RECOMB'99 - accepted papers

Gregory Kucherov Gregory.Kucherov at loria.fr
Tue Jan 5 18:35:08 EST 1999

Accepted Papers for
the 3rd Annual International Conference on Computational 
Molecular Biology (RECOMB'99)
April 11-14, 1999 
Lyon, France


--------------- [in no apparent order] --------------------------------

Algorithms for Whole Genome Shotgun Sequencing 
Eric Anson, Gene Myers

Classifying proteins by family using the product of correlated p-values 
Timothy L. Bailey, William Noble Grundy

A Dictionary Based Approach for Gene Annotation 
Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky,
  Eric S. Lander, Bonnier Berger, Daniel J. Kleitman

Winnowing Sequences from a Database Search 
Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller

Faster reliable phylogenetic analysis 
Vincent Berry, David Bryant

A method for optimal design of a threading scoring function 
Jadwiga R. Bienkowska, Robert G. Rogers Jr., Temple F. Smith

Searching gene transfers on Bacillus subtilis using hidden Markov models 
Laurent Bize, Florence Muri, Franck Samson, Francois Rodolphe,
  Stanislav D. Ehrlich, Bernard Prum

An Analytic Study of the Phase Transition Line in Local Sequence
  Alignment with Gaps
R. Bundschuh, T. Hwa

q-gram Based Database Searching Using a Suffix Array 
Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-Peter Lenhof,
  Eric Rivals, Martin Vingron

Formulations and Complexity of Multiple Sorting by Reversals 
Alberto Caprara

Fast Detection of Common Geometric Substructure in Proteins 
L. Paul Chew, Klara Kedem, Jon Kleinberg, Dan Huttenlocher

Computing physical maps of chromosomes with nonoverlapping probes by
Thomas Christof, John Kececioglu

Optimizing Combinatorial Library Construction via Split Synthesis 
Barry Cohen, Steven Skiena

Protein Sequencing Using Tandem Mass Spectrometry 
Vlado Dancik, Theresa Addona, Karl Clauser, Jim Vath, Pavel A. Pevzner

A Solvation Potential with Improved Contact Definitions and Optimized
  by Extensive Threading
Alan A. Dombkowski, Gordon M. Crippen

Reconstructing the Pre-Doubling Genome 
Nadia El-Mabrouk, David Bryant, David Sankoff

Sequence Homology Detection Through Large-Scale Pattern Discovery 
Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Gustavo Stolovitzky,
  Yuan Gao

Evolution of Metabolisms A New Method for the Comparison of
  Metabolic Pathways 
Christian V. Forst, Klaus Schulten

Significance Testing for Genomic Mismatch Scanning 
G.R. Grant, R.S. Spielman, E. Manduchi, V.G. Cheung, W.J. Ewens

An Algorithm for Clustinering cDNAs for Gene Expression Analysis 
Erez Hartuv, Armin Schmitt, Jorg Lange, Sebastian Meirer-Ewert,
  Hans Lehrach, Ron Shamir

Obtaining Highly Accurate Topology Estimates of Evolutionary Trees
  From Very Short Sequences 
Daniel Huson, Scott Nettles, Tandy Warnow

Algorithms for Choosing Differential Gene Expression Experiments 
Richard M. Karp, Ka Yee Yeung

Recognition of remote protein homologies using three-dimensional
  information to generate a position specific scoring matrix in
  the program 3D-PSSM 
Lawrence Kelley, Robert MacCullum, Michael J. E. Sternberg

Efficient Algorithms for Protein Sequence Design and the Analysis
  of Certain Evolutionary Fitness Landscapes 
Jon M. Kleinberg

An Anytime Algorithm for Gapped Block Protein Threading with Pair
Richard H. Lathrop

Efficient Database Screening for Rational Drug Design Using
  Pharmacophore-Constrained Conformational Search 
Steven M. LaValle, Lydia E. Kavraki, Paul W. Finn, Jean-Claude Latombe

Internal loops in RNA secondary structure prediction 
Rune B. Lyngso, Michael Zuker, Christian N. S. Pedersen

Construction of Physical Maps From Oligonucleotide Fingerprints Data
Guy Mayraz, Ron Shamir

On the Power of Universal Bases in Sequencing by Hybridization 
Franco P. Preparata, Alan M. Frieze, Eli Upfal

Optimization in Protein Docking 
Ben Rosen, Lynn TenEyck, Julie C. Mitchell, Andy Phillips

Probability Models for Genome Rearrangement and Linear Invariants
  for Phylogenetic Inference 
David Sankoff, Mathieu Blanchette

Identifying Gene Regulatory Networks from Experimental Data 
Ting Chen, Vladimir Filkov, Steven S. Skiena

Derivation of sensitive discrimination potential for virtual
  ligand screening 
Maxim Totrov, Ruben Abagyan

Clustering Gene Expression Patterns 
Amir Ben-Dor, Zohar Yakhini

Modeling protein families using probabilistic suffix trees
G. Bejerano, G. Yona

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