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 'genomes'. Sat, 03 Sep 2011 02:08:53 +0100 http://www.medworm.com/index.php?rid=5103510&cid=t_104789_150_f&fid=34768&url=http%3A%2F%2Fpharmagossip.blogspot.com%2F2011%2F08%2Fsynthetic-personal-genomes_07.html (Source: PharmaGossip) PharmaGossip blogs http://www.medworm.com/rss/comments.php?id=5103510 Sun, 07 Aug 2011 06:09:00 +0100 5103510 http://www.medworm.com/index.php?rid=3827292&cid=t_104789_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F08%2Fwhat-is-medical-testing-why-it-matters.html I just was threatened by Daniel MacArthur over at GenomesUnzipped that he was about to delete my comments.He called it trivial. I think he is missing the tremendously simple point.Why is the FDA mad as hell? Medical Claims.Hell, they even told Mary Carmichael in the interview.Alberto Gutierrez = AG"AG: The concern is with everything.""AG: The law requires us to clear devices or approve devices BEFORE they go into the marketplace when they make medical claims"This to me is crystal clear. Make a medical claim. Get regulated.Which is interesting. Because I would say some of what DTCG did was, infer medical claims without making outright claims- silly games . I happen to think that is a shitty way to sell something. But heck it is a way to create a discussion rather than instant regs....."AG: ... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3827292 Fri, 06 Aug 2010 00:45:00 +0100 3827292 http://www.medworm.com/index.php?rid=3552476&cid=t_104789_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F05%2Fpersonal-genomes-in-clinical-care-quake.html With all due respect to the scientists involved in analyzing Stephen Quake's genome in clinical context.You did a major league $h!tty job.No offense. I can only assume this based on what you reported in the lancet paper.Start by asking yourself."Is Stephen healthier because of what that genome and clinical assessment added to his care?"I am speaking precisely on this topic at the Consumer Genomics Conference on June 3rd at 830 AM. So I will hold off on all my arguments....But,The Paper even says"We noted that most of the sequence information is difficult to interpret, and discussed error rates"Ummm, ok. Nice counseling session."patients with whole genome sequence data need information about more diseases with a wide clinical range"Perhaps that person could actually be a physician, maybe a ... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3552476 Tue, 11 May 2010 00:34:00 +0100 3552476 http://www.medworm.com/index.php?rid=3437869&cid=t_104789_134_f&fid=34841&url=http%3A%2F%2Fwww.diabetesmine.com%2F2010%2F04%2Fteam-type-1-working-with-23andme-to-probe-genes-behind-diabetes.html The high-powered diabetic cycling group Team Type 1 has once again pulled off a jaw-dropping feat: they’ve somehow caught the attention of 23andMe, one of just three celeb-status companies in the world offering “personal genomics services” — they scan people’s DNA for details on their ancestry and individual health risks — and convinced them to [...] (Source: Diabetes Mine) Diabetes Mine blogs http://www.medworm.com/rss/comments.php?id=3437869 Mon, 05 Apr 2010 12:00:10 +0100 3437869 http://www.medworm.com/index.php?rid=3291975&cid=t_104789_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F_ZpmUxmMoI4%2F Next week a collection of international scientists with stakes in seeing fungal genome databases evolve and rise to meet the tide of genome data being produced and analyzed from fungi will be meeting in DC.  I am hopeful we’ll come up with some strategies and principles that can guide how this data can be more effectively managed and provided to researchers.  This includes web-based resources, tools, and simply adhering to a standardized formats for genome annotations (like GFF3), automated methods for gene ontology associations on newly annotated genomes, and integration of what I expect to be the major amount of data in the years to come: individual lab produced  genomic, ChIP, resequencing, and RNA-sequencing results. This means the integration (and sharing) of individual labs ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3291975 Sun, 21 Feb 2010 06:14:18 +0100 3291975 http://www.medworm.com/index.php?rid=3223022&cid=t_104789_139_f&fid=38879&url=http%3A%2F%2Fwww.virology.ws%2F003_W3310_10.mp4 Download: .wmv (333 MB) | .mp4 (75 MB) Visit the virology W3310 home page for a complete list of course resources. (Source: virology blog) virology blog blogs http://www.medworm.com/rss/comments.php?id=3223022 Fri, 29 Jan 2010 22:00:18 +0100 3223022 http://www.medworm.com/index.php?rid=1984949&cid=t_104789_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F463183919%2F Genome survey sequencing (1.9X coverage) was generated for Moniliophthora perniciosa, the cause of witches' broom disease on cacao plants. The sequence for this basidiomycete plant pathogen was published in BMC Genomics this week. The authors report a higher number of ROS metabolism and P450 genes. Evaluating whether these copy number differences are significantly different from other basidiomycete fungi and are lineage specific expansions will help determine if these families played a role in the adaptation of this plant pathogen. This work provides an important stepping stone in understanding and eventually controlling this pathogen which is devastating cacao plantations. An associated review describes what we have and can learn about Witches' broom disease. See related: Will you alway... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1984949 Sun, 23 Nov 2008 21:23:17 +0100 1984949 http://www.medworm.com/index.php?rid=1768952&cid=t_104789_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F384488166%2F If you are interested in fungal genetics and genomics, comparative biology, and of course dancing with fungal geneticists, plan to attend the 25th Fungal Genetics Meeting held at the beautiful Asilomar Conference Grounds in Pacific Grove, California. Below is info sent out from the Policy Committee and registration opens in a little over a month.  Budding (and conidiating) artists can also submit a Logo design so we have cool T-shirts to wear. 25th Fungal Genetics Conference Registration and Program The Fungal Genetics Policy Committee invites you to attend the 25th Fungal Genetics Conference, sponsored by the Genetics Society of America.   The meeting will be held March  17-22, 2009 at the Asilomar Conference Center, Pacific Grove, California (near Monterey, California). The FGSC i... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1768952 Fri, 05 Sep 2008 20:41:06 +0100 1768952 http://www.medworm.com/index.php?rid=1658166&cid=t_104789_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F347809614%2F Report concludes that a fungal genome database is of "the highest priority". This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom. The need for a comprehensive database for information about fungi, starting at least with systematic collections of genomic and transcript data, is highlighted as a major need.  Really and sort of new database effort should strive to be more comprehensive and include genetic and population data (alleles, strains) and information like protein-protein, protein-nucleic acid interactions (as Pedro mentioned). But on top of that it, it needs to be comparative so that information from systems that serve as great models can be transferred to other fungal... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1658166 Sun, 27 Jul 2008 23:01:00 +0100 1658166 http://www.medworm.com/index.php?rid=1634966&cid=t_104789_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F338156072%2F Just noticed that the JGI has released the Cochliobolus heterostrophus genome sequence at their site predicting 9,633 protein-coding genes.  Torrey Mesa Research Institute had access to a sequence many years ago, but it isn't until now that public version of this genome is available.  Cochliobolus is has been a model plant pathogen system and its production of T-Toxin by a PKS gene (Yang et al). © Jason Stajich for The Hyphal Tip: Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under pezizomycota. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1634966 Thu, 17 Jul 2008 15:49:31 +0100 1634966 http://www.medworm.com/index.php?rid=1603096&cid=t_104789_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F331008458%2F The American Academy of Microbiology has released a report (PDF) on the Fungal Kingdom outlining importance of research in the kingdom and recommending several areas of priority for future areas of research. One recommendation that makes the top of the list is an integrated database for fungal genomes, something we're keenly interested in seeing happen.  This sort of centralized repository of functional annotation, literature links, and genome sequences and annotation is critical given the 150+ genomes that are available or on their way.  Systematic re-annotation with consistent tools, comparative analyses and gene predictions, and linking gene sequences by homology and ortholog predictions are a critical component to fully utilizing the genomic data that has been produced for the fungi ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1603096 Wed, 09 Jul 2008 18:49:15 +0100 1603096 http://www.medworm.com/index.php?rid=1522208&cid=t_104789_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F312751464%2F NPR had a story this weekend on Cocoa plantation collapse and the ecological aftermath of the changes the witches' broom fungus Moniliophthora perniciosa has wreaked. The genome sequence project for this Homobasidiomycete fungus (also known as Crinipellis perniciosa, phylogenetic relationships discussed by Aime and Philips-Mora 2005) is underway at the Laboratory Genomica e Expressao at UNICAMP, Brazil.  The witches's broom (not this witches' broom) is named because of the bristly form it induces in the cacao plants. The genome project will hopefully improve the diagnosis and treatment work that is needed.  Beyond the insatiable need for chocolate, the NPR story does talk about the impact on farmers, the economy, and the environment with the loss of these cacao plantations. Some links:... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1522208 Mon, 16 Jun 2008 03:57:26 +0100 1522208 http://www.medworm.com/index.php?rid=1484935&cid=t_104789_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F302439648%2F Just finished attending Genetics and Cell Biology of Basidiomycetes in Cape Girardeau, MO which was an intimate gathering of basidiomycetaphiles.  I learned about systems that are used for studying fruiting body development, genetic mapping, pheromone and mating genes, kinesin dynamics, meoitic gene regulation, and a host of topics.  