Bioinformatics, Volume 18

Volume 18, Number 1, January 2002

Editorial

• 
  Chris Sander:
  The Journal Bioinformatics, key medium for computational biology. 1-2

Original Papers

• 
  James K. Bonfield, Rodger Staden:
  ZTR: a new format for DNA sequence trace data. 3-10
• 
  Trond Hellem Bø, Inge Jonassen, Ingvar Eidhammer, Carsten Helgesen:
  A fast top-down method for constructing reliable radiation hybrid frameworks. 11-18
• 
  Vladimir Pavlovic, Ashutosh Garg, Simon Kasif:
  A Bayesian framework for combining gene predictions. 19-27
• 
  Jirí Macas, Tibor Mészáros, Marcela Nouzová:
  PlantSat: a specialized database for plant satellite repeats. 28-35
• 
  Bernhard Haubold, Thomas Wiehe:
  Calculating the SNP-effective sample size from an alignment. 36-38
• 
  Danh V. Nguyen, David M. Rocke:
  Tumor classification by partial least squares using microarray gene expression data. 39-50
• 
  Wolfram Liebermeister:
  Linear modes of gene expression determined by independent component analysis. 51-60
• 
  Roman Sásik, N. Iranfar, Terence Hwa, W. F. Loomis:
  Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development. 61-66
• 
  Christian Siehs, Rainer Oberbauer, Gert Mayer, Arno Lukas, Bernd Mayer:
  Discrete simulation of regulatory homo- and heterodimerization in the apoptosis effector phase. 67-76
• 
  Weizhong Li, Lukasz Jaroszewski, Adam Godzik:
  Tolerating some redundancy significantly speeds up clustering of large protein databases. 77-82
• 
  Philip J. Cotter, Daniel R. Caffrey, Denis C. Shields:
  Improved database searches for orthologous sequences by conditioning on outgroup sequences. 83-91
• 
  Christian E. V. Storm, Erik L. L. Sonnhammer:
  Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. 92-99
• 
  Gary W. Stuart, Karen Moffett, Steve Baker:
  Integrated gene and species phylogenies from unaligned whole genome protein sequences. 100-108
• 
  Ursula Rost, Erich Bornberg-Bauer:
  TreeWiz: interactive exploration of huge trees. 109-114
• 
  Tae-Kun Seo, Jeffrey L. Thorne, Masami Hasegawa, Hirohisa Kishino:
  A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. 115-123
• 
  Alexander Goesmann, Martin Haubrock, Folker Meyer, Jörn Kalinowski, Robert Giegerich:
  PathFinder: reconstruction and dynamic visualization of metabolic pathways. 124-129
• 
  Xi Chen, Yuhmei Lin, Ming Liu, Michael K. Gilson:
  The Binding Database: data management and interface design. 130-139
• 
  Hiroshi Nagata, Hiroshi Mizushima, Hiroshi Tanaka:
  Concept and prototype of protein-ligand docking simulator with force feedback technology. 140-146
• 
  Rachel Karchin, Kevin Karplus, David Haussler:
  Classifying G-protein coupled receptors with support vector machines. 147-159
• 
  Amanda Clare, Ross D. King:
  Machine learning of functional class from phenotype data. 160-166
• 
  Sabine Dietmann, Cornelius Frömmel:
  Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networks. 167-174
• 
  Lee C. Allcorn, Andrew C. R. Martin:
  SACS-Self-maintaining database of antibody crystal structure information. 175-181

Discovery Notes

• 
  Darrell Conklin, Inge Jonassen, Rein Aasland, William R. Taylor:
  Association of nucleotide patterns with gene function classes: application to human 3' untranslated sequences. 182-189
• 
  Edouard Yeramian, Serge Bonnefoy, Gordon Langsley:
  Physics-based gene identification: proof of concept for Plasmodium falciparum. 190-193

Applications Notes

• 
  James K. Bonfield, Kathryn F. Beal, Matthew J. Betts, Rodger Staden:
  Trev: a DNA trace editor and viewer. 194-195
• 
  Biju Issac, Harpreet Singh, Harpreet Kaur, G. P. S. Raghava:
  Locating probable genes using Fourier transform approach. 196-197
• 
  Vladimir B. Bajic, Seng Hong Seah, Allen Chong, Guanglan Zhang, Judice L. Y. Koh, Vladimir Brusic:
  Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. 198-199
• 
  Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali:
  LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. 200-201
• 
  Scott C. Chapman, Peer Schenk, Kemal Kazan, John Manners:
  Using biplots to interpret gene expression patterns in plants. 202-204
• 
  Daniel R. Rhodes, Jeremy C. Miller, Brian B. Haab, Kyle A. Furge:
  CIT: identification of differentially expressed clusters of genes from microarray data. 205-206
• 
  Alexander Sturn, John Quackenbush, Zlatko Trajanoski:
  Genesis: cluster analysis of microarray data. 207-208
• 
  A. Hofmann, A. Wlodawer:
  PCSB-a program collection for structural biology and biophysical chemistry. 209-210
• 
  Anna E. Lobley, Lee Whitmore, B. A. Wallace:
  DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra. 211-212
• 
  Christophe Combet, Martin Jambon, Gilbert Deléage, Christophe Geourjon:
  Geno3D: automatic comparative molecular modelling of protein. 213-214

Letter

• 
  Donald R. Forsdyke:
  Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia. 215-217

Erratum

• 
  Steffen Möller, Michael D. R. Croning, Rolf Apweiler:
  Erratum: Evaluation of methods for the prediction of membrane spanning regions. 218

