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  • My lab has a new paper that just came out on the sequencing and analysis of the genome of a pretty cool (or hot actually) bacterium, Thermomicrobium roseum, which was isolated from a Toadstool Spring, an alkaline siliceous hotspring in Yellowstone National

    http://phylogenomics.blogspot.com/2009/02/please-bash-my-latest-paper-fo...

    Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. Wu D (2009) PLoS One.
    February 2, 2009
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  • Associated PressBad news for Benedict?Ever wonder why so much health news seems contradictory? One week theres a study saying that drinking coffee raises the risk of pancreatic cancer, or miscarriage, or lowers the risk of colorectal cancer; a few weeks later,

    http://feeds.wsjonline.com/~r/wsj/health/feed/~3/UPz6h6y9OPI/

    Why most published research findings are false. Ioannidis JP (2005) PLoS Med.
    January 26, 2009
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  • Since youre a Bitesize Bio reader, youre well aware that there is an abundance of both broad and specialized bioinformatics tools freely available for researchersif you know where and how to find them.Recently emerging is a push to combine or link some of the

    http://bitesizebio.com/2009/01/26/taming-the-data-stampede-with-wikis/

    Calling on a million minds for community annotation in WikiProteins. Mons B (2008) Genome Biol.
    Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Hodis E (2008) Genome Biol.
    ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. Stokes TH (2008) BMC Bioinformatics.
    WikiPathways: pathway editing for the people. Pico AR (2008) PLoS Biol.
    A gene wiki for community annotation of gene function. Huss JW (2008) PLoS Biol.
    January 25, 2009
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  • Another mechanism by which synonymous mutations may affect protein function is by altering the kinetics of protein folding. Researchers have proposed that synonymous substitutions that change a codon read by an abundant tRNA to a codon read by a rare tRNA could

    http://feeds.nature.com/~r/chemistry/rss/the_sceptical_chymist_with_comm...

    A "silent" polymorphism in the MDR1 gene changes substrate specificity. Kimchi-Sarfaty C (2007) Science.
    January 22, 2009
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  • I have decided to post a question here to my blog requesting help from phylogeneticists everywhere in doing phylogenetic analysis of data from metagenomic projects. Here I will try to describe the problem and then hopefully people out there can chime in on

    http://phylogenomics.blogspot.com/2008/01/calling-all-phylogeneticists-w...

    Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. Eisen JA (2007) PLoS Biol.
    January 13, 2009
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  • Altruism is a very heavily loaded word  in evolutionary psychology/ biology and I would not add to the confusion by defining the term myself. Suffice it to say , that I will use it in all of its various intuitive and theoretical usages. The evolution of

    http://feedproxy.google.com/~r/TheMouseTrap/~3/OpyEo87DPz8/varieties-of-...

    Generalized Reciprocity in Rats. Rutte C (2007) PLoS Biol.
    January 13, 2009
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  • Altruism is a very heavily loaded word  in evolutionary psychology/ biology and I would not add to the confusion by defining the term myself. Suffice it to say , that I will use it in all of its various intuitive and theoretical usages. The evolution of

    http://the-mouse-trap.blogspot.com/2009/01/varieties-of-altrusitic-exper...

    Generalized Reciprocity in Rats. Rutte C (2007) PLoS Biol.
    January 13, 2009
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  • Just a little plug for a new paper of which I am a co-author. This is a report on the analysis of the genome sequence of Acidithiobacillus ferrooxidans which was just published in BMC Genomics (an open access journal, by the way). This paper was a long long

    http://phylogenomics.blogspot.com/2009/01/acid-rock-bacteria-genome.html

    Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. Valdés J (2008) BMC Genomics.
    January 12, 2009
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  • It is with great sadness that I learned that Dr.Greg Cahill died a few days ago, at the Houston airport, waiting for his flight. I have met Greg at several meetings of the Society for Research on Biological Rhythms and while, those being fairly large meetings,

    http://www.scienceblogs.com/clock/2008/12/greg_cahill_19582008.php

    Light-dependent development of circadian gene expression in transgenic zebrafish. Kaneko M (2005) PLoS Biol.
    December 30, 2008
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  • A 21st century plague might be called the "Syndrome of Inappropriate Over-Confidence in Computing" (SICC syndrome for short).It's bad enough that we are placing major decisions about industrial policy at the tender mercies of computer models. For example, whether

    http://hcrenewal.blogspot.com/2008/12/21st-century-plague-syndrome-of.html

    Why most published research findings are false. Ioannidis JP (2005) PLoS Med.
    December 21, 2008
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  • No, not really. Mind reading software cannot record your dreams:'Mind-reading' software could record your dreams18:05 12 December 2008 by Celeste BieverPictures you are observing can now be recreated with software that uses nothing but scans of your brain.

    http://neurocritic.blogspot.com/2008/12/more-mindreading.html

    Visual image reconstruction from human brain activity using a combination of multiscale local image decoders. Miyawaki Y (2008) Neuron.
    Identifying natural images from human brain activity. Kay KN (2008) Nature.
    December 19, 2008
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  • Pages: 1 2 3 Next »     Single Page As another year comes to a close, it’s time to review what made the biggest news in 2008 in mental health and psychology. Of course, the biggest news of the year — the historic election of

    http://psychcentral.com/blog/archives/2008/12/17/mental-health-year-in-r...

