All posts; Tags Include "genomics"
- August 31, 2010
- 11:02 AM
- 45 views
The Price of Sequencing Versus the Cost
by Mike in Mike the Mad Biologist
So, Nature Reviews Genetics has an article, "Computational solutions to large-scale data management and analysis", which claims the following in the abstract (italics mine):
Today we can generate hundreds of gigabases of DNA and RNA sequencing data in a week for less than US$5,000. The astonishing rate of data generation by these low-cost, high-throughput technologies in genomics is being matched by that of other technologies, such as real-time imaging and mass spectrometry-based flow cytomet........ Read more »
Schadt EE, Linderman MD, Sorenson J, Lee L, & Nolan GP. (2010) Computational solutions to large-scale data management and analysis. Nature reviews. Genetics, 11(9), 647-57. PMID: 20717155
- August 21, 2010
- 04:53 AM
- 132 views
More (you know you wanted it) on fecal transplants and the microbiome
by Jonathan Eisen in The Tree of Life
Image fromI Heart Guts blogThere is an interesting mini review in the Journal of Clinical Gastroenterology's September issue that may be of interest to some out there. It is entitled "Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome" by Martin Floch and well, the title is indicative of the article.Yes, the fecal transplant meme is here to stay. Sure, the cognoscenti already knew about fecal transplants. Perhaps they had read Tara Smith's discussion of it in her Aetiology blog in 20........ Read more »
Floch, M. (2010) Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome. Journal of Clinical Gastroenterology, 44(8), 529-530. DOI: 10.1097/MCG.0b013e3181e1d6e2
Grehan, M., Borody, T., Leis, S., Campbell, J., Mitchell, H., & Wettstein, A. (2010) Durable Alteration of the Colonic Microbiota by the Administration of Donor Fecal Flora. Journal of Clinical Gastroenterology, 44(8), 551-561. DOI: 10.1097/MCG.0b013e3181e5d06b
Khoruts, A., Dicksved, J., Jansson, J., & Sadowsky, M. (2009) Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium Difficile-associated Diarrhea. Journal of Clinical Gastroenterology, 1. DOI: 10.1097/MCG.0b013e3181c87e02
Yoon, S., & Brandt, L. (2010) Treatment of Refractory/Recurrent C. difficile-associated Disease by Donated Stool Transplanted Via Colonoscopy. Journal of Clinical Gastroenterology, 44(8), 562-566. DOI: 10.1097/MCG.0b013e3181dac035
- August 20, 2010
- 12:30 AM
- 63 views
The evolutionary ecology of the genome
by Graves in Down the Cellar
A new paper by Pierre Durand and Richard Michod suggests an interesting line of inquiry in the "post-genomic" era. Instead of focusing on the genome as a mere collection of genes, there is an opportunity to study the selective processes that result in both the origin and subsequent evolution of the genome. This is something we can approach with data now that the genomes of so many organisms are ... Read more »
Durand, P., & Michod, R. (2010) Genomics in the light of evolutionary transitions. Evolution, 64(6), 1533-1540. DOI: 10.1111/j.1558-5646.2009.00907.x
- August 9, 2010
- 08:47 PM
- 133 views
Lack of neutrality in bacteria and where pseudogenes go when they die
by Jonathan Eisen in The Tree of Life
Pseudogenes, which are in essence regions of the genome that used to be genes but no longer able to produce a functional unit, have long been considered to be models of the genetic equivalent of Switzerland's neutrality. With this assumption of neutrality in hand, researchers have used studies of pseudogenes to better understand what happens to DNA when it is not visible to any form of natural selection. That is, pseudogenes have been thought to be neither harmful (as in, they are........ Read more »
Kuo, C., & Ochman, H. (2010) The Extinction Dynamics of Bacterial Pseudogenes. PLoS Genetics, 6(8). DOI: 10.1371/journal.pgen.1001050
- August 2, 2010
- 02:25 PM
- 183 views
The MolBio Carnival: the first edition
by Alejandro Montenegro-Montero in MolBio Research Highlights
I’m pleased to host the very first edition of the MolBio Carnival, your monthly roundup of interesting posts in molecular biology from the science blogosphere. There has been a great response to this initiative and I had a great time reviewing submissions and writing this post.