Volume 18, Number 2, February 2002

Editorial

• 
  Steven Henikoff:
  Beyond the central dogma. 223-225

Original Papers

• 
  Dirk Husmeier, Frank Wright:
  A Bayesian approach to discriminate between alternative DNA sequence segmentations. 226-234
• 
  Marc Sebban, Igor Mokrousov, Nalin Rastogi, Christophe Sola:
  A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis. 235-243
• 
  Zhengdong Zhang, Richard C. Willson, George E. Fox:
  Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset. 244-250
• 
  Alexander D. Tsodikov, Aniko Szabo, David Jones:
  Adjustments and measures of differential expression for microarray data. 251-260
• 
  Ilya Shmulevich, Edward R. Dougherty, Seungchan Kim, Wei Zhang:
  Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. 261-274
• 
  Debashis Ghosh, Arul M. Chinnaiyan:
  Mixture modelling of gene expression data from microarray experiments. 275-286
• 
  Hiroyuki Toh, Katsuhisa Horimoto:
  Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling. 287-297
• 
  Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano:
  Extensive feature detection of N-terminal protein sorting signals. 298-305
• 
  Melissa S. Cline, Richard Hughey, Kevin Karplus:
  Predicting reliable regions in protein sequence alignments. 306-314
• 
  Elmar Krieger, Gert Vriend:
  Models@Home: distributed computing in bioinformatics using a screensaver based approach. 315-318

Applications Notes

• 
  Francisco Azuaje:
  A cluster validity framework for genome expression data. 319-320
• 
  Henrik Bjørn Nielsen, Steen Knudsen:
  Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays. 321-322
• 
  Christopher M. L. S. Bouton, Jonathan Pevsner:
  DRAGON View: information visualization for annotated microarray data. 323-324
• 
  Wuju Li, Momiao Xiong:
  Tclass: tumor classification system based on gene expression profile. 325-326
• 
  Klaus Bumm, Mingzhong Zheng, Clyde Bailey, Fenghuang Zhan, M. Chiriva-Internati, Paul Eddlemon, Julian Terry, Bart Barlogie, John D. Shaughnessy Jr.:
  CGO: utilizing and integrating gene expression microarray data in clinical research and data management. 327-328
• 
  A. Collette, Adrien Six:
  ISEApeaks: an Excel platform for GeneScan and Immunoscope data retrieval, management and analysis. 329-330
• 
  Gert Thijs, Yves Moreau, Frank De Smet, Janick Mathys, Magali Lescot, Stephane Rombauts, Pierre Rouzé, Bart De Moor, Kathleen Marchal:
  INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. 331-332
• 
  Xavier Messeguer, Ruth Escudero, Domènec Farré, Oscar Núñez, Javier Martínez, M. Mar Albà:
  PROMO: detection of known transcription regulatory elements using species-tailored searches. 333-334
• 
  Alex Kozik, Elena Kochetkova, Richard W. Michelmore:
  GenomePixelizer-a visualization program for comparative genomics within and between species. 335-336
• 
  Richard R. Hudson:
  Generating samples under a Wright-Fisher neutral model of genetic variation. 337-338
• 
  George Seaton, Chris S. Haley, Sara A. Knott, Mike Kearsey, Peter M. Visscher:
  QTL Express: mapping quantitative trait loci in simple and complex pedigrees. 339-340
• 
  J. Signorovitch, Rasmus Nielsen:
  PATRI-paternity inference using genetic data. 341-342
• 
  Alexander Kanapin, Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Youla Karavidopoulou, Paul J. Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Thomas M. Oinn, Isabelle Phan, Florence Servant, Evgeni M. Zdobnov:
  Interactive InterPro-based comparisons of proteins in whole genomes. 374-375

GCB2000 Papers

• 
  Artemis G. Hatzigeorgiou:
  Translation initiation start prediction in human cDNAs with high accuracy. 343-350
• 
  Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar:
  Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. 351-361
• 
  Inge Jonassen, Ingvar Eidhammer, Darrell Conklin, William R. Taylor:
  Structure motif discovery and mining the PDB. 362-367
• 
  Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold:
  The EBI SRS server-recent developments. 368-373

Volume 18, Number 3, March 2002

Editorial

• 
  Christos A. Ouzounis:
  Bioinformatics and the theoretical foundations of molecular biology. 377-378

Original Papers

• 
  Martti T. Tammi, Erik Arner, Tom Britton, Björn Andersson:
  Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. 379-388
• 
  Mattias Wahde, Gregory T. Klus, Michael L. Bittner, Yidong Chen, Zoltan Szallasi:
  Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices. 389-394
• 
  Graham R. Ball, Shahid Mian, F. Holding, R. O. Allibone, James Lowe, S. Ali, G. Li, S. McCardle, Ian O. Ellis, Colin Creaser, Robert C. Rees:
  An integrated approach utilizing artificial neural networks and SELDI mass spectrometry for the classification of human tumours and rapid identification of potential biomarkers. 395-404
• 
  Winston Patrick Kuo, Tor-Kristian Jenssen, Atul J. Butte, Lucila Ohno-Machado, Isaac S. Kohane:
  Analysis of matched mRNA measurements from two different microarray technologies. 405-412
• 
  Geoffrey J. McLachlan, Richard W. Bean, David Peel:
  A mixture model-based approach to the clustering of microarray expression data. 413-422
• 
  Kurt Fellenberg, Nicole C. Hauser, Benedikt Brors, Jörg D. Hoheisel, Martin Vingron:
  Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis. 423-433
• 
  Martin J. Blythe, Irini A. Doytchinova, Darren R. Flower:
  JenPep: a database of quantitative functional peptide data for immunology. 434-439
• 
  Bin Ma, John Tromp, Ming Li:
  PatternHunter: faster and more sensitive homology search. 440-445
• 
  Pierre Vincens, Anne Badel-Chagnon, Cécile André, Serge A. Hazout:
  D-ASSIRC: distributed program for finding sequence similarities in genomes. 446-451
• 
  Christopher J. Lee, Catherine S. Grasso, Mark F. Sharlow:
  Multiple sequence alignment using partial order graphs. 452-464
• 
  Mark Ettinger:
  The complexity of comparing reaction systems. 465-469
• 
  Andrzej M. Kierzek:
  STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm. 470-481

