Bioinformatics, Volume 20

Volume 20, Number 1, January 2004

• Shao-Wu Meng, Zhuo Zhang, Jinyan Li: Twelve C2H2 zinc-finger genes on human chromosome 19 can be each translated into the same type of protein after frameshifts. 1-4

• Sofia Wichert, Konstantinos Fokianos, Korbinian Strimmer: Identifying periodically expressed transcripts in microarray time series data. 5-20
• Ying Huang, Yanda Li: Prediction of protein subcellular locations using fuzzy k-NN method. 21-28
• Tetsuo Shibuya, Hisashi Kashima, Akihiko Konagaya: Efficient filtering methods for clustering cDNAs with spliced sequence alignment. 29-39
• Saejoon Kim: Protein ß-turn prediction using nearest-neighbor method. 40-44
• Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho: ClusPro: an automated docking and discrimination method for the prediction of protein complexes. 45-50
• Stephan Philippi: Light-weight integration of molecular biological databases. 51-57
• Jianhua Ruan, Gary D. Stormo, Weixiong Zhang: An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. 58-66
• O. Michael Melko, Arcady R. Mushegian: Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes. 67-74
• Qiang Tu, Haixu Tang, Dafu Ding: MedBlast: searching articles related to a biological sequence. 75-77
• Karan Vasudeva, Upinder S. Bhalla: Adaptive stochastic-deterministic chemical kinetic simulations. 78-84
• Li Zhang, Aidong Zhang, Murali Ramanathan: VizStruct: exploratory visualization for gene expression profiling. 85-92
• Jelle J. Goeman, Sara A. van de Geer, Floor de Kort, Hans C. van Houwelingen: A global test for groups of genes: testing association with a clinical outcome. 93-99
• Song Wang, Stewart Ethier: A generalized likelihood ratio test to identify differentially expressed genes from microarray data. 100-104
• Monica Benito, Joel Parker, Quan Du, Junyuan Wu, Dong Xiang, Charles M. Perou, James Stephen Marron: Adjustment of systematic microarray data biases. 105-114
• Ney Lemke, Fabiana Herédia, Cláudia K. Barcellos, Adriana Neves dos Reis, José C. M. Mombach: Essentiality and damage in metabolic networks. 115-119

• Jung-Hsien Chiang, Hsu-Chun Yu, Huai-Jen Hsu: GIS: a biomedical text-mining system for gene information discovery. 120-121
• Aaron E. Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna: GRIL: genome rearrangement and inversion locator. 122-124
• Nils Blüthgen, Szymon M. Kielbasa, Branka Cajavec, Hanspeter Herzel: HOMGL - comparing genelists across species and with different accession numbers. 125-126
• Andreas Prlic, Francisco S. Domingues, Peter Lackner, Manfred J. Sippl: WILMA - automated annotation of protein sequences. 127-128
• David P. Leader: BugView: a browser for comparing genomes. 129-130
• Liam J. McGuffin, Stefano A. Street, Søren-Aksel Sørensen, David T. Jones: The Genomic Threading Database. 131-132
• Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, Alain Trubuil: PARIS: a proteomic analysis and resources indexation system. 133-135
• Miklós Cserzo, Frank Eisenhaber, Birgit Eisenhaber, István Simon: TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. 136-137

Volume 20, Number 2, January 2004

• Richard M. Bruskiewich:
  Guest Editor Preface: Plant & Animal Genome (PAG) Meeting Bioinformatics Session Paper Competition. 139
  

• Scott J. Emrich, Srinivas Aluru, Yan Fu, Tsui-Jung Wen, Mahesh Narayanan, Ling Guo, Daniel A. Ashlock, Patrick S. Schnable:
  A strategy for assembling the maize (Zea mays L.) genome. 140-147
  
• Lei Liu, George Gong, Yong Liu, Shreedhar Natarajan, Denis M. Larkin, Annelie Everts-van der Wind, Mark Rebeiz, Jonathan E. Beever:
  Multi-species comparative mapping in silico using the COMPASS strategy. 148-154
  
• Nikoleta Juretic, Thomas E. Bureau, Richard M. Bruskiewich:
  Transposable element annotation of the rice genome. 155-160
  
