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 [...]
Displaying posts tagged with
“metagenomics”
Biochemistry, Bioinformatics, Genomics, Health, Metagenomics, Microbiology, Travel
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Lake Arrowhead Microbial Genomics Conference
By Iddo on September 14th, 2010
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 [...]
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. [...]
The Craigslist of Antibiotic Resistance
By Iddo on September 6th, 2009
(Before we get going: this the the 100th post on Byte Size Biology. Happy Birthday to me!) Resistance to antibiotics is a huge clinical problem. In the US, more people die of methicillin-resistant Staphylococcus aureus (MRSA) infections (nearly 19,000 in 2006) than of AIDS (14,627). We know that antibiotic resistance is carried on mobile genetic [...]
Bioinformatics, Microbiology, Software, Technology
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Absolut standards: report from the M3-2009 meeting, part 2: signature genes and big science
By Iddo on July 27th, 2009
Some more presentations from the metagenomics, metadata, and metaanalysis (M3) meeting, Stockholm June 27, 2009 Pathway Signature Genes Lucas A. Brouwers, Martijn A. Huynen and Bas E. Dutilh CMBI / NCMLS, Radboud University Nijmegen Medical Centre, The Netherlands If we take a sample of soil, how can we know whether it is adequate for growing [...]
Bioinformatics, Evolution, Genomics, Microbiology
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Absolut standards: report from the Metagenomics Metadata and Metaanalysis 2009 meeting. Part 1
By Iddo on July 20th, 2009
The first metagenomics, metadata and metaanalysis meeting held in Stockholm June 27 2009 was a raging success. People were standing all the way back to the hall jostling for elbow room, while all the other concurrent meetings were pitifully empty after word has made it about how awesome we were. OK, I may be exaggerating [...]
Microbiology
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Skin Flick 2: Statistic Boogaloo
By Iddo on June 1st, 2009
Reports on the first metagenomic survey of skin bacteria (see my previous post) did not go unnoticed by the popular media. Reports appear in US News & world Report, LA Times, Times of India, National Geographic, and Scientific American. All these articles have one thing in common: they are wrong. Yes, even Scientific American. All [...]
Bioinformatics, Microbiology
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Skin flick
By Iddo on May 29th, 2009
Interesting report in Science today about the human skin metagenome. The skin is a fairly large organ, and it is home to an estimated 1012 bacteria. It is the first barrier our body poses against pathogens, toxins, and sarcastic comments. An adult’s skin area is about 2m2, virtually all of it exposed to the outside [...]
Bioinformatics, Biology, Microbiology
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The Metagenomics Metadata and Metaanalysis meeting is coming up
By Iddo on April 22nd, 2009
It is fun chairing the program committee of a new meeting: you get all this cutting edge research getting thrown your way. Scientists will submit their latest to meetings, True, it is usually incomplete work and very rough around the edges. But it’s great being one of the first to know what’s cooking in other [...]
Bioinformatics, Biotechnology, Software
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Challenges with Data Quality, Sharing, and Versioning in Next-Generation Sequencing
By Iddo on March 27th, 2009
An fine talk by David Dooling highlighting some of the false impressions about second generation sequencing. A partial list: Why sequencing quality trump base pair output Why genomes are really probabilities rather than strings Why centralized repositories break down when it comes to second generation sequencing data. Collaborative Software development and versioning has been moving [...]
Microbiology
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Metagenomes as a diagnostic tool?
By Iddo on February 15th, 2009
Can we learn about an environment by looking at the bacteria living in it? Can we sequence a metagenome, and then say: ”according to the active genes in this water sample it appears to be too rich in metal ions / sewage products / other pollutants” ? In the foreseeable future could we sequence a [...]
Every Man an Island, Pt. 2
By Iddo on January 26th, 2009
(Continued from part 1) Why we are islands In the previous post we have seen how our bacterial population affects our weight and that by changing our dietary habits we can change the species composition in our guts. Also, we saw how a metagenomic analysis can lead to verifiable hypotheses: using a metagenomic analysis, Gordon’s [...]