Discovery Notes

• 
  Heikki Mannila, Anne Patrikainen, Jouni K. Seppänen, Juha Kere:
  Long-range control of expression in yeast. 482-483

Applications Notes

• 
  S. R. Ness, W. Terpstra, Martin Krzywinski, Marco A. Marra, Steven J. M. Jones:
  Assembly of fingerprint contigs: parallelized FPC. 484-485
• 
  Jean-Marie Rouillard, Christopher J. Herbert, Michael Zuker:
  OligoArray: genome-scale oligonucleotide design for microarrays. 486-487
• 
  Pinglang Wang, Fei Ding, Hsienyuan Chiang, Robert C. Thompson, Stanley J. Watson, Fan Meng:
  ProbeMatchDB-a web database for finding equivalent probes across microarray platforms and species. 488-489
• 
  Gilles Didier, Pierre Brézellec, Elisabeth Remy, Alain Hénaut:
  GeneANOVA-gene expression analysis of variance. 490-491
• 
  Glenn Tesler:
  GRIMM: genome rearrangements web server. 492-493
• 
  Raphaël Leplae, Tim J. P. Hubbard:
  MaxBench: evaluation of sequence and structure comparison methods. 494-495
• 
  Robel Y. Kahsay, Guoli Wang, Nataraj Dongre, Guang R. Gao, Roland L. Dunbrack Jr.:
  CASA: a server for the critical assessment of protein sequence alignment accuracy. 496-497
• 
  Harpreet Kaur, G. P. S. Raghava:
  BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms. 498-499
• 
  Xun Gu, Kent Vander Velden:
  DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. 500-501
• 
  Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, Arndt von Haeseler:
  TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. 502-504

Volume 18, Number 4, April 2002

Editorial

• 
  Rainer Fuchs:
  From Sequence to Biology: The Impact on Bioinformatics. 505-506

Original Papers

• 
  Mark J. Schreiber, Chris M. Brown:
  Compensation for nucleotide bias in a genome by representation as a discrete channel with noise. 507-512
• 
  Steven Hampson, Dennis F. Kibler, Pierre Baldi:
  Distribution patterns of over-represented k-mers in non-coding yeast DNA. 513-528
• 
  Charles J. Colbourn, Alan C. H. Ling, Martin Tompa:
  Construction of optimal quality control for oligo arrays. 529-535
• 
  Ying Xu, Victor Olman, Dong Xu:
  Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. 536-545
• 
  Wei Pan:
  A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. 546-554
• 
  Ilya Shmulevich, Wei Zhang:
  Binary analysis and optimization-based normalization of gene expression data. 555-565
• 
  Thomas D. Moloshok, R. R. Klevecz, Jeffrey D. Grant, Frank J. Manion, W. F. Speier IV, Michael F. Ochs:
  Application of Bayesian Decomposition for analysing microarray data. 566-575
• 
  David C. Hoyle, Magnus Rattray, Ray Jupp, Andy Brass:
  Making sense of microarray data distributions. 576-584
• 
  Dov Greenbaum, Ronald Jansen, Mark Gerstein:
  Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. 585-596
• 
  Daniel Aguilar, Baldomero Oliva, Francesc X. Avilés, Enrique Querol:
  TranScout: prediction of gene expression regulatory proteins from their sequences. 597-607
• 
  Shigeki Mitaku, Takatsugu Hirokawa, Toshiyuki Tsuji:
  Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces. 608-616
• 
  Mauro Delorenzi, Terence P. Speed:
  An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. 617-625

Discovery Notes

• 
  Riccardo Bennett-Lovsey, Sarah E. Hart, Hiroki Shirai, Kenji Mizuguchi:
  The SWIB and the MDM2 domains are homologous and share a common fold. 626-630

Applications Notes

• 
  Loïc Ponger, Dominique Mouchiroud:
  CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. 631-633
• 
  Adalberto T. Castelo, Wellington Santos Martins, Guang R. Gao:
  TROLL-Tandem Repeat Occurrence Locator. 634-636
• 
  Maria Elena Ochagavía, Jean Richelle, Shoshana J. Wodak:
  Advanced pairwise structure alignments of proteins and analysis of conformational changes. 637-640
• 
  M. Madan Babu, K. Sankaran:
  DOLOP-database of bacterial lipoproteins. 641-643
• 
  Filippo Rusconi, Maya Belghazi:
  Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert. 644-645
• 
  Coral del Val, Peter Ernst, Rüdiger Bräuning, Karl-Heinz Glatting, Sándor Suhai:
  PATH: a task for the inference of phylogenies. 646-647