You can read all about this Carnival here (submission guidelines, scope, etc), but right now, let’s get down to ... Read more »
Niethammer, P., Grabher, C., Look, A., & Mitchison, T. (2009) A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish. Nature, 459(7249), 996-999. DOI: 10.1038/nature08119
Quyn, A., Appleton, P., Carey, F., Steele, R., Barker, N., Clevers, H., Ridgway, R., Sansom, O., & Näthke, I. (2010) Spindle Orientation Bias in Gut Epithelial Stem Cell Compartments Is Lost in Precancerous Tissue. Cell Stem Cell, 6(2), 175-181. DOI: 10.1016/j.stem.2009.12.007
van Bakel H, Nislow C, Blencowe BJ, & Hughes TR. (2010) Most "dark matter" transcripts are associated with known genes. PLoS biology, 8(5). PMID: 20502517
Altschuler, S., & Wu, L. (2010) Cellular Heterogeneity: Do Differences Make a Difference?. Cell, 141(4), 559-563. DOI: 10.1016/j.cell.2010.04.033
- August 2, 2010
- 01:00 PM
- 45 views
An Inactive Mine Provides Active Opportunities
by Moselio Schaechter in Small Things Considered
by Elio
Metagenomics is a fine tool indeed for surveying a microbial community in concert, treating both the cultured and uncultured equally. When the sample studied is rich in microbial variety, as often is the case, the pieces of genomes can be reluctant to reveal the genetic heritage of whole microbes. But there are a few particular environments that are dominated by a handful of species at most, and here this approach allows the reconstruction of complete genomes. That is the case with t........ Read more »
Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, & Banfield JF. (2010) Enigmatic, ultrasmall, uncultivated Archaea. Proceedings of the National Academy of Sciences of the United States of America, 107(19), 8806-11. PMID: 20421484
- July 5, 2010
- 10:18 AM
- 140 views
Boney lumps and fast ways to the genetic cause of a disease
by Grant Jacobs in Code for life
We all have our lumps, the quirky features we develop with time.
Some of these are bone spurs, extra growths of bone.
These can be caused from damage to joints, like the lumpy joints seen in elderly people with arthritis. Bone spurs from differing causes can develop in many parts of the body, spine, toes, heel and [...]... Read more »
Sobreira NL, Cirulli ET, Avramopoulos D, Wohler E, Oswald GL, Stevens EL, Ge D, Shianna KV, Smith JP, Maia JM.... (2010) Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS genetics, 6(6). PMID: 20577567
- June 29, 2010
- 01:35 PM
- 90 views
A mushroom on the cover
by stajich in The Hyphal Tip
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 [...]... Read more »
Stajich, J., Wilke, S., Ahren, D., Au, C., Birren, B., Borodovsky, M., Burns, C., Canback, B., Casselton, L., Cheng, C.... (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proceedings of the National Academy of Sciences, 107(26), 11889-11894. DOI: 10.1073/pnas.1003391107
- June 10, 2010
- 07:39 AM
- 156 views
Autism genetics, how do you copy?
by Grant Jacobs in Code for life
Subtitle: Recent research identifies many changes in copy number that may point to genes that cause or are associated with autism.
