Call for Posters
Scope
Topics
Submission
Accepted Papers
Program
Important Dates
Program Committee
WABI Steering Committee
Registration and Hotel Reservation Form
3rd Workshop on Algorithms in
Bioinformatics
Budapest, Hungary, 15-20 September, 2003
Contents
Call
for Posters
Scope
Topics
Submission
Accepted
Papers
Program
Important
Dates
Program
Committee
WABI
Steering Committee
Registration and Hotel
Reservation Form
A poster session
will be organized during the workshop. The emphasis is on algorithmic work that
addresses an important problem in molecular biology.
Graduate students with significant work in progress are especially
invited to submit posters. A printed version of the poster abstracts will be distributed at
the workshop.
Poster abstracts must be one or two pages long and must contain: the title; the
authors and their addresses (including email addresses); a short abstract using
10 point font or larger and single line spacing. A standard PDF file must be sent to Gary Benson (benson@camelot.mssm.edu),
by
July 25th, 2003. Authors will be notified
about acceptance by August 1, 2003.
▲
to contents
The Workshop on Algorithms in Bioinformatics covers
research in all aspects of algorithmic work in bioinformatics and computational
biology. The emphasis is on discrete algorithms that address important problems
in molecular biology, genomics and genetics, that are founded on sound models,
that are computationally efficient, that have been implemented and tested in
simulations and on real datasets and that provide new biological results. The
goal is to present recent research results, including significant
work-in-progress, and to identify and explore directions for future research.
WABI
2003 will be held as part of ALGO
2003 in
Budapest, Hungary, 15-20 September, 2003.
Original research papers (including significant
work-in-progress) or state-of-the-art surveys are solicited in all aspects of
algorithms in bioinformatics and computational biology, including, but not
limited to:
* Exact and
approximate algorithms for genomics, genetics, sequence analysis, gene
and signal recognition, alignment, molecular evolution, phylogenetics,
structure determination or prediction, gene expression and gene networks,
proteomics, functional genomics, and drug design.
*
Methods, software and dataset repositories for development and testing of such
algorithms and their underlying models.
*
High-performance computing approaches to computationally hard problems in
bioinformatics, particularly optimization problems.
The proceedings of the workshop will be published in
the Lecture Notes in Computer Science (LNCS) series of Springer Verlag.
Submissions should consist of an extended abstract of
no more than 15 pages (including title page, all figures and bibliography) in
11pt font, preferably using the Springer LNCS style (see: http://www.springer.de/comp/lncs/authors.html).
An abstract should start with a presentation of the biological motivation, the
algorithmic problem, the results achieved, their significance and a comparison
with previous work. This material should be understandable to non-specialists. A
more technical exposition should follow and an optional short appendix may
contain details or additional data to be consulted at the discretion of the
program committee. The submission must include the corresponding author's email
address.
Submissions
must be made using the online submission server at (http://wabi.biomath.mssm.edu).
Deadline is 23:59 (GMT) on 28 April 2003, for your submission to be
considered. Three formats will be supported this year, postscript, pdf, and doc.
Each submission must be submitted as a single file.
Authors using other than latex to generate their document are cautioned
that as of the date of this call for papers, the
final version of accepted papers must be submitted as a latex file.
Simultaneous
submission to another conference or journal is allowed. Authors are asked to
inform the program co-chairs at the time of submission of the simultaneous
submission. If the submission has been accepted to another conference or a
journal before WABI 2003, the abstract will not be published in the proceedings
of WABI 2003.
In order to ensure inclusion of their
work in the proceedings, authors must present their accepted papers at the
workshop.
Address any
questions to the program committee co-chairs, Gary Benson
(benson@camelot.mssm.edu) and Roderic Page (r.page@bio.gla.ac.uk).