Volume 18, Number 5, May 2002

Editorial

• 
  Ken Nishikawa:
  Information Concept in Biology. 649-651

Original Papers

• 
  Jacek Blazewicz, Piotr Formanowicz, Frédéric Guinand, Marta Kasprzak:
  A heuristic managing errors for DNA sequencing. 652-660
• 
  Zhou Yu, Tao Li, Jindong Zhao, Jingchu Luo:
  PGAAS: a prokaryotic genome assembly assistant system. 661-665
• 
  Yu-hua Hao, Zheng Tan:
  The generation of long telomere overhangs in human cells: a model and its implication. 666-671
• 
  M. Mar Albà, Roman A. Laskowski, John M. Hancock:
  Detecting cryptically simple protein sequences using the SIMPLE algorithm. 672-678
• 
  Olga G. Troyanskaya, Ora Arbell, Yair Koren, Gad M. Landau, Alexander Bolshoy:
  Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity. 679-688
• 
  Nela Zavaljevski, Fred J. Stevens, Jaques Reifman:
  Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions. 689-696
• 
  Ernesto Estrada:
  Characterization of the folding degree of proteins. 697-704
• 
  T. Oyama, K. Kitano, Kenji Satou, Takashi Ito:
  Extraction of knowledge on protein-protein interaction by association rule discovery. 705-714
• 
  Suzanne M. Paley, Peter D. Karp:
  Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. 715-724
• 
  Jinyan Li, Limsoon Wong:
  Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns. 725-734
• 
  Frank De Smet, Janick Mathys, Kathleen Marchal, Gert Thijs, Bart De Moor, Yves Moreau:
  Adaptive quality-based clustering of gene expression profiles. 735-746
• 
  Daniel Bozinov, Jörg Rahnenführer:
  Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering. 747-756
• 
  Wasco Wruck, Huw Griffiths, Matthias Steinfath, Hans Lehrach, Uwe Radelof, John O'Brien:
  Xdigitise: visualization of hybridization experiments. 757-760

Applications Notes

• 
  Wei Zhu, Volker Brendel:
  Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions. 761-762
• 
  Vincent Lombard, E. B. Camon, Helen E. Parkinson, Pascal Hingamp, Guenter Stoesser, Nicole Redaschi:
  EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database. 763-764
• 
  Jeffrey D. Grant, Roland L. Dunbrack Jr., Frank J. Manion, Michael F. Ochs:
  BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. 765-766
• 
  Patrice Gouet, Emmanuel Courcelle:
  ENDscript: a workflow to display sequence and structure information. 767-768
• 
  Flavio Monigatti, Elisabeth Gasteiger, Amos Bairoch, Eva Jung:
  The Sulfinator: predicting tyrosine sulfation sites in protein sequences. 769-770
• 
  M. R. Fielden, R. G. Halgren, E. Dere, Timothy R. Zacharewski:
  GP3: GenePix post-processing program for automated analysis of raw microarray data. 771-773
• 
  Mary E. Edgerton, Ronald C. Taylor, John I. Powell, Lawrence Hunter, Richard Simon, Edison T. Liu:
  A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis. 774-775

Volume 18, Number 6, June 2002

Original Papers

• 
  Burkhard Morgenstern, Oliver Rinner, Saïd Abdeddaïm, Dirk Haase, Klaus F. X. Mayer, Andreas W. M. Dress, Hans-Werner Mewes:
  Exon discovery by genomic sequence alignment. 777-787
• 
  Alpan Raval, Zoubin Ghahramani, David L. Wild:
  A Bayesian network model for protein fold and remote homologue recognition. 788-801
• 
  Ingolf Sommer, Alexander Zien, Niklas von Öhsen, Ralf Zimmer, Thomas Lengauer:
  Confidence measures for protein fold recognition. 802-812
• 
  Angela C. M. Luyf, J. de Gast, Antoine H. C. van Kampen:
  Visualizing metabolic activity on a genome-wide scale. 813-818
• 
  Shandar Ahmad, M. Michael Gromiha:
  NETASA: neural network based prediction of solvent accessibility. 819-824
• 
  Mor Peleg, Iwei Yeh, Russ B. Altman:
  Modelling biological processes using workflow and Petri Net models. 825-837
• 
  Andrey M. Leontovich, L. I. Brodsky, V. A. Drachev, V. K. Nikolaev:
  Adaptive algorithm of automated annotation. 838-844
• 
  Maximilian Schlosshauer, Mattias Ohlsson:
  A novel approach to local reliability of sequence alignments. 847-854
• 
  Upinder S. Bhalla:
  The chemical organization of signaling interactions. 855-863
• 
  Yi-Kuo Yu, Ralf Bundschuh, Terence Hwa:
  Hybrid alignment: high-performance with universal statistics. 864-872
• 
  Eldar Giladi, Michael G. Walker, James Ze Wang, Wayne Volkmuth:
  SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size. 873-877

Discovery Notes

• 
  Ehud Gazit:
  Global analysis of tandem aromatic octapeptide repeats: The significance of the aromatic-glycine motif. 880-883

Applications Notes

• 
  Christiaan Karreman:
  AiO, combining DNA/protein programs and oligo-management. 884-885
• 
  Matthew J. Gonzales, Jonathan M. Dugan, Robert W. Shafer:
  Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN). 886-887
• 
  Philippe Marc, Claude Jacq:
  Arrayplot for visualization and normalization of cDNA microarray data. 888-889
• 
  Florian Burckhardt:
  MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population genetic markers. 890-891
• 
  Julien Dutheil, Nicolas Galtier:
  BAOBAB: a Java editor for large phylogenetic trees. 892-893
• 
  Jeff P. Reeve, Bruce Rannala:
  DMLE+: Bayesian linkage disequilibrium gene mapping. 894-895

