Bioinformatics

Søren Brunak and Anders Krogh

ISMB 2001
Bioinformatics 2001 17: S1-S4; doi:10.1093/bioinformatics/17.suppl_1.S1 [Print PDF][Screen PDF]  

Ezekiel F. Adebiyi, Tao Jiang, and Michael Kaufmann

An efficient algorithm for finding short approximate non-tandem repeats
Bioinformatics 2001 17: S5-S12; doi:10.1093/bioinformatics/17.suppl_1.S5 [Abstract] [Print PDF][Screen PDF]  

Vineet Bafna and Nathan Edwards

SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database
Bioinformatics 2001 17: S13-S21; doi:10.1093/bioinformatics/17.suppl_1.S13 [Abstract] [Print PDF][Screen PDF]  

Ziv Bar-Joseph, David K. Gifford, and Tommi S. Jaakkola

Fast optimal leaf ordering for hierarchical clustering
Bioinformatics 2001 17: S22-S29; doi:10.1093/bioinformatics/17.suppl_1.S22 [Abstract] [Print PDF][Screen PDF]  

Mathieu Blanchette and Saurabh Sinha

Separating real motifs from their artifacts
Bioinformatics 2001 17: S30-S38; doi:10.1093/bioinformatics/17.suppl_1.S30 [Abstract] [Print PDF][Screen PDF]  

James Borneman, Marek Chrobak, Gianluca Della Vedova, Andres Figueroa, and Tao Jiang

Probe selection algorithms with applications in the analysis of microbial communities
Bioinformatics 2001 17: S39-S48; doi:10.1093/bioinformatics/17.suppl_1.S39 [Abstract] [Print PDF][Screen PDF]  

Derek Y. Chiang, Patrick O. Brown, and Michael B. Eisen

Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
Bioinformatics 2001 17: S49-S55; doi:10.1093/bioinformatics/17.suppl_1.S49 [Abstract] [Print PDF][Screen PDF]  

John S. Chuang and Dan Roth

Gene recognition based on DAG shortest paths
Bioinformatics 2001 17: S56-S64; doi:10.1093/bioinformatics/17.suppl_1.S56 [Abstract] [Print PDF][Screen PDF]  

Eleazar Eskin, William N. Grundy, and Yoram Singer

Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences
Bioinformatics 2001 17: S65-S73; doi:10.1093/bioinformatics/17.suppl_1.S65 [Abstract] [Print PDF][Screen PDF]  

Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, and Andrey Rzhetsky

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles
Comput. Appl. Biosci. 2001 17: S74-S82; doi:10.1093/bioinformatics/17.suppl_1.S74 [Abstract] [Print PDF][Screen PDF]  

Gordana Apic, Julian Gough, and Sarah A. Teichmann

An insight into domain combinations
Bioinformatics 2001 17: S83-S89; doi:10.1093/bioinformatics/17.suppl_1.S83 [Abstract] [Print PDF][Screen PDF]  

Sridhar Hannenhalli and Samuel Levy

Promoter prediction in the human genome
Bioinformatics 2001 17: S90-S96; doi:10.1093/bioinformatics/17.suppl_1.S90 [Abstract] [Print PDF][Screen PDF]  

Vasileios Hatzivassiloglou, Pablo A. Duboué, and Andrey Rzhetsky

Disambiguating proteins, genes, and RNA in text: a machine learning approach
Bioinformatics 2001 17: S97-S106; doi:10.1093/bioinformatics/17.suppl_1.S97 [Abstract] [Print PDF][Screen PDF]  

Anja von Heydebreck, Wolfgang Huber, Annemarie Poustka, and Martin Vingron

Identifying splits with clear separation: a new class discovery method for gene expression data
Bioinformatics 2001 17: S107-S114; doi:10.1093/bioinformatics/17.suppl_1.S107 [Abstract] [Print PDF][Screen PDF]  

Lawrence Hunter, Ronald C. Taylor, Sonia M. Leach, and Richard Simon

GEST: a gene expression search tool based on a novel Bayesian similarity metric
Bioinformatics 2001 17: S115-S122; doi:10.1093/bioinformatics/17.suppl_1.S115 [Abstract] [Print PDF][Screen PDF]  

Dirk Husmeier and Frank Wright

Probabilistic divergence measures for detecting interspecies recombination
Bioinformatics 2001 17: S123-S131; doi:10.1093/bioinformatics/17.suppl_1.S123 [Abstract] [Print PDF][Screen PDF]  

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, and Eugene W. Myers

Design of a compartmentalized shotgun assembler for the human genome
Bioinformatics 2001 17: S132-S139; doi:10.1093/bioinformatics/17.suppl_1.S132 [Abstract] [Print PDF][Screen PDF]  

Ian Korf, Paul Flicek, Daniel Duan, and Michael R. Brent

Integrating genomic homology into gene structure prediction
Bioinformatics 2001 17: S140-S148; doi:10.1093/bioinformatics/17.suppl_1.S140 [Abstract] [Print PDF][Screen PDF]  

Michael Lappe, Jong Park, Oliver Niggemann, and Liisa Holm

Generating protein interaction maps from incomplete data: application to fold assignment
Bioinformatics 2001 17: S149-S156; doi:10.1093/bioinformatics/17.suppl_1.S149 [Abstract] [Print PDF][Screen PDF]  

Fabian Model, Péter Adorján, Alexander Olek, and Christian Piepenbrock

Feature selection for DNA methylation based cancer classification
Bioinformatics 2001 17: S157-S164; doi:10.1093/bioinformatics/17.suppl_1.S157 [Abstract] [Print PDF][Screen PDF]  