• Qingsong Zhu, Youping Deng, Phaneendra Vanka, Susan J. Brown, Subbaratnam Muthukrishnan, Karl J. Kramer:
  Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome. 161-169
  
• Kimmen Sjölander:
  Phylogenomic inference of protein molecular function: advances and challenges. 170-179
  

• Brad A. Chapman, John E. Bowers, Stefan R. Schulze, Andrew H. Paterson:
  A comparative phylogenetic approach for dating whole genome duplication events. 180-185
  

• Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler:
  Prediction of locally stable RNA secondary structures for genome-wide surveys. 186-190
  
• Jonathan D. Wren, Harold R. Garner:
  Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. 191-198
  
• Michal Brylinski, W. Jurkowski, Leszek Konieczny, Irena Roterman:
  Limited conformational space for early-stage protein folding simulation. 199-205
  
• Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S. Almeida:
  Comparative evaluation of word composition distances for the recognition of SCOP relationships. 206-215
  
• Jeffrey T. Chang, Hinrich Schütze, Russ B. Altman:
  GAPSCORE: finding gene and protein names one word at a time. 216-225
  
• Steffen Klamt, Ernst Dieter Gilles:
  Minimal cut sets in biochemical reaction networks. 226-234
  
• Susmita Datta, Glen A. Satten, Dale J. Benos, Jiazeng Xia, Martin J. Heslin, Somnath Datta:
  An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments. 235-242
  
• Hideya Kawaji, Yoichi Takenaka, Hideo Matsuda:
  Graph-based clustering for finding distant relationships in a large set of protein sequences. 243-252
  
• Ulisses Braga-Neto, Ronaldo Fumio Hashimoto, Edward R. Dougherty, Danh V. Nguyen, Raymond J. Carroll:
  Is cross-validation better than resubstitution for ranking genes? 253-258
  
• Albert Burger, Duncan Davidson, Richard A. Baldock:
  Formalization of mouse embryo anatomy. 259-267
  

• Torsten Crass, Iris Antes, Rico Basekow, Peer Bork, Christian Buning, Maik Christensen, Holger Claussen, Christian Ebeling, Peter Ernst, Valérie Gailus-Durner, Karl-Heinz Glatting, Rolf Gohla, Frank Gößling, Korbinian Grote, Karsten R. Heidtke, Alexander Herrmann, Sean O'Keeffe, O. Kießlich, Sven Kolibal, Jan O. Korbel, Thomas Lengauer, Ines Liebich, Mark van der Linden, Hannes Luz, Kathrin Meissner, Christian von Mering, Heinz-Theodor Mevissen, Hans-Werner Mewes, Holger Michael, Martin Mokrejs, Tobias Müller, Heike Pospisil, Matthias Rarey, Jens G. Reich, Ralf Schneider, Dietmar Schomburg, Steffen Schulze-Kremer, Knut Schwarzer, Ingolf Sommer, Stephan Springstubbe, Sándor Suhai, Gnanasekaran Thoppae, Martin Vingron, Jens Warfsmann, Thomas Werner, Daniel Wetzler, Edgar Wingender, Ralf Zimmer:
  The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. 268-270
  
• Nancie Reymond, Hubert Charles, Laurent Duret, Federica Calevro, Guillaume Beslon, Jean-Michel Fayard:
  ROSO: optimizing oligonucleotide probes for microarrays. 271-273
  
• Daniel Barker:
  LVB: parsimony and simulated annealing in the search for phylogenetic trees. 274-275
  
• Shir-Ly Huang, Li-Cheng Wu, Han-Kuen Liang, Kuan-Ting Pan, Jorng-Tzong Horng, Ming-Tat Ko:
  PGTdb: a database providing growth temperatures of prokaryotes. 276-278
  
• Ryan Brodie, Rachel L. Roper, Chris Upton:
  JDotter: a Java interface to multiple dotplots generated by dotter. 279-281
  
• Jeffrey D. Grant, Luke A. Somers, Yue Zhang, Frank J. Manion, Ghislain Bidaut, Michael F. Ochs:
  FGDP: functional genomics data pipeline for automated, multiple microarray data analyses. 282-283
  
