Scope:

Integration of language technologies in bioinformatics/computational biology research

Protein sequences from different organisms may be viewed as texts written in different languages. The mapping of protein sequence to their structure, dynamics and function then becomes analogous to the mapping of words to meaning in natural languages. This analogy can be exploited by application of statistical language modeling and text classification techniques to biological sequences, thereby generating testable hypotheses regarding the fundamental building blocks of “protein sequence language”.

The biology-language analogy enables novel applications of language technologies to the biology domain, but is to a great extent overlapping with existing other computational biology/bioinformatics applications. The purpose of the Biological Language Conference is to facilitate scientific exchange between researchers using the language analogy approach directly and researchers using other approaches.

We invite papers in the following areas of interest:

secondary structure prediction
tertiary structure prediction
repetitive fold prediction
membrane protein-specific prediction challenges
protein folding/misfolding
conformational dynamics

genome evolution/comparison
sequence alignment
protein family classification
immune system
protein-protein interactions
protein/gene networks and pathways

Because of the challenge in bioinformatics research of involvement of non-biology domain experts in biology research, we also encourage submission of papers describing new approaches to cross-disciplinary education.

Venue and dates:

November 20-21, 2003 at Carnegie Mellon University in Pittsburgh, USA

The conference is organized by Profs. Raj Reddy and Judith Klein-Seetharaman of the NSF-funded Center for Biological Language Modeling (http://www.cs.cmu.edu/~blmt). Papers should be a maximum of 15 pages and will be peer-reviewed. All accepted papers will appear in the conference proceedings. Papers should be prepared according to the guidelines (http://flan.blm.cs.cmu.edu/meeting2003/template.doc) and submitted online here. Further information on the conference will be available at http://flan.blm.cs.cmu.edu/meeting2003/.

September 20^th, 2003	(Optional) White-paper abstract and indication of intention to submit a paper by email to judithks@cs.cmu.edu
October 20^th, 2003	Deadline for electronic paper submission
November 1^st, 2003	Notification of acceptance
November 10^th, 2003	Final camera-ready manuscript due

Contact

Judith Klein-Seetharaman,
Language Technologies Institute,
School of Computer Science,
Carnegie Melon University,
email: judithks@cs.cmu.edu,
phone: 412 383 7325,
fax: 412 648 1945.

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