Bioinformatics

Janice Glasgow and Burkhard Rost

ISMB 2002
Bioinformatics 2002 18: S1; doi:10.1093/bioinformatics/18.suppl_1.S1 [Print PDF]  

ISMB 2002 Organization
Bioinformatics 2002 18: S2-S4; doi:10.1093/bioinformatics/18.suppl_1.S2 [Print PDF]  

Ajit Narayanan, Xikun Wu, and Z. Rong Yang

Mining viral protease data to extract cleavage knowledge
Bioinformatics 2002 18: S5-S13; doi:10.1093/bioinformatics/18.suppl_1.S5 [Abstract] [Print PDF][Screen PDF]  

Ori Sasson, Nathan Linial, and Michal Linial

The metric space of proteins—comparative study of clustering algorithms
Bioinformatics 2002 18: S14-S21; doi:10.1093/bioinformatics/18.suppl_1.S14 [Abstract] [Print PDF][Screen PDF]  

N.R. Steffen, S.D. Murphy, L. Tolleri, G.W. Hatfield, and R.H. Lathrop

DNA sequence and structure: direct and indirect recognition in protein-DNA binding
Bioinformatics 2002 18: S22-S30; doi:10.1093/bioinformatics/18.suppl_1.S22 [Abstract] [Print PDF][Screen PDF]  

Amy M. Hauth and Deborah A. Joseph

Beyond tandem repeats: complex pattern structures and distant regions of similarity
Bioinformatics 2002 18: S31-S37; doi:10.1093/bioinformatics/18.suppl_1.S31 [Abstract] [Print PDF][Screen PDF]  

Michael J. Wise

The POPPs: clustering and searching using peptide probability profiles
Bioinformatics 2002 18: S38-S45; doi:10.1093/bioinformatics/18.suppl_1.S38 [Abstract] [Print PDF][Screen PDF]  

Pier Luigi Martelli, Piero Fariselli, Anders Krogh, and Rita Casadio

A sequence-profile-based HMM for predicting and discriminating ß barrel membrane proteins
Bioinformatics 2002 18: S46-S53; doi:10.1093/bioinformatics/18.suppl_1.S46 [Abstract] [Print PDF][Screen PDF]  

Christopher Bystroff and Yu Shao

Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA
Bioinformatics 2002 18: S54-S61; doi:10.1093/bioinformatics/18.suppl_1.S54 [Abstract] [Print PDF][Screen PDF]  

G. Pollastri and P. Baldi

Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
Bioinformatics 2002 18: S62-S70; doi:10.1093/bioinformatics/18.suppl_1.S62 [Abstract] [Print PDF][Screen PDF]  

Tal Pupko, Rachel E. Bell, Itay Mayrose, Fabian Glaser, and Nir Ben-Tal

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
Bioinformatics 2002 18: S71-S77; doi:10.1093/bioinformatics/18.suppl_1.S71 [Abstract] [Print PDF][Screen PDF]  

Rajesh Nair and Burkhard Rost

Inferring sub-cellular localization through automated lexical analysis
Bioinformatics 2002 18: S78-S86; doi:10.1093/bioinformatics/18.suppl_1.S78 [Abstract] [Print PDF][Screen PDF]  

E. Myasnikova, A. Samsonova, M. Samsonova, and J. Reinitz

Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns
Bioinformatics 2002 18: S87-S95; doi:10.1093/bioinformatics/18.suppl_1.S87 [Abstract] [Print PDF][Screen PDF]  

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

Variance stabilization applied to microarray data calibration and to the quantification of differential expression
Bioinformatics 2002 18: S96-S104; doi:10.1093/bioinformatics/18.suppl_1.S96 [Abstract] [Print PDF][Screen PDF]  

B.P. Durbin, J.S. Hardin, D.M. Hawkins, and D.M. Rocke

A variance-stabilizing transformation for gene-expression microarray data
Bioinformatics 2002 18: S105-S110; doi:10.1093/bioinformatics/18.suppl_1.S105 [Abstract] [Print PDF][Screen PDF]  

M. Sultan, D.A. Wigle, C.A. Cumbaa, M. Maziarz, J. Glasgow, M.S. Tsao, and I. Jurisica

Binary tree-structured vector quantization approach to clustering and visualizing microarray data
Bioinformatics 2002 18: S111-S119; doi:10.1093/bioinformatics/18.suppl_1.S111 [Abstract] [Print PDF][Screen PDF]  

