ISMB2001 - The 9th International Conference on Intelligent Systems for Molecular Biology,
 Tivoli Gardens, Copenhagen, Denmark, July 22 - 25, 2001

PROGRAMME
SATURDAY, JULY 21 SUNDAY, JULY 22 MONDAY, JULY 23 TUESDAY, JULY 24 WEDNESDAY, JULY 25

SATURDAY, JULY 21
7:00Registration and information desk opens at the Tietgensgade entrance
8:30 - 12:30TUTORIALS 1 to 7, morning
12:30 - 13:30Lunch
13:30 - 17:30TUTORIALS 1 to 7, afternoon
19:00 - 22:00Opening Reception at Restaurant NIMB
SUNDAY, JULY 22
7:00Registration and information desk opens at the Tietgensgade entrance
8:30 - 9:00Opening remarks, Søren Brunak and Anders Krogh
Protein Structure and Modeling
Chair: Anna Tramontano
9:00 - 9:45 Protein folding, molecular evolution, and human disease
Keynote talk by CHRISTOPHER DOBSON
9:45 - 10:10 An insight into domain combinations
Gordana Apic, Julian Gough, Sarah A. Teichmann
10:10 - 10:50Coffee break
10:50 - 11:15 Prediction of the coupling specificity of G protein coupled receptors to their G proteins
Steffen Möller, Jaak Vilo, Michael D.R. Croning
11:15 - 11:40 Improved prediction of the number of residue contacts in proteins by recurrent neural networks
Gianluca Pollastri, Pierre Baldi, Pietro Fariselli, Rita Casadio
11:40 - 12:05 Non-symmetric score matrices and the detection of homologous transmembrane proteins
Tobias Mueller, Sven Rahmann, Marc Rehmsmeier
12:05 - 12:30 Generating protein interaction maps from incomplete data: application to fold assignment
Michael Lappe, Jong Park, Oliver Niggemann, Liisa Holm
12:30 - 14:00Lunch
Sequence Motifs, Alignments and Families
Chair: Michael Gribskov
14:00 - 14:45 Structural genomics
Keynote talk by CHRIS SANDER
14:45 - 15:10 0j.py: a software tool for low complexity proteins and protein domains
Michael J. Wise
15:10 - 15:50Coffee break
15:50 - 16:15 Separating real motifs from their artifacts
Mathieu Blanchette, Saurabh Sinha
16:15 - 16:40 Feature selection for DNA methylation based cancer classification
Fabian Model, Peter Adorjan, Alexander Olek, Christian Piepenbrock
16:40 - 17:05 An algorithm for finding signals of unknown length in DNA sequences
Giulio Pavesi, Giancarlo Mauri, Graziano Pesole
17:05 - 17:35 Discussion: Public Library of Science Initiative
Organized by Michael B. Eisen, University of California, Berkeley
17:00 - 19:00 POSTER SESSION 1 at Restaurant NIMB
INDUSTRY NIGHT
18:00 - 21:00 Industry Night Reception at Restaurant NIMB, Exhibition stands open untill 21:00
18:00 - 21:00 Software Demonstrations by Platinum Sponsors in Concert Hall
MONDAY, JULY 23
8:00Registration and information desk opens at the Tietgensgade entrance
Networks and Modeling
Chair: Alvis Brazma
8:30 - 9:15 Protein interactions
Keynote talk by DAVID EISENBERG
9:15 - 9:40 Protein-protein interaction map inference using interacting domain profile pairs
Jérôme Wojcik, Vincent Schächter
9:40 - 10:05 Inferring subnetworks from perturbed expression profiles
Dana Pe'er, Aviv Regev, Gal Elidan, Nir Friedman
10:05 - 10:40Coffee break
10:40 - 11:05 GEST: a gene expression search tool based on a novel Bayesian similarity metric
Lawrence Hunter, Ronald C. Taylor, Sonia M. Leach, Richard Simon
11:05 - 11:30 Rich probabilistic models for gene expression
Eran Segal, Ben Taskar, Audrey Gasch, Nir Friedman, Daphne Koller
11:30 - 11:55 Molecular classification of multiple tumor types
Chen-Hsiang Yeang, Sridhar Ramaswamy, Pablo Tamayo, Sayan Mukherjee, Ryan M. Rifkin, Michael Angelo,
Michael Reich, Eric Lander, Jill P. Mesirov, Todd Golub
11:55 - 12:20 Centralization: a new method for the normalization of gene expression data
Alexander Zien, Thomas Aigner, Ralf Zimmer, Thomas Lengauer
12:20 - 13:50Lunch
Networks and Modeling, continued
Chair: Søren Brunak
13:50 - 14:35 The phenomenon of the web
Keynote talk by BERNARDO HUBERMAN
14:35 - 15:00 Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
Derek Y. Chiang, Patrick O. Brown, Michael B. Eisen
15:00 - 15:35Coffee break
15:35 - 16:00 Identifying splits with clear separation: a new class discovery method for gene expression data
Anja von Heydebreck, Wolfgang Huber, Annemarie Poustka, M.Vingron
16:00 - 16:25 CLIFF: Clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts
Eric P. Xing, Richard M. Karp
16:25 - 17:55 Workshop: Bioethics and Fiction Science
Organized by Pierre Baldi, University of California, Irvine
16:00 - 18:00 POSTER SESSION 2 at Restaurant NIMB
BOAT TRIP AND BANQUET DINNER AT RESTAURANT BASECAMP ON HOLMEN
18:00 Busses depart from Tietgensgade just outside Tivoli Gardens
TUESDAY, JULY 24
Gene Structure, Regulation, and Modeling
Chair: Gary Stormo
9:00 - 9:45 The modern RNA world: many genes don't encode proteins
Keynote talk by SEAN EDDY
9:45 - 10:10 Promoter prediction in the human genome
Sridhar Hannenhalli, Samuel Levy
10:10 - 10:45Coffee break
10:45 - 11:10 Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition
Uwe Ohler, Heinrich Niemann, Guo-chun Liao, Gerald M. Rubin
11:10 - 11:35 Computational expansion of genetic networks
Amos Tanay, Ron Shamir
11:35 - 12:00 GENIES: a natural-language processing system for the Extraction of Molecular Pathways from Journal Articles
Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, Andrey Rzhetsky
12:00 - 12:25 Designing better phages
Steven S. Skiena
12:25 - 14:00Lunch
13:15 - 13:45NorFA Meeting
Gene Structure, Regulation, and Modeling, continued
Chair: Anders G. Pedersen
14:00 - 14:50 Computational analysis of RNA splicing
Overton Lecture by CHRIS BURGE
14:50 - 15:15 Disambiguating proteins, genes, and RNA in text: a machine learning approach
Vasileios Hatzivassiloglou, Pablo A. Duboue, Andrey Rzhetsky
15:15 - 15:50Coffee break
15:50 - 16:15 Gene recognition based on DAG shortest paths
John S. Chuang, Dan Roth
16:15 - 16:40 An efficient algorithm for finding short approximate non-tandem repeats
Ezekiel F. Adebiyi, Tao Jiang, Michael Kaufmann
16:40 - 17:05 Integrating genomic homology into gene structure prediction
Ian Korf, Paul Flicek, Daniel Duan, Michael R. Brent
17:00 - 19:00 POSTER SESSION 3 at Restaurant NIMB
17:05 - 19:00 IP WORKSHOP: Putting Informatics to Work: Intellectual Property and Business Promises
presented by Heller Ehrman White & McAuliffe LLP
WEDNESDAY, JULY 25
8:00 - 8:30 ISCB welcome & presentation of ISMB2002
Methods
Chair: Pierre Rouzé
8:30 - 9:15 Membrane proteins: from the computer to the bench and back
Keynote talk by GUNNAR VON HEIJNE
9:15 - 9:40 Design of a compartmentalized shotgun assembler for the human genome
Daniel H. Huson, Knut Reinert, Saul A. Kravitz, Karin A. Remington, Art L. Delcher, Ian M. Dew, Mike Flanigan, Aaron L. Halpern, Zhongwu Lai, Clark M. Mobarry, Granger G. Sutton, Eugene W. Myers
9:40 - 10:05 Probabilistic approaches to the use of higher order clone relationships in physical map assembly
David J. States, Volker Nowotny, Thomas W. Blackwell
10:05 - 10:35Coffee break
10:35 - 11:00 Fragment assembly with double-barreled data
Pavel A. Pevzner, Haixu Tang
11:00 - 11:25 SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database
Vineet Bafna, Nathan Edwards
11:25 - 11:50 Probe selection algorithms with applications in the analysis of microbial communities
James Borneman, Marek Chrobak, Gianluca Della Vedova, Andres Figueroa, Tao Jiang
11:50 - 12:15 Fast optimal leaf ordering for hierarchical clustering
Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola
12:15 - 13:00 ISCB open meeting
12:30 - 14:00 Lunch
14:00 - 14:25 Separation of samples into their constituents using gene expression data
D. Venet, F. Pecasse, C. Maenhaut, H. Bersini
Sequence and Phylogeny
Chair: Frédérique Galisson
14:25 - 14:50 New approaches for reconstructing phylogenies from gene order data
Bernard M.E. Moret, Li-San Wang, Tandy Warnow, Stacia K. Wyman
14:50 - 15:20Coffee break
15:20 - 15:45 Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences
Eleazar Eskin, William N. Grundy, Yoram Singer
15:45 - 16:10 Designing fast converging phylogenetic methods
Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow
16:10 - 16:35 Probabilistic divergence measures for detecting interspecies recombination
Dirk Husmeier, Frank Wright
16:40 - 17:10 Awards for best paper and poster
Closing remarks
SATURDAY, JULY 21 SUNDAY, JULY 22 MONDAY, JULY 23 TUESDAY, JULY 24 WEDNESDAY, JULY 25

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Last update: July 9, 2001
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