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 'genome'. Sat, 03 Sep 2011 01:53:04 +0100 http://www.medworm.com/index.php?rid=5125968&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FgEUN4aYZF2A%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? And here is our regular feature. Send us a photo and we will spotlight a different person each week. This time around, we note that Acucela hired Michelle Carpenter as senior vp for regulatory affairs and development operations. Most recently, she executive director for regulatory affairs at Dow Pharmaceutical Sciences. Before that, she was vp of regulatory affairs at Oculu... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=5125968 Fri, 12 Aug 2011 12:11:41 +0100 5125968 http://www.medworm.com/index.php?rid=5076973&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FVQLvzLRbR7U%2F Hosts: Vincent Racaniello, Michael Schmidt, Margaret McFall-Ngai, and Elio Schaechter On episode #12 of the podcast This Week in Microbiology, Vincent, Margaret, Michael and Elio review the use of photothermal nanoblades to dissect the Burkholderia intracellular life cycle, and manipulation of chromosomes in vivo for genome-wide codon replacement in E. coli. Click the arrow above to play, or right click to download TWiM #12 (52 MB, .mp3, 75 minutes). Subscribe to TWiM (free) on iTunes, Zune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app. Links for this episode: Using a photothermal nanoblade to study intracellular life cycle (PNAS) Reynolds number Theriot lab movie collection Manipulation of chromosomes in vivo (Science) Stop codons Church... virology blog blogs http://www.medworm.com/rss/comments.php?id=5076973 Fri, 29 Jul 2011 17:27:48 +0100 5076973 http://www.medworm.com/index.php?rid=5077936&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2011%2F07%2F28%2Fsynthetic-life-craig-venter-ted-talk%2F TEDMED just released the presentation of Craig J. Venter, the father of the human genome project and other interesting initiatives including the race for the synthetic life. (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=5077936 Thu, 28 Jul 2011 19:56:23 +0100 5077936 http://www.medworm.com/index.php?rid=5051238&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FbCFE16uqAmc%2F And so, another working week will soon draw to a close. As you know, this is our welcome signal to daydream about weekend plans. Our agenda is modest - a dip in the pool, an evening of soccer with one of the short people and catching up on some reading. What about you? Given the heat, a few indoor activities may be in order. How about an air-conditioned drive in the country or a movie marathon (if you avoid paying for more than one flick, you have a bargain). You could take a trip to the mall and spur the economy. Or you could stay home and turn on the telly for updates on the debt talks. Whatever you do, have a good time and stay cool. See you soon… Bristol-Myers Buys Amira Pharmaceuticals For Up To $475M (Xconomy) Merck And Simcere Pharmaceutical Form Joint Venture (China Daily) Ex... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=5051238 Fri, 22 Jul 2011 11:44:20 +0100 5051238 http://www.medworm.com/index.php?rid=4975123&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FafmmTOiAVac%2F Hosts: Vincent Racaniello, Alan Dove, and Dickson Despommier Vincent, Alan, and Dickson discuss the reduction in genome size of Mimivirus upon passage in amoeba, and analysis of the microbiome of honeybees. Click the arrow above to play, or right-click to download TWiV #139 (96 MB .mp3, 80 minutes). Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, by email, or listen on your mobile device with the Microbeworld app. Links for this episode: Mimivirus genome reduction after amoebal culture (PNAS) Carbohydrate-Active enZYmes database Analysis of the honey bee microbiome (PLoS One) The colony-collapse blues (TWiV 104) Blessed are the beekeepers (Wall Street Journal) TWiV on Facebook Letters read on TWiV 139 Weekly Science Picks Alan – Life Before the Dinos... virology blog blogs http://www.medworm.com/rss/comments.php?id=4975123 Sun, 26 Jun 2011 18:18:27 +0100 4975123 http://www.medworm.com/index.php?rid=4848154&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FkTurjNnKuyc%2F And so another working week will soon draw to a close. This is, of course, our signal to daydream about weekend plans. Our modest agenda includes yardwork, hanging with assorted short people and another installment in the ‘Let’s-see-them-before-they-die‘ concert series. And you? Anything special in the pipeline? How about curling up with a good e-book? Or a dinner with a favorite someone? Or maybe just a walk in the park? Whatever you do, have a great time and be safe. See you soon… FDA Approves J&J HIV Med For Combo Use (Reuters) EU OKs Bloodthinner From Pfizer And Bristol (Associated Press) EMA Approves Glaxo And Human Genome’s Benlysta For Lupus (Reuters) Pfizer Truck Robbed On Way To CVS (Securing Pharma) AstraZeneca To Eliminate 135 Jobs In Massachus... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4848154 Fri, 20 May 2011 11:39:57 +0100 4848154 http://www.medworm.com/index.php?rid=4848028&cid=t_104781_113_f&fid=34634&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FEmrAndHipaa%2F%7E3%2FKu2UJfCTGwo%2F Katherine Rourke, on my sister site EMR and EHR, wrote an interesting piece on Adding Genomic Info to the EMR. Here’s a short excerpt from the post. You should go and read the rest of the post as well. As the author notes, some specialties have already begun to tailor drug treatments to individual patients based on their genomic profile. For example, DNA sequencing of tumors in non-Hodgkin’s and Mantle Cell lymphoma can lead to personalized cancer vaccines that can produce great results, notes writer Gerry Higgins of the NIH. Such data can also be used for a growing number of clinical situations, such as tailoring Coumadin doses to specific patients and providing psychiatric patients with the appropriate drug. I’d been meaning to write about genomics and EMR for a while and ... EMR and HIPAA blogs http://www.medworm.com/rss/comments.php?id=4848028 Tue, 17 May 2011 18:27:02 +0100 4848028 http://www.medworm.com/index.php?rid=4733273&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FhsKU3_uGzUg%2F Hosts: Vincent Racaniello, Cliff Mintz, Michael Schmidt, and Ronald Atlas. Vincent, Cliff, Michael and Ron discuss the genome sequqnce of a mercury-methylating bacterium and the antimicrobial effects of nanoparticles. Click the arrow above to play, or right click to download TWiM #5 (52.5 MB .mp3, 76 minutes). Subscribe to TWiM (free) on iTunes,  Zune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app. Image of Biofilm of Desulfovibrio desulfuricans by PNNL – Pacific Northwest National Laboratory via flickr Links for this episode: Genome sequence of a mercury-methylating Desulfovibrio strain Dusulfovibrio commentary in ScienceDaily Review on the genus Desulfovibrio (pdf) Perturbation of an Artic soil microbe community by nanoparticles N... virology blog blogs http://www.medworm.com/rss/comments.php?id=4733273 Thu, 21 Apr 2011 00:00:46 +0100 4733273 http://www.medworm.com/index.php?rid=4734446&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2011%2F04%2F20%2Fopening-your-genome-to-the-public%2F Ramūnas Janavičius, a clinical geneticist (MD) and blogger at Cancer Genetics, just made his genomic data open to the public. The Personal Genome project did the same with 10 volunteers. An excerpt from the entry of Ramunas: Today is a good day. I can not imagine a better day than personal birthday (and forthcoming DNA Day) to share my personal genome scan information, which you can find in this blog HERE* [GenomeScan_RJv2]. This is quite low density profile generated through 23andMe v.2 genotyping on Illumina Hap550+ array while a year ago. He shared his genomic data under Creative Commons 3.0 license. Though it would be better to see his genomic raw data, but the Excel file with the SNP variants is also very interesting. The first commenter pointed out that he doesn’t have curly ... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=4734446 Wed, 20 Apr 2011 08:04:47 +0100 4734446 http://www.medworm.com/index.php?rid=4636107&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FHO2eJzZBWaY%2F Hosts: Vincent Racaniello, Cliff Mintz, Jo Handelsman, and Ronald Atlas. On episode #3 of the podcast This Week in Microbiology, Vincent, Jo, Cliff, and Ron explore the genome analysis done in support of the Amerithrax investigation, and an insecticidal enterotoxin-deficient mutant of Bacillus thurigiensis. Click the arrow above to play, or right-click to download TWiM #3 (55 MB .mp3, 60 minutes). Subscribe to TWiM (free) at iTunes, the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with the Microbeworld App. Links for this episode: Bacillus anthracis genome analysis for Amerithrax investigation (PNAS) US Department of Justice summary of Amerithrax investigation (pdf) Anthrax expert comments on FBI Amerithrax report Genome data not sufficient for convicti... virology blog blogs http://www.medworm.com/rss/comments.php?id=4636107 Fri, 25 Mar 2011 16:36:43 +0100 4636107 http://www.medworm.com/index.php?rid=4611003&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FWXsonFvU_bM%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? And here is our regular feature. Send us a photo and we will spotlight a different person each week. This time around, we note that MTI Information Technologies, which provides marketing services to healthcare providers, hired Brian Tvenstrup as sr vp of business analytics. Previously, he headed analytics for First Equity Card, a commercial lender to small businesses, and w... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4611003 Fri, 18 Mar 2011 12:03:11 +0100 4611003 http://www.medworm.com/index.php?rid=4605985&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FRltCYzZI5qs%2F Here’s the schedule for the Tools session we’re having on Friday at Asilomar. I hope to be able to post everyone’s slides after the meeting as well. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4605985 Thu, 17 Mar 2011 15:00:13 +0100 4605985 http://www.medworm.com/index.php?rid=4592394&cid=t_104781_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fa-new-treatment-for-lupus%2F2011.03.15 Lupus, an autoimmune disease, [recently] turned up on the front page of the Wall Street Journal (WSJ). It cropped up, also, on the first page of the New York Times business section, and elsewhere. Scientific American published a nice online review just now. The reason is that the FDA has approved a new monoclonal antibody for treatment of this condition. The drug belimumab (Benlysta), targets a molecule called BlyS (B-lymphocyte Stimulator). The newspapers uniformly emphasize that this drug marks some sort of triumph for Human Genome Sciences, a biotech company that first reported on BlyS in the journal Science way back in 1999. BlyS triggers B cells to produce antibodies that in patients with lupus tend to bind and destroy their own cells’ needed machinery, causing various joint, lung... Better Health blogs http://www.medworm.com/rss/comments.php?id=4592394 Tue, 15 Mar 2011 18:00:36 +0100 4592394 http://www.medworm.com/index.php?rid=4570762&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FP1ew3fxxnEE%2F Every so often, a new approval generates significant attention. And the FDA endorsement of Benlysta, the first new treatment for lupus in 56 years, is one of those moments. The injectable med, which will be marketed by Human Genome Sciences and GlaxoSmithKline, is forecast to generate at least $2 billion in annual sales thanks to a $35,000 price tag, despite cautionary language for certain patients. The med, which will actually about cost $40,000 in the first year, will become available later this month. There is no REMS requirement or Black Box warning, which heartened Wall Street. Nonetheless, insurance reimbursement remains somewhat fuzzy. Meanwhile, Human Genome Sciences agreed to conduct another clinical trial in African-American lupus patients. Here’s why… “As expec... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4570762 Thu, 10 Mar 2011 13:40:03 +0100 4570762 http://www.medworm.com/index.php?rid=4570763&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FNmT5C8tDVOY%2F Hello, everyone, and nice to see you again. A spot of rain is falling on the Pharmalot corporate campus, but our spirits remain sunny thanks to the Morning Mayor, who would always say: ‘Every brand new day should be unwrapped like a precious gift.’ So while you tug on the ribbon, please join us for a cup of stimulation and help us scan the news of the world. Hope your day goes well and do stay in touch… FDA Approves First New Lupus Drug In 56 Years (Associated Press) Vertex Moves Ahead With Epilepsy Drug (Boston Business Journal) J&J Hip Replacement Has 49 Percent UK Failure Rate (Bloomberg News) Epizyme And Eisai Form A Partnership (Boston Globe) FDA OKs Hospira Generic Of Taxotere Cancer Med (Reuters) Quintiles Eyes More Deals With Credit Facility (Outsourcing Phar... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4570763 Thu, 10 Mar 2011 12:59:47 +0100 4570763 http://www.medworm.com/index.php?rid=4560491&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F1ryY5ataWZ8%2F As an update to previous post, the N. crassa annotation has been updated to version 5 on the Broad Institute website. Previously the data was not yet available for this update, but as of 8-Mar-2011 it is.  The assembly hasn’t changed but the annotation is updated and includes some fixes to improperly renamed locus names.  On the N. crassa genome site you can see files with the history of loci through this to determine if a locus name was improperly changed in the past. This should be rectified in the currently released annotation, and definitely encourage you to take it for a spin and report back to the Broad Institute if you have any questions. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4560491 Tue, 08 Mar 2011 22:43:27 +0100 4560491 http://www.medworm.com/index.php?rid=4507281&cid=t_104781_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fthe-human-genome-turns-10%2F2011.02.22 The human genome has been around for a bit more than ten years, but on February 15, 2001, the first complete human genome sequence was published. This was nothing short of a revolution within medicine. Since then, great advancements have been made in our understanding of genetics and its associations with human traits and diseases. Nature is celebrating this tenth birthday with a special titled “Human Genome at Ten.” In it, multiple papers reflect on what we learned and discovered, what is still unknown, and what we can expect for the near future. Best of all, Nature has packaged the special in a free iPad app for everyone to read, which features interactive graphs, videos, and audio commentaries. Nature special: The Human Genome at Ten… iTunes link: Nature Human Genome S... Better Health blogs http://www.medworm.com/rss/comments.php?id=4507281 Tue, 22 Feb 2011 18:00:52 +0100 4507281 http://www.medworm.com/index.php?rid=4477979&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FG1cDclcbn9Q%2F Here is a message from the Broad Institute about a gene annotation update that was made recently in response to an issue that was revealed in the June 2010 release.  This new version is called V5 and should be on its way to GenBank. Dear Neurospora scientists, Recently we discovered an issue with the way locus tags were assigned to our most recent Neurospora gene set, released publicly on the Broad website in June of 2010. Many genes in this gene set have mismatched locus numbers compared to the same genes released in February 2010. Adding to the confusion, both releases were labeled version 4. To remedy this we have recalled the June locus numbers and released a new, version 5 gene set. Genes in this set have been numbered to preserve historical locus numbers (back to the original gen... