ISMB2007 Summary

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SIG-AS
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1. Alan Zahler from UCSC
uses evolutionary conservation of sequences in introns flanking alternative spliced exons to identify splicing regulatory elements;
statistical analysis to find significant pentamer and hexamer
use microarray to detect out 400 high-confidence exon-skipping event (developmental stage-specific splicing regulation)
Browser: the Intronerator

2. Jamal Tazi from Montpellier II (France)
An interesting story.
use some small chemical molecules to target the splicing factor to correct the aberrant splicing caused by the mutation which could cause disease.
examples:
AS and Disease (ASF/SF2 on SR protein factor)
AS and development (eye/ey2a)

3. Uwe Ohler @ Duke University
transcript diversity on the 5' and 3' ends
for 5': use EST libraries, CAGE data?
for 3': use PolyA_DB

4. Mihaela Zavolan from Erik van Nimwegan's group
Title:Computational Evidence for the association btw transcription initiation and internal splicing
use FANTOM3 (mouse cDNA) and H-Invitational (human cDNA)

5. Erik @ Micro-SIG same time
Comparative genomic inference of bacterial regulatory systems
Interested point: develop a method to quantify selection at non-coding positions genome-wide from multi-alignments of clades of related bacterial genomes.
use simplified Halpern-Bruno model of site specific evolution (quick flash, not too much detail)
found: whereas silent sites evolve according to a neutral background model, intergenic regions show significant evidence of selection in all clades with consistently more selection upstream than downstream of gene.
strong avoidance of RNA 2nd structure in the region immediatelly around the translation start site (probably due to the selection for translation initiation efficiency)

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Tutourial
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1. Phylogenetic workflow using BioPerl by Jason
multiple alignment using bioperl/EnsEMBL; tree-construction using PhyLip; Molecular Evolution analysis using PAML/HyPHY; build gene family using MCL / OrthoMCL (for orthologous family); gene family size change (Computational Analysis of gene Family Evolution: CAFE)

2. Genome Browser and database by Peter Schattner
http://genome-test.cse.ucsc.edu

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Main Meeting
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1. RNA special session
Michael Zhang: Insulator (CTCF / BORIS)

Q: whether it's possible to observe the insulators like CTCF around breakpoint in GRB?
Two parts in GRB could be seperated due to the looser strength of pressure caused by the CTCF; We could really screen the evolution of GRB, to show the cases/events;

2. RNA keynote from John Mattick (?)
one of sharking(at least for me) points is "~98% transcripts output is non-coding RNA";
show lots of RNA papers, including some BIG or intertesting ones:
-Rapid evolution of noncoding RNA, K.C.Pang, 2006
-Widely distributed noncoding purifying selection in the human genome, PNAS, 2007 July, Saurabh Asthana... John A. Stamatoyannopoulos (@Washington University)
He also mentioned that 1300/1600 ncRNA expressed in brain, in some paper.

Q: whether to see ncRNA in GRB?
The hypothesis is that ncRNA overlapping(or anti-sensing) with the regulator gene makes the gene as a 'bystander' gene

3. Keynote from Michael Eisen (@Berkeley Lab)
For me, one important msg from his report is to use high level feature linked to function to re-define conservation, not just simply seqeunce similarity.
BTW, I just got to know that the director of Berkeley Lab is the famous Chinese scientist Steve Chu(朱棣文)