Consensus
networks: A method for visualising incompatibilities in collections of trees
Barbara
Holland, Vincent Moulton
Parsimonious
Reconstruction of Sequence Evolution and Haplotype Blocks: Finding the Minimum
Number of Recombination Events
Yun
Song, Jotun Hein
A
Local Chaining Algorithm and its Applicationsin Comparative Genomics
Mohamed
Ibrahim Abouelhoda, Enno Ohlebusch
Pattern
discovery allowing gaps, substitution matrices and multiple score functions
Alban
Mancheron, Irena Rusu
A
Combinatorial Approach to Automatic Discovery of Cluster-Patterns
Revital
Eres, Gad Landau, Laxmi Parida
Efficient
Generation of Uniform Samples from Phylogenetic Trees
Paul
Kearney, Ian Munro, Derek Phillips
New
Efficient Algorithm for Detection of Horizontal Gene Transfer Events
Alic
Boc, Vladimir Makarenkov
Side-chain
Structure Prediction based on Dead-End Elimination: Single Split DEE-criterion
Implementation and Elimination Power.
Jan
Spriet, Niles Pierce, Johan Desmet, Stephen Mayo
Efficient
Energy Computation for Monte Carlo Simulation
Itay
Lotan, Fabian Schwarzer, Jean-Claude Latombe
Speedup LP Approach to Protein Threading via Graph Reduction
Jinbo
Xu
Match
Chaining Algorithms for cDNA Mapping
Tetsuo
Shibuya, Igor Kurochkin
Identifying
Blocks and Sub-Populations in Noisy SNP Data
Gad
Kimmel, Roded Sharan, Ron Shamir
A
stochastic approach to count RNA molecules using DNA sequencing methods
Boris
Hollas, Rainer Schuler
A Large Version of the Small Parsimony Problem
Jakob
Fredslund, Jotun Hein, Tejs Scharling
Designing
Optimally Multiplexed SNP Genotyping Assays
Yonatan
Aumann, Efrat Manisterski, Zohar Yakhini
Ancestral
Maximum Likelihood of Phylogenetic Trees is Hard
Louigi
Addario-Berry, Benny Chor, Mike Hallett, Jens Lagergren, Alessandro Panconesi,
Tod Wareham
A
systematic statistical analysis of ion trap tandem mass spectra in view of
peptide scoring
Jacques
Colinge, Alexandre Masselot, Jerome Magnin
Vector
seeds: an extension to spaced seeds allows substantial improvements in
sensitivity and specificity
Brona
Brejova, Daniel Brown, Tomas Vinar
New
Algorithm for the Simplified Partial Digest Problem
Jacek
Baewicz, Marcin Jaroszewski
A Linear-time Majority Tree Algorithm
Nina
Amenta, Frederick Clarke, Katherine St. John
Common
intervals of two sequences
Gilles
Didier
Sequencing
from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+ nt
Sebastian
Boecker
Bayesian
phylogenetic inference under a statistical insertion--deletion model
Gerton
Lunter, Istvan Miklos, Jens Ledet Jensen, Alexei Drummond
Bounds
for Resequencing By Hybridization
Dekel
Tsur
Noisy
Data Make the Partial Digest Problem NP-hard
Mark
Cieliebak, Stephan Eidenbenz, Paolo Penna
Better
hill-climbing searches for parsimony
Ganeshkumar
Ganapathy, Vijaya Ramachandran, Tandy Warnow
Optimal
Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree
Bjarne
Knudsen
Minimum
Recombinant Haplotype Configuration on Pedigrees without Mating Loops
Koichiro
Doi, Jing Li, Tao Jiang
Dynamic
Programming Algorithms for Two Statistical Problems in Computational Biology
Sven
Rahmann
Computing
Refined Buneman Trees in Cubic Time
Gerth
Stolting, Rolf Fagerberg, Anna Ostlin, Christian N. S. Pedersen, S. Srinivasa
Rao
Composition
Alignment
Gary
Benson
Phylogenetic
Analysis of Recombinant Sequences
David
Bryant, Daniel Huson, Thomas Kloepper, Kay Nieselt-Struwe
Optimal
DNA signal recognition models with a fixed amount of intrasignal dependency
Brona
Brejova, Daniel G. Brown, Tomas Vinar
A
Method to detect alternative splicing by agreeing ESTs to a genomic sequence
Paola
Bonizzoni, Graziano Pesole, Raffaella Rizzi
Homology
Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment
Jahnavi
Prasad, Michael Silberstein, Carlos Camacho, Sandor Vajda
Selecting
Degenerate Multiplex PCR Primers
Richard
Souvenir, Jeremy Buhler, Gary Stormo, Weixiong Zhang
16
September
***
Protein Structure ***
09.00-09.25
Efficient Energy Computation for Monte Carlo Simulation of
Proteins
I. Lotan, F. Schwarzer, and J.-C. Latombe
09.25-09.50
Speedup LP Approach to Protein Threading via Graph Reduction
J. Xu
10.20-10.45
Homology Modeling of Proteins Using Multiple Models and
Consensus Sequence Alignment
J. C. Prasad, M. Silberstein, C.J. Camacho, and S. Vajda
10.45-11.10
Side-chain Structure Prediction Based on Dead-End
Elimination: Single Split
DEE-criterion Implementation and Elimination Power
J. A. Spriet
***
Phylogenetic Analysis ***
14.00-14.25
Better Hill-Climbing Searches for Parsimony
G. Ganapathy, V. Ramachandran, and T. Warnow
14.25-14.50
Parsimonious Reconstruction of Sequence Evolution and
Haplotype Blocks
Y.S. Song and J. Hein
14.50-15.15
Distance Corrections on Recombinant Sequences
D. Bryant, D. Huson, T. Kloepper, and K. Nieselt-Struwe
15.45-16.10
New Efficient Algorithm for Detection of Horizontal Gene
Transfer Events
A. Boc and V. Makarenkov
16.10-16.35
Efficient Generation of Uniform Samples from Phylogenetic
Trees
P. Kearney, J. Ian Munro, and
Derek Phillips
17
September
***
Sequence Alignment ***
09.00-09.25
Large Version of the Small Parsimony Problem
J. Fredslund, J. Hein, and T.
Scharling
09.25-09.50
Optimal Multiple Parsimony Alignment with Affine Gap Cost
Using a Phylogenetic Tree
B. Knudsen
***
Sequence Composition ***
10.20-10.45
A Combinatorial Approach to Automatic Discovery of
Cluster-Patterns
R. Eres, G. M. Landau, and L.
Parida
10.45-11.10
Composition Alignment
G. Benson
***
Polymorphism ***
14.00-14.25
Minimum Recombinant Haplotype Configuration on Tree Pedigrees
K. Doi J. Li, and T. Jiang
14.25-14.50
Identifying Blocks and Sub-Populations in Noisy SNP Data
G. Kimmel, R. Sharan, and R.
Shamir
14.50-15.15
Designing Optimally Multiplexed SNP Genotyping Assays
Y. Aumann, E. Manisterski,
and Z. Yakhini
***
Comparative Genomics ***
15.45-16.10
A Local Chaining Algorithm and its Applications in
Comparative Genomics
M. I. Abouelhoda and E.
Ohlebusch
16.10-16.35
Common Intervals of Two Sequences
G. Didier
18
September
***
Pattern and Motif Discovery ***
09.00-09.25
Pattern Discovery Allowing Wild-Cards, Substitution Matrices
and Multiple Score Functions
A. Mancheron and I. Rusu
09.25-09.50
Dynamic Programming Algorithms for Two Statistical Problems
in Computational Biology
S. Rahmann
***
Database Searching ***
10.20-10.45
Vector Seeds: An Extension to Spaced Seeds Allows Substantial
Improvements in Sensitivity and Specificity
B. Brejova, D.G. Brown, and T. Vinar
10.45-11.10
A Systematic Statistical Analysis of Ion Trap Tandem Mass
Spectra in View of Peptide Scoring
J. Colinge, A. Masselot, and J. Magnin
***
Phylogeny ***
14.00-14.25
Computing Refined Buneman Trees in Cubic Time
G. S. Brodal, R. Fagerberg,
A. Ostlin, C. N. S. Pedersen, and S. S. Rao
14.25-14.50
Ancestral Maximum Likelihood of Evolutionary Trees is Hard
L. Addario-Berry, B. Chor, M.
Hallett, J. Lagergren, A. Panconesi, and T. Wareham
14.50-15.15
Bayesian Phylogenetic Inference under a Statistical
Insertion-deletion Model
G. Lunter, I. Miklos, A.
Drummond, J.L. Jensen, and J. Hein
15.45-16.10
Consensus Networks: A Method for Visualising
Incompatibilities in Collections of Trees
B. Holland and V. Moulton
16.10-16.35
A Linear-time Majority Tree Algorithm
N. Amenta, F. Clarke, and K.
St. John
19
September
*** String Algorithms ***
09.00-09.25
Match Chaining Algorithms for cDNA Mapping
T. Shibuya and I. Kurochkin
09.25-09.50
Sequencing from Compomers: Using Mass Spectrometry for DNA
de-novo Sequencing of 200+ nt
S. Bocker
10.20-10.45
Bounds for Resequencing By Hybridization
D. Tsur
10.45-11.10
Selecting Degenerate Multiplex PCR Primers
R. Souvenir, J. Buhler, G.
Stormo, and W. Zhang
***
Gene Finding and Expression ***
14.00-14.25
A Method to Detect Gene Structure and Alternative Splice
Sites by Agreeing ESTs to a Genomic Sequence
P. Bonizzoni, G. Pesole, and R. Rizzi
14.25-14.50
A Stochastic Approach to Count RNA Molecules Using DNA
Sequencing Methods
B. Hollas and R. Schuler
14.50-15.15
Optimal DNA Signal Recognition Models with a Fixed Amount of
Intrasignal Dependency
B. Brejova, D. G. Brown, and
T. Vinar
***
Genome Mapping ***
15.45-16.10
Noisy Data Make the Partial Digest Problem NP-hard
M. Cieliebak, S. Eidenbenz, and P. Penna
16.10-16.35
New Algorithm for the Simplified Partial Digest Problem
J. Blazewicz and M.
Jaroszewski
Submission deadline: 28 April,
2003
Notification to authors: 2
June, 2003
Final version due:
30 June,
2003
Symposium: 15-20 September,
2003
Amihood Amir (Bar Ilan University, Israel)
Alberto Apostolico (Purdue University)
Pierre Baldi (UC Irvine)
Gary Benson (Mount Sinai School of
Medicine, New York; Co-chair)
Benny Chor (Tel Aviv University)
Nadia El-Mabrouk (University of Montreal)
Olivier Gascuel (LIRMM-CNRS,
Montpellier)
Raffaele Giancarlo (U. di Palermo)
David Gilbert (University of Glasgow)
Jan Gorodkin (The Royal Veterinary and
Agricultural University, Denmark)
Roderic Guigo (IMIM, Barcelona)
Dan Gusfield (UC Davis)
Jotun Hein (University of Oxford)
Daniel
Huson (Tübingen University)
Simon Kasif (Boston University)
Gregory Kucherov (INRIA-Lorraine/LORIA)
Gad Landau (University of Haifa)
Thierry Lecroq (Université de Rouen)
Bernard M.E. Moret (U. New Mexico)
Vincent Moulton (Uppsala University,
Sweden)
Roderic Page (University of Glasgow;
Co-chair)
Sophie Schbath (INRA,
Jouy-en-Josas)
Charles Semple (University of Canterbury, New Zealand)
Jens Stoye (Universität Bielefeld)
Fengzhu Sun (U. Southern California)
Alfonso Valencia (Centro Nacional de
Biotecnologia, Madrid)
Jacques Van Helden (Université Libre de
Bruxelles)
Louxin Zhang (National
University
Olivier Gascuel
Raffaele Giancarlo
Roderic Guigo
Dan Gusfield
Bernard Moret
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Reservation Form
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