In order to verify that important information has been conveyed over radio, the sender might ask “how do you copy” or, more briefly, “how copy” asking the receiver to tell the sender the information they [...]... Read more »
Pinto, D., Pagnamenta, A., Klei, L., Anney, R., Merico, D., Regan, R., Conroy, J., Magalhaes, T., Correia, C., Abrahams, B.... (2010) Functional impact of global rare copy number variation in autism spectrum disorders. Nature. DOI: 10.1038/nature09146
- June 6, 2010
- 02:01 PM
- 162 views
RNA Journal Club 5/27/10
by YPAA in You'd Prefer An Argonaute
Most “Dark Matter” Transcripts Are Associated With Known Genes Harm van Bakel, Corey Nislow, Benjamin J. Blencowe, Timothy R. Hughes PLoS Biology, 8 (5): e1000371, 18 May 2010. doi:10.1371/journal.pbio.1000371 This week’s illuminating summary and analysis by Igor Ulitsky. It’s Igor’s second contribution to the blog: The paper is one of at least five interesting RNA-Seq [...]... Read more »
van Bakel H, Nislow C, Blencowe BJ, & Hughes TR. (2010) Most "dark matter" transcripts are associated with known genes. PLoS biology, 8(5). PMID: 20502517
- May 28, 2010
- 09:49 AM
- 215 views
I remember because my DNA was methylated
by Grant Jacobs in Code for life
Our memories keep our yesterdays, our friends’ faces, the distinctive smell of previous partners, if we’ve read that book before, what clothes you wore to the party.
Movies and books have been written about memories. Or the trials not being able to keep them.2
Poets and lyricists evoke them, talk about them and reminiscence over them: “Preserve your memories, [...]... Read more »
Miller CA, Gavin CF, White JA, Parrish RR, Honasoge A, Yancey CR, Rivera IM, Rubio MD, Rumbaugh G, & Sweatt JD. (2010) Cortical DNA methylation maintains remote memory. Nature neuroscience, 13(6), 664-6. PMID: 20495557
- May 8, 2010
- 07:38 PM
- 160 views
Better the metagenome you know than the metagenome you don't...
by Daemios in Rudimenthos
Morgan, J., Darling, A., & Eisen, J. (2010). Metagenomic Sequencing of an In Vitro-Simulated Microbial Community PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010209A new era for the design of metagenomic controls starts! Morgan et al. present the benchmarking of metagenomic tools using artificial "microbial communities" mixed up in the lab.The Hook...Metagenomics is a fancy name for what's actually a large and obscure toolbox of molecular biology procedures and computational algorithms that p........ Read more »
Morgan, J., Darling, A., & Eisen, J. (2010) Metagenomic Sequencing of an In Vitro-Simulated Microbial Community. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010209
- May 7, 2010
- 02:28 AM
- 81 views
Better the metagenome you know than the metagenome you don't
by Daemios in Rudimenthos
A look into an in-vitro approach of metagenome benchmarking...... Read more »
Morgan, J., Darling, A., & Eisen, J. (2010) Metagenomic Sequencing of an In Vitro-Simulated Microbial Community. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010209
- May 6, 2010
- 11:19 PM
- 280 views
There is a little bit of Neanderthal in many of us
by Iddo Friedberg in Byte Size Biology
Big party at Science journal today, with the publication of a comprehensive draft Neanderthal genome. (Free access, nice going Science). Actually, it is a partially assembled draft of 60% of the total genome, but 60% of the genome from a human that was last seen on Earth 28,000 years ago is quite an achievement. The [...]... Read more »
Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.... (2010) A Draft Sequence of the Neandertal Genome. Science, 328(5979), 710-722. DOI: 10.1126/science.1188021
- May 6, 2010
- 05:19 PM
- 170 views
A Draft Sequence of the Neandertal Genome
by Olexandr Isayev in isayev.info
After extracting ancient DNA from the 40,000-year-old bones of Neanderthals, scientists have obtained a draft sequence of the Neanderthal genome, yielding important new insights into the evolution of modern humans.[1] Among the findings, published in the May 7 issue of Science, is evidence that shortly after early modern humans migrated out of Africa, some of [...]... Read more »
Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.... (2010) A Draft Sequence of the Neandertal Genome. Science, 328(5979), 710-722. DOI: 10.1126/science.1188021
