Chor, Hendy, Holland, Penny
Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic
Approach
 

Akutsu, Miyano, Kuhara
Algorithms for Identifying Boolean Networks and Related Biological
Networks Based on Matrix Multiplication and Fingerprint Function
 

Marsan, Sagot
Extracting structured motifs using a suffix tree - Algorithms and
application to promoter consensus identification
 

Linial, Portugaly
Probabilities for having a new fold on the basis of a map of all
protein sequences
 

Chen, Kwong, Li
A Compression Algorithm for DNA Sequences and Its Applications in Genome
Comparison
 

Liwo, Pillardy, Czaplewski, Lee, Ripoll, Groth, Rodziewicz-Motowidlo,
Kazmierkiewicz, Wawak, Oldziej,  Scheraga
UNRES -- a united-residue force field for energy-based prediction
of protein structure - origin and significance of multibody terms
 

Kann, Goldstein
Optimizing for Success: A New Score Function For Distantly Related
Protein Sequence Comparison
 

Akutsu, Arimura, Shimozono
On Approximation Algorithms for Local Multiple Alignment
 

Teichmann, Chothia, Church, Park
PDB-ISL: an intermediate sequence library for fast assignment of
protein structures to sequences
 

Pevzner, Dancik, Tang
Mutation-Tolerant Protein Identification by Mass-Spectrometry
 

Batzoglou, Berger, Mesirov, Lander
Sequencing a Genome by Walking with Clone-end Sequences: A
Mathematical Analysis
 

Batzoglou, Pachter, Mesirov, Berger, Lander
Comparative Analysis of Mouse and Human DNA and Applications to
Exon Prediction
 

Bienkowska, Yu, Zarakhovich, Rogers, Smith
Comprehensive statistical method for protein fold recognition
 

Ohkubo, Crippen
Determining Contact Energy Function for Continuous State Models
of Globular Protein Conformations
 

Bundschuh
An Analytic Approach to Significance Assessment in Local Sequence
Alignment with Gaps
 

Apostolico, Bejerano
Optimal Amnesic Probabilistic Automata or How to Learn and Classify
Proteins in Linear Time and Space
 

Heber, Stoye, Hoheisel, Vingron
Contig Selection in Physical Mapping
 

Hallett, Lagergren
New Algorithms for the Duplication-Loss Model
 

Desper, Vingron
Tree Fitting: an Algebraic Approach Using Profile Distances
 

Lyngso, Pederson
Pseudonknots in RNA Secondary Structures
 

Chen, Durand, Farach-Colton
Notung: Dating gene duplications using gene family trees
 

Xu, Xu, Crawford, Einstein, Serpersu
Protein Structure Determination using Protein Threading and
Sparse  NMR Data
 

Slonim, Tamayo, Mesirov, Golub, Lander
Class prediction and discovery using gene expression data
 

Sorenson, Head-Gordon
Matching simulation and experiment: a new simplified model for
simulating protein folding
 

Zien, Zimmer, Lengauer
A simple iterative approach to parameter optimization
 

Ben-Dor, Karp, Schwikowski, Yakhini
Universal DNA tag systems: a combinatorial design scheme
 

Sankoff, Bryant, Deneault, Lang, Burger
Early Eukaryote Evolution Based on Mitochondrial Gene Order
Breakpoints
 

Yona, Levitt
A unified sequence-structure classification of protein sequences:
combining sequence and structure in a map of the protein space
 

Bailey-Kellogg, Widge, Kelley, Berardi, Bushweller, Donald
The NOESY Jigsaw: automated protein secondary structure and
main-chain assignment from sparse, unassigned NMR data
 

Ben-Dor, Bruhn, Friedman, Nachman, Schummer, Yakhini
Tissue classification with gene expression profiles
 

Kececioglou, Shete, Arnold
Reconstructing distances in physical maps of chromosomes with
nonoverlapping probes
 

Hart, Royyuru, Stolovitzky, Califano
Systematic and Automated Discovery of Patterns in PROSITE Families
 

Althaus, Kohlbacher, Lenhof, Mueller
A combinatorial approach to protein docking with flexible side-chains
 

Friedman, Linial, Nachman, Pe'er
Using Bayesian Networks to Analyze Expression Data
 

Preparata, Upfal
Sequencing-by-hybridization at the information-theory bound:
an optimal algorithm
 

Tomita, Hashimoto, Takahashi, Matsuzaki, Matsushima, Yugi, Miyoshi,
Nakano, Saito, Shimizu, Nakayama
The E-CELL project: towards integrative simulation of cellular
processes