Volume 18, Number 7, July 2002

Structural Genomics

• 
  Burkhard Rost, Barry Honig, Alfonso Valencia:
  Bioinformatics in structural genomics - Editorial. 897
• 
  Elon Portugaly, Ilona Kifer, Michal Linial:
  Selecting targets for structural determination by navigating in a graph of protein families. 899-907
• 
  Federico Abascal, Alfonso Valencia:
  Clustering of proximal sequence space for the identification of protein families. 908-921
• 
  Jinfeng Liu, Burkhard Rost:
  Target space for structural genomics revisited. 922-933
• 
  Manuel C. Peitsch:
  About the use of protein models. 934-938
• 
  Xavier Fradera, Xavier de la Cruz, Carlos H. Tomich P. Silva, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco:
  Ligand-induced changes in the binding sites of proteins. 939-948

Original Papers

• 
  G. Charles Ostermeier, David J. Dix, Stephen A. Krawetz:
  A bioinformatic strategy to rapidly characterize cDNA libraries. 949-952
• 
  J. M. Dodson, P. T. Charles, David A. Stenger, Joseph J. Pancrazio:
  Quantitative assessment of filter-based cDNA microarrays: gene expression profiles of human T-lymphoma cell lines. 953-960
• 
  Adam B. Olshen, Ajay N. Jain:
  Deriving quantitative conclusions from microarray expression data. 961-970
• 
  Fabrizio Lillo, Salvatore Basile, Rosario N. Mantegna:
  Comparative genomics study of inverted repeats in bacteria. 971-979
• 
  Alessandro Pintar, Oliviero Carugo, Sándor Pongor:
  CX, an algorithm that identifies protruding atoms in proteins. 980-984
• 
  Jerry Tsai, Mark Gerstein:
  Calculations of protein volumes: sensitivity analysis and parameter database. 985-995
• 
  Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, Gurkan Nisanci, Rengül Çetin-Atalay, Mehmet Ozturk:
  PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. 996-1003
• 
  Jan-Jaap Wesselink, Beatriz de la Iglesia, Stephen A. James, Jo L. Dicks, Ian N. Roberts, Victor J. Rayward-Smith:
  Determining a unique defining DNA sequence for yeast species using hashing techniques. 1004-1010

Applications Notes

• 
  Yuki Saka, Mariel Vázquez:
  TangleSolve: topological analysis of site-specific recombination. 1011-1012
• 
  Michael Bober, Kevin Wiehe, Christina K. Yung, Tugba Onal Suzek, Matthew Lin, William Baumgartner Jr., Raimond L. Winslow:
  CaGE: Cardiac gene expression knowledgebase. 1013-1014
• 
  Pierre Tufféry:
  CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints. 1015-1016
• 
  Grigory Kolesov, Hans-Werner Mewes, Dmitrij Frishman:
  SNAPper: gene order predicts gene function. 1017-1019

Volume 18, Number 8, August 2002

Original Papers

• 
  Pierre-François Baisnée, Steven Hampson, Pierre Baldi:
  Why are complementary DNA strands symmetric? 1021-1033
• 
  Sanja Rogic, B. F. Francis Ouellette, Alan K. Mackworth:
  Improving gene recognition accuracy by combining predictions from two gene-finding programs. 1034-1045
• 
  Atul A. Shah, Michael C. Giddings, Jasmin B. Parvaz, Raymond F. Gesteland, John F. Atkins, Ivaylo P. Ivanov:
  Computational identification of putative programmed translational frameshift sites. 1046-1053
• 
  Gregory Stephanopoulos, Daehee Hwang, William A. Schmitt, Jatin Misra, George Stephanopoulos:
  Mapping physiological states from microarray expression measurements. 1054-1063
• 
  Brad Love, David R. Rank, Sharron G. Penn, David A. Jenkins, Russell S. Thomas:
  A conditional density error model for the statistical analysis of microarray data. 1064-1072
• 
  Shuta Tomida, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi:
  Analysis of expression profile using fuzzy adaptive resonance theory. 1073-1083
• 
  Bill C. H. Chang, Saman K. Halgamuge:
  Protein motif extraction with neuro-fuzzy optimization. 1084-1090
• 
  Pedro Gonnet, Frédérique Lisacek:
  Probabilistic alignment of motifs with sequences. 1091-1101
• 
  Nicola Cannata, Stefano Toppo, Chiara Romualdi, Giorgio Valle:
  Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices. 1102-1108
• 
  Zheng Yuan, Rohan D. Teasdale:
  Prediction of Golgi Type II membrane proteins based on their transmembrane domains. 1109-1115
• 
  Tal Pupko, Itsik Pe'er, Masami Hasegawa, Dan Graur, Nir Friedman:
  A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. 1116-1123
• 
  Lorraine K. Tanabe, W. John Wilbur:
  Tagging gene and protein names in biomedical text. 1124-1132

Applications Notes

• 
  Jeppe S. Spicker, Friedrik Wikman, Ming-Lan Lu, Carlos Cordon-Cardo, Christopher T. Workman, Torben F. Ørntoft, Søren Brunak, Steen Knudsen:
  Neural network predicts sequence of TP53 gene based on DNA chip. 1133-1134
• 
  Boris Lenhard, Wyeth W. Wasserman:
  TFBS: Computational framework for transcription factor binding site analysis. 1135-1136
• 
  Eyal Seroussi, Micha Ron, Darek Kedra:
  ShiftDetector: detection of shift mutations. 1137-1138
• 
  Junbai Wang, Vigdis Nygaard, Birgitte Smith-Sørensen, Eivind Hovig, Ola Myklebost:
  MArray: analysing single, replicated or reversed microarray experiments. 1139-1140
• 
  Bruno Contreras-Moreira, Paul A. Bates:
  Domain Fishing: a first step in protein comparative modelling. 1141-1142
• 
  Farid Chetouani, Philippe Glaser, Frank Kunst:
  DiffTool: building, visualizing and querying protein clusters. 1143-1144
• 
  Yuh-Jyh Hu:
  The NCTU BioInfo Archive of biological data sets for bioinformatics research and experimentation. 1145-1146
• 
  Lichun Wang, Jean-Jack M. Riethoven, Alan J. Robinson:
  XEMBL: distributing EMBL data in XML format. 1147-1148
• 
  Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold:
  The EBI SRS server-new features. 1149-1150

