Greetings from CSHL

Greetings from Cold Spring Harbor.

So far the sessions I've attended have comprised of a variety of focus-applications of large sequencing projects.
These have been:
Functional and Cancer Genomics
Genetics of Complex Traits
and
High Throughput Genomics & Genetics

The latter session was really all about new sequencing technologies and large genome sequencing projects. The most news-worthy talk was Chad Nusbaum's presentation of preliminary findings from their research using the SOLiD(TM) System. There were a number of science publications that covered this this morning (for instance here's the CNBC piece), so I won't go into it here.

One of the interesting ideas promoted by EA Grice from NISC comparative sequencing program was to look for a core microbiome. First, is there a core microbiome? In her talk titled "core diversity profile of human skin microbiome in health and in disease," the center is asking whether we should consider the dominant and rare bacterial populations in normal individuals as a taxonomic
unit when we're predicting disease or drug response (given that our drug digestion or response is sometimes dependent on the response of our microbiome). Their approach was all about the "Phylogenetic architecture" of the microbiome. While they were looking at skin microbiome, they said that the results (and ability to differentiate healthy and diseased tissue) could be generalized. However, they did recognize that skin is special because they have terminal differentiation.

I also presented my poster last night. The set-up is a bit weird because they make you put your poster up and down within a 4 hour period. We got some interest from the usual suspects, but I think there was greater interest in J.D. Watson's wine and cheese birthday party taking place on the lawn. So I got to see J. Watson in a cowboy hat. Personal opinion aside, everyone questioned CSHL's love-hate relationship with Watson...
J.D. Watson's wine and cheese birthday party






It was hard for me to see other posters last night since I was attending my own, but a few interesting things I saw:
Adam Siepel's lab is looking at some interesting ways of finding already characterized regulatory motifs under selection in multiple genomes with a phyloHMM approach (fabsCons derivative method)
Manuel Garber, Michelle Clamp and Xiaohui Xie looking for selection signatures. The idea is to identify sites with unlikely substitution patterns using diversion from stationary distribution that is in background. They tried this over the encode regions.

The evening session went until 11:30pm (!) finishing with R. Durbin's talk on the "1000 genome project." Since the meeting is oversubscribed, many of us are staying several miles away (and I didn't bring my car) so I'm dependent on the shuttle. So I didn't get to leave the labs until 11:45, and it wasn't because I hung out at the bar...

This morning's session is on Computational Genomics.
From JGI: Microbial genomes are a rich source of biological info. Doing comparative prokaryote genomics, they identified antimicrobial peptides, small RNAs and new restriction enzymes that may act as barriers to horizontal gene transfer (see Sorek, Science 2007).

From E birney's lab:
Herrero presented Enredo (which we heard about from Birney on his April 22nd visit)
Also introdued Ortheus
addressing inference of insertion deletion histories and substitution events
Uses a multiple alignment as guiding input
subs are using tamura nei nucleotide subs model
ancestral sequences are represented using weighted sequence graphs, but works progressively.
so check out
enredo, pecan and ortheus.
at their respective websites (which went past on the screen way too fast for me to catch).

Manolis Kellis talking about comparative genomics of mammalian phylogeny and drosophila.

In mammals: want to discover regions of increased selection, detect func elements by increased conservation, and add more genomes in which we can detect smaller elements, and subtle selection
also: discover diff classes of fun elements, patters of change that distinguish diff types of func element.
(I'm not sure what is new here)
They were promoting the "evolutionary signatures" of protein coding genes respecting frame shifting gaps and synonymous substitution signature (again, not new)
built a model for expected substitution counts (diff codons have diff distribution for synonymous subs counts) and score windows for depletion of syn subs-- but this only looks for purifying selection.
Also looking for signatures for microRNA genes (in Drosophila) (see Stark et al, Genome Research 2007)