I'm happy I got a chance to meet more folks in the community and learned about where informatics and computational approaches are really needed to push along some of the interpretation of the more than a dozen basidiomycete genomes.  In particular it sounds like the Pleurotus, Schizophyllum, Agaricus bisporus, and Serpula genomes are all marching along to completion with some already in 4X assembly or further.   So we'll further have more samples from... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1484935 Sun, 01 Jun 2008 17:04:19 +0100 1484935 http://www.medworm.com/index.php?rid=1469733&cid=t_104789_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F298471576%2F This month's Genetics has a series of articles exploring the genome (published last year & freely available at Science) of the green algae Chlamydomonas reinhardtii. These manuscripts are primarily genome analyses making for a very bioinformatics focused issue of Genetics. Some of the highlights include: Exploration of snoRNAs finding that a large fraction are clustered in the genome and located in introns. Description of transcription factors and their evolutionary conservation and potential link to multicellularity. Duplication and diversification of the RNA processing machinery for small RNA mediated silencing. Gleaning additional information from Chlamy ESTs that have been over-trimmed. Integrating metabolomics and proteomics into better genome annotation. Evolution of s... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1469733 Tue, 27 May 2008 00:25:59 +0100 1469733 http://www.medworm.com/index.php?rid=1392570&cid=t_104789_134_f&fid=36049&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FDiabetesNotes%2F%7E3%2F261946808%2F The new magic number is 16 among diabetic researchers. Scientists identified 6 new genes which play a role in the development of type 2 diabetes and among the group is the second gene known to also play a role in prostate cancer. By researching how the prostate and diabetic related gene works, we see how raising the risk of one condition can also protect against the other.  These type of results are promising for further medications and sources of treatment. This promises the development of new therapies, and should help scientists to avoid designing drugs aimed at one disorder that inadvertently trigger the other. As these type of results are yielded and with continuing research, we get one step closer to completely understanding type 2 diabetes. We are nearing 200 million persons world... Diabetes Notes blogs http://www.medworm.com/rss/comments.php?id=1392570 Wed, 23 Apr 2008 00:39:51 +0100 1392570 http://www.medworm.com/index.php?rid=1340862&cid=t_104789_134_f&fid=36049&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FDiabetesNotes%2F%7E3%2F261946808%2F The new magic number is 16 among diabetic researchers. Scientists identified 6 new genes which play a role in the development of type 2 diabetes and among the group is the second gene known to also play a role in prostate cancer. As these type of results are yielded with continuing research we get one step closer to completely understanding type 2 diabetes. We are nearing 200 million persons worldwide that are affected by this disease process. “The remarkable recent progress in identifying regions of the genome that increase risk to diabetes—from 3 to 16 in only a year—will help us unravel the complex basis diabetes and may suggest new and better tailored methods to prevent or treat this disease.,” said U-M’s Michael Boehnke, the lead scientist on the Finland-... Diabetes Notes blogs http://www.medworm.com/rss/comments.php?id=1340862 Tue, 01 Apr 2008 13:02:49 +0100 1340862 http://www.medworm.com/index.php?rid=1198081&cid=t_104789_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2008%2F02%2Fof-slelling-and-men.html Way back in 2004 I was bouncing off the ideas of Helix Health. My ex-partner and I even spoke of how great it would be to have datasets with genomes, biomarkers, physical exam and medical history data. We posited how great it would be to sell these datasets to pharma.....We even thought about creating a CRO to carry out the genetic integration of pharma testing creating PGx specialized research.I only mention this because I got a little blasted for tying 23andME with Tuskegee. Well, not really blasting, just a blog post from a really great new blog called Genetic Future.First, we said "Is this a viable business model?" The answer, a resounding yesSecond we said "Will patients be ok with us giving their data to Pharma companies?" The answer, maybe...but only if they received something back.... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=1198081 Sun, 03 Feb 2008 14:51:00 +0100 1198081 http://www.medworm.com/index.php?rid=847516&cid=t_104789_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2007%2F09%2Flrp8-and-familial-miho-hum.html This month in the American Journal of Human Genetics we have some interesting publications. Including an association study identifying a gene known as LRP8. So what is LRP8? It is a receptor for bad cholesterol. When bad cholesterol binds this receptor, platelets (the bricks in your blood that build a clot) become sticky making it easier to thrombose (form a clot).I am interested in this study for several reasons. First, it has been shown that platelets get stick even after ingesting a Big Mac. That's correct. Just one fast food hamburger can theoretically precipitate a heart attack. So naturally we would love to know who. Think Personalized Diet/Nutrigenomics. I wonder if Salugen can hear me now? I still haven't received their "Scientific Data" yet. I will publicize it if they do.Back to ... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=847516 Thu, 06 Sep 2007 23:36:00 +0100 847516 http://www.medworm.com/index.php?rid=812272&cid=t_104789_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2007%2F08%2Fnice-commercial-bogus-advertisement.html Has anyone seen a company named Navigenics....Unless I have been sleeping and missed my daily rss feeds searching pubmed for pharmacogenomics, personalized medicine, genomics, and GWAS I feel they are lying.......They have partnered with Affymetrix and plan to NAVigate GENomICS.The way the Navigenics process works is that you submit a saliva sample and.......They present your future!!!Please take a look at the commercial! What blew me away was this quote......after a misleading commercial where you think that a simple report, delivered in your email, describing your genome will alter your life......"Now is the time when people should be getting this information(their genome). The Science is there, The Information is there....and Now Navigenics is there"Even more disturbing is the fact that... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=812272 Tue, 21 Aug 2007 02:36:00 +0100 812272 http://www.medworm.com/index.php?rid=738945&cid=t_104789_107_f&fid=35025&url=http%3A%2F%2Frrresearch.blogspot.com%2F2007%2F07%2Fmore-about-reduced-variation-at-usss.html The analysis I showed in my last post deserves more discussion. First, it could be improved in a couple of ways. Second, is this an expected result for sequences subject to a molecular drive resulting form biased DNA uptake and unbiased homologous recombination?Improvement one: better controls. As it stands, the comparisons of variation at USS positions is compared to adjacent positions that are not part of the USS motif. This is a bit weak, because some of these positions may contribute to DNA uptake but not show up as 'motif'. A better control comparison would be with random segments of the genome. This is easy to do, as I already have a set of 3500 segments of 39bp (like the USS-centered segments) that I used as a control for the analysis of covariation. Well, 'easy' to see how to do (c... RRResearch blogs http://www.medworm.com/rss/comments.php?id=738945 Tue, 17 Jul 2007 00:07:00 +0100 738945 http://www.medworm.com/index.php?rid=687120&cid=t_104789_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2007%2F05%2Fhemochromatosis-stories.html Lisa Lee posted about "House" last night. It made me laugh. I couldn't help but think how the media really portrays health care. It is down right scary. Most, like the media over-hype the non-dramatic and fail to catch the essence of medical culture. It is also scary how they miss the REAL issues. Did you know that in real life if you are "coded" you have less than a 15% chance of leaving the hospital? On TV it is over 75% And the way they portray disease......don't get me started :(But what's even scarier is having to suffer through disease. I always like to check out the support blogs and this is one I feel strongly about. They express their difficulty with phlebotomy, the traditional treatment for Hemochromatosis.Which brings me to my last comment. The American Gastroenterological Assoc... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=687120 Wed, 30 May 2007 22:03:00 +0100 687120 http://www.medworm.com/index.php?rid=623758&cid=t_104789_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F118106455%2F Things I noticed returns for another week. A lot happened this past week, and I’m still way behind on my feed reading. The following is just a smattering of some of the news items that caught my attention. Trying a simpler format as well. Intel hosted the Intel science and engineering fair, the “world’s largest pre-college celebration of science”. The press release is here A couple of people I know are big fans of the Java posse podcast. Our friends at Google have taken a page from Java posse and launched the Google Developer podcast. Enjoy My favorite event, Ignite continues to spread Hari has already blogged on this subject, so just a small mention at bbgm. Say what you want about Jonathan Rothberg, but no one can accuse him of a lack of enthusiasm or of not thin... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=623758 Sun, 20 May 2007 05:47:18 +0100 623758 http://www.medworm.com/index.php?rid=486421&cid=t_104789_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F102813755%2F Science writer Carl Zimmer of The Loom has done the count and arrived at 18,308 genes in the human genome. The pie shows that we’re now down to just 18,308 genes. That’s over 8,000 genes fewer than six years ago. Many sequences that once looked like full-fledged genes, capable of generating a protein, now don’t make the grade. Some genes turned out to be pseudogenes–vestiges of genes that once worked but have been since wrecked by mutations. In other cases, DNA segments that appeared to be parts of separate genes have turned out to be part of the same gene. At this rate, we won’t be much better than fruit flies as the gene count continues to be refined. Carl’s organism of choice, E. coli, stands at 3200 genes on one chromosome. Tags: carl zimmer, genet... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=486421 Mon, 19 Mar 2007 14:35:33 +0100 486421