Systems Biology Workshop Highlights Avalanche of Protein Interaction Data; Video Now Available

By Doug Ramsey, 858-822-5825,

Systems Biology Poster Session
UCSD bioengineering postdoc Andreas Beyer, who works in Trey Ideker's lab, answers questions about his research project (with Ideker and bioinformatics grad student Silpa Suthram) during a Dec. 1 RECOMB poster session at Calit2.
San Diego, CA, December 14, 2006  -- The second annual RECOMB Satellite Workshop on Systems Biology took place Dec. 1-2 at Calit2 in San Diego. Chaired by UCSD Bioengineering professor Trey Ideker, the conference received funding from the UC Discovery Grant program, Calit2, and Pfizer La Jolla. Collaborating institutions included the International Society for Computational Biology (ISCB), which co-organized the meeting, and the journal Molecular Systems Biology , which will publish nearly half of the workshop's 20 accepted papers (others will appear in Lecture Notes in Bioinformatics ).

In his opening remarks, Ideker showed a graph charting the exponential increase in the total number of protein interactions available in public databases -- from just over zero in 2000, to 80,000 in 2005. "It's certainly consistent with exponential growth," Ideker pointed out. "In 2005 we saw roughly twice the number of interactions [in databases] as in 2004, and 2004 was roughly double the number in 2003. So there is this rise in all kinds of data in addition to sequence data. These are the golden years of understanding networks, and one would hope that by 2010 we would no longer be holding these conferences [focused on protein interactions], and will be talking about something else!"

At the request of presenters, several talks were not webcast, typically because a publication is pending. Below are several talks that are now archived and available for on-demand viewing, and others will be added over time. To watch the individual presentations, click on the image or video link below [Real player and broadband connection required].

Trey Ideker
Introductory Remarks
Friday, December 1, 2006
Trey Ideker, Conference Chair
Jacobs School of Engineering, UCSD
Length: 11:47 [video]
Eric Davidson, Caltech
Experimental System Analysis of the Genomic Regulatory Code for Embryonic Development
Eric Davidson, Caltech
Length: 55:00 [video][abstract]
Tomer Shlomi, Tel Aviv University A Genome-Scale Computational Study of the Interplay Between Regulation and Metabolism
Tomer Shlomi, Tel Aviv University
Length: 22:24  [video][abstract]
Mark Gerstein, Yale Understanding Protein Function on a Genome Scale Using Networks
Mark Gerstein, Yale University
Length: 53:06  [video][abstract]
Jianhua Ruan, WUSTL Identification and Evaluation of Functional Modules in Gene Co-expression Networks
Jianhua Ruan, Washington University in St. Lous
Length: 19:17  [video][abstract]
Xin Lu, UCSD Hubs in Gene Network Exhibit Low Changes in Expression in Allergic Response in Experimental Asthma
Xin Lu, UCSD School of Medicine
Length:  18:48  [video][abstract]
Igor Ulitsky Pathway Redundancy and Protein Essentiality Revealed in the S. cerevisiae Interaction Networks
Igor Ulitsky, Tel Aviv University
Length: 20:16  [video][abstract]

The Systems Biology conference was held in conjunction with the Dec. 2-3 RECOMB Satellite Workshop on Computational Proteomics. Those presentations are also available in streaming video. To watch selected talks, click here.

Related Links

RECOMB Satellite Workshop on Systems Biology
RECOMB Satellite Workshop on Computational Proteomics
Computational Proteomics Videos