Volume 18, Number 9, September 2002

Original Papers

• 
  Koichi Nishigaki, Ayumu Saito:
  Genome structures embossed by oligonucleotide-stickiness. 1153-1161
• 
  Allen J. Gavin, Todd E. Scheetz, Chad A. Roberts, Brian O'Leary, Terry A. Braun, Val C. Sheffield, Marcelo Bento Soares, John P. Robinson, Thomas L. Casavant:
  Pooled library tissue tags for EST-based gene discovery. 1162-1166
• 
  Sündüz Keles, Mark J. van der Laan, Michael B. Eisen:
  Identification of regulatory elements using a feature selection method. 1167-1175
• 
  S. A. Rifkin, Junhyong Kim:
  Geometry of gene expression dynamics. 1176-1183
• 
  Daehee Hwang, William A. Schmitt, George Stephanopoulos, Gregory Stephanopoulos:
  Determination of minimum sample size and discriminatory expression patterns in microarray data. 1184-1193
• 
  Mario Medvedovic, Siva Sivaganesan:
  Bayesian infinite mixture model based clustering of gene expression profiles. 1194-1206
• 
  Yidong Chen, Vishnu G. Kamat, Edward R. Dougherty, Michael L. Bittner, Paul S. Meltzer, Jeffrey M. Trent:
  Ratio statistics of gene expression levels and applications to microarray data analysis. 1207-1215
• 
  Danh V. Nguyen, David M. Rocke:
  Multi-class cancer classification via partial least squares with gene expression profiles. 1216-1226
• 
  Robert F. Stengel, Raffaele M. Ghigliazza, Nilesh V. Kulkarni:
  Optimal enhancement of immune response. 1227-1235
• 
  Yonil Park, John L. Spouge:
  The correlation error and finite-size correction in an ungapped sequence alignment. 1236-1242
• 
  Sam Griffiths-Jones, Alex Bateman:
  The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs. 1243-1249
• 
  Christophe G. Lambert, Nadia Léonard, Xavier De Bolle, Eric Depiereux:
  ESyPred3D: Prediction of proteins 3D structures. 1250-1256
• 
  Ville-Veikko Rantanen, Mats Gyllenberg, Timo Koski, Mark S. Johnson:
  A dissimilarity matrix between protein atom classes based on Gaussian mixtures. 1257-1263

Applications Notes

• 
  Nick Moseyko, Lewis J. Feldman:
  VIZARD: analysis of Affymetrix Arabidopsis GeneChi® data. 1264-1265
• 
  Meena K. Sakharkar, Pandjassarame Kangueane, Dmitri A. Petrov, Ashok S. Kolaskar, S. Subbiah:
  SEGE: A database on 'intron less/single exonic' genes from eukaryotes. 1266-1267
• 
  Yan Zhou, Guyang Matthew Huang, Liping Wei:
  UniBLAST: a system to filter, cluster, and display BLAST results and assign unique gene annotation. 1268
• 
  Jens Kleinjung, Nigel Douglas, Jaap Heringa:
  Parallelized multiple alignment. 1270-1271
• 
  Volker Hollich, Christian E. V. Storm, Erik L. L. Sonnhammer:
  OrthoGUI: graphical presentation of Orthostrapper results. 1272-1273
• 
  Oleksandr V. Buzko, Kevan M. Shokat:
  A kinase sequence database: sequence alignments and family assignment. 1274-1275
• 
  Iddo Friedberg, Hanah Margalit:
  PeCoP: automatic determination of persistently conserved positions in protein families. 1276-1277
• 
  Patrick McConnell, Kimberly F. Johnson, Simon M. Lin:
  Applications of Tree-Maps to hierarchical biological data. 1278-1279
• 
  Douglas S. Greer, John D. Westbrook, Philip E. Bourne:
  An ontology driven architecture for derived representations of macromolecular structure. 1280-1281

Erratum

• 
  Erratum. Bioinform. 18(9): 1282 (2002)

Volume 18, Number 10, October 2002

SAC 2002 Paper

• 
  Mathew J. Palakal, Snehasis Mukhopadhyay, Javed Mostafa, Rajeev R. Raje, Mathias N'Cho, Santosh Mishra:
  An intelligent biological information management system. 1283-1288
• 
  Rhonda Harrison, Charles DeLisi:
  Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae. 1289-1296
• 
  Gianluca Della Vedova, Todd Wareham:
  Optimal algorithms for local vertex quartet cleaning. 1297-1304
• 
  David Sankoff:
  Short inversions and conserved gene cluster. 1305