Burbano, H., Hodges, E., Green, R., Briggs, A., Krause, J., Meyer, M., Good, J., Maricic, T., Johnson, P., Xuan, Z.... (2010) Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture. Science, 328(5979), 723-725. DOI: 10.1126/science.1188046
Dalton, R. (2010) Neanderthals may have interbred with humans. Nature. DOI: 10.1038/news.2010.194
- May 3, 2010
- 03:33 PM
- 194 views
Holy lateral transfer batman; amazing story on fungal to aphid transfer from Nancy Moran
by Jonathan Eisen in The Tree of Life
As many know, I generally do not write a lot about papers in non open access journal because I like readers to be able to access all the papers which I write about. But this is one of the exceptions to my normal rule. An amazing paper was published a few days ago in Science by Nancy Moran and Tyler Jarvik. Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids -- Moran and Jarvik 328 (5978): 624 -- ScienceI first found out about this from Ed Yong's blog post here (just........ Read more »
Moran, N., & Jarvik, T. (2010) Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids. Science, 328(5978), 624-627. DOI: 10.1126/science.1187113
, . (2010) Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biology, 8(2). DOI: 10.1371/journal.pbio.1000313
- April 30, 2010
- 12:49 PM
- 268 views
Well, color me surprised
by Iddo Friedberg in Byte Size Biology
Nature is colorful. And the family of pigments that is mostly responsible for these colors are carotenoids. Carotenoids make the apples red, the lemons yellow, the pumpkins oranges and, yes carrots, (from which their name is derived), orange.
Carotenoids also make flamingos and salmon pink, and color the puffin’s bill orange. But those animals cannot produce [...]... Read more »
Moran, N., & Jarvik, T. (2010) Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids. Science, 328(5978), 624-627. DOI: 10.1126/science.1187113
- April 27, 2010
- 07:04 PM
- 149 views
The specialization of novel genes
by Leonardo Martins in bioMCMC
Recently a paper about the software MANTiS called my attention, and I’ve been trying to write about it for a while. This announcement at the EvolDir list seemed like the perfect opportunity. I must warn you though that I’ve never used the software and I don’t have any intimacy with the underlying databases, but the [...]... Read more »
Milinkovitch, M., Helaers, R., & Tzika, A. (2009) Historical Constraints on Vertebrate Genome Evolution. Genome Biology and Evolution, 13-18. DOI: 10.1093/gbe/evp052
Tzika, A., Helaers, R., Van de Peer, Y., & Milinkovitch, M. (2007) MANTIS: a phylogenetic framework for multi-species genome comparisons. Bioinformatics, 24(2), 151-157. DOI: 10.1093/bioinformatics/btm567
- April 25, 2010
- 12:34 PM
- 278 views
Obesity: the role of the immune system
by Iddo Friedberg in Byte Size Biology
Obesity is one symptom of several, which together constitute what is now termed metabolic syndrome. Morbid obesity is also associated with a host of other symptoms including high blood sugar, high blood lipids, insulin resistance and liver disorders. The root causes of which are traced back to excessive food consumption, reduced physical activity and in some cases, genetic predisposition.
I have written before on the connection found between gut microbe populations and metabolic syndrome.... Read more »
Vijay-Kumar, M., Aitken, J., Carvalho, F., Cullender, T., Mwangi, S., Srinivasan, S., Sitaraman, S., Knight, R., Ley, R., & Gewirtz, A. (2010) Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5. Science, 328(5975), 228-231. DOI: 10.1126/science.1179721
- March 23, 2010
- 02:07 PM
- 212 views
Does gene function predict molecular evolutionary rate?
by stajich in The Hyphal Tip
Gene sequences evolve at different rates due to different constraints, either due to chromosome position, functional constraint, and status as a single-copy or multi-copy gene. In a recent paper, Allen Rodrigo (the new NESCent director by the, way, congrats!) the authors hypothesize that correlation in branch lengths of gene trees suggest they operate in the [...]... Read more »
Li WL, & Rodrigo AG. (2009) Covariation of branch lengths in phylogenies of functionally related genes. PloS one, 4(12). PMID: 20041191
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