EXTRACTING BIOLOGICAL KNOWLEDGE FROM DNA SEQUENCES 2nd Call

Denis Thieffry denis at cifn.unam.mx
Wed Sep 4 11:26:29 EST 1996


EXTRACTING BIOLOGICAL KNOWLEDGE FROM DNA SEQUENCES
          Track of the PACIFIC SYMPOSIUM ON BIOCOMPUTING 1997
                 Kapalua, Maui, Hawaii - January 6-9, 1997
        Chairs: F. M. De La Vega, D. Thieffry & J. Collado-Vides
               http://www.cgl.ucsf.edu/psb/delavega.html
                         2d Announcement
             Call for poster/computer demonstrations


We would like to invite you to submit an abstract for a poster and/or a
computer demonstration in the context of the PSB=9297 track we are
organizing. Abstracts (one page) can be sent by physical mail or email
to Russ Altman (altman at camis.stanford.edu), to arrive no later than
September 15, 1996. An abstract book will be assembled and distributed
at the meeting. More information about format, registration, lodging,
support, and other PSB=9297 tracks can be found at the url:
http://www.cgl.ucsf.edu/psb.


INTRODUCTION

A growing number of ambitious sequencing projects are in progress, and
there is an increasing need for integration and analysis of these huge
amounts of sequence data. The central question that remains is: how to
leap from pure sequence information to useful biological knowledge?
There are many theoretical, mathematical and computational approaches
useful in this enterprise. Examples of these are statistics, artificial
intelligence, linguistics and information theory. A common goal is to
identify functional units in the sequences, looking for characteristic
patterns and regularities found in a set of examples. Some of the
identified units also maintain complex relationships among themselves,=20
allowing to explain regulatory phenomena. As some complete genomic
sequences become available, there are new opportunities for comparative
analyses involving global questions dealing with complete genomes. A new
type of sequence analysis focusing on higher order sequence patterns is
emerging.


PURPOSE

This session will address the different theoretical and computational
approaches aimed to extract biological information from DNA sequences.

This includes but is not limited to:

* Statistical analysis of DNA sequences
* Analysis of codon usage and compositional patterns
* Gene identification and localization
* Definition and recognition of regulatory signals
* Characterization of complex functional patterns
* Knowledge extraction from sequence databases
* Comparative genome analysis
* New tools for automated analysis
* Cross validation of existing tools


ORAL COMMUNICATIONS

Fretch, K. & Werner, T. (GSF-FUG, Germany). =93Specific modelling of
regulatory units in DNA sequences=94.

Kulp, D., Haussler, D., Reese, M.G. & Eeckman, F.H. (UC-Santa Cruz -
LBNL, CA). =93Integrating database homology in a probabilistic gene
structure model=94.

Ponomarenko, M.P., Ponomarenko, J.V., Kel, A.E. & Kolchanov, N.A. (ICG,
Russia). =93Search fo DNA conformational features for functional sites.
Investigation of the pro- and eukaryotic TATA box=94.

Shibuya, T. & Imai, H. (Universityof Tokyo, Japan). =93Enumerating
suboptimal alignments of multiple biological sequences efficiently=94.

Thieffry, D., Rosenblueth, D.A., Huerta, A.M., Salgado, H. &
Collado-Vides, J. (UNAM, Mexico). =93Definite-Clause Grammars for the
analysis of cis-regulatory regions in E.coli=94.=94

Widgenger, E., Karas, H. & Kn=FCppel, R. (GBF, Germany). =93TRANSFAC
Database as a bridge between sequence data libraries and biological
function=94.


DEADLINES

Abstract submission deadline: September 15, 1996

Meeting: January 6-9, 1997


TRACK CHAIRS

J. Collado-Vides
Centro de Investigacion sobre la Fijacion de Nitrogeno,
UNAM Cuernavaca, A.P. 565-A, Morelos, Mexico
Fax: (527)317-55-81
E-mail: collado at cifn.unam.mx

F. M. De La Vega
Depto. de Genetica y Biologia Molecular,
CINVESTAV-IPN, A.P. 14-740, Mexico D.F.
07000, Mexico.
Fax:+752-6330
E-mail: FVega at gene.cinvestav.mx

D. Thieffry
DBM-ULB, Rhode-Saint-Genese, Belgium
Current address:
Centro de Investigacion sobre la Fijacion de Nitrogeno,
UNAM Cuernavaca, A.P. 565-A, Morelos, Mexico
Fax: (527)317-55-81
E-mail: denis at cifn.unam.mx

Note: The preferred means of contact with the track co-chairs for any
subject refering the track, is the E-mail address:
psb97 at gene.cinvestav.mx




_______________________________________________________________________
Dr Denis THIEFFRY (Ed. CSTB Bulletin)
Laboratorio de Biologia Computacional              Tel: (52-73)13-20-63
CIFN - UNAM                                        Fax: (52-73)17-55-81
A.P. 565-A,  Cuernavaca, Morelos 62100, Mexico     =20
______________________________________________________________________




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