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 'comparative genomics'. Sat, 03 Sep 2011 02:39:36 +0100 http://www.medworm.com/index.php?rid=4953226&cid=t_176982_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FgVptTyL-3Q8%2F [via Teun Boekhout] This year looks like another great lineup of speakers for the EMBO Comparative Genomics of Microorganisms: ‘Understanding the Complexity of Diversity’ 15-20 Oct 2011 Sant Feliu de Guixols, Spain. Andrew Allen J. Craig Venter Institute US Anders Blomberg Göteborg University SE Chris Bowler École Normale Supérieure FR Gertraud Burger University of Montreal CA Bernard Dujon Institut Pasteur FR Toni Gabaldón CRG, Barcelona ES Ursula Goodenough Washington University US Michael Gray Dalhousie University CA Joseph Heitman Duke University US Christiane Hertz-Fowler University of Liverpool UK Regine Kahmann Max Planck Institute DE Patrick Keeling University of British Columbia CA Nicole King UC, Berkeley US Edda Klipp Humboldt Univers... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4953226 Mon, 20 Jun 2011 20:18:12 +0100 4953226 http://www.medworm.com/index.php?rid=4714227&cid=t_176982_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2011%2F04%2Fphylogenetics-and-phylogenomics-for-microbial-genomes.html from Luo et al (2011) in Microbial Population GeneticsGenerally, microorganisms, in particular prokaryotes often lack morphological and behavioral characters amenable to phylogenetic analysis. Such a lack of information in these areas makes gene sequence information the most prevalent source of data for phylogenetic analysis in pre-genomic era. Molecular phylogenetics based on single genes, in particular the small-subunit rRNA (SSU rRNA) , has laid the foundation for a modern classification system, conceptually represented by the 'universal tree of life'. However, phylogenetic trees based on single genes or gene families may show conflict results due to a variety of problem, such as mutational saturation of the single genes and horizontal gene transfer. Consequently, although SSU rRNA gene... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=4714227 Fri, 15 Apr 2011 04:00:12 +0100 4714227 http://www.medworm.com/index.php?rid=4450452&cid=t_176982_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FsUICiC0b8Ac%2F Announcing an upcoming conference in October. Comparative Genomics Of Eukaryotic Microorganisms: Understanding The Complexity Of Diversity It will be held in Sant Feliux, Spain October  15-20, 2011. The website has more details including an impressive slate of speakers. I can attest to it being a great meeting from my attendance 2 years ago. A great venue and excellent speakers and plenty of time to linger and discuss ideas and research over meals and coffee breaks.   (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4450452 Tue, 08 Feb 2011 18:00:05 +0100 4450452 http://www.medworm.com/index.php?rid=4285301&cid=t_176982_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FrYtx4OOtgDY%2F Though a bit cliche, I think the metaphor of “presents under the tree” of some new plant pathogen genomes summarized in 4 recent publications is still too good to resist.  There are 4 papers in this week’s Science that will certainly make a collection of plant pathogen biologists very happy. There are also treats for the general purpose genome biologists with descriptions of next generation/2nd generation sequencing technologies, assembly methods, and comparative genomics. Much more inside these papers than I am summarizing so I urge you to take look if you have access to these pay-for-view articles or contact the authors for reprints to get a copy. These include the genome of biotrophic oomycete and Arabidopsis pathogen Hyaloperonospora arabidopsidis (Baxter et al). Wh... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4285301 Thu, 23 Dec 2010 16:11:50 +0100 4285301 http://www.medworm.com/index.php?rid=4229035&cid=t_176982_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F12%2Fcomparative-genomics-of-metabolic-pathways-in-microbial-genomes.html from Luo et al (2011) in Microbial Population GeneticsUnderstanding the regulatory mechanisms should allow the examination of engineering pathways with pre-determined expression patterns (i.e. expression is activated by a given compound or in a specific environmental or physiological condition). Metabolic pathways have evolved to execute their function efficiently, while tolerating perturbations, such as changes in environmental parameters or in the physiological status of the cell. Below we describe some of the databases and programs for integrated analyses of metabolic pathways.KEGGKEGG (Kyoto Encyclopedia of Genes and Genomes) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking ge... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=4229035 Sat, 04 Dec 2010 05:00:08 +0100 4229035 http://www.medworm.com/index.php?rid=4224706&cid=t_176982_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F12%2Fcomparative-genomics-microarray-analyses-technology.html from Luo et al (2011) in Microbial Population GeneticsThe advent of DNA microarray technology has greatly expanded our ability to monitor changes in the abundance of transcripts. Such a development has been a milestone in several areas of microbiology. In clinical microbiology, microarrays are used for microorganism detection and identification and gene-expression analysis. DNA microarrays have allowed us to monitor the effects of pathogens on host-cell gene expression in a much greater depth and on a significantly broader scale than previous single gene studies. The results generated by these studies are complex, and few systematic studies have been carried out to compare results among studies. Comparative transcriptomics - whole genome mRNA transcript profiling using microarrays.Whole-ge... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=4224706 Fri, 03 Dec 2010 12:34:05 +0100 4224706 http://www.medworm.com/index.php?rid=4189707&cid=t_176982_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F11%2Fanalytic-tools-in-comparative-genomics.html from Luo et al (2011) in Microbial Population GeneticsThe rapid accumulation of bacterial genome sequences has opened up a new field of research, that of comparative genomics. Interpretation of raw DNA sequence data involves the identification and annotation of genes, proteins, and regulatory and/or metabolic pathways. Therefore, there is a natural shift towards the creation of tools for viewing and manipulating data in a comparative genomics context. In addition, genome annotations need to be reprocessed on a regular basis to take into account the newly characterized functions of genes. Furthermore, large-scale functional analyses generate additional data that contribute to the interpretation of genomic data. These considerations are driving the research community to think about how to ma... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=4189707 Mon, 22 Nov 2010 17:23:46 +0100 4189707 http://www.medworm.com/index.php?rid=3354513&cid=t_176982_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F03%2Fproblem-with-comparative-whole-genomics.html I have been having this debate with a good friend and mentor. I think Complete Genome Comparison could be a Killer App.He thinks it could be a legal and scientific nightmare.I think he's right.Let's really think about this for a second. If history has anything to say about human behavior we need look no further than the secrecy with which gene sequences were hunted.Hell, even Science makes mention of it several times. The Article "Data Hoarding Blocks Progress in Genetics" might be a good read if you are interested.Guys like Daniel MacArthur over at Genetic future point out some good points about the difficulty in making sense of all the noise that exists in genomes. But the problems go even further than that. Hell, CNV can differ in IDENTICAL TWINS!!!! Say Wha?So what do we have to say ab... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3354513 Thu, 11 Mar 2010 15:11:00 +0100 3354513 http://www.medworm.com/index.php?rid=3231108&cid=t_176982_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F02%2Fmicrobial-phylogenetics-methods.html The purpose of phylogenetic analysis is to understand the past evolutionary path of organisms. Even though we will never know for certain the true phylogeny of any organism, phylogenetic analysis provides best assumptions, thereby providing a framework for various disciplines in microbiology. Due to the technological innovation of modern molecular biology and the rapid advancement in computational science, accurate inference of the phylogeny of a gene or organism seems possible in the near future. There has been a flood of nucleic acid sequence information, bioinformatic tools and phylogenetic inference methods in public domain databases, literature and worldwide web space. Phylogenetic analysis has long played a central role in basic microbiology, for example in taxonomy and ecology. In a... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3231108 Tue, 02 Feb 2010 14:25:00 +0100 3231108 http://www.medworm.com/index.php?rid=3159499&cid=t_176982_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2010%2F01%2Fmolecular-phylogeny-of-microorganisms.html A proper understanding of the diversity, systematics and nomenclature of microbes is increasingly important in many branches of biological science. The molecular approach to phylogenetic analysis, pioneered by Carl Woese in the 1970s and leading to the three-domain model (Archaea, Bacteria, Eucarya), has revolutionized our thinking about evolution in the microbial world. The technological innovation of modern molecular biology and the rapid advancement in computational science have led to a flood of nucleic acid sequence information, bioinformatic tools and phylogenetic inference methods. Phylogenetic analysis has long played a central role in microbiology and the emerging fields of comparative genomics and phylogenomics require substantial knowledge and understanding of phylogenetic analy... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3159499 Mon, 11 Jan 2010 16:06:00 +0100 3159499 http://www.medworm.com/index.php?rid=2793358&cid=t_176982_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2Ft8b-RRiEZtg%2F A nice series of comparative genomics articles have been published in the last few weeks. The pace of genome sequencing has accelerated to the point that we have lots of sequencing projects coming from individual labs and small consortia not necessarily from genome centers. We are seeing a preview of what next (2nd) generation sequencing will enable and can start to imagine what happens when even cheaper 3rd generation sequencing technologies are applied. I’m behind in reviewing these papers for you, dear reader, but I hope you’ll click through and take a look at some of these papers if you are interested in the topics. In the following set of papers we have some nice examples of comparative genomics of closely related species and among a clade of species. The papers mentioned ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2793358 Mon, 14 Sep 2009 18:14:35 +0100 2793358 http://www.medworm.com/index.php?rid=2630307&cid=t_176982_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FM-HrlX4ETbE%2F If you can make plans to head to Spain in October you should consider attending the EMBO conference on Comparative Genomics of Eukaryotic Microorganisms October 17-22 outside of Barcelona. Lots of very interesting speakers and I’ve got the chance to be there to speak about ideas and results using comparative genomics to study evolution of early diverging fungal lineages. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2630307 Wed, 22 Jul 2009 17:41:49 +0100 2630307 http://www.medworm.com/index.php?rid=2902920&cid=t_176982_132_f&fid=35001&url=http%3A%2F%2Farchive.nodalpoint.org%2F2008%2F07%2F02%2Ftree_of_life I'm not much of an evolutionary biologist, but Jonathan Eisen asked for help and I can't resist. So, in the name of Science, and via the goodness of nodalpoint, here is some deserved Google Juice for various Trees of Life on the Web. Jonathan Eisen's "Tree of Life" blog Tree of Life Web Project Tree of life (science) - Wikipedia, the free encyclopedia Green Tree of Life at Berkeley Fungal Tree of Life Project Beetle Tree of Life project Fly Tree of Life project Mammal Tree of Life project Cypriniformes Tree of Life project Liverwort Tree of Life Project Early Bird Tree of Life project Angiosperm Tree of Life project Cnidaria Tree of Life Project Decapoda Tree of Life Project There, I've done my bit for Science, no... nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=2902920 Wed, 02 Jul 2008 22:44:17 +0100 2902920 http://www.medworm.com/index.php?rid=1492123&cid=t_176982_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F303770716%2F We're excited that a Penicillium marneffei grant to Mat Fisher and collaborators has been funded by the Welcome Trust. It includes a collaboration with University College London, our lab, JCVI, and Univ of Melbourne. This project will explore functional and comparative genomics approaches to studying the fungus which primarily infects immune compromised individuals in south-east asia where it is found associated with bamboo rats.  Scientists at Imperial College London have received almost £350 000 from the Wellcome Trust, the UK's largest medical research charity, to study Penicillium marneffei, the only Penicillium fungus to cause serious disease in humans. The researchers aim to find out what makes this particular fungus pathogenic. Read the rest of the release. © Jason Staji... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1492123 Tue, 03 Jun 2008 21:10:13 +0100 1492123 http://www.medworm.com/index.php?rid=1354055&cid=t_176982_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F265427447%2F The Broad Institute has made available the Schizosaccharomyces octosporus genome sequence producing another model system (S.pombe) with several related species for comparative genomics.  I believe S. octosporus genome was entirely sequenced with 454 technology.   The other genome sequences in the Taphrina clade include the S. japonicus genome. S. octosporus is pretty interesting as it grows filamentously and is 8-spored unlike S. pombe. The origin of this filamentous growth would be quite important to understand how reversions to simpler fission yeast forms form and whether this is loss of whole gene families or remodeling of gene networks. There is also some preliminary (old) sequence from Pneumocystis (although it is hard to track down that sequence, a paper from 2006 says there is... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1354055 Mon, 07 Apr 2008 04:50:17 +0100 1354055