Bernard M.E. Moret, Li-San Wang, Tandy Warnow, and Stacia K. Wyman

New approaches for reconstructing phylogenies from gene order data
Bioinformatics 2001 17: S165-S173; doi:10.1093/bioinformatics/17.suppl_1.S165 [Abstract] [Print PDF][Screen PDF]  

Steffen Möller, Jaak Vilo, and Michael D.R. Croning

Prediction of the coupling specificity of G protein coupled receptors to their G proteins
Bioinformatics 2001 17: S174-S181; doi:10.1093/bioinformatics/17.suppl_1.S174 [Abstract] [Print PDF][Screen PDF]  

Tobias Müller, Sven Rahmann, and Marc Rehmsmeier

Non-symmetric score matrices and the detection of homologous transmembrane proteins
Bioinformatics 2001 17: S182-S189; doi:10.1093/bioinformatics/17.suppl_1.S182 [Abstract] [Print PDF][Screen PDF]  

Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, and Tandy Warnow

Designing fast converging phylogenetic methods
Bioinformatics 2001 17: S190-S198; doi:10.1093/bioinformatics/17.suppl_1.S190 [Abstract] [Print PDF][Screen PDF]  

Uwe Ohler, Heinrich Niemann, Guo-chun Liao, and Gerald M. Rubin

Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition
Bioinformatics 2001 17: S199-S206; doi:10.1093/bioinformatics/17.suppl_1.S199 [Abstract] [Print PDF][Screen PDF]  

Giulio Pavesi, Giancarlo Mauri, and Graziano Pesole

An algorithm for finding signals of unknown length in DNA sequences
Bioinformatics 2001 17: S207-S214; doi:10.1093/bioinformatics/17.suppl_1.S207 [Abstract] [Print PDF][Screen PDF]  

Dana Pe’er, Aviv Regev, Gal Elidan, and Nir Friedman

Inferring subnetworks from perturbed expression profiles
Bioinformatics 2001 17: S215-S224; doi:10.1093/bioinformatics/17.suppl_1.S215 [Abstract] [Print PDF][Screen PDF]  

Pavel A. Pevzner and Haixu Tang

Fragment assembly with double-barreled data
Bioinformatics 2001 17: S225-S233; doi:10.1093/bioinformatics/17.suppl_1.S225 [Abstract] [Print PDF][Screen PDF]  

Gianluca Pollastri, Pierre Baldi, Pietro Fariselli, and Rita Casadio

Improved prediction of the number of residue contacts in proteins by recurrent neural networks
Bioinformatics 2001 17: S234-S242; doi:10.1093/bioinformatics/17.suppl_1.S234 [Abstract] [Print PDF][Screen PDF]  

Eran Segal, Ben Taskar, Audrey Gasch, Nir Friedman, and Daphne Koller

Rich probabilistic models for gene expression
Bioinformatics 2001 17: S243-S252; doi:10.1093/bioinformatics/17.suppl_1.S243 [Abstract] [Print PDF][Screen PDF]  

Steven S. Skiena

Designing better phages
Bioinformatics 2001 17: S253-S261; doi:10.1093/bioinformatics/17.suppl_1.S253 [Abstract] [Print PDF][Screen PDF]  

David J. States, Volker Nowotny, and Thomas W. Blackwell

Probabilistic approaches to the use of higher order clone relationships in physical map assembly
Bioinformatics 2001 17: S262-S269; doi:10.1093/bioinformatics/17.suppl_1.S262 [Abstract] [Print PDF][Screen PDF]  

Amos Tanay and Ron Shamir

Computational expansion of genetic networks
Bioinformatics 2001 17: S270-S278; doi:10.1093/bioinformatics/17.suppl_1.S270 [Abstract] [Screen PDF]  

D. Venet, F. Pecasse, C. Maenhaut, and H. Bersini

Separation of samples into their constituents using gene expression data
Bioinformatics 2001 17: S279-S287; doi:10.1093/bioinformatics/17.suppl_1.S279 [Abstract] [Print PDF][Screen PDF]  

Michael J. Wise

0j.py: a software tool for low complexity proteins and protein domains
Bioinformatics 2001 17: S288-S295; doi:10.1093/bioinformatics/17.suppl_1.S288 [Abstract] [Print PDF][Screen PDF]  

Jérôme Wojcik and Vincent Schächter

Protein-protein interaction map inference using interacting domain profile pairs
Bioinformatics 2001 17: S296-S305; doi:10.1093/bioinformatics/17.suppl_1.S296 [Abstract] [Print PDF][Screen PDF]  

Eric P. Xing and Richard M. Karp

CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts
Bioinformatics 2001 17: S306-S315; doi:10.1093/bioinformatics/17.suppl_1.S306 [Abstract] [Print PDF][Screen PDF]  

Chen-Hsiang Yeang, Sridhar Ramaswamy, Pablo Tamayo, Sayan Mukherjee, Ryan M. Rifkin, Michael Angelo, Michael Reich, Eric Lander, Jill Mesirov, and Todd Golub

Molecular classification of multiple tumor types
Bioinformatics 2001 17: S316-S322; doi:10.1093/bioinformatics/17.suppl_1.S316 [Abstract] [Print PDF][Screen PDF]  

Alexander Zien, Thomas Aigner, Ralf Zimmer, and Thomas Lengauer

Centralization: a new method for the normalization of gene expression data
Bioinformatics 2001 17: S323-S331; doi:10.1093/bioinformatics/17.suppl_1.S323 [Abstract] [Print PDF][Screen PDF]  

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