    Selective publication of antidepressant trials and its influence on apparent efficacy. Turner EH (2008) N Engl J Med.
    Initial severity and antidepressant benefits: a meta-analysis of data submitted to the Food and Drug Administration. Kirsch I (2008) PLoS Med.
    December 17, 2008
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  • Here's the abstract from a recent article in Neuron:Visual Image Reconstruction from Human Brain Activity using a Combination of Multiscale Local Image Decoders Yoichi Miyawaki1, 2, 6, Hajime Uchida2, 3, 6, Okito Yamashita2, Masa-aki Sato2, Yusuke Morito4,

    http://kolber.typepad.com/ethics_law_blog/2008/12/fmri-visual-image-reco...

    Visual image reconstruction from human brain activity using a combination of multiscale local image decoders. Miyawaki Y (2008) Neuron.
    December 16, 2008
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  • 350James Hansen, NASA's chief climate scientist and the first to warn about global warming more than two decades ago, recently wrote: If humanity wishes to preserve a planet similar to that on which civilization developed and to which life on Earth is adapted,

    http://crnano.typepad.com/crnblog/2008/12/350-or-bust.html

    Target atmospheric CO2: Where should humanity aim?. J. Hansen (2008) arXiv [physics.ao-ph].
    December 15, 2008
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  • Before a clinical trial can commence a protocol - a plan of exactly how a trial will be conducted - will be formulated. As part of the planning, the individuals undertaking the trial will calculate approximately how many patients need to take part for the results

    http://www.helenjaques.co.uk/blog/2008/are-researchers-fudging-clinical-...

    Discrepancies in sample size calculations and data analyses reported in randomised trials: comparison of publications with protocols. Chan AW (2008) BMJ.
    Bias, spin, and misreporting: time for full access to trial protocols and results. Chan AW (2008) PLoS Med.
    December 12, 2008
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  • Nice little bit in the New York Times tomorrow about aphids and their symbionts. Henry Fountain writes (Observatory - How Tiny Insects, With a Little Help, Survive on Plant Sap - NYTimes.com) about a new article by Angela Douglas, one of the true pioneers of

    http://phylogenomics.blogspot.com/2008/12/aphid-bacterial-symbiosis-in-m...

    Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. Wu D (2006) PLoS Biol.
    December 8, 2008
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  • Publication bias became a big blogging topic last week as a PLoS Medicine paper was picked up by several influential sites. Lisa Bero and colleagues found that a quarter of trials submitted to the Food and Drug Administration between 2001 and 2002 in support

    http://www.plos.org/cms/node/424

    Reporting Bias in Drug Trials Submitted to the Food and Drug Administration: Review of Publication and Presentation. Rising Kristin (2008) Plos Med.
    Publication of clinical trials supporting successful new drug applications: a literature analysis. Lee K (2008) PLoS Med.
    Bias, spin, and misreporting: time for full access to trial protocols and results. Chan AW (2008) PLoS Med.
    December 7, 2008
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  • ormal {margin:0.0pt; margin-top:0.0pt; margin-bottom:0.0pt; margin-left:0.0pt; margin-right:0.0pt; text-indent:0.0pt; font-family:"Times New Roman"; font-size:10.0pt; color:Black; font-weight:normal; } H1 {margin:0.0pt; margin-top:0.0pt; margin-bottom:6.0pt;

    http://clinpsyc.blogspot.com/2008/12/lamictal-break-out-shovel.html

    Reporting Bias in Drug Trials Submitted to the Food and Drug Administration: Review of Publication and Presentation. Rising Kristin (2008) Plos Med.
    December 3, 2008
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  • Drug companies are not publishing all the trial data that they submit to the FDA, and those trials that are published are more likely to show positive results. Rising et al. compared all the New Drug Applications (NDAs) (the vehicle for initiating a new clinical

    http://www.scienceblogs.com/purepedantry/2008/12/drug_trial_publication_...

    Reporting Bias in Drug Trials Submitted to the Food and Drug Administration: Review of Publication and Presentation. Rising Kristin (2008) Plos Med.
    December 1, 2008
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  • Maxine Clarke, Positive skew of clinical-trial publication, Peer-to-Peer, November 27, 2008. A news story in Nature Medicine discusses an investigation into the publication status of the clinical-trials literature, which concludes that positive results of clinical

    http://www.earlham.edu/~peters/fos/2008/11/impact-of-oa-to-clinical-tria...

    Publication is positively skewed. Bjorn G (2008) Nat Med.
    Medicine. Moving toward transparency of clinical trials. Zarin DA (2008) Science.
    Publication of clinical trials supporting successful new drug applications: a literature analysis. Lee K (2008) PLoS Med.
    November 28, 2008
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  • A news story in Nature Medicine (14, 1133; 2008) discusses an investigation into the publication status of the clinical-trials literature (PLoS Med., doi: 10.1371/journal.pmed.0050191; 2008), which concludes that positive results of clinical trials for drugs

    http://blogs.nature.com/peer-to-peer/2008/11/positive_skew_of_clinicaltr...