Original Papers

• 
  Irmtraud M. Meyer, Richard Durbin:
  Comparative ab initio prediction of gene structures using pair HMMs. 1309-1318
• 
  Ilya Shmulevich, Edward R. Dougherty, Wei Zhang:
  ayesian automatic relevance determination algorithms for classifying gene expression data. 1332-1339
• 
  Lars Kaderali, Alexander Schliep:
  Selecting signature oligonucleotides to identify organisms using DNA arrays. 1340-1349
• 
  Kuang Lin, Alex C. W. May, William R. Taylor:
  Threading Using Neural nEtwork (TUNE): the measure of protein sequence-structure compatibility. 1350-1357
• 
  Ovidiu Ivanciuc, Catherine H. Schein, Werner Braun:
  Data mining of sequences and 3D structures of allergenic proteins. 1358-1364
• 
  Brendan J. McConkey, Vladimir Sobolev, Marvin Edelman:
  Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure. 1365-1373
• 
  Uri Keich, Pavel A. Pevzner:
  Finding motifs in the twilight zone. 1374-1381
• 
  Uri Keich, Pavel A. Pevzner:
  U Subtle motifs: defining the limits of motif finding algorithms. 1382-1390

Discovery Notes

• 
  Janusz M. Bujnicki, Leszek Rychlewski, Daniel Fischer:
  Fold-recognition detects an error in the Protein Data Bank. 1391-1395

Application Notes

• 
  Eugene Berezikov, Ronald H. A. Plasterk, Edwin Cuppen:
  GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. 1396-1397
• 
  Mark D. Wilkinson, David Block, William L. Crosby:
  Genquire: genome annotation browser/editor. 1398-1399
• 
  Tra Thi Vu, Jiri Vohradsky:
  Genexp-a genetic network simulation environment. 1400-1401
• 
  Phillip W. Lord, J. N. Selley, Terri K. Attwood:
  CINEMA-MX: a modular multiple alignment editor. 1402-1403
• 
  Oliver G. Pybus, Andrew Rambaut:
  GENIE: estimating demographic history from molecular phylogenies. 1404-1405

Corrigendum

• 
  Jinyan Li, Limsoon Wong:
  Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns . 1406-1407

Volume 18, Number 11, November 2002

Editorial

• 
  Catherine A. Ball, Gavin Sherlock, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank C. P. Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald C. Taylor, Alvis Brazma, John Quackenbush:
  An open letter to the scientific journals. 1409

Original Papers

• 
  Amit V. Kulkarni, Noelle Sevilir Williams, Yun Lian, Jonathan D. Wren, David Mittelman, Alexander Pertsemlidis, Harold R. Garner:
  ARROGANT: an application to manipulate large gene collections. 1410-1417
• 
  Nikola Stojanovic, Jean L. Chang, Jessica Lehoczky, Michael C. Zody, Ken Dewar:
  Identification of mixups among DNA sequencing plates. 1418-1426
• 
  Long-Cheng Li, Rajvir Dahiya:
  MethPrimer: designing primers for methylation PCRs. 1427-1431
• 
  Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou, Ying Xu:
  PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. 1432-1437
• 
  Kevin Dobbin, Richard Simon:
  Comparison of microarray designs for class comparison and class discovery. 1438-1445
• 
  Seferina Mavroudi, Stergios Papadimitriou, Anastasios Bezerianos:
  Gene expression data analysis with a dynamically extended self-organized map that exploits class information. 1446-1453
• 
  Olga G. Troyanskaya, Mitchell E. Garber, Patrick O. Brown, David Botstein, Russ B. Altman:
  Nonparametric methods for identifying differentially expressed genes in microarray data. 1454-1461
• 
  Lisa M. McShane, Michael D. Radmacher, Boris Freidlin, Ren Yu, Ming-Chung Li, Richard M. Simon:
  Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data. 1462-1469
• 
  William J. Lemon, Jeffrey J. T. Palatini, Ralf Krahe, Fred A. Wright:
  Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arrays. 1470-1476
• 
  Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano:
  Statistical analysis of a small set of time-ordered gene expression data using linear splines. 1477-1485
• 
  Ashish Bhan, David J. Galas, T. Gregory Dewey:
  A duplication growth model of gene expression networks. 1486-1493
• 
  Jonathan M. Keith, Peter Adams, Darryn E. Bryant, Dirk P. Kroese, Keith R. Mitchelson, Duncan A. E. Cochran, Gita H. Lala:
  A simulated annealing algorithm for finding consensus sequences. 1494-1499
• 
  J. T. Reese, William R. Pearson:
  Empirical determination of effective gap penalties for sequence comparison. 1500-1507
• 
  Harpreet Kaur, G. P. S. Raghava:
  An evaluation of ß-turn prediction methods. 1508-1514
• 
  Julie E. Leonard, Jeffrey B. Colombe, Joshua L. Levy:
  Finding relevant references to genes and proteins in Medline using a Bayesian approach. 1515-1522
• 
  Vyacheslav N. Grishin, Nick V. Grishin:
  Euclidian space and grouping of biological objects. 1523-1534

Discovery Notes

• 
  Stefan Janecek:
  A motif of a microbial starch-binding domain found in human genethonin. 1534-1537

Applications Notes

• 
  Sheldon J. McKay, Steven J. M. Jones:
  AcePrimer: automation of PCR primer design based on gene structure. 1538-1539
• 
  Carlo Colantuoni, George Henry, Scott Zeger, Jonathan Pevsner:
  SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis. 1540-1541
• 
  Marilyn Safran, Irina Solomon, Orit Shmueli, Michal Lapidot, Shai Shen-Orr, Avital Adato, Uri Ben-Dor, Nir Esterman, Naomi Rosen, Inga Peter, Tsviya Olender, Vered Chalifa-Caspi, Doron Lancet:
  GeneCardsTM 2002: towards a complete, object-oriented, human gene compendium. 1542-1543
• 
  Angelika Ehlers, John Osborne, Stephanie Slack, Rachel L. Roper, Chris Upton:
  Poxvirus Orthologous Clusters (POCs). 1544-1545
• 
  Kevin L. Howe, Alex Bateman, Richard Durbin:
  QuickTree: building huge Neighbour-Joining trees of protein sequences. 1546-1547
• 
  S. S. Sheik, Prasanna Sundararajan, A. S. Z. Hussain, Krishna Sekar:
  Ramachandran plot on the web. 1548-1549