• Richard J. Orton, William I. Sellers, Dietlind L. Gerloff:
  YETI: Yeast Exploration Tool Integrator. 284-285
  
• Lakshmi K. Matukumalli, John J. Grefenstette, Tad S. Sonstegard, Curtis P. Van Tassell:
  EST-PAGE - managing and analyzing EST data. 286-288
  
• Emmanuel Paradis, Julien Claude, Korbinian Strimmer:
  APE: Analyses of Phylogenetics and Evolution in R language. 289-290
  
• Antonio Jesús Pérez, Guillermo Thode, Oswaldo Trelles:
  AnaGram: protein function assignment. 291-292
  

• Torgeir R. Hvidsten, Andriy Kryshtafovych, Henryk Jan Komorowski, Krzysztof Fidelis:
  A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins. 293
  

Volume 20, Number 3, February 2004

• Lugang Li, Renchao Jin, Poh-Lin Kok, Honghui Wan:
  Pseudo-periodic partitions of biological sequences. 295-306
  
• Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, Rafael A. Irizarry:
  affy - analysis of Affymetrix GeneChip data at the probe level. 307-315
  
• Thomas R. Kiehl, Robert M. Mattheyses, Melvin K. Simmons:
  Hybrid simulation of cellular behavior. 316-322
  
• Leslie Cope, Rafael A. Irizarry, Harris A. Jaffee, Zhijin Wu, Terence P. Speed:
  A benchmark for Affymetrix GeneChip expression measures. 323-331
  
• Yihui Luan, Hongzhe Li:
  Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data. 332-339
  
• Natasa Przulj, Dennis A. Wigle, Igor Jurisica:
  Functional topology in a network of protein interactions. 340-348
  
• Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, A. Ayaz, Gürcan Gülesir, Gurkan Nisanci, Rengül Çetin-Atalay:
  An ontology for collaborative construction and analysis of cellular pathways. 349-356
  
• Zoltan Kutalik, Jacqueline Inwald, Steve V. Gordon, R. Glyn Hewinson, Philip D. Butcher, Jason Hinds, Kwang-Hyun Cho, Olaf Wolkenhauer:
  Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis. 357-363
  
• Jeanne Kowalski, Charles Drake, Ronald H. Schwartz, Jonathan Powell:
  Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypes. 364-373
  
• Ulisses Braga-Neto, Edward R. Dougherty:
  Is cross-validation valid for small-sample microarray classification? 374-380
  
• Sung Geun Lee, Jung Uk Hur, Yang Seok Kim:
  A graph-theoretic modeling on GO space for biological interpretation of gene clusters. 381-388
  
• Jonathan D. Wren, Raffi Bekeredjian, Jelena A. Stewart, Ralph V. Shohet, Harold R. Garner:
  Knowledge discovery by automated identification and ranking of implicit relationships. 389-398
  
• Jacques van Helden:
  Metrics for comparing regulatory sequences on the basis of pattern counts. 399-406
  
• Gautam Altekar, Sandhya Dwarkadas, John P. Huelsenbeck, Fredrik Ronquist:
  Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. 407-415
  

• Mikael Thollesson:
  LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. 416-418
  
• Matthew J. Wood, Jonathan D. Hirst:
  Predicting protein secondary structure by cascade-correlation neural networks. 419-420
  
• Manoj Bhasin, G. P. S. Raghava:
  SVM based method for predicting HLA-DRB1^*0401 binding peptides in an antigen sequence. 421-423
  
• Nir Orlev, Ron Shamir, Yosef Shiloh:
  PIVOT: Protein Interacions VisualizatiOn Tool. 424-425
  
• Michele E. Clamp, James A. Cuff, Stephen M. J. Searle, Geoffrey J. Barton:
  The Jalview Java alignment editor. 426-427
  
• Henrik Hornshøj, Henrik Stengaard, Frank Panitz, Christian Bendixen:
  SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target T_m algorithm for reducing cross-hybridization in microarray gene expression experiments. 428-429
  
• Natasha Levenkova, Qingjuan Gu, John J. Rux:
  Gene specific siRNA selector. 430-432
  
• Michael Spitzer, Georg Fuellen, Paul Cullen, Stefan Lorkowski:
  VisCoSe: visualization and comparison of consensus sequences. 433-435
  
• Susanna L. Lamers, Scott Beason, Luke Dunlap, Robert Compton, Marco Salemi:
  HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data. 436-438
  
• Tu H. Nguyen, Chunyu Liu, Elliot S. Gershon, Francis J. McMahon:
  Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers. 439-443
  

Volume 20, Number 4, March 2004

• Alexey V. Kochetov, Akinori Sarai:
  Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana.
  