    Publication is positively skewed. Bjorn G (2008) Nat Med.
    Medicine. Moving toward transparency of clinical trials. Zarin DA (2008) Science.
    Publication of clinical trials supporting successful new drug applications: a literature analysis. Lee K (2008) PLoS Med.
    November 27, 2008
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  • A news story in Nature Medicine (14, 1133; 2008) discusses an investigation into the publication status of the clinical-trials literature (PLoS Med., doi: 10.1371/journal.pmed.0050191; 2008), which concludes that positive results of clinical trials for drugs

    http://feeds.nature.com/~r/peer_review/rss/peer_to_peer/~3/481916490/pos...

    Publication is positively skewed. Bjorn G (2008) Nat Med.
    Publication of clinical trials supporting successful new drug applications: a literature analysis. Lee K (2008) PLoS Med.
    November 27, 2008
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  • For all out there who love ciliates and their relatives, you might want to check out the second paper to come out of my Tetrahymena thermophila Genome Sequencing Project for which the preprint is available in BMC Genomics. In this project we have been sequencing,

    http://phylogenomics.blogspot.com/2008/11/tackling-hairy-beast-ii.html

    Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Eisen JA (2006) PLoS Biol.
    Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. Coyne RS (2008) BMC Genomics.
    November 26, 2008
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  • Dana's online mind and brain magazine Cerebrum has a critical and thought-provoking article arguing that mental illnesses like ADHD and child bipolar disorder are too often being used as fig leaves for social problems that we prefer to think of as blame-free

    http://www.mindhacks.com/blog/2008/11/mental_illness_in_ch.html

    Reporting Bias in Drug Trials Submitted to the Food and Drug Administration: Review of Publication and Presentation. Rising Kristin (2008) Plos Med.
    November 25, 2008
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  • According to John Ioannidis, most published research findings are false. This is because of the Winner’s Curse: scientists need to oversell to get heard, published and funded.Does this affect agrobiodiversity research?Yes, it does.Take this press release

    http://agro.biodiver.se/2008/11/truth-or-consequences/

    Why most published research findings are false. Ioannidis JP (2005) PLoS Med.
    November 21, 2008
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  • Michael Nierenberg, Medical Director of Navigenics comments on “Absence of High Penetrance in SNP Genomic Services” regarding my statement “existing SNP genomic services just arent that useful.” (comment appended below)Rather than entertain

    http://www.thinkgene.com/challenge-to-michael-nierenberg-medical-directo...

    Why most published research findings are false. Ioannidis JP (2005) PLoS Med.
    November 10, 2008
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  • by Merry and ElioOrganelles were endosymbionts that either made good or were enslaved, depending on your point of view. Either way, some of their genes now reside in the nuclear genome of their eukaryote host. We also know that there are some bacterial endosymbionts

    http://schaechter.asmblog.org/schaechter/2008/11/jumping-genes-wolbachia...

    Horizontal gene transfer in eukaryotic evolution. Keeling PJ (2008) Nat Rev Genet.
    Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. Wu M (2004) PLoS Biol.
    Phylogenetic relationships of the Wolbachia of nematodes and arthropods. Fenn K (2006) PLoS Pathog.
    Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Hotopp JC (2007) Science.
    Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Kondo N (2002) Proc Natl Acad Sci U S A.
    November 10, 2008
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  • Continuing with the series of posts highlighting sessions in the Program at the upcoming ScienceOnline09, here are some sessions that deal with collaboration and networking between scientists and between their data.Community intelligence applied to gene annotation:This

    http://www.scienceblogs.com/clock/2008/11/scienceonline09_tapping_into_t...

    Calling on a million minds for community annotation in WikiProteins. Mons B (2008) Genome Biol.
    A wiki for the life sciences where authorship matters. Hoffmann R (2008) Nat Genet.
    WikiPathways: pathway editing for the people. Pico AR (2008) PLoS Biol.
    A gene wiki for community annotation of gene function. Huss JW (2008) PLoS Biol.
    November 3, 2008
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  • news.thinkgene.comTop 10 genomic news as voted by the genomics community. Week of 19 Oct 08PLoS Medicine - Why Most Published Research Findings Are FalseYouTube - Current Issues in Computational Biology and BioinformaticsAfter whole genome sequencing comes

    http://www.thinkgene.com/top-10-genomics-news-from-newsthinkgenecom-week...

    Why most published research findings are false. Ioannidis JP (2005) PLoS Med.
    October 26, 2008
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  • Kevin: Very cool. It’s going to be a while before this is ready for any sort of practical application, but it is another great tool for the cyborg scientists of the future to use.Engineers from the California Institute of Technology have created a “plug-and-play”

    http://www.thinkgene.com/caltech-engineers-build-first-ever-multi-input-...

    Higher-order cellular information processing with synthetic RNA devices. Win MN (2008) Science.
    October 18, 2008
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