Volume 18, Number 12, December 2002

Editorial

• 
  Alfonso Valencia:
  Bioinformatics: Biology by other means. 1551-1552

Reviews

• 
  Lynette Hirschman, Jong-Chan Park, Jun'ichi Tsujii, Limsoon Wong, Cathy H. Wu:
  Accomplishments and challenges in literature data mining for biology. 1553-1561

Discovery Notes

• 
  Demelo Madrazo Lao, Masafumi Arai, Masami Ikeda, Toshio Shimizu:
  The presence of signal peptide significantly affects transmembrane topology prediction. 1562-1566

Original Papers

• 
  Alistair M. Chalk, Erik L. L. Sonnhammer:
  Computational antisense oligo prediction with a neural network model. 1567-1575
• 
  Peter J. Park, Atul J. Butte, Isaac S. Kohane:
  Comparing expression profiles of genes with similar promoter regions. 1576-1584
• 
  Earl Hubbell, Wei-Min Liu, Rui Mei:
  Robust estimators for expression analysis. 1585-1592
• 
  Wei-Min Liu, Rui Mei, Xiaojun Di, Thomas B. Ryder, Earl Hubbell, S. Dee, Teresa A. Webster, C. A. Harrington, Ming-Hsiu Ho, J. Baid, S. P. Smeekens:
  Analysis of high density expression microarrays with signed-rank call algorithms. 1593-1599
• 
  Aedín C. Culhane, Guy Perrière, Elizabeth C. Considine, Thomas G. Cotter, Desmond G. Higgins:
  Between-group analysis of microarray data. 1600-1608
• 
  Michael A. Black, Rebecca W. Doerge:
  Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments. 1609-1616
• 
  Ann-Marie Martoglio, James W. Miskin, Stephen K. Smith, David J. C. MacKay:
  A decomposition model to track gene expression signatures: preview on observer-independent classification of ovarian cancer. 1617-1624
• 
  Danh V. Nguyen, David M. Rocke:
  Partial least squares proportional hazard regression for application to DNA microarray survival data. 1625-1632
• 
  Roman Sásik, E. Calvo, Jacques Corbeil:
  Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model. 1633-1640
• 
  Walter R. Gilks, Benjamin Audit, Daniela De Angelis, Sophia Tsoka, Christos A. Ouzounis:
  Modeling the percolation of annotation errors in a database of protein sequences. 1641-1649
• 
  An-Suei Yang, Lu-Yong Wang:
  Local structure-based sequence profile database for local and global protein structure predictions. 1650-1657
• 
  An-Suei Yang:
  Structure-dependent sequence alignment for remotely related proteins. 1658-1665
• 
  Adrian J. Shepherd, Nigel J. Martin, Roger G. Johnson, Paul Kellam, Christine A. Orengo:
  PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources. 1666-1672
• 
  Mikhail A. Roytberg, Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Alexey S. Kondrashov:
  A hierarchical approach to aligning collinear regions of genomes. 1673-1680
• 
  Alberto Riva, Isaac S. Kohane:
  SNPper: retrieval and analysis of human SNPs. 1681-1685

Applications Notes

• 
  Ralf Mrowka, Johannes Schuchhardt, Christoph Gille:
  Oligodb-interactive design of oligo DNA for transcription profiling of human genes. 1686-1687
• 
  Xiayi Ke, Andrew Collins, Shu Ye:
  PCR designer for restriction analysis of various types of sequence mutation. 1688-1689
• 
  Jianghui Hou:
  Design of endonuclease restriction sites into primers for PCR cloning. 1690-1691
• 
  Rebecca Everitt, Stephanie E. Minnema, Michael A. Wride, C. S. Koster, J. E. Hance, Fiona C. Mansergh, Derrick E. Rancourt:
  RED: the analysis, management and dissemination of expressed sequence tags. 1692-1693
• 
  Jing Hua Zhao, Sebastien Lissarrague, Laurent Essioux, Pak Chung Sham:
  GENECOUNTING: haplotype analysis with missing genotypes. 1694-1695
• 
  Xin Chen, Ming Li, Bin Ma, John Tromp:
  DNACompress: fast and effective DNA sequence compression. 1696-1698
• 
  Li Zhi Sun, Zhi Liang Ji, Xin Chen, J. F. Wang, Yuzong Chen:
  ADME-AP: a database of ADME associated proteins. 1699-1700
• 
  Jean Marc Kwasigroch, Dimitri Gilis, Yves Dehouck, Marianne Rooman:
  PoPMuSiC, rationally designing point mutations in protein structures. 1701-1702
• 
  Aleksey Y. Ogurtsov, Mikhail A. Roytberg, Svetlana A. Shabalina, Alexey S. Kondrashov:
  OWEN: aligning long collinear regions of genomes. 1703-1704
• 
  Junko Tanoue, Masatoshi Yoshikawa, Shunsuke Uemura:
  The GeneAround GO viewer. 1705-1706

Supplements

• 
  Proceedings of the European Conference on Computational Biology (ECCB 2002), October 6-9, 2002, Saarbrücken, Germany. 2002 [contents]