• Zoltán Gáspári, Csaba P. Ortutay, András Perczel:
  A simple fold with variations: the pacifastin inhibitor family.
  

• Elisabetta Manduchi, Gregory R. Grant, H. He, Junmin Liu, Matthew D. Mailman, A. D. Pizarro, Patricia L. Whetzel, Christian J. Stoeckert Jr.:
  RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.
  
• Yue Huang, Ling Zhang:
  Rapid and sensitive dot-matrix methods for genome analysis.
  
• Christina S. Leslie, Eleazar Eskin, Adiel Cohen, Jason Weston, William Stafford Noble:
  Mismatch string kernels for discriminative protein classification.
  
• Shandar Ahmad, M. Michael Gromiha, Akinori Sarai:
  Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information.
  
• Daehee Hwang, George Stephanopoulos, Christina Chan:
  Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function.
  
• Tzu-Ming Chu, B. S. Weir, Russell D. Wolfinger:
  Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays.
  
• Tatiana V. Karpinets, Brent D. Foy, John M. Frazier:
  Tailored gene array databases: applications in mechanistic toxicology.
  
• Neil D. Lawrence, Marta Milo, Mahesan Niranjan, Penny Rashbass, Stephan Soullier:
  Reducing the variability in cDNA microarray image processing by Bayesian inference.
  
• Eytan Adar:
  SaRAD: a Simple and Robust Abbreviation Dictionary.
  
• Olivier Bastien, Jean-Christophe Aude, Sylvaine Roy, Eric Maréchal:
  Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics.
  
• Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita:
  A multi-algorithm, multi-timescale method for cell simulation.
  
• Zhiyong Lu, Duane Szafron, Russell Greiner, Paul Lu, David S. Wishart, Brett Poulin, John Anvik, Cam Macdonell, Roman Eisner:
  Predicting subcellular localization of proteins using machine-learned classifiers.
  
• Florence Horn, Anthony L. Lau, Fred E. Cohen:
  Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors.
  
• Wen Xue, Jin Wang, Zhirong Shen, Huaiqiu Zhu:
  Enrichment of transcriptional regulatory sites in non-coding genomic region.
  

• Sven Ekdahl, Erik L. L. Sonnhammer:
  ChromoWheel: a new spin on eukaryotic chromosome visualization.
  
• Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo:
  FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.
  
• Soohyun Lee, Changwon Kang:
  CHOISS for selection of single nucleotide polymorphism markers on interval regularity.
  
• Giovanni Lavorgna, Luca Sessa, Alessandro Guffanti, Lelio Lassandro, Giorgio Casari:
  AntiHunter: searching BLAST output for EST antisense transcripts.
  
• Paul Pavlidis, Ilan Wapinski, William Stafford Noble:
  Support vector machine classification on the web.
  
• Kevin Murphy, Towfique Raj, R. Scott Winters, Peter S. White:
  me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements.
  
• Marijke J. van Baren, Peter Heutink:
  The PCR Suite.
  
• Kentaro Tomii, Yutaka Akiyama:
  FORTE: a profile-profile comparison tool for protein fold recognition.
  
• Yukimitsu Yabuki, Yuri Mukai, Mark B. Swindells, Makiko Suwa:
  GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures.
  

Volume 20, Number 5, March 22 2004

• Yong Zhang, Zhihua Zhang, Lunjiang Ling, Baochen Shi, Runsheng Chen:
  Conservation analysis of small RNA genes in Escherichia coli. 599-603
  

• Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Svetlana Novichkova, Alexander Nikitin, Ilya Mazo:
  Extracting human protein interactions from MEDLINE using a full-sentence parser. 604-611
  
• Ren Zhang, Chun-Ting Zhang:
  A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I. 612-622
  
• Paul H. C. Eilers, