In no particular order or ranking, recent and not-so-recent articles from PLoS-1. The common thread (if any): I thought they were pretty cool in one way or another. 1. Men don’t tell the truth about their penis. No kidding? But this is somewhat more serious. It has been accepted for some time that male [...]
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Metagenomics
Bioinformatics, Free Culture, Metagenomics, Microbiology, Psychology, Science publication
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Circumcision, preventing fraud, and icky toilets. You know you’re going to read this.
By Iddo on December 4th, 2011
Bioinformatics, Evolution, Metagenomics, Microbiology, programming
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The Friedberg Lab is Recruiting Graduate Students
By Iddo on October 18th, 2011
The Friedberg Lab is recruiting graduate students, for both Master’s and Ph.D. WE ARE: A dynamic young lab interested in gene, gene cluster and genome evolution, understanding microbial communities and microbe-host interactions by metagenomic analyses, developing algorithms for understanding gene cluster evolution, and prediction of protein function from protein sequence and structure. YOU ARE: [...]
Biochemistry, Bioinformatics, Genomics, Health, Metagenomics, Microbiology, Travel
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Lake Arrowhead Microbial Genomics Conference
By Iddo on September 14th, 2010
Quick post: at the Lake Arrowhead Microbial Genomics Conference. I’m a bad microblogger, but thankfully Jonathan Eisen and Ruchira Datta are doing a great job of covering this conference live. There is a friendfeed room. The Twitter hashtag is #LAMG10. The science, people, food and location are all great. My student, David Ream, is presenting [...]
Obesity: the role of the immune system
By Iddo on April 25th, 2010
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 [...]
I never metagenomics I didn’t like
By Iddo on April 7th, 2010
“Let another man praise thee, and not thine own mouth; a stranger, and not thine own lips.” — Proverbs 27:2 “What-ever” – Me In PLoS Computational Biology this week, a trio of researchers provides a review of the challenges that metagenomics might ― and already do ― pose for bioinformaticians. The authors refer to metagenomic [...]
A sh*tload of data
By Iddo on March 4th, 2010
There are more microbial cells in our body than our own. Those microbes are not just passive hitchhikers or conversely, malicious agents of disease. They affect our well-being and health in a much broader spectrum than simply “bad” or “passive”. Among other things our gut microbes play an important role in digestion, have been linked [...]
blogging, Evolution, Genomics, Metagenomics
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Blogosphere catches: Marco Island, finding Ada and blog carnivals
By Iddo on March 2nd, 2010
Some interesting events cropped up recently. The Marco Island Advances in Genome Biology and Technology meeting was heavily tweeted and blogged about. Pacific Biosciences unveiled their third generation sequencer. Ostensibly, it can sequence reads of 20,000 length, but the fraction of actual long reads in a run, and their quality is still a bit hazy. [...]
Biology, Biotechnology, Genomics, Metagenomics
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Videos on sequencing
By Iddo on December 4th, 2009
A few cool vids on sequencing. Company infomercials, but still entertaining and informative. Thanks to my student, David Ream, for finding these. Pyrosequencing: Helicos: SOLiD: BASETM nanopore sequencing:
Bioinformatics, Metagenomics, Microbiology, stuctural biology
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Photosynthesis, phages and structures: there’s treasure everywhere!
By Iddo on November 24th, 2009
Here’s a really cool work, published this September in Nature.. Why did I choose this work? Well, it’s a major discovery, and it’s all done using bioinformatics, and fairly simple bioinformatics at that. The power of metagenomics and bioinfromatics: in a mass of data you just have to know what you are looking for, and [...]
The medium-rare biosphere
By Iddo on October 9th, 2009
All the roots hang down Swing from town to town They are marching around Down under your boots All the trucks unload Beyond the gopher holes There’s a world going on Underground — Tom Waits, “Underground” Our picture of the microbial biosphere is heavily skewed towards what we can see, culture, and are interested in. [...]
Bioinformatics, Biology, Genomics, Metagenomics
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Metagenomics Metadata and Metaanalysis
By Iddo on February 9th, 2009
I am a co-organizer of this… see for yourself. Cutting edge metagenomics research, discussion of standards applications to genomics and metagenomics, all in beautiful Stockholm this summer. If you are coming to ISMB/ECCB 2009, consider coming to the M3 SIG. Link to announcement 1-page poster, because you really want to tack this to your departmental [...]
