Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures
Nancy M. Amato, Ken A. Dill, Guang Song
Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion
Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe
Monotony of Surprise And Large-Scale Quest for Unusual Words (Extended Abstract)
Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi
DNA Sequence Evolution with Neighbor-Dependent Mutation
Peter F. Arndy, Christopher B. Burge, Terence Hwa
A New Approach to Analyzing Gene Expression Time Series Data
Ziv Bar-Joseph, Georg Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon
Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem
Amir Ben-Dor, Benny Chor, Richard Karp, Zohar Yakhini
The Restriction Scaffold Problem
Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir
Comparison of Minisatellites
S\`everine B\'erard, \'Eric Rivals
Trilogy: Discovery of Sequence-Structure Patterns Across Diverse Proteins
Phil Bradley, Peter S. Kim, Bonnie Berger
Provably Sensitive Indexing Strategies for Biosequence Similarity Search
Jeremy Buhler
Structural Alignment of Large-Size Proteins via Lagrangian Relaxation (Extended Abstract)
Alberto Caprara, Giuseppe Lancia
Designing RNA Structures: Natural and Artificial Selection (Extended Abstract)
Barry Cohen, Steven Skiena
Inferring Domain-Domain Interactions from Protein-Protein Interactions
Minghua Deng, Shipra Mehta, Fengzhu Sun, Ting Chen
Analysis of Gene Expression Profiles: Class Discovery and Leaf Ordering (Extended Abstract)
Chris H.Q. Ding
A Bayesian Approach to Transcript Estimation from Gene Array Data: The BEAM Technique
Ron O. Dror, Jonathan G. Murnick, Nicola A. Rinaldi
Tests for Gene Clustering
Dannie Durand, David Sankoff
Approximate Matching of Secondary Structures (Extended Abstract)
Nadia El-Mabrouk, Mathieu Raffinot
Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions (Extended Abstract)
Dan Gusfield
Handling Long Targets and Errors in Sequencing by Hybridization
Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir
Sequencing by Hybridization using Direct and Reverse Cooperating Spectra
Samuel A. Heath, Franco P. Preparata, Joel Young
Finding Motifs in the Twilight Zone
Uri Keich, Pavel A. Pevzner
Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns
Christopher James Langmead, Anthony K. Yan, C. Robertson McClung, Bruce Randall Donald
Significance of Inter-Species Matches When Evolutionary Rate Varies
Jia Li, Webb Miller
Combining Pairwise Sequence Similarity and Support Vector Machines for Remote Protein Homology Detection
Li Liao, William Stafford Noble
Revealing Protein Structures: A New Method for Mapping Antibody Epitopes
Brendan M. Mumey, Brian W. Bailey, Edward A. Dratz
Set Association Analysis of SNP Case-Control and Microarray Data
Jurg Ott, Josephine Hoh
Picking Alignments from (Steiner) Trees
Lior Pachter, Fumei Lam, Marina Alexandersson
String Barcoding: Uncovering Optimal Virus Signatures
Sam Rash, Dan Gusfield
From Promoter Sequence to Expression: A Probabilistic Framework
Eran Segal, Yoseph Barash, Itamar Simon, Nir Friedman, Daphne Koller
Probabilistic Hierarchical Clustering for Biological Data
Eran Segal, Daphne Koller
An Algorithm to Find All Sorting Reversals
Adam C. Siepel
Discriminative Motifs
Saurabh Sinha
A Dimensionality Reduction Approach to Modeling Protein Flexibility
Miguel L. Teodoro, George N. Phillips Jr., Lydia E. Kavraki
Deconvolving Sequence Variation in Mixed DNA Populations
Andy Wildenberg, Steven Skiena, Pavel Sumazin
Microarrays: How Many Do You Need?
Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer
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