Peter J. Park, Lu Tian, and Isaac S. Kohane

Linking gene expression data with patient survival times using partial least squares
Bioinformatics 2002 18: S120-S127; doi:10.1093/bioinformatics/18.suppl_1.S120 [Abstract] [Print PDF][Screen PDF]  

Rohan J. Fernandes and Steven S. Skiena

Microarray synthesis through multiple-use PCR primer design
Bioinformatics 2002 18: S128-S135; doi:10.1093/bioinformatics/18.suppl_1.S128 [Abstract] [Print PDF][Screen PDF]  

Amos Tanay, Roded Sharan, and Ron Shamir

Discovering statistically significant biclusters in gene expression data
Bioinformatics 2002 18: S136-S144; doi:10.1093/bioinformatics/18.suppl_1.S136 [Abstract] [Print PDF][Screen PDF]  

Daniel Hanisch, Alexander Zien, Ralf Zimmer, and Thomas Lengauer

Co-clustering of biological networks and gene expression data
Bioinformatics 2002 18: S145-S154; doi:10.1093/bioinformatics/18.suppl_1.S145 [Abstract] [Print PDF][Screen PDF]  

Fabian Model, Thomas König, Christian Piepenbrock, and Péter Adorján

Statistical process control for large scale microarray experiments
Bioinformatics 2002 18: S155-S163; doi:10.1093/bioinformatics/18.suppl_1.S155 [Abstract] [Print PDF][Screen PDF]  

J. B. Tobler, M.N. Molla, E.F. Nuwaysir, R.D. Green, and J.W. Shavlik

Evaluating machine learning approaches for aiding probe selection for gene-expression arrays
Bioinformatics 2002 18: S164-S171; doi:10.1093/bioinformatics/18.suppl_1.S164 [Abstract] [Print PDF][Screen PDF]  

Chaim Linhart and Ron Shamir

The degenerate primer design problem
Bioinformatics 2002 18: S172-S181; doi:10.1093/bioinformatics/18.suppl_1.S172 [Abstract] [Print PDF][Screen PDF]  

Steffen Heber, Max Alekseyev, Sing-Hoi Sze, Haixu Tang, and Pavel A. Pevzner

Splicing graphs and EST assembly problem
Bioinformatics 2002 18: S181-S188; doi:10.1093/bioinformatics/18.suppl_1.S181 [Abstract] [Print PDF][Screen PDF]  

M. Fishelson and D. Geiger

Exact genetic linkage computations for general pedigrees
Bioinformatics 2002 18: S189-S198; doi:10.1093/bioinformatics/18.suppl_1.S189 [Abstract] [Print PDF][Screen PDF]  

Teemu Kivioja, Mikko Arvas, Kari Kataja, Merja Penttilä, Hans Söderlund, and Esko Ukkonen

Assigning probes into a small number of pools separable by electrophoresis
Bioinformatics 2002 18: S199-S206; doi:10.1093/bioinformatics/18.suppl_1.S199 [Abstract] [Print PDF][Screen PDF]  

Daniel L. Rubin, Farhad Shafa, Diane E. Oliver, Micheal Hewett, and Russ B. Altman

Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models
Bioinformatics 2002 18: S207-S215; doi:10.1093/bioinformatics/18.suppl_1.S207 [Abstract] [Print PDF][Screen PDF]  

V. Anne Smith, Erich D. Jarvis, and Alexander J. Hartemink

Evaluating functional network inference using simulations of complex biological systems
Bioinformatics 2002 18: S216-S224; doi:10.1093/bioinformatics/18.suppl_1.S216 [Abstract] [Print PDF][Screen PDF]  

Peter D. Karp, Suzanne Paley, and Pedro Romero

The Pathway Tools software
Bioinformatics 2002 18: S225-S232; doi:10.1093/bioinformatics/18.suppl_1.S225 [Abstract] [Print PDF][Screen PDF]  

Trey Ideker, Owen Ozier, Benno Schwikowski, and Andrew F. Siegel

Discovering regulatory and signalling circuits in molecular interaction networks
Bioinformatics 2002 18: S233-S240; doi:10.1093/bioinformatics/18.suppl_1.S233 [Abstract] [Print PDF][Screen PDF]  