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4477979 Mon, 14 Feb 2011 23:36:32 +0100 4477979 http://www.medworm.com/index.php?rid=4436886&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2011%2F02%2F04%2Flinked-electronic-medical-records-for-genomic-research%2F I’ve just come across an interesting study on BMC Medical Genomics. Authors aim at linking electronic medical records and genomic data which is I believe a very promising approach. The Personal Genome Project did something similar but only with 10 participants. The eMERGE (electronic MEdical Records and GEnomics) Network is an NHGRI-supported consortium of five institutions to explore the utility of DNA repositories coupled to Electronic Medical Record (EMR) systems for advancing discovery in genome science. eMERGE also includes a special emphasis on the ethical, legal and social issues related to these endeavors. Current progress: The primary site-specific phenotypes for which samples have undergone genome-wide association study (GWAS) genotyping are cataract and HDL, dementia, elec... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=4436886 Fri, 04 Feb 2011 14:24:23 +0100 4436886 http://www.medworm.com/index.php?rid=4429047&cid=t_104781_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fspectroscopynow-february-1-issue.html Valentine’s Day science – Spring may not quite be in the air, but Valentine's Day is on the way and love is certainly on the minds of researchers in the US. A small functional magnetic resonance imaging has been used to investigate love. The study revealed brain activity in 10 women and 7 men when they looked at photos of their spouses to whom they had been married an average of 21 years. The results? Apparently, love lasts. Grapes of worth – The position in which a grape in a bunch matures on the vine seems to influence the production of different metabolites more than the specific genetic clone from which the vine is raised, according to new NMR data. Researchers have turned to NMR spectroscopy to help them analyse and characterise the chemistry of grape berries. T... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4429047 Mon, 31 Jan 2011 16:09:50 +0100 4429047 http://www.medworm.com/index.php?rid=4419182&cid=t_104781_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fspectroscopynow-february-1-issue.html Valentine’s Day science – Spring may not quite be in the air, but Valentine's Day is on the way and love is certainly on the minds of researchers in the US. A small functional magnetic resonance imaging has been used to investigate love. The study revealed brain activity in 10 women and 7 men when they looked at photos of their spouses to whom they had been married an average of 21 years. The results? Apparently, love lasts. Grapes of worth – The position in which a grape in a bunch matures on the vine seems to influence the production of different metabolites more than the specific genetic clone from which the vine is raised, according to new NMR data. Researchers have turned to NMR spectroscopy to help them analyse and characterise the chemistry of grape berries. T... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4419182 Mon, 31 Jan 2011 16:09:50 +0100 4419182 http://www.medworm.com/index.php?rid=4382950&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F-uLkBowhkas%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? And here is our regular feature. Send us a photo and we will spotlight a different person each week. This time around, we note that Concert Pharmaceuticals hired James Shipley as chief medical officer. Previously, he was was senior vp of clinical development, medical and regulatory affairs at Indevus Pharmaceuticals, which is now owned by Endo Pharmaceuticals, and before th... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4382950 Fri, 21 Jan 2011 13:08:51 +0100 4382950 http://www.medworm.com/index.php?rid=4377789&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FaVe4cHW2HSM%2F In a move that some may consider long overdue, more than a dozen of the most prestigious medical journals will consider requiring doctors who submit studies to disclose any payments received from hedge funds and other large investors. The proposal is expected to be discussed at the next annual meeting of The International Committee of Medical Journal Editors, which is scheduled for June, according to a spokeswoman for the New England Journal of Medicine. The possibility follows ongoing concerns about conflicts of interest between researchers and the pharmaceutical industry and the extent to which undisclosed financial relationships may unduly influence medical research and, from there, medical practice. But the issue is also encompassing financial ties to large investors, given the growing... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4377789 Thu, 20 Jan 2011 15:21:05 +0100 4377789 http://www.medworm.com/index.php?rid=4322636&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FgRRZQti7WfU%2F New genomes from Microsporidia are on the way from the Broad Institute and other groups, and will be a boon to those working on these fascinating creatures. Microsporidia are obligate intracellular parasites of eukaryotic cells and many can cause serious disease in humans. Some parasitize worms and insects too. The evolutionary placement of these species in the fungi is still debated with recent evidence placing them as derived members of the Mucormycotina based on shared synteny (conserved gene order), in particular around the mating type locus.  There is still some debate as to where this group belongs in the Fungal kingdom, with their highly derived characteristics and long branches they are still make them hard to place.  The synteny-based evidence was another way to find a phyloge... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4322636 Fri, 07 Jan 2011 19:24:01 +0100 4322636 http://www.medworm.com/index.php?rid=4298767&cid=t_104781_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2010%2F12%2F29%2Fuh-biochemist-works-to-revolutionize-ovarian-cancer-treatment-by-unleashing-the-power-of-micrornas-nanotechnology%2F The day when an ovarian cancer patient can treat her tumor with a single, painless pill instead of a toxic drug cocktail is the ultimate goal of the pioneering research of a University of Houston (UH) scientist.  Preethi Gunaratnee, assistant professor in the department of biology and biochemistry, is studying a class of tiny genetic [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=4298767 Wed, 29 Dec 2010 23:01:17 +0100 4298767 http://www.medworm.com/index.php?rid=4285301&cid=t_104781_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=4233424&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F69Q-JUDmm-A%2F Welcome to the working week. We hope the weekend was refreshing and restful, although now, of course, the routine resumes. To prepare, we are brewing the mandatory cup of stimulation. Meanwhile, we would like to note that we are hosting a webinar on Thurs., Dec. 9 about the FDA’s Accelerated Approval process (please look here). Please join us. And now, the news of the world. Have a great day and if you run into Jeff Kindler, please send our regards… Celgene Stock Hurt By Revlimid Cancer Data (TheStreet) Elan Replaces Martin With Former Glaxo CEO Ingram (Bloomberg News) AstraZeneca Bloodthinner Gets EU Approval (Reuters) FDA Delays Decision On Benlysta Lupus Med (Associated Press) China To Lead Innovation By 2020: AstraZeneca Survey (PharmaTimes) (Source: Pharmalot) Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4233424 Mon, 06 Dec 2010 12:45:55 +0100 4233424 http://www.medworm.com/index.php?rid=4159501&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F63gV3zwM57s%2F On Tuesday, an FDA advisory panel will review the first new treatment for lupus in decades. And the early indications are that Benlysta, which is being developed by Human Genome Sciences, will win an endorsement. At least that’s how some Wall Street analysts are interpreting the FDA briefing documents filed this morning, even though the stock is trading down. If approved, Benlysta is widely expected to become a blockbuster and possibly make Human Genome a takeover target. The drugmaker, by the way, is developing Benlysta with GlaxoSmithKline. But what issues did the FDA raise? The agency noted two large studies demonstrated a statistically significant difference in the number of lupus patients who responded to Benlysta compared with a placebo. But there were reservations: infections ... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4159501 Fri, 12 Nov 2010 15:01:25 +0100 4159501 http://www.medworm.com/index.php?rid=4159506&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FUn-ROdfR8Lc%2F Good morning, everyone. Once again, the time has come to daydream, just a little, about the upcoming weekend. We envision long walks with the official Pharmalot mascots, entertaining our short people and, in the name of getting exercise, raking countless leaves shed by our towering pin oaks. What about you? How about a drive in the country? Some time with that special someone? Maybe a good book is in order. Whatever you do, have a great time and be safe. Meanwhile, here is the news of the world. See you soon… The AHA Meeting And Some Big Heart Drugs (Reuters) UK’s NICE Rejects Roche’s Avastin For Colorectal Cancer (Bloomberg News) J&J To Release Bloodthinner Results (The Wall Street Journal) Japan’s Otuska To Raise $2.8 Billion In Record IPO (Reuters) AstraZene... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4159506 Fri, 12 Nov 2010 12:54:49 +0100 4159506 http://www.medworm.com/index.php?rid=4142559&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Fmedia.rawvoice.com%2Fpmn_twiv%2Ftraffic.libsyn.com%2Ftwiv%2FTWiV106.flv Hosts: Vincent Racaniello, Dickson Despommier, and Rich Condit On episode #106 of the podcast This Week in Virology, Vincent, Dickson, and Rich continue Virology 101 with a second installment of their discussion of how viruses with DNA genomes replicate their genetic information. Download TWiV #106 (69 MB .mp3, 95 minutes) Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with Stitcher Radio. Links for this episode: Figures for this episode (pdf) Letters read on TWiV 106 Video of this episode – download .mov or .wmv or view below Weekly Science Picks Rich – Google Health Dickson – The Neandertal genome Vincent – Lab techniques videos (thanks, Erik!) Send your virology questions ... virology blog blogs http://www.medworm.com/rss/comments.php?id=4142559 Sat, 06 Nov 2010 21:29:20 +0100 4142559 http://www.medworm.com/index.php?rid=4025618&cid=t_104781_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fadhd-is-it-genetic%2F2010.10.02 British scientists announced that attention-deficit/hyperactivity disorder (ADHD) has been linked to deleted or duplicated DNA segments (copy number variants), which leads to developmental difference in the brains of children with the condition. Researchers scanned genomes of 366 children with ADHD and compared them with 1,047 unrelated, ethnically matched control subjects. They reported full results in The Lancet. Rare copy number variants were almost twice as common in children with ADHD compared to the other children. Researchers commented to Reuters that there was a significant overlap between copy number variants found in ADHD and elements of the genome linked to autism and schizophrenia, specifically in a region on chromosome 16. *This blog post was originally published at AC... Better Health blogs http://www.medworm.com/rss/comments.php?id=4025618 Sat, 02 Oct 2010 19:00:00 +0100 4025618 http://www.medworm.com/index.php?rid=3999178&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F09%2F24%2Fwhole-genome-sequencing-in-diagnostics%2F Using whole genome sequencing in diagnostics has been an issue for years, and as the cost of sequencing is rapidly declining, it seems it can pave the way for personalized medicine. A new research published in Genome Biology, Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors, just proves this point: Adenocarcinomas of the tongue are rare and represent the minority (20 to 25%) of salivary gland tumors affecting the tongue. We investigated the utility of massively parallel sequencing to characterize an adenocarcinoma of the tongue, before and after treatment. We conclude that complete genomic characterization of a rare tumor has the potential to aid in clinical decision making and identifying therapeutic approaches where no established treatment protoco... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3999178 Fri, 24 Sep 2010 16:39:33 +0100 3999178 http://www.medworm.com/index.php?rid=3976637&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F79B_MJ5P7io%2F The Broad Institute released their sequence of the genome of Geomyces destructans implicated in the White Nose Syndrome that is causing a massive die-offs of bats. The researchers sequenced a North America isolated strain in this project which is part of an epidemic spreading across the Northeastern United States. This is just the assembly of the genome not the annotation which will be forthcoming. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3976637 Thu, 16 Sep 2010 20:46:56 +0100 3976637 http://www.medworm.com/index.php?rid=3976639&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F09%2F16%2Fpersonal-genomics-in-the-news%2F There are 4 articles focusing on personalized medicine I would like to share with you today. Personal Genotyping Course Progress Report At the Stanford School of Medicine’s Scope blog, Lia Steakley recounts student participation in the school’s summer elective course that offered the physicians-in-training the option to study their own genotype data. “Overall, 33 students in the class of 60 … opted for personal genotyping. Ten others analyzed their genetic background using commercial services before the class,” Steakley reports, adding that a Stanford task force will deliberate to determine whether to offer the course again. Our sister publication Genome Technology spoke with Stuart Kim, one of the course organizers, and professors at other medical schools who&#82... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3976639 Thu, 16 Sep 2010 15:58:51 +0100 3976639 http://www.medworm.com/index.php?rid=3965703&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FDWqutsIp8sY%2F Following through on plans announced earlier this year, Lonza is eliminating 106 jobs from its plant in Conshohocken, Pennsylvania, which makes various pharmaceutical ingredients. The Swiss company, which recently signed supply deals with GlaxoSmithKline and Human Genome Sciences (see here and here), confirmed the planned job losses in a filing with the Pennsylvania Department of Labor. At the time the closure was first announced in January, Lonza also signaled plans to shutter two other plants - one in Shawinigan, Canada, and another in Workingham, UK - and eliminate a total of 175 jobs. A report at the time indicated that about 140 people work at the Conshohocken facility, although the status of those jobs is not clear. Lonza employs about 8,500 people worldwide. This is only the latest ... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3965703 Mon, 13 Sep 2010 12:04:56 +0100 3965703 http://www.medworm.com/index.php?rid=3921011&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F08%2F31%2Fpersonalized-genomics-on-slideshows%2F When preparing for this year’s Researchers’ Night (details below), I was trying to collect some information and updates about the consumer genomics market for my presentation and found great slideshows. Enjoy! If you thought that research was all about lab coats and Bunsen burners, think again. Like everyone else, researchers come from numerous backgrounds, have diverse interests and pursue a spectrum of hopes and dreams. One thing they all have in common is a passion for research – and they want to share it with you. The European Commission’s ‘Researchers in Europe’ (RIE) initiative allows citizens to get closer to our researchers and gives a face to European research. (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3921011 Tue, 31 Aug 2010 19:42:35 +0100 3921011 http://www.medworm.com/index.php?rid=3953616&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Fmedia.rawvoice.com%2Fpmn_twiv%2Fwww.twiv.tv%2FTWiV096.flv Hosts: Vincent Racaniello, Dickson Despommier, and Rich Condit On episode #96 of the podcast This Week in Virology, Vincent, Dickson, and Rich continue Virology 101 with a discussion of how viruses with DNA genomes replicate their genetic information. Download TWiV #96 (65 MB .mp3, 90 minutes) Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with Stitcher Radio. Links for this episode: Figures for this episode (pdf) RNA silencing as a plant immune system (Trends in Genetics) Photos of transgenic petunia (PLoS Biology) Letters read on TWiV 96 Video of this episode – download .mov or .wmv or view below Weekly Science Picks Rich – Breast milk sugars give infants a protective coat (NY Times a... virology blog blogs http://www.medworm.com/rss/comments.php?id=3953616 Sun, 22 Aug 2010 15:46:21 +0100 3953616 http://www.medworm.com/index.php?rid=3805966&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F07%2F30%2Fpersonalized-genomics-dtc-companies-are-in-huge-trouble%2F Federal ‘Sting’ Slams Gene Tests (New York Times): Watch this video A sad day for personal genomics (Genetic Future): Today’s US Congress Committee on Energy and Commerce hearing into the direct-to-consumer genetic testing industry was a vicious affair. Representatives from testing companies 23andMe, Navigenics and Pathway faced a barrage of questions about the accuracy and utility of their tests, made all the worse by the fact that many of the Committee’s members seemed unable to distinguish between the more responsible companies in the field and the scammers and bottom-feeders. Consumer Genetics Needs More Transparency, Not Excessive Regulation: Daniel MacArthur and Daniel Vorhaus provide potential solutions. What If Your Genetics Defined Your Community? How I go... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3805966 Fri, 30 Jul 2010 11:36:35 +0100 3805966 http://www.medworm.com/index.php?rid=3780500&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F07%2F22%2Fgenomes-unzipped%2F A new group blog was just launched under the name Genomes Unzipped featuring the best genomics blogger out there.The sponsor is the PHG Foundation. With a range of experience in the group, the aim of GNZ is to provide the basic knowledge and tools that individuals interested in personal genomics need to explore their own genetic information in a responsible, informed manner. GNZ will feature technical analyses of personal genomics developments and services, including detailed analysis of the scientific basis of tests offered direct-to-consumer by personal genomics companies. It will also include dissections of important new papers in the field and discussion of the ethical, legal and social issues presented by new developments in this rapidly evolving field. Here is the list of contributor... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3780500 Thu, 22 Jul 2010 13:08:29 +0100 3780500 http://www.medworm.com/index.php?rid=3767235&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F07%2F19%2Fnumber-of-genomes-sequenced%2F I remember when Hsien-Hsien Lei tried to list all the people who had their genomes sequenced. Here is a more comprehensive list from SNPedia. Now the FuturePundit blog shared some interesting projections about the number of people who would have their genomes sequenced in the future: 2001-2009: A Human Genome 2010: 1,000 Genomes – Learning the Ropes 2011: 50,000 Genomes – Clinical Flirtation 2012: 250,000 Genomes – Clinical Early Adoption 2013: 1 Million Genomes – Consumer Awareness 2014: 5 Million Genomes – Consumer Reality 2015-2020: 25 Million Genomes And Beyond – A Brave New World The cost of sequencing is still decreasing, but the cost of data analysis and whether it can affect medical decision-making are different questions. Even if many of us thought we would be quite ... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3767235 Mon, 19 Jul 2010 13:54:59 +0100 3767235 http://www.medworm.com/index.php?rid=3743644&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FqAGH5CCKq5k%2F I am excited to announce the publication of another mushroom genome this week. The mushroom Schizophyllum commune is an important model system for mushroom biology, development of genome was sequenced as part of efforts at the Joint Genome Institute and a collection of international researchers.  The data and analyses from these efforts are presented in a publication appearing in Nature Biotechnology today. Studies in mushrooms can have important impact on other research areas.  They can be useful in biotechnology as protein biosynthesis factories for producing compounds or even as an edible delivery mechanism for new drugs.  What we found in the analysis of this genome include clues to mechanisms of how white rotting fungi degrade lignin through analysis of enzyme families.  We also ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3743644 Mon, 12 Jul 2010 07:12:10 +0100 3743644 http://www.medworm.com/index.php?rid=3714362&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F06%2F30%2F5949%2F 23andMe is a direct-to-consumer genetic company that also launched the 23andWe project in which they tried to use the data they obtain from patients in studies. Now the results are published in PLoS Genetics. Despite the recent rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data. We have developed a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort. The approach takes advantage of the interactivity of the Web both to gather data and to present genetic information to research participants, while taking care to correct for the... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3714362 Wed, 30 Jun 2010 15:47:23 +0100 3714362 http://www.medworm.com/index.php?rid=3710720&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FHmUqNNb51wE%2F I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus.  You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some of the high points in the paper. Stajich, J., Wilke, S., Ahren, D., Au, C., Birren, B., Borodovsky, M., Burns, C., Canback, B., Casselton, L., Cheng, C., Deng, J., Dietrich, F., Fargo, D., Farman, M., Gathman, A., Goldberg, J., Guigo, R., Hoegger, P., Hooker, J., Huggins, A., James, T., Kamada, T., Kilaru, S., Kodira, C., Kues, U., Kupfer, D., Kwan, H., Lomsadze, A., Li, W., Lilly, W., Ma, L., Mackey, A., Manning, G., Martin, F., Muraguchi, H., Natvig, D.,... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3710720 Tue, 29 Jun 2010 17:35:11 +0100 3710720 http://www.medworm.com/index.php?rid=3691022&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FMmHPW-7YeJU%2F There are several databases that include orthology prediction for fungi. These all have pros and cons. Some are more comprehensive and have many more species. Some are curated orthologies and paralogy which should be pretty stable. Some are automated and groupings and ortholog group IDs change at each iteration. A phylogenetic approach from a Saccharomyces perspective is at PhylomeDB. Fungal Orthogroups is based on Synergy algorithm from I. Wapinski formerly of the Regev group at the Broad Institutue. Yeast gene order browser (YGOB) for Saccharomyces spp and CGOB for Candida spp. OrthoMCL database based on whole genomes, not a ton of fungi but useful starting set. Ensembl Genomes provides ortholog prediction as part of the Compara pipeline though there is a limited phylogenetic diversity ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3691022 Thu, 24 Jun 2010 01:13:09 +0100 3691022 http://www.medworm.com/index.php?rid=3687297&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F06%2F22%2Fpersonalized-genetics-fda-dtc-and-gina%2F Here are some interesting news and announcements to keep you absolutely up-to-date regarding the improvements of personalized medicine. Why 23andMe’s Sample Swap is Actually an Argument In Favor of DTC Genetic Testing There are a number of reasons why DTC genetic testing may soon find itself subject to increased federal regulatory oversight. However, 23andMe’s widely publicized data error should not be one of those reasons. In fact, the sample swap, while unfortunately timed, actually presents a compelling argument in favor of the direct-to-consumer model for genetic testing. Challenging the FDA: A History Lesson for DTC Genetics A Positive Response to Genetic Testing A personalized medicine study from the Coriell Institute for Medical Research suggests that patients who underg... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3687297 Tue, 22 Jun 2010 15:58:44 +0100 3687297 http://www.medworm.com/index.php?rid=3676833&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F06%2F18%2Festher-dyson-about-genomics%2F Esther Dyson answers questions about the direct-to-consumer genome market at the recent New York City Quantified Self Show&Tell meetup: (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3676833 Fri, 18 Jun 2010 10:23:47 +0100 3676833 http://www.medworm.com/index.php?rid=3671928&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FQxLvqBv_sO4%2F Francis Martin has written up a delightful summary pointing to our publication of the genome of Coprinopsis cinereus which appears in the early edition of PNAS and will grace the cover at the end of the month.  I encourage you to take a look at Francis’s post and the paper, available as Open Access from PNAS.  I’ll do my best to post a summary of the paper when I get a free moment. For now I’ll leave you with a picture of this cute little mushroom fruting in the lab and a link to many more at Flickr. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3671928 Thu, 17 Jun 2010 21:05:32 +0100 3671928 http://www.medworm.com/index.php?rid=3662930&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FlG3_0WmNlLQ%2F Rise and shine. Another day is on the way. To top it off, the sun is shining here on the Pharmalot corporate campus, where we are hustling the short people off to the schoolhouse. Wish us luck. Meanwhile, there is much to do. So why not start with the mandatory cup of stimulation and the news of the world. Have a great day, everyone… Glaxo Wins FDA OK For Prostate Combo Drug (Reuters) Cheap Generic May Save Lives After Bleeding From Accidents (Bloomberg News) ACRO Wants More US & European Trial Investigators (Outsourcing Pharma) Waiting For The Human Genome To Yield Drugs (The New York Times) Georgia Creates Bioscience Center (Atlanta Journal-Constitution) Cleveland Clinics Inks Research Deal With Lipitor Creator (Crain’s Cleveland Business) (Source: Pharmalot) Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3662930 Tue, 15 Jun 2010 11:54:48 +0100 3662930 http://www.medworm.com/index.php?rid=3644932&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F06%2F08%2Fpersonalized-genomics-news-from-virtuality-to-the-streets%2F DNA As Crystal Ball: Buyer Beware (Newsweek): A genome-wide association study identified a new gene variant associated with Alzheimer’s disease but it turned out clinically it’s not useful. “Adding these genes to traditional risk factors, such as age and sex, does nothing to aid prediction” of whether someone will develop Alzheimer’s, she told me. “Knowing your genetic status will not help. We may still be in the Stone Age when it comes to gene-based prediction.” Breaking: Congress to Investigate DTC Genetic Testing (Genomics Law Report): A really detailed and interesting review. The United States House of Representatives Committee on Energy and Commerce today launched an investigation into direct-to-consumer (DTC) genetic testing, sending letters to three promine... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3644932 Tue, 08 Jun 2010 16:43:26 +0100 3644932 http://www.medworm.com/index.php?rid=3629636&cid=t_104781_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fsynthetic-life-created-the-first-micro-avatar%2F2010.06.03 For the first time in history, a living organism has been manufactured with the help of a computer-generated genome. Dr. Jon LaPook reports on the groundbreaking discovery’s widespread implications. Watch CBS News Videos Online The First Micro-Avatar Craig Venter and his team of scientists recently announced that they had created the first “synthetic cell” — a bacterium controlled by genetic material that they had designed on a computer and concocted from four bottles of chemicals. This is the closest thing to creating life that has happened outside of a science-fiction movie. If it doesn’t fire your imagination, then you should fire your imagination. Basically, what Venter et al did was remove the “brain” (the genetic material that runs the cell) from one species o... Better Health blogs http://www.medworm.com/rss/comments.php?id=3629636 Thu, 03 Jun 2010 19:51:56 +0100 3629636 http://www.medworm.com/index.php?rid=3603755&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F05%2F27%2Fdiygenomics-on-smartphones%2F In personal or direct-to-consumer genomics, what we need is reliable, scientifically correct smartphone applications. Here is DIY Genomics, and Android app, which performs a side-by-side comparison of consumer genomic services such as deCODEme, Navigenics and 23andme by loci and variants for 20 conditions. It also does the same for drug responses and health risks. What can you do? Select 1 of 20 top conditions covered by consumer genomic services Side-by-side locus, gene and SNP comparison of deCODEme, Navigenics and 23andme Selecting any SNP row, comparison of underlying studies cited by company Click-through to PubMed study listing Actually it provides the user with reliable pieces of information that might help interprete the data. (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3603755 Thu, 27 May 2010 10:23:06 +0100 3603755 http://www.medworm.com/index.php?rid=3585767&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FCyx0pBSS2FU%2F Several groups working on Fungi are submitting proposals to the JGI Community Sequencing Program.  Several proposals relating to the JGI’s interest in an encyclopedia of fungal genomes sequencing genomes of ascomycete and basidiomycete yeasts, filamentous ascomycetes, basidiomycetes,  and early diverging fungi are being put forward.  If you haven’t been contacted by these community members but would like to write a letter of support in these areas, please get in touch as the deadline for the proposals in early next week. There are also other proposals going in for Neurospora mutant strain resequencing, more Fusarium species, transcriptomes of mycorrhizal fungi, and other topics.  If you are are a user of data from any of the previous fungal projects that you know how imp... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3585767 Thu, 20 May 2010 20:49:13 +0100 3585767 http://www.medworm.com/index.php?rid=3570008&cid=t_104781_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2010%2F05%2Fpotential-of-genomic-medicine-lost.html I was reading and often read Mark Henderson of the TimesThe piece I just read about the "Potential of genomic medicine could be lost, say science think-tanks"The piece basically comes down to one conclusion. We have no proof that most of this stuff is useful in any form.This is something that I have been shouting from the roof tops ever since some self deluded socialite from Mountain View decided to say "Genetic testing is for fun"Seriously DTCG. You knew this day was coming. You tried to play yourself off as hip, cool, sexy/ Yet at the same time to avoid regulation you played, not serious, not clinical, and in essence, not valuable.I was deeply concerned about precisely this issue. By putting yourselves out there as an invalid in the clinical world, you cheapened the field and some of the... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=3570008 Mon, 17 May 2010 14:11:00 +0100 3570008 http://www.medworm.com/index.php?rid=3552476&cid=t_104781_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=3538332&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F05%2F05%2Freally-personalized-medicine%2F Stephen Quake had his genome sequenced a year ago and since then he and 30 collegues have been working on the medical aspects of this huge amount of data. They try to make connections between genetic background and medical decisions. The results they found were published in The Lancet. Analysis of 2·6 million single nucleotide polymorphisms and 752 copy number variations showed increased genetic risk for myocardial infarction, type 2 diabetes, and some cancers. We discovered rare variants in three genes that are clinically associated with sudden cardiac death—TMEM43, DSP, and MYBPC3. A variant in LPA was consistent with a family history of coronary artery disease. The patient had a heterozygous null mutation in CYP2C19 suggesting probable clopidogrel resistance, several variants associa... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3538332 Wed, 05 May 2010 16:54:39 +0100 3538332 http://www.medworm.com/index.php?rid=3494487&cid=t_104781_134_f&fid=34841&url=http%3A%2F%2Fwww.diabetesmine.com%2F2010%2F04%2Fdesign-challenge-five-minutes-with-our-venture-capitalist-judge.html A new addition to our DiabetesMine Design Challenge Judges’ Panel this year is John Steuart, Managing Director of Claremont Creek Ventures, a venture capital firm that invests in early stage information technology companies. John himself has spent the last 20 years building and investing in technology and life science companies, so you might say [...] (Source: Diabetes Mine) Diabetes Mine blogs http://www.medworm.com/rss/comments.php?id=3494487 Thu, 22 Apr 2010 13:00:31 +0100 3494487 http://www.medworm.com/index.php?rid=3480887&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F04%2F18%2Fdnatwist-teaching-students-about-pharmacogenomics%2F Berlin et al. published a very interesting paper in Clinical Pharmacology and Therapeutics about DNATwist which is an online tool for teaching middle and high school students about pharmacogenomics. DNATwist is a Web-based learning tool that explains pharmacogenomics concepts to middle- and high-school students. Its features include (i) a focus on drug responses of interest to teenagers (e.g., alcohol intolerance), (ii) reusable graphical interfaces that reduce extension costs, and (iii) explanations of molecular and cellular drug responses. In testing, students found the tool and topic understandable and engaging. The tool is being modified for use at the Tech Museum of Innovation in California. (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3480887 Sun, 18 Apr 2010 00:18:23 +0100 3480887 http://www.medworm.com/index.php?rid=3471972&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FoHra8g2mYaY%2F A couple of papers should have captured your attention lately in the realm of fungal genomics. One is the publication of the genome of the black truffle Tuber melanosporum. This appears as an advanced publication at Nature (OA by virtue of Nature’s agreement on genome papers) along with a NYT writeup and is a tasty exploration of the genome of an ascomycete ectomycorrhizal (ECM) fungus. There are several gems in there including the differences in transposable element content, content of gene families related to carbohydrate metabolism. This genome helps open the doorway for exploring the several independent origins of ECM in both ascomycete and basidiomycete fungi. I’ll also point out there is some work on the analysis of mating type locus found in this genome has applied aspe... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3471972 Thu, 15 Apr 2010 15:03:53 +0100 3471972 http://www.medworm.com/index.php?rid=3467950&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F04%2F13%2Fgenomics-education-videos%2F Genome British Columbia has come up with a series of educational videos describing genomics, gene expression or genomics in everyday life. (Via Genome Web) (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3467950 Tue, 13 Apr 2010 20:47:17 +0100 3467950 http://www.medworm.com/index.php?rid=3463592&cid=t_104781_87_f&fid=38368&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FDisruptiveWomenInHealthCare%2F%7E3%2FyKMxlwsv7PI%2F It’s been awhile since I read a book that has influenced  my thinking.  Maybe it’s because I don’t read as many books for “fun” as I used to.  Maybe it’s because I’ve been pre-occupied with ARRA and HITECH related work or my graduate school course on medical ethics or my teenager’s triumphs and despair as she awaited college acceptance decisions.   But there I was driving in my car listening to a National Public Radio (NPR) segment.  Actually it was Fresh Air with Terry Gross. For the next several minutes I found myself drawn in by an interview with a science journalist named Rebecca Skloot, who wrote a book called “The Immortal Life of Henrietta Lacks.” Now I’ve worked in the health care field for more than 35 years and lived in the Maryland-DC area for... Disruptive Women in Health Care blogs http://www.medworm.com/rss/comments.php?id=3463592 Tue, 13 Apr 2010 12:33:05 +0100 3463592 http://www.medworm.com/index.php?rid=3399104&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F03%2F24%2Fpersonalized-genomics-genetic-testing-registry-and-next-gen-sequencing%2F I know I have not been updating you about the improvements of personalized genomics lately, but here are the most interesting and important news focusing on this emerging field of medicine. When DNA means do not ask (TIME): Quite a negative (but partly valid) article from Camilla Long about genetic testing and DTC companies. And the answer for this piece by Genetic Future point by point. If Long wishes to stay ignorant of her own genetic risks – just as she has managed to remain ignorant of the entire field of genetics, even while writing an op-ed piece about it – that should be her choice. But her criticism of others who choose to pursue a greater understanding of their own genetic risk is entirely, horrendously misplaced. Next-Gen Sequencing in 2010 (Mass Genomics): Ever... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3399104 Wed, 24 Mar 2010 01:10:39 +0100 3399104 http://www.medworm.com/index.php?rid=3395314&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FXlcBOyfI7mU%2F I’m at the JGI user meeting, which is starting with a Basidiomycete genomics workshop/jamboree, later a meeting of JGI fungal genome advisory board, and the main show: the User Meeting. Looking forward to catching  up with scientists from a wide variety of projects and  some twitter/blogger types and twittering about it @#JGIUM. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3395314 Mon, 22 Mar 2010 20:19:27 +0100 3395314 http://www.medworm.com/index.php?rid=3385501&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F03%2F19%2Fpathway-genomics-lets-see-my-genes%2F As I’m doing PhD in clinical genomics and I’m really interested in the connection between internet and medicine, so I was very happy when Pathway Genomics, one of the newest direct-to-consumer genetic companies, offered me a free genetic test. After an interview I did with them, I sent my saliva sample back and 3-4 weeks later, I received an e-mail that my results were ready. This is just an entry about my experience and the things I found interesting. As I got a free test from Navigenics a year ago, I plan to compare these services in a future entry. The reason why I was very interested in the service of Pathway Genomics is what they analyze: Risk markers for 70+ diseases Maternal and paternal ancestry Drug responses Carrier status 1) Sampling: It was quite an easy process... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3385501 Fri, 19 Mar 2010 19:17:47 +0100 3385501 http://www.medworm.com/index.php?rid=3359215&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FCkbiyODkbig%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? Portola Pharmaceuticals promoted William Lis to ceo; BayBio Jeremy Leffler chief operating officer; Human Genome Sciences named David Southwell exec vp and cfo; Teva Pharmaceuticals named Phillip Frost as chairman; Sandoz promoted Don DeGolyer to head No. American commercial ops; Cornerstone Pharmaceuticals named Robert Shepard as chief medical officer; EUSA Pharma hired Ia... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3359215 Fri, 12 Mar 2010 13:00:53 +0100 3359215 http://www.medworm.com/index.php?rid=3342245&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Fmedia.rawvoice.com%2Fpmn_twiv%2Fwww.twiv.tv%2FTWiV072.mp3 Hosts: Vincent Racaniello, Dickson Despommier, Alan Dove, and Rich Condit This week the TWiV team explains CRISPR/Cas, the immune system of bacteria and archaea, how novel viruses are discovered by deep sequencing of small RNAs, and the relationship between dry weather and outbreaks of West Nile virus infection. This episode is sponsored by Data Robotics Inc. Use the promotion code VINCENT to receive $50 off a Drobo or $100 off a Drobo S. Win a free Drobo S! Contest rules here. Download TWiV #72 (62 MB .mp3, 85 minutes) Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email. Links for this episode: Review on the CRISPR/cas system of bacteria and archaea Virus discovery by sequencing small virus-derived RNAs (paper one and two) Dry weather induces outbre... virology blog blogs http://www.medworm.com/rss/comments.php?id=3342245 Mon, 08 Mar 2010 02:30:37 +0100 3342245 http://www.medworm.com/index.php?rid=3301987&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Fwww.virology.ws%2F009_W3310_10.mp4 Download: .wmv (352 MB) | .mp4 (74 MB) Presented by guest lecturer Saul Silverstein, Ph.D. 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=3301987 Tue, 23 Feb 2010 22:00:26 +0100 3301987 http://www.medworm.com/index.php?rid=3244050&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FvsxrDoBSY9s%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? And here is something we hope to make a regular feature. Send us a photo and we will spotlight a different person each week. This time around, we note that Genzyme hired Lilly’s former head of manufacturing, Scott Canute, to run manufacturing and operations. He will be in charge of pulling rabbits out of hats, given Genzyme’s embarassing problems at a plant that... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3244050 Fri, 05 Feb 2010 12:50:14 +0100 3244050 http://www.medworm.com/index.php?rid=3212502&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F01%2F26%2Fsmartphone-as-a-personal-genome-assistant%2F A few months ago, I wrote about a press release: Using the Google Phone’s built-in bar code reader, Dr. Pellionisz demonstrated how personal genome computing can detect genome-friendly and genome-supportive products from foods to cosmetics to building materials and beyond. You upload data from personal health record system such as Microsoft Healthvault or Google Health; genomic data from 23andMe or Navigenics to your smartphone and then by using the bar code reader, you can find products that are probably good for you based on your genomic and health profiles. Though the system has several limitations (e.g. how useful genomic data is right now regarding medical decisions), it sounds quite interesting. Here is the process on video: (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3212502 Tue, 26 Jan 2010 21:15:32 +0100 3212502 http://www.medworm.com/index.php?rid=3180368&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2010%2F01%2F17%2Fgenome-sequencing-under-10000%2F The estimated cost of the Human Genome Project that aimed to sequence the human genome was around $350 million. The dream line is around $1000, and now here is a new milestone. Illumina HiSeq 2000 costs $650,000, but it can sequence a genome for $10,000 and generates 200 gigabytes per run. Though even if we cross the $1000 line somewhere in the near future, I don’t think we are ready to implement this huge amont of data into medical decision making effectively. Technology moves faster than our understanding of clinical genomics. Fellow bloggers’ reports: GenomeWeb Pathogens Genetic Future Genomics Law Report PolITiGenomics The race for the $1000 genome is serious. Do you remember the new genome sequencer of Helicos? 1 billion basepairs a day: (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3180368 Sun, 17 Jan 2010 12:14:08 +0100 3180368 http://www.medworm.com/index.php?rid=3166775&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2F7ABuOXRMEo4%2F The chromosomal DNA of several mammals has been found to contain sequences related to the nucleoprotein (N) gene of bornaviruses, enveloped viruses with a negative-strand RNA genome. I am amazed by this finding. How did bornaviral DNA get in our chromosomes, and what is it doing there? A search of the human genome sequence revealed DNA copies of the bornaviral N protein gene. This 370 amino acid viral protein is wrapped around the viral RNA, where it functions during RNA synthesis. Four different insertions of N protein DNA were found, all encoding proteins that are shorter than the viral counterpart.  DNA encoding bornaviral N protein was also found in the genomes of the chimpanzee, gorilla, orangutan, rhesus macaque, lemur, Garnett’s galago, African elephant, Cape hyrax, rat, mou... virology blog blogs http://www.medworm.com/rss/comments.php?id=3166775 Wed, 13 Jan 2010 15:22:03 +0100 3166775 http://www.medworm.com/index.php?rid=3172143&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FALk2EqU95xw%2F These papers got lost in my drafts of things to write about.  Grants and overdue manuscripts are keeping me away from the blog. Published work from Gary Foster’s lab in Applied Env Micro show progress on genetic engineering tools to express introduced genes in the basidiomycete mushroom system Clitopilus passeckerianus. C. passeckarianus produces an antibiotic, pleuromutilin, an important antibiotic. Cover photo [Press] They also showed the  5′ intron is important for efficient expression, something that has been shown several times in fungi and provides more evidence for the role of introns in promoting or regulating an aspect of gene expression or translation. Perhaps by splicing-dependent export. Corradi et al – the genome of the microsporidia parasite of Daphn... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3172143 Wed, 13 Jan 2010 00:25:10 +0100 3172143 http://www.medworm.com/index.php?rid=3159560&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Fmedia.rawvoice.com%2Fpmn_twiv%2Fwww.twiv.tv%2FTWiV065.mp3 Hosts: Vincent Racaniello, Alan Dove, and Matthew Frieman Vincent, Alan, and Matt discuss a project to study the RNA virome of Northeastern American bats, failure to detect XMRV in UK chronic fatigue syndrome patients, and DNA of bornavirus, an RNA virus, in mammalian genomes. This episode is sponsored by Data Robotics Inc. To receive $50 off a Drobo or $100 off a Drobo S, visit drobostore.com and use the promotion code VINCENT. Download TWiV #65 (58 MB .mp3, 80 minutes) Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email. Links for this episode: Mist net Indigo Tunnel, Western Maryland Railway (jpg) Eric Donaldson and Amy Haskew with bat in holding bag (jpg) XMRV not detected in UK chronic fatigue syndrome patients (virology blog) Bornavirus DNA in ... virology blog blogs http://www.medworm.com/rss/comments.php?id=3159560 Mon, 11 Jan 2010 01:53:19 +0100 3159560 http://www.medworm.com/index.php?rid=3092892&cid=t_104781_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2009%2F12%2F15%2Fprinceton-scientists-find-way-to-catalog-all-that-goes-wrong-in-a-cancer-cell%2F A team of Princeton University scientists has produced a systematic listing of the ways a particular cancerous cell has “gone wrong,” giving researchers a powerful tool that eventually could make possible new, more targeted therapies for patients. A team of Princeton University scientists has produced a systematic listing of the ways a particular cancerous cell has [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=3092892 Tue, 15 Dec 2009 22:53:24 +0100 3092892 http://www.medworm.com/index.php?rid=3089475&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F12%2F14%2Fethical-legal-and-social-implications-in-genomics-e-book%2F Dan Vorhaus at Genomics Law Report launched a great series featuring many scientists, legal and social experts who talked about the possible implications in genomics. My commentary focused on the web 2.0 aspect of personalized medicine. Now the series is over and they published an e-book which is a must-read for everyone who wants to know more about the ELSI of genomics or personalized medicine. From October 5 to December 8, 2009, the Genomics Law Report featured a series of thirty-six guest commentaries by industry, academic and thought leaders in the fields of genomics and personalized medicine. Entitled What ELSI is New?, the series, which we have organized into an e-book (pdf), asked each contributor to briefly respond to the following question: “What do you believe is the most im... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3089475 Mon, 14 Dec 2009 22:17:09 +0100 3089475 http://www.medworm.com/index.php?rid=3044941&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F11%2F30%2Fpathway-genomics-interview%2F Some months ago, I wrote about the importance of customer service in the life of direct-to-consumer genomic companies. After the post, Pathway Genomics contacted me and said they were excited to speak more openly about their service. They also want to educate the community on genetic testing services and what these test results will and will not tell you. Here is the interview they have recently given to me. Pathway Genomics is one of the newest competitors in the DTC genomics market. How do you aim to make a difference? Quality. Pathway has a wholly owned federal CLIA and California State licensed laboratory. This onsite lab removes any “middle-man” issues. DNA samples are collected in Pathway’s custom-designed DNA collection kits and shipped directly to Pathway’s laboratory in... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3044941 Mon, 30 Nov 2009 20:46:15 +0100 3044941 http://www.medworm.com/index.php?rid=3044307&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Fmedia.rawvoice.com%2Fpmn_twiv%2Fwww.twiv.tv%2FTWiV060video.wmv Hosts: Vincent Racaniello and Dickson Despommier Vincent and Dick continue Virology 101 with a discussion of how RNA viruses produce mRNA and replicate their genomes. Download TWiV #60 (51 MB .mp3, 71 minutes) Subscribe to TWiV in iTunes, by the RSS feed, or by email Links for this episode: Diagrams of viral RNA synthesis Animations of influenza virus and HIV-1 replication Video for this episode – see below Weekly Science Picks Dick The Double Helix by James D. Watson Vincent Worms and Germs Blog Send your virology questions and comments (email or mp3 file) to twiv@twiv.tv or leave voicemail at Skype: twivpodcast. You can also send articles that you would like us to discuss to delicious and tag them with to:twivpodcast. Below is a video of TWiV 60, which highlights the diagrams I r... virology blog blogs http://www.medworm.com/rss/comments.php?id=3044307 Sun, 29 Nov 2009 16:30:17 +0100 3044307 http://www.medworm.com/index.php?rid=3008306&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F11%2F18%2Fagenda-for-personalized-medicine-answers%2F A few weeks ago, Pauline C. Ng, Sarah S. Murray, Samuel Levy and J. Craig Venter published a quite an interesting piece  in the October 8, 2009 issue of Nature. In this publication, they had really relevant suggestions for Direct-to-consumer genomics companies such as Navigenics or 23andMe. Now, surprisingly, they two giants published an answer together: Dear Editor: We read with interest the Opinion piece entitled “An agenda for personalized medicine” in the October 8, 2009 edition of Nature. Our two companies, though commercially distinct with differentiated products, would like to respond to this piece jointly to show our commitment to working together in an open, transparent fashion. Our companies agree with most of the recommendations Ng and colleagues made.  Without doubt, geno... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=3008306 Wed, 18 Nov 2009 20:06:21 +0100 3008306 http://www.medworm.com/index.php?rid=2993889&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F11%2F15%2Feuropean-personalised-medicine-diagnostics-association%2F We all know about the Personalised Medicine Coalition: The Personalized Medicine Coalition (PMC) is an independent, non-profit group that works to advance the understanding and adoption of personalized medicine for the ultimate benefit of patients. Our diverse members work together to educate opinion leaders and the public about the issues that will shape how personalized medicine develops — and how quickly all of us can benefit from it. Now I was glad to see the European Personalised Medicine Diagnostics Association just launched as reported by GenomeWeb. Made up of biotechnology firms, academic and institutional researchers, small and large businesses, and patient advocacy groups, the European Personalised Medicine Diagnostics Association (EPEMED) announced its board of directors this ... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2993889 Sun, 15 Nov 2009 13:22:05 +0100 2993889 http://www.medworm.com/index.php?rid=2962863&cid=t_104781_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F11%2Ftrichomonas-vaginalis-genome.html The genome of Trichomonas vaginalis, the first from a parabasalid to be sequenced, was published in 2007, the culmination of a project marked by several surprises and not a little distress. The ~160 Mb genome was found to be significantly larger than first described, presenting new challenges to the standard genome sequencing pipeline.from Anaerobic Parasitic Protozoa: Genomics and Molecular BiologyFurther reading:Anaerobic Parasitic ProtozoaAcanthamoeba: Biology and PathogenesisLeishmania: After The GenomeFull range of books on microbiology at Microbiology Books (Source: Microbiology Blog: The weblog for microbiologists.) Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2962863 Thu, 05 Nov 2009 12:42:00 +0100 2962863 http://www.medworm.com/index.php?rid=2950984&cid=t_104781_150_f&fid=34768&url=http%3A%2F%2Fpharmagossip.blogspot.com%2F2009%2F11%2Flupus.html Yes, lupus! (Source: PharmaGossip) PharmaGossip blogs http://www.medworm.com/rss/comments.php?id=2950984 Mon, 02 Nov 2009 14:14:00 +0100 2950984 http://www.medworm.com/index.php?rid=2950995&cid=t_104781_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FGLpICeeuy88%2F Welcome back. We hope your weekend was fun. After all, there was Halloween and the World Series for baseball fans. And there was plenty of opportunity to get some exercise raking leaves, at least for those who live in the US Northeast. Now, though, another week beckons. And so as you prepare for those meetings and deadlines, here are a few items to help you along. Have a nice day everyone… Will Pfizer Buy Protalix? (Globes) Amylin And Takeda To Develop Obesity Drugs (Reuters) Dendreon Seeks FDA Approval For Provenge Vaccine (Reuters) Human Genome Sciences’ Lupus Drug Cuts Symptoms (Bloomberg) Schering-Plough Reports Hepatitis C Drug Results (Associated Press) Vertex Pitches Its Hepatitis C Drug (The Boston Globe) (Source: Pharmalot) Pharmalot blogs http://www.medworm.com/rss/comments.php?id=2950995 Mon, 02 Nov 2009 12:21:12 +0100 2950995 http://www.medworm.com/index.php?rid=2912383&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F10%2F20%2Fpersonalized-medicine-in-the-web-2-0-era%2F A few weeks ago, Daniel Vorhaus from the Genomics Law Report asked me to provide a commentary on what I think about the future of personalized medicine regarding ethical, legal and social aspects. Now my commentary was published and here is an excerpt: Educating medical professionals and preparing the public to be able to provide informed consent for these activities is crucial to this next phase; as is the accessibility of the enormous and growing amount of genomic data. A new generation of web services, the so-called web 2.0, seems to be playing an important role in this movement. Through such tools, people can interact with their doctors and each other easily and they can share the results of genomic tests, resulting in a self-maintained database of human genomic information. Examples i... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2912383 Tue, 20 Oct 2009 18:16:50 +0100 2912383 http://www.medworm.com/index.php?rid=2894689&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FrAbaB3MBQM0%2F Dr. Hsien Lei of the DNA Network informed us about a new blog launch, HUGO MATTERS from the International Human Genome Organization (HUGO). The HUGO is a group of scientists involved in genetic and genomic research whose aims are to assist coordination of research and foster collaboration of scientists. HUGO Matters will be a central hub for HUGO’s HUGO’s social networking efforts. Readers can discuss relevant topics in genomics including research, ethics, social issues and even education, according to HUGO president Prof. Edison T Liu. As part of the blog launch, HUGO is offering a free meeting registration at the HUGO Genomics and Ethics, Law and Society Symposium in Switzerland on November 1- 3. Check out this page for details. And if you are attending the 59th Annual American ... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2894689 Thu, 15 Oct 2009 03:58:26 +0100 2894689 http://www.medworm.com/index.php?rid=2871608&cid=t_104781_87_f&fid=38368&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FDisruptiveWomenInHealthCare%2F%7E3%2FHa0wmbppsG4%2F Well – sadly it’s been one year since I have posted a blog with Disruptive Women in Healthcare so I really need to update you all on the fascinating science occurring in the genomics community. Shortly after I wrote my last blog in October 2008, I attended a meeting at one of our country’s finest scientific institutions– Cold Spring Harbor Laboratories – where some of the world’s foremost scientific discoveries have occurred. At this inaugural meeting entitled “Personal Genomes”, scientists discussed the tremendous potential for understanding the genome and translating this knowledge into our quest for the personalization of healthcare – yet at this meeting one year ago, we were acknowledging that we had sequenced less than a handful of genomes, the task at hand enorm... Disruptive Women in Health Care blogs http://www.medworm.com/rss/comments.php?id=2871608 Wed, 07 Oct 2009 11:05:33 +0100 2871608 http://www.medworm.com/index.php?rid=2793358&cid=t_104781_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=2792869&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Fmedia.rawvoice.com%2Fpmn_twiv%2Fwww.twiv.tv%2FTWiV049.mp3 Hosts: Vincent Racaniello and Dick Despommier On episode 49 of the podcast ‘This Week in Virology”, Vincent and Dick continue Virology 101 with a discussion of the seven different types of viral genomes, and how to use the pathway to mRNA to understand viral replication. Download TWiV #49 (45 MB .mp3, 62 minutes) Subscribe to TWiV in iTunes, by the RSS feed, or by email Links for this episode: Dick talks about hookworm on Radio Lab Dick’s video page at BigThink The seven types of viral genome Animation of HIV replication (thanks axiomatically atypical!) Changes in transcript abundance relating to colony collapse disorder in honey bee (thanks Judi!) Weekly Science Picks Dick Discovery Channel: Planet Green Vincent Influenza videos at BigThink: one, two, three, four, ... virology blog blogs http://www.medworm.com/rss/comments.php?id=2792869 Sun, 13 Sep 2009 18:45:35 +0100 2792869 http://www.medworm.com/index.php?rid=2778668&cid=t_104781_137_f&fid=35426&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheAlzheimersReadingRoom%2F%7E3%2FSvrw5fO0SxM%2Fscientists-identify-two-gene-variants.html In the largest genome-wide association study (GWAS) reported to date involving Alzheimer's disease, scientists have identified two new possible genetic risk factors for late-onset Alzheimer's, the most common form of the disease. The study, which pooled DNA samples from a number of European and U.S. groups, not only associated variations in the sequence of the CLU and PICALM genes with increased risk, but also found another 13 gene variants that merit further investigation, according to findings presented in the September 6, 2009, online issue of Nature Genetics. Involving more than 16,000 DNA samples, one feature of this research was its use of publicly shared DNA samples and databases, including several supported by the National Institute on Aging (NIA) and other components of the Natio... Alzheimer's Reading Room, The blogs http://www.medworm.com/rss/comments.php?id=2778668 Tue, 08 Sep 2009 23:31:25 +0100 2778668 http://www.medworm.com/index.php?rid=2762085&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F09%2F02%2Fchoose-a-genome-to-sequence%2F What Olivia Judson, an evolutionary biologist, did on the New York Times is called science journalism, I mean science journalism. A few excerpts of her recent article, The Fantasy Genome Project: Here’s a game for a rainy afternoon. If you could pick any organism to have its whole genome sequenced — what would it be? At the moment, our ability to interpret whole genomes is patchy: it’s like trying to read a foreign language with an incomplete dictionary and grammar. We don’t yet know what most genes do, or how they interact with each other. But just because we don’t yet understand all the information that genomes contain doesn’t mean they aren’t useful. Consider, for example, the single-celled being Cryptosporidium parvum. This is an intestinal parasite of humans and other an... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2762085 Wed, 02 Sep 2009 20:05:28 +0100 2762085 http://www.medworm.com/index.php?rid=2752087&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FkDNsa2XdrJs%2F Testing for one’s genetic risk has become increasingly popular in recent years with the mapping of the human genome. Now, you have the opportunity to know if you carry the BRCA genes, or know your risk for Alzheimer’s, other cancers, heart diseases and other diseases and traits, and even one’s genetic ancestry, based on the presence of certain DNA segments in your genome. Direct-to-Consumer (DTC) DNA testing, also known as personal genome services, allows a person to get his genetic profile just simply by swabbing one’s cheeks or spitting into a test tube and sending the sample back to the genetic testing company. In a few weeks you have your results back in print and at a password-controlled website. Pretty nifty, right? Actor Ernie Hudson swabs cheek for African Ancestry DNA ... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2752087 Tue, 01 Sep 2009 03:59:12 +0100 2752087 http://www.medworm.com/index.php?rid=2752088&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FM8OLs7FOhjI%2F Persistence really pays off, and this is especially true in genetic studies. After 35 years of combined research, a father-and-son team has finally identified the source of the gene that causes the heart’s electricity to go awry. For three hundred years, a South African family has been plagued by progressive familial heart block, a disease of the electrical system of the heart. The disease causes an affected person to have irregular heart beats, fainting spells, seizures or sudden death. The risk is greatest soon after birth, during puberty and early twenties and returns in the middle age, and a timely installment of a pacemaker is the best treatment. Using data from the human genome project, Professors Andries and Paul Brink were able to trace the origin of this disease to one man: A... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2752088 Tue, 01 Sep 2009 03:13:01 +0100 2752088 http://www.medworm.com/index.php?rid=2719896&cid=t_104781_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F08%2Fwhere-from-here.html This is the question I am asked so often.1. We have the steady progress towards cheap genomes. 2. We have the biggest supporter of personalized medicine running the NIH 3. We have "some" clinical awareness of personalized medicine 4. We have the government aware of the shenanigans of some unscrupulous DTC advertising, etc 5. We have several milemarkers under our belts with genome science..... We are moving in the "right" direction, but where do we go from here There are several areas we need to investigate. I would like to sum a few of them, both basic science and clinical. Basic Science first. 1. We need to understand precisely how gene regulation occurs in the face of certain common environmental exposures. Trans Fat, Tobacco Smoke, Alcohol, Stress. Is it RNA? Is it Methylation? What pr... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2719896 Thu, 20 Aug 2009 14:26:00 +0100 2719896 http://www.medworm.com/index.php?rid=2712287&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F08%2F18%2Fgenome-the-future-is-now-webisodes%2F Here are a few videos that everyone interested in personal genomics should watch. GENOME: THE FUTURE IS NOW, a multi-media documentary project with a film and interactive website, has exclusive access to Harvard scientist Dr. George Church and his Personal Genome Project (PGP) in which he unlocks the genome sequences of the first ten volunteers offering themselves up as guinea pigs, pioneers, genomic astronauts for an unprecedented experiment at the crossroads of science, health, and ethics. (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2712287 Tue, 18 Aug 2009 21:00:56 +0100 2712287 http://www.medworm.com/index.php?rid=2705158&cid=t_104781_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fmetabolic-fingerprint-of-your-urine.html For decades, the word “fingerprint” has been used to denote a set of unique characteristics, whether literally the complex patterns of arches, loops, and whorls on one’s fingertips or entirely figuratively and more recently, the notion of a genetic fingerprint based on an analysis of an individual’s DNA sequence. Most recently though, scientists have turned to another “omic” metabonomic fingerprinting using the analytical technique of NMR spectroscopy to obtain a unique view of an individual based on the complete range of metabolites produced by their body. In the press release that discussed the research and in my follow-up news story on Spectroscopynow.com, there was an allusion to the idea that each one of the 6.7 billion people on earth would have a ... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=2705158 Mon, 17 Aug 2009 12:00:39 +0100 2705158 http://www.medworm.com/index.php?rid=2691703&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F1Rts0G29jXk%2F There is an article in Wine Spectator (Seen on the JGI feed) on sequencing the wine spoilage yeast bruxellensis (correct name is now Dekkera bruxellensis) which adds the not-so-excellent taste of “sweaty horse” to wines.  There is already some survey sequencing done by Ken Wolfe and Jurge Piskur’s groups so a full genome sequencing project will help work out how this yeast is able to out compete Saccharomyces and cause dramatic wine spoilage.  This is also relevant on the bio-fuel side since this yeast can also taint an ethanol bio-reactor.  It is an interesting ecology inside the wine bottle and this competition for resources can lead to bad tasting wine. The competition presumably originated in some form in the rotting fruit where these yeasts compete for space and ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2691703 Tue, 11 Aug 2009 19:17:04 +0100 2691703 http://www.medworm.com/index.php?rid=2688838&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FjqxKb-XZnKA%2F Thirteen years and US $10 billion later, the first of several human genomes were completely sequenced in 2003 in what is now known as The Human Genome Project. From then on, scientists dreamed of and aimed to get the cost of DNA sequencing down to $1,000 per person. Although the running cost was around $250,000 per genome last year, well, that’s still thousands more expensive than most people can afford. No wonder only seven people have had their DNA fully sequenced! But that could all change from now on. A whole genome has been sequenced for only $50,000. Stanford engineer Stephen R. Quake invented the Heliscope Single Molecule Sequencer and sequenced his own DNA in one week – one short week! – using only three staff personnel, which was much faster and cheaper than first project... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2688838 Tue, 11 Aug 2009 05:06:56 +0100 2688838 http://www.medworm.com/index.php?rid=2683953&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F08%2F09%2Fwhat%25e2%2580%2599s-on-the-web-a-genome-application%2F Genetics & Medicine Online – ScienceRoll.WordPress.com (Killer Startups) One of the main ideas that originated this blog’s creation is to introduce medical professionals to the 21st century so they can get ready to get in touch with their patients online. In fact, patients could be called e-patients and it is very possible that they change the way medicine is actually being provided and practiced. No matter what you want to find in relation to medicine and health, this is a scientific blog where you will accomplish that goal. Your Genome: There’s an App for That (Med Tech): How personal genome computing can detect genome-friendly and genome-supportive products, from foods to cosmetics to building materials. Is Wikipedia in Decline? Scientists Search for Answers in Wik... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2683953 Sun, 09 Aug 2009 12:09:13 +0100 2683953 http://www.medworm.com/index.php?rid=2683961&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FM32MyPH8T1w%2F Just a short note and congratulations to Dr. Francis Collins for being confirmed as director of the National Institutes of Health. Francis Collins is new NIH director According to the Associated Press, Collins was confirmed by the US Senate yesterday via voice vote (say “aye” or “nay”), so I’d have to say this was an even easier confirmation than Judge Sonia Sotomayor, who took her oath today from Chief Justice Roberts as the first Hispanic justice of the US Supreme Court after a non-event of hearings. Collins is a familiar face and name at the NIH, having been one of the prime-movers of the human genome project as head of the Human Genome Research Institute for 15 years. He also authored the controversial book “The Language of God: A Scientist Presents Evidence for Belief ” ... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2683961 Sun, 09 Aug 2009 01:40:00 +0100 2683961 http://www.medworm.com/index.php?rid=2741080&cid=t_104781_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FcEH9tDc1aKQ%2F For the first 60 years of virus discovery, there was no system for classifying viruses. Consequently viruses were named haphazardly, a practice that continues today. Vertebrate viruses may be named according to the associated diseases (poliovirus, rabies), the type of disease caused (murine leukemia virus), or the sites in the body affected or from which the virus was first isolated (rhinovirus, adenovirus). Some viruses are named for where they were first isolated (Sendai virus, Coxsackievirus), for the scientists who discovered them (Epstein-Barr virus), or for the way people imagined they were contracted (dengue = ‘evil spirit’; influenza = ‘influence’ of bad air). By the early 1960s, new viruses were being discovered and studied by electron microscopy. As partic... virology blog blogs http://www.medworm.com/rss/comments.php?id=2741080 Fri, 07 Aug 2009 13:00:32 +0100 2741080 http://www.medworm.com/index.php?rid=2653979&cid=t_104781_136_f&fid=36162&url=http%3A%2F%2Fmyelomablog.com%2F2009%2F07%2F29%2Fmultiple-myeloma-genome-unlocked%2F Have you seen this news? Multiple Myeloma Genome Unlocked Discovery paves way for better therapies for some blood cancer patients, experts say Posted July 29, 2009 WEDNESDAY, July 29 (HealthDay News) — The sequencing of the first three multiple myeloma whole genomes has been completed by U.S. scientists, who said this success will lead to a better understanding of this form of blood cancer and advance efforts to develop new therapies. The analysis of DNA from more than 50 patient samples was conducted as part of the Multiple Myeloma Genomics Initiative. Overall, more than 250 patient samples have been collected and additional multiple myeloma genomes are being sequenced, according to a news release from The Broad Institute. The first three complete genomes should be available online ... beth's myeloma blog blogs http://www.medworm.com/rss/comments.php?id=2653979 Thu, 30 Jul 2009 00:18:15 +0100 2653979 http://www.medworm.com/index.php?rid=2649197&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F07%2F28%2Fpersonalized-genetics-news-genetic-test-registry-and-profiling%2F I try to keep you really up-to-date about news and announcements focusing on personalized genetics on Gene Genie, but I must share some other articles with you now. Navigenics reduced the price of its kit to 999$. You may also be interested in seeing the Navigenics HQ of which I published some images I took myself in Redwood, CA. 23andMe Research Revolution: “23andMe wants to advance genetic research into diseases that affect countless people, and make healthcare more personalized. The Research Revolution program is a way of kicking off that effort by seeding an inaugural set of communities focused on diseases. These diseases were chosen in part because we have identified pre-existing communities that have developed around them — we are excited to expand this list, and welcome f... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2649197 Tue, 28 Jul 2009 13:00:33 +0100 2649197 http://www.medworm.com/index.php?rid=2645476&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FSHq0DHhi37g%2F It looks like Proctor & Gamble scientists have just discovered the secret to youthful skin: it’s in 1,500 genes. Using data from the Human Genome Project, P&G scientists identified some 1,500 genes that are responsible for how skin ages. Of those, up to 700 genes control how skin collects and retains moisture. Genomics has key to keeping skin healthy and young. According to an article in the Daily Mail, there are separate ways that skin ages, and each of these are controlled by their own set of genes: Collagen (the protein that gives skin its structure and strength) degrades. Skin loses its ability to keep it hydrated. Fewer skin cells are produced with time. Wrinkles are produced when the skin becomes more inflamed. Age weakens our skin’s natural defense against free-radicals... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2645476 Tue, 28 Jul 2009 08:01:28 +0100 2645476 http://www.medworm.com/index.php?rid=2639675&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F07%2F26%2Fwhole-genome-sequencing-any-useful-data%2F I met George Church at this year’s Scifoo event in San Francisco and we talked about how useful the data is that was obtained from whole genome sequencing methods. There are almost 50 people in the world right now whose genomes were sequenced like that but the number of useful genomes is very low (e.g. who made it public) . That’s one reason why the ClinSeq project is really promosing. ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicine, including the exploration of issues related to the genetic architecture of di... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2639675 Sun, 26 Jul 2009 11:43:58 +0100 2639675 http://www.medworm.com/index.php?rid=2594576&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FI15UfjUj7GE%2F After the genome maps of an African, two Europeans, and a Chinese have been published, a Korean professor claims to have completed the “most accurate” genomic map yet – that of a 30-some healthy Korean male. The map is 99.94 accurate, having repeated analyses say, on chromosome 20, an average of 150 times. A research team lead by Professor Seo Jeong-seon, from Seoul National University, published its finding on Nature. Professor Seo emphasized the importance of having an accurate map as a foundation of personalized medicine. "It is important to have precise and accurate genome information of an individual since it is going to be fundamentals of personalized medicine. From this study, we found a way to obtain precise and accurate genome information.” The newest map is the sec... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2594576 Mon, 13 Jul 2009 11:43:00 +0100 2594576 http://www.medworm.com/index.php?rid=2594568&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F07%2F12%2Fbioweathermap-genomic-surveillance%2F Yesterday, I attended the session of George Church that focused on personalized genomics. He mentioned one of his new projects, Bioweathermap, an experiment in collaborative environmental surveillance and discovery. The BioWeatherMap initiative is a global, grassroots, distributed environmental sensing effort aimed at answering some very basic questions about the geographic and temporal distribution patterns of microbial life. Utilizing the power of high-throughput, low cost DNA sequencing and harnessing the drive of an enlightened public we propose a new collaborative research approach aimed at generating a steady stream of environmental samples from many geographic locations to produce high quality data for ongoing discovery and surveillance. Our approach will provide a unique opportunit... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2594568 Sun, 12 Jul 2009 17:28:34 +0100 2594568 http://www.medworm.com/index.php?rid=2584182&cid=t_104781_107_f&fid=36905&url=http%3A%2F%2Fjemmasbiologyblog.blogspot.com%2F2009%2F07%2Fartificial-sperm.html Read this news story about how human sperm have been made in the lab (Source: Jemma's Biology Blog) Jemma's Biology Blog blogs http://www.medworm.com/rss/comments.php?id=2584182 Thu, 09 Jul 2009 08:25:00 +0100 2584182 http://www.medworm.com/index.php?rid=2570472&cid=t_104781_90_f&fid=36413&url=http%3A%2F%2Fwww.dcscience.net%2F%3Fp%3D1848 On July 1st. the journal Nature, published three reports that described genetic differences between people with schizophrenia and the rest of us. Nature held a big press conference, at the World Conference of Science Journalists,  Many of the individual institutions involved in the studies also issued press releases.  As so often in press releases, descriptions like “landmark”, “major step forward” and “real scientific breakthrough” were used liberally. In short, there is no simple genetic basis for schizophrenia. The pooled results of the three studies gave 8,014 cases and 19,090 controls.  A huge amount of genetic analysis was involved. Many thousands of small genetic differences were found between the schizophrenics and the controls, bu... DC's goodscience blogs http://www.medworm.com/rss/comments.php?id=2570472 Fri, 03 Jul 2009 10:43:20 +0100 2570472 http://www.medworm.com/index.php?rid=2571006&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F5rYRQ7HKCbw%2F Tremella mesenterica (from K. Findley) The Tremella mesenterica genome portal is now live at the JGI. The genome is ~28Mb and the JGI annotation group predicted 8,313 genes, a significantly larger number of peptides predicted for C. neoformans (~7000; 18Mb genome) which may represent new and interesting genes or aspects of gene loss in the Cryptococcus yeast lineage. Tremella is a Basidiomycete jelly fungus and an interesting study system from the perspective of discovery of novel lignin degrading enzymes.  It also occupies an interesting phylogenetic position being an outgroup to the human pathogenic yeast Cryptococcus neoformans and C. gattii. Comparative genomics on this system may also provide insight into the interesting evolution of the large mating-type locus that was formed throug... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2571006 Thu, 02 Jul 2009 20:43:42 +0100 2571006 http://www.medworm.com/index.php?rid=2512320&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F06%2F23%2Ffamily-history-is-the-cheapest-genome%2F Steve Murphy, the gene sherpa, published a great post on his blog yesterday. An excerpt: But more importantly, we have a healthy respect for family history in common…… This guy and his team at the CDC have been researching Family History tools and the state of the science of family history pretty aggressively. This team is a heavyweight in the field and I am blown away by what they are doing. Why? It is the cheapest whole genome, phenome, metabolome scan we have today. The best part is that it covers multiple people with just one take! Just to make sure the message is transmitted: Family history is the cheapest whole genome, phenome, metabolome scan we have today. Thank you, Steve! Couldn’t say it better. Every physician in all the medical specialties should read this. (S... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2512320 Tue, 23 Jun 2009 20:30:54 +0100 2512320 http://www.medworm.com/index.php?rid=2512324&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F06%2F21%2Fyour-mobile-and-your-genomic-data%2F Dr. Andrad Pellionisz shared a press release with me today: Sunnyvale, CA (PRWEB) June 19, 2009 — The Google Phone demonstration introduced the imminent reality of the Genome Based Economy, as presented by HolGenTech Founder Dr. Andras Pellionisz at the Consumer Genetics in Boston the morning of June 10. HolGenTech Founder Dr. Andras Pellionisz demonstrated use of PDA for customers at the Consumer Genetics Conference in Boston in in the morning of June 10. Within hours, Illumina’s CEO Jay Flately featured a different business model application for personal genomes in the Apple iPhone. The demonstrations of hand held device applications intended for personal genomes stunned the audience of approximately 400 with a view into how practical applications of our personal genomes will... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2512324 Sun, 21 Jun 2009 20:25:56 +0100 2512324 http://www.medworm.com/index.php?rid=2512405&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FHEThPiK8Qy0%2F What does mega-search engine Google and mega-genome services company 23andMe have in common? Two actually, and maybe more… First – investments and second, spouses. This week, Google invested $2.6 million in 23andMe on top of the $7 million invested so far. No surprise there, since Google’s co-founder Sergey Bring is the spouse of 23andMe’s co-founder Anne Wojcicki. But as CNN remarked, it’s one the perks of marrying Google.   In another news, biotech giant Illumina has launched a personal genome sequencing service. That is, you can have your entire genome sequenced – all 3 billion DNA - for a hefty price of $48,000. Unlike 23andMe and other genome-testing services where only genotypes are provided, Illumina will provide your entire DNA sequence. But you need a prescr... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2512405 Sun, 21 Jun 2009 06:58:59 +0100 2512405 http://www.medworm.com/index.php?rid=2512326&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F06%2F20%2Fpersonalized-medicine-genetic-tests-for-drugs%2F Pharmacogenetics of warfarin – is testing clinically indicated?: A must-read about warfarin and Coumadin issues. This page catalogues drugs with pharmacogenomic information in the context of FDA-approved drug labels and lists drugs with mounting pharmacogenomic evidence. Have you ever seen a Promethease Report? Promethease is a tool to build a report based on SNPedia and a file of genotypes. Customers of testing services (23andMe, deCODEme, Navigenics, …) can use it to learn more about their DNA. It can also pool the data from multiple testing services. The program runs for approximately 2 hours. If you make an optional $2 payment via Amazon.com the program runs faster. Actually, I cannot download my genomic data from Navigenics, but will be able to do so after the summer. Any... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2512326 Sat, 20 Jun 2009 07:15:10 +0100 2512326 http://www.medworm.com/index.php?rid=2473875&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FU0yUCF_qeUo%2F Genome sequencing is underway on several early branches in the Opisthokont and some related linages as part of the “Origins of Multicellularity” project at the Broad Institute (BI) include some recently made available assemblies for: Allomyces macrogynus (Blastocladiomycota “Chytrid”) Capsaspora owczarzaki (Ichthyosporea) Already available data from Monosiga brevicolis (JGI) Batrachochytrium dendrobatidis (JGI, BI) (Chytridiomycota) Still in progress (BI) Amastigomonas sp Amoebidium parasiticum Nuclearia simplex Salpingoeca or Codosiga sp. Sphaeroforma arctica Stephanoeca or Acanthocopis sp. Mortierella verticulata Spizellomyces punctatus Still in progress (Other centers) Monosiga ovata (WashU) Physarum polycephalum (WashU) (Source: Fungal Genomes and Compa... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2473875 Sun, 14 Jun 2009 00:04:26 +0100 2473875 http://www.medworm.com/index.php?rid=2473507&cid=t_104781_107_f&fid=36905&url=http%3A%2F%2Fjemmasbiologyblog.blogspot.com%2F2009%2F06%2Ftransgenic-monkeys.html News story about how transgenic monkeys may be used to find cures for human diseases.What does transgenic mean? (Source: Jemma's Biology Blog) Jemma's Biology Blog blogs http://www.medworm.com/rss/comments.php?id=2473507 Thu, 11 Jun 2009 09:52:00 +0100 2473507 http://www.medworm.com/index.php?rid=2474070&cid=t_104781_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2009%2F06%2F10%2Fone-in-three-billion-found-single-mutation-in-the-foxl2-gene-may-cause-granulosa-cell-ovarian-cancer%2F “… Vancouver scientists from the Ovarian Cancer Research (OvCaRe) Program at BC Cancer Agency and Vancouver Coastal Health Research Institute have discovered that there appears to be a single spelling mistake in the genetic code of granulosa cell tumours, a rare and often untreatable form of ovarian cancer. This means that out of the three [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=2474070 Thu, 11 Jun 2009 06:05:16 +0100 2474070 http://www.medworm.com/index.php?rid=2452494&cid=t_104781_93_f&fid=36982&url=http%3A%2F%2Fprep4md.blogspot.com%2F2009%2F06%2Fhow-accurate-is-this.html Lecturer explains how humans came to have 46 chromosomes while chimpanzees have 48 and discusses the evolutionary significance of this discvery.Its the first time I hear this argument, so I would like to know what you think of it.Thanks for reading :) ... http://prep4md.blogspot.com/ (Source: My M.D. Journey!) My M.D. Journey! blogs http://www.medworm.com/rss/comments.php?id=2452494 Thu, 04 Jun 2009 00:25:00 +0100 2452494 http://www.medworm.com/index.php?rid=2447969&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F05%2F30%2Fpathway-genomics-a-new-contestant%2F There already are plenty of companies offering direct-to-consumer genetic testing such as Navigenics, 23andMe, DecodeMe or Knome. Now, here is Pathway Genomics that aims to offer “the fastest, easiest and most secure DNA testing available, providing information that can save your life” for $249. Quite a brave mission statement, but the service seems to be promising. You can order the test online, send your salive sample back and then they will share the genomic results of your sample with you through a secure form. You can get information about: Risk markers for 90+ diseases Maternal and paternal ancestry Drug responses including statins and warfarin. Carrier status (pre-pregnancy) Personal inheritable traits for eye color and back pain, among others. Here they discuss priva... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2447969 Sat, 30 May 2009 20:44:27 +0100 2447969 http://www.medworm.com/index.php?rid=2442308&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2Fw9bjwy5bfkw%2F Francis Collins, one of the major players who cracked the genetic code, is in final talks for taking the helm of the National Institutes of Health, reports the Bloomberg News. As director of the National Human Genome Research Institutes (NHGRI) for 15 years, Collins spearheaded efforts to map the human genetic code. With a lot of help from J. Craig Venter at Celera, the project was completed ahead of schedule in 2003, and opened up a plethora of applications and implications for research into our genetic blueprint. Collins resigned from the NHGRI position last year, in his own words, to have “greater latitude than my current position allows to pursue other potential positions of service without encountering any possible conflicts of interest, whether real or perceived." Post from:... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2442308 Tue, 26 May 2009 20:18:12 +0100 2442308 http://www.medworm.com/index.php?rid=2441375&cid=t_104781_93_f&fid=36982&url=http%3A%2F%2Fprep4md.blogspot.com%2F2009%2F05%2Fgenomics-and-future-of-medicine-francis.html The molecular understanding of disease has transformed the pharmaceutical industry. In the future, one can anticipate an increasing number of new drugs whose derivation depended upon a precise genomic understanding of disease. National Human Genome Research Director Dr. Francis Collins explains how genomics could play a role in medicine by improving public health.Thanks for reading :) ... http://prep4md.blogspot.com/ (Source: My M.D. Journey!) My M.D. Journey! blogs http://www.medworm.com/rss/comments.php?id=2441375 Tue, 26 May 2009 16:37:00 +0100 2441375 http://www.medworm.com/index.php?rid=2442266&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2Fftge7ud1tlI%2F Too much on my plate as of late, so I’m woefully behind on posting much on interesting papers or news.  Here’s a short list of links and papers that are worth a look though. “Evolution of pathogenicity and sexual reproduction in eight Candida genomes” published (Nature) NYT Science article sort of summarizing the good, bad, and ugly of fungi and human interactions Attempts to save amphibians from chytridiomycosis “Riders of a Modern-Day Ark” (PLoS Biology) Looks like Scott Baker with the JGI are in the process of resequencing several classical mutant strains of Phycomyces, Neurospora and Cochliobolus, Cryphonectria for sequence-based mapping of mutants (i.e. here and here and here). (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2442266 Tue, 26 May 2009 16:26:02 +0100 2442266 http://www.medworm.com/index.php?rid=2415617&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F05%2F15%2Fnavigenics-customers-speak%2F I’ve found two videos about Navigenics in which their customers share their experiences with personal genetic testing. Navigenics is a company focusing on direct-to-consumer genetic testing. I analyzed their service in details a few weeks ago. (Via HumanGeneticsDisorders.com) (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2415617 Fri, 15 May 2009 21:50:41 +0100 2415617 http://www.medworm.com/index.php?rid=2398773&cid=t_104781_107_f&fid=35041&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2Fdigitalbio%2F%7E3%2F8UfMlI5piEA%2Fwhy_dont_we_finish_the_human_g.php One of the interesting things I learned today was that many people are calling for the genome sequences of the chimps and Macaques to be finished. This is especially amusing because the human genome isn't quite done. We're primates, too! Why not finish our genome? Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World) Discovering Biology in a Digital World blogs http://www.medworm.com/rss/comments.php?id=2398773 Fri, 08 May 2009 13:00:18 +0100 2398773 http://www.medworm.com/index.php?rid=2358018&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FcxMadoakYds%2F Have a look at this post by Larry Moran on Takao Kasuga’s PLoS One paper on phylogenetic distribution of genes in N. crassa genome. The interesting next step with this paper, some of which we’re exploring as part of the Neuropsora tetrasperma and N.discreta genome sequencing, is how many of these N.crassa genes are at least shared with other Neurospora spp and whether they show a nucleotide conservation pattern that suggests they are protein coding genes. We also haves some RNASeq and microarray gene expression data to test if these species-specific genes are expressed any under conditions. So far there isn’t much evidence to throw out many of the 10k or so genes as artifacts, but the analysis is still a work in progress. Figure 1. Lineage specificity classification of ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2358018 Wed, 22 Apr 2009 22:11:38 +0100 2358018 http://www.medworm.com/index.php?rid=2349214&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F04%2F20%2Fwhat%25e2%2580%2599s-on-the-web-20-april-2009%2F What is the Physician’s Role in a Web-based World? (The Health Care Blog): Jay Parkinson, the founder of Hello Health, expressed his views. Worst Jobs in Science 2009 (Popsci.com) SHITTER: The social messaging service for IBS patients (Placebo Journal): What I can say now is OMG… Doctor, I’ve got a problem with my genome… (Times Online) Is Twitter Making You a Cold, Heartless Being? (Medgadget): Of course, it is not… X PRIZE for Healthcare Overview - Initial Design and Prize Guidelines (Crossover health) Social Networking, Semantic Searching and Science (Dennis’ Blog) (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2349214 Mon, 20 Apr 2009 18:53:07 +0100 2349214 http://www.medworm.com/index.php?rid=2349230&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F04%2F11%2Fwhat-is-pharmacogenomics%2F My good friend, Chavonne Jones at HumanGeneticsDisorders.com shared a great video with us that focuses on describing the main concept of pharmacogenomics. Read more about this interesting field here. (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2349230 Sat, 11 Apr 2009 19:02:13 +0100 2349230 http://www.medworm.com/index.php?rid=2323374&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F04%2F08%2Fa-catalog-of-published-genome-wide-association-studies%2F We desperately need a database of genome-wide association studies and now here it is (organized by Genome.gov). The genome-wide association study (GWAS) publications listed here include only those attempting to assay at least 100,000 single nucleotide polymorphisms (SNPs) in the initial stage. Publications are organized from most to least recent date of publication, indexing from online publication if available. Studies focusing only on candidate genes are excluded from this catalog. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator). What is a genome-wide association study? In genetic epidemiology, a genome-wide association ... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2323374 Wed, 08 Apr 2009 17:42:48 +0100 2323374 http://www.medworm.com/index.php?rid=2312608&cid=t_104781_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F03%2Fopen-innovation-in-drug-design-i-do-not.html Triggered by slides and a discussion from Cameron Neylon was I wondering, to which degree people believe in open innovation for the drug design community?Though the principle seems valid for a few software companies, is there little support for life sciences on this topic."It's an area that's just not been explored much. The usual flow is very much linear. Can be developed in academia, is then licensed via tech transfer." [Deepak]"The question is whether a business can make money by a route that doesn't involve patents (or copyright). There are examples of that, O'Reilly publishing being the most obvious but they are pretty thin." [Cameron]In other words, if you do not need the money, do whatever you like openly. If you need the money, e.g. for clinical trials, then please make sure stayin... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2312608 Mon, 30 Mar 2009 17:30:00 +0100 2312608 http://www.medworm.com/index.php?rid=2274488&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FvBv9bKMjBKQ%2F In preparation for Asilomar, JGI is releasing lots of the genome sequencing project portals. The Schizophyllum commune Genome Portal is now publicly available. Go get your white-rot gene investigation on! (Though please respect the community rules for 1st rights to publication of the genome-wide analyses). © Jason Stajich for The Hyphal Tip, 2009. | 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 Agaricomycota, genome, genome annotation, genome sequencing. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2274488 Mon, 16 Mar 2009 22:55:14 +0100 2274488 http://www.medworm.com/index.php?rid=2260106&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FdtNrZqSK434%2F The Mucormycotina (formerly Zygomycota) fungus Mucor circinelloides Genome Portal is now publicly available at http://www.jgi.doe.gov/Mucor. If you are planning to attend the Fungal Conference in Asilomar, there will be a JGI Workshop on March 19, 2009 at noon in Chapel to show how to use the manual curation tools. © Jason Stajich for The Hyphal Tip, 2009. | 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 genome, zygomycete. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2260106 Thu, 12 Mar 2009 19:55:53 +0100 2260106 http://www.medworm.com/index.php?rid=2260108&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FYGrts5CFiSk%2F Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. I mocked up a homage to his earlier street art — here we’ll discuss the growing Aspergillus genome posse. But the work from mainly the JCVI, Broad Institute, JGI, NITE, and Sanger centre has generated an excellent collection of genome sequences for the Eurotiales clade (feel free to get a login for the wiki and add other that are missing).  The Aspergillus community now has a AGD - Aspergillus Genome Database project that includes a curator of genome annotation (they are hiring) and presumably literature in the SGD and CGD model of curation. I think a lot of other projects have a Posse too (or maybe just a loosely organized band) in terms of a community of peop... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2260108 Thu, 12 Mar 2009 18:09:35 +0100 2260108 http://www.medworm.com/index.php?rid=2249293&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F03%2F07%2Fnavigenics-what-my-genome-tells-me-to-do%2F A few months ago, Navigenics.com offered me to analyze my saliva sample and genome. I happily accepted the offer and was curious to see what they could tell me. After graduating from medical school, I will start PhD training in personalized genetics this September so I’m quite into this emerging field of medicine. I sent my saliva sample back to their laboratory this January and received the results in about 3-4 weeks. I clicked on View my results and saw what kind of risks I have for certain medical conditions such as glaucoma, heart disease, prostate cancer, Crohn’s disease or osteoarthritis (9 conditions all together). When I check one medical condition, I see something like that: They tell me my risk compared to the whole population. And how that medical condition is af... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2249293 Sat, 07 Mar 2009 19:15:28 +0100 2249293 http://www.medworm.com/index.php?rid=2227456&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FrldRjqU82Kw%2F I have cheered the Sanger-Wellcome SGRP group work to generate multiple Saccharomyces cerevisiae and S. paradoxus strain genome sequences.   The group had previously submitted a version of the manuscript to Nature precedings and it is now published in Nature AOP showing that submitting to a preprint server doesn’t necessarily hurt your manuscript getting published…  The research groups explored the impact of domestication (as was also recently done for the sake and soy sauce worker fungus, Aspergillus oryzae) on the Saccharomyces genome by comparing individuals from wild strains of S. paradoxus. This paper addressed several challenges including methodology for light genome sequencing for population genomics. This data represents in a way, a pilot project on for genome reseq... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2227456 Sun, 01 Mar 2009 10:00:06 +0100 2227456 http://www.medworm.com/index.php?rid=2177560&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2009%2F02%2Fntetrasperma-ndiscreta%2F The JGI in collaboration with our lab at Berkeley have released the Neurospora tetrasperma (mat A) and N. discreta (mat A) genome sequences and annotation after about two years of work.  These are two closely related species to the well studied laboratory workhorse Neurospora crassa. The N.tetrasperma assembly (8X) has an N50 of 976kb and is highly colinear with the N.crassa genome.  With the JGI, we’ve also done some additional 454 sequencing which will represent an improved assembly and 23X coverage in the next release.  We also did some comparative scaffolding and can basically double that N50 - most of which looks good when compared to the improved V2 assembly. The N.discreta assembly (8X) is also quite good with an N50 of 2.3 Mb. For comparison, the V7 of N.crassa has an N50 ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2177560 Wed, 11 Feb 2009 07:08:50 +0100 2177560 http://www.medworm.com/index.php?rid=2167712&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FCAIJslFGq0M%2F Postia placenta genome is now published in early edition of PNAS.   Brown rotting fungi are import part of the cellulose degrading ecology of the forest as well (hopefully) providing some enzymes that will help in the ligin to biofuels process. Brown rotters break down cellulose but cannot break down lignin or lignocellulose while white rotters (like the previously sequenced Phanerochaete chrysosporium) are able to break down the lignin.  This fungus was chosen for sequencing as it is another potentially helpful fungus in the war on sugars (turning them into fuels) including recently published Trichoderma reesei and 1st basidiomycete genome Phanerochaete (all incidentally with the Diego Martinez as first author - go Diego!). It is also helpful to contrast the white and brown rotters t... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2167712 Fri, 06 Feb 2009 07:29:42 +0100 2167712 http://www.medworm.com/index.php?rid=2156525&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F02%2F03%2Fpersonal-genome-computing-breakthroughs-risks-and-opportunities%2F One more short post today. A video about personal genome computing: breakthroughs, risks and opportunities featured in the The Churchill Club which is Silicon Valley’s premier business and technology forum. Silicon Valley changed the world as the driving force in the development of computers and the internet. Could we play a similar role in advancing a genome-based economy?”. Panelists: •Linda Avey, Founder, 23andMe. •David Medina, HP Chief Technologist, Worldwide Health & Life Sciences •Karoly Nikolich., Dievini Hopp Biotech Holding, CEO of Amnestix •Andras Pellionisz, founder, International Hologenomics Society and HolGenTech •Dietrich Stephan, founder, Navigenics, founder of Amnestix        (Source: ScienceRoll) ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2156525 Tue, 03 Feb 2009 21:29:21 +0100 2156525 http://www.medworm.com/index.php?rid=2156526&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F02%2F03%2Fgenome-medicine-new-journal-from-biomed-central%2F I added Genome Medicine Journal to the new free medical information tracking tool of Webicina, PeRSSonalized Medicine yesterday so it’s time to say a few words about it. Genome Medicine is an online peer-reviewed journal which publishes open access research articles of outstanding quality in all areas of medicine studied from a genomic or post-genomic perspective. The journal will have a special focus on the latest technologies and findings that impact on the understanding and management of human health and disease. In addition to publishing high-quality research, Genome Medicine serves the international research community as a forum for the discussion and critical review of information about all areas of medicine informed by genomic research. Subjects include, but are not limited to... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2156526 Tue, 03 Feb 2009 21:24:01 +0100 2156526 http://www.medworm.com/index.php?rid=2150842&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FniC0Uc_RKKA%2F   After describing himself as an “unemployed geneticist”, Francis Collins now reveals that he has been “working night and day” with the White House transition for health and human services with Tom Daschle.  Now that that’s over, he is ready to discuss the progress that personalized medicine needs for it to move forward in a responsible way. Francis Collins, the public face of the human genome research and former director of the National Human Genome Research Institute, spoke to biomedical researchers, biotech execs and policy people at a meeting in Washington DC organized by the Personalized Medicine Coalition. "If we’re serious about preventive medicine, and using personalized genomics to inform that, we’re not going to change the genome," he s... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2150842 Sun, 01 Feb 2009 14:54:00 +0100 2150842 http://www.medworm.com/index.php?rid=2149663&cid=t_104781_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FOYsK0PypSK4%2F I hear so much about genetic testing these days that I’ve always wanted to find out what that experience is like for people who had the test done. Sure, it’s painless (just a saliva or cheek scrape will do). But more than the test itself, I want to know what your life is like these days. What was it like to know you are at risk for this X disease? What did you do with your results? Are you now eating, living better? Do you feel trapped, empowered, confused? I do want to know. Maybe I’m the coward who can’t face the mortality of my future. I don’t know that if I knew, I would do something about it, or I would be scared stiff to change. (What’s the point, right?) So hearing from other people who are more adventurous than me would probably help. It turns out, I’m not the only... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2149663 Sat, 31 Jan 2009 15:02:12 +0100 2149663 http://www.medworm.com/index.php?rid=2147612&cid=t_104781_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F527593699%2F I’m working to make more data available in the genome browsers for fungi. One is adding in the Primer information from the Neurospora KO project to the Neurospora browser to indicate the position and primer sequences for all the gene knockouts being (or already) constructed.  At least 60% of the genes have been knocked out and are available from the FGSC. We’re also integrating SNP data using the HapMap glyphs in which you can see one way to view this information in the Genome Browser for Coccidioides.  Working on other information including PhastCons conservation profiles and other information in our development server and hope to make this public soon. © Jason Stajich for The Hyphal Tip, 2009. | Permalink | No comment Add to del.icio.us Search blogs linking... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2147612 Fri, 30 Jan 2009 22:12:54 +0100 2147612 http://www.medworm.com/index.php?rid=2147604&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F01%2F30%2Fhave-you-used-the-services-of-23andme-decodeme-navigenics-or-knome%2F Marcie Lambrix (Research Assistant at Case Western University, School of Medicine) asked me to post this announcement: Early adopters of Direct to Consumer Genome Scans, researchers at Case Western Reserve University want to talk with YOU! We’re currently conducting in-depth interviews with early-adopter/consumers of such tests to learn more about an individuals’ decision to us Direct to Consumer genome scanning, what they understand to be the benefits and risks of this technology, both for individuals and society. Our interview question will address how the participant learned of whole genome scanning services, why they were interested in trying the technology, how they feel about the results that they have received, what they have done with the results, and if and how they have u... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2147604 Fri, 30 Jan 2009 18:01:16 +0100 2147604 http://www.medworm.com/index.php?rid=2141405&cid=t_104781_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F01%2F28%2Fnavigenics-interview-annual-insight%2F In my post about the predictions for 2009 in genomics, I said Navigenics would rule the market even if its service was more expensive than the kit of 23andMe. Now I had a chance to do an interview about the scientific background of the service and I have already sent my saliva sample back to their lab so the results should arrive soon. Now, they came up with a totally new website, a new product and a lower price (read the press release). I’m always saying such genetic tests should be ordered by physicians. Well, here is an excerpt from the press release: Accessible through Navigenics’ website, the secure portal empowers physicians with a suite of tools including a single access point to all of their participating patients’ genomic information, along with learning tools and case s... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2141405 Wed, 28 Jan 2009 21:17:30 +0100 2141405 http://www.medworm.com/index.php?rid=2131849&cid=t_104781_93_f&fid=36982&url=http%3A%2F%2Fprep4md.blogspot.com%2F2009%2F01%2Fintroduction-to-genomics.html Genomics is the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of single genes, their functions and roles, something very common in today's medical and biological research, and a primary focus of molecular biology, does not fall into the definition of genomics, unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks.For the United States Environmental Protection Age... My M.D. Journey! blogs http://www.medworm.com/rss/comments.php?id=2131849 Sat, 24 Jan 2009 16:48:00 +0100 2131849