou Ide4, Timothy A. Rowe5Check it out at PLoS One. This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist at the University of California, Davis. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1030170 Thu, 15 Nov 2007 22:33:00 +0100 1030170 http://www.medworm.com/index.php?rid=996486&cid=t_321732_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2007%2F11%2F01%2Fa-small-achievement%2F Moving to a new group and a new project is always difficult. However, one of the better aspects of being a bioinformatician is that you can often contribute to other projects - which can be a bonus when your own are not progressing so well. I’m happy to announce: Thakur, A.S., Robin, G., Guncar, G., Saunders, N.F.W., Newman, J., Martin, J.L. and Kobe, B. (2007). Improved Success of Protein Crystallization Sparse Matrix Screening with Heterogeneous Nucleating Agents. PLoS ONE 2:e1091. Open Access My contribution was very minor; some writing and a little statistical evaluation (although the method that I had in mind didn’t make it to the final version). The take-home message is: if your protein won’t crystallise, try throwing some dried seaweed into the mix! It’s no... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=996486 Thu, 01 Nov 2007 03:59:54 +0100 996486 http://www.medworm.com/index.php?rid=935301&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2007%2F10%2Fgme-2007-getting-feedback-on-plos-one.html While at the GME meeting - I have now been approached by 3 people saying they really liked the discussion I initiated on PLoS One for a paper on metagenomics a few weeks ago. They were not saying they liked my comments but that there was an active discussion about some important topics. I think the function on PLoS One has great potential to engage the broad scientific community in discussions that might have previously been limited to journal clubs. So it is nice to see (1) that people are reading stuff on PLoS One and (2) that they seem to like the commenting function.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist at the University of California, Davis. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=935301 Mon, 08 Oct 2007 23:41:00 +0100 935301 http://www.medworm.com/index.php?rid=737577&cid=t_321732_107_f&fid=35026&url=http%3A%2F%2Fphylogenomics.blogspot.com%2F2007%2F07%2Frated-my-first-paper-in-plos-one.html Well, PLoS One has announced its rating system is open. See Chris Surridge's Blog for more detail here. This is basically the first good system for trying out ratings for scientific publications in much the way it is done at YouTube and other Web 2.0 type systems.I personally am not sure if I think PLoS One is the perfect system for scientific publishing. But we desperately need to try out new systems and as an Open Access Web 2.0 scientific publishing system, the concept is worth trying. So - I decided to try it.I rated my first paper. I picked a paper by Xiang Xia Min and Donal Hickey on DNA barcoding. Why did I pick this paper. Well a few reasons. First, when I searched PLoS One for "metagenomics" and "metagenomic" it was one of the papers that came up. As soon as I saw the Barcoding ti... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=737577 Mon, 16 Jul 2007 23:29:00 +0100 737577 http://www.medworm.com/index.php?rid=723240&cid=t_321732_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F132181958%2F The new release candidate allows you to rate articles using the following criteria Insight - How thought-provoking a user found the article or how much it advances our scientific understanding Style - How well performed and presented a user considers a study to be Reliability - How secure a user feels the results and conclusion are in a study The criteria are interesting. They are along the lines of peer review, in a more open, wisdom of crowds kind of way. Are these criteria sufficient? Are they the most important ones? Pedro has some nice screenshots, and as a member of the group, I should really start following what’s being posted on Facebook Technorati Tags: PLoS One, Wisdom of Crowds, Peer Review (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=723240 Tue, 10 Jul 2007 05:09:02 +0100 723240 http://www.medworm.com/index.php?rid=559949&cid=t_321732_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F110993705%2F Another hectic week that has left me over 200 feed articles behind, so it is quite likely that Things I Noticed will be missing some of the best stuff from the past week. Let’s start with some non-scientific news FeistyFawn is now available Hari declares it “grandma worthy”. The latest release of Ubuntu, codenamed Feisty Fawn is now available and all the people I know who have tried it seem to like it quite a bit Better Gmail Better Gmail is a Firefox extension that combines some of the best Greasemonkey scripts for gmail. As a user of several of the scripts, downloading the extension was a no brainer, especially after such rave reviews Jon Udell talks Darwin An interesting take on Darwin from an unlikely source Biotech in India Krish points to an article in Nature about ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=559949 Sun, 22 Apr 2007 07:52:14 +0100 559949