Irene M. Ong, Jeremy D. Glasner, and David Page

Modelling regulatory pathways in E. coli from time series expression profiles
Bioinformatics 2002 18: S241-S248; doi:10.1093/bioinformatics/18.suppl_1.S241 [Abstract] [Print PDF][Screen PDF]  

Michael Krauthammer, Pauline Kra, Ivan Iossifov, Shawn M. Gomez, George Hripcsak, Vasileios Hatzivassiloglou, Carol Friedman, and Andrey Rzhetsky

Of truth and pathways: chasing bits of information through myriads of articles
Bioinformatics 2002 18: S249-S257; doi:10.1093/bioinformatics/18.suppl_1.S249 [Abstract] [Print PDF][Screen PDF]  

Dana Pe'er, Aviv Regev, and Amos Tanay

Minreg: Inferring an active regulator set
Bioinformatics 2002 18: S258-S267; doi:10.1093/bioinformatics/18.suppl_1.S258 [Abstract] [Print PDF][Screen PDF]  

Koji Tsuda, Taishin Kin, and Kiyoshi Asai

Marginalized kernels for biological sequences
Bioinformatics 2002 18: S268-S275; doi:10.1093/bioinformatics/18.suppl_1.S268 [Abstract] [Print PDF][Screen PDF]  

Jean-Philippe Vert

A tree kernel to analyse phylogenetic profiles
Bioinformatics 2002 18: S276-S284; doi:10.1093/bioinformatics/18.suppl_1.S276 [Abstract] [Print PDF][Screen PDF]  

Cara Stockham, Li-San Wang, and Tandy Warnow

Statistically based postprocessing of phylogenetic analysis by clustering
Bioinformatics 2002 18: S285-S293; doi:10.1093/bioinformatics/18.suppl_1.S285 [Abstract] [Print PDF][Screen PDF]  

Daniel Fasulo, Aaron Halpern, Ian Dew, and Clark Mobarry

Efficiently detecting polymorphisms during the fragment assembly process
Bioinformatics 2002 18: S294-S302; doi:10.1093/bioinformatics/18.suppl_1.S294 [Abstract] [Print PDF][Screen PDF]  

Dmitry Korkin and Lev Goldfarb

Multiple genome rearrangement: a general approach via the evolutionary genome graph
Bioinformatics 2002 18: S303-S311; doi:10.1093/bioinformatics/18.suppl_1.S303 [Abstract] [Print PDF][Screen PDF]  

Michael Höhl, Stefan Kurtz, and Enno Ohlebusch

Efficient multiple genome alignment
Bioinformatics 2002 18: S312-S320; doi:10.1093/bioinformatics/18.suppl_1.S312 [Abstract] [Print PDF][Screen PDF]  

Kyungsook Han, Yujin Lee, and Wootaek Kim

PseudoViewer: automatic visualization of RNA pseudoknots
Bioinformatics 2002 18: S321-S328; doi:10.1093/bioinformatics/18.suppl_1.S321 [Abstract] [Print PDF][Screen PDF]  

Gabriel Moreno-Hagelsieb and Julio Collado-Vides

A powerful non-homology method for the prediction of operons in prokaryotes
Bioinformatics 2002 18: S329-S336; doi:10.1093/bioinformatics/18.suppl_1.S329 [Abstract] [Print PDF][Screen PDF]  

Brian Tjaden, David R. Haynor, Sergey Stolyar, Carsten Rosenow, and Eugene Kolker

Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
Bioinformatics 2002 18: S337-S344; doi:10.1093/bioinformatics/18.suppl_1.S337 [Abstract] [Print PDF][Screen PDF]  

Dirk Husmeier and Gráinne McGuire

Detecting recombination with MCMC
Bioinformatics 2002 18: S345-S353; doi:10.1093/bioinformatics/18.suppl_1.S345 [Abstract] [Print PDF][Screen PDF]  

Eleazar Eskin and Pavel A. Pevzner

Finding composite regulatory patterns in DNA sequences
Bioinformatics 2002 18: S354-S363; doi:10.1093/bioinformatics/18.suppl_1.S354 [Abstract] [Print PDF][Screen PDF]  

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