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[Gofriends] COMBREX Workshop for Computational and Experimental Determination of Protein Function

Iddo Friedberg idoerg at
Wed Jun 9 09:57:55 PDT 2010

Announcing the first COMBREX Workshop for
Computational and Experimental Determination of Protein Function
Lake Arrowhead, California   Sep. 15, 2010

(Apologies for cross-posting. Please forward appropriately).

COMBREX (Computational Bridge to Experiments) is a new NIH funded effort
that aims to increase the pace of experimental determination of the
function of large and high priority gene families in bacterial genomes.
Led by Richard Roberts (New England Biolabs) Simon Kasif (Boston
University) and Martin Steffen (Boston University), this effort will
form a consortium of experimental and computational biologists that
would collaborate directly to test the predicted functions or
specificity of high-priority genes. Central to this effort would be the
creation of a community web-based database that would allow
computational and experimental scientists to communicate easily and
assist experimentalists in identifying high-priority genes with
high-quality computational predictions. Experimentalists will be able to
submit bids (proposals) to validate individual predictions, and if
successful, will receive modest funding from COMBREX to perform the
validation. The website can be found at <>.

A workshop to discuss issues related to the formation and operation of
COMBREX will take place on Wednesday, September 15, 2010, as part of the
18th Annual International Meeting on Microbial Genomics at Lake
Arrowhead, CA, outside of Los Angeles. A preliminary program can be
found at (COMBREX is
formerly SciBay). Confirmed speakers include Richard Roberts, Simon
Kasif, Manuel Ferrer (CSIC, Madrid), Patricia Babbit (UCSF), John Gerlt
(Illinois), Peter Karp (SRI), Alexander Yakunin (Toronto) Steven
Brenner (UC Berkeley) and Bruno Sobral (Virginia Tech).

The morning session will provide an overview of COMBREX, including both
the experimental and  computational challenges, related talks, and a
description of topics to be discussed by breakout groups. These groups
will convene in the afternoon to discuss the topics and prepare a short
summary, for presentation to the entire workshop after dinner.

Topics to be discussed by the breakout groups will roughly divide into
the following areas:  (1) whole genome annotation, (2) assessment of
computational predictions, (3) use of structure to predict function, and
(4) infrastructure for function annotation. General topics to be
discussed include:

        1. How to prioritize predictions?
        2. How to evaluate experimental bids?
        3. How to handle non-enzymatic proteins?
        4. How best to handle predictions/phenotypes from high-throughput

A key desired outcome of the workshop is identifying opportunities and
catalyzing collaborations between computational and experimental

We hope you will be able to join us for this event. You can register at

For further information please contact the organizers:

Co-chairs: Martin Steffen, Boston University, steffen at
Iddo Friedberg, Miami University, i.friedberg at

Steering Committee: Simon Kasif and Richard J. Roberts

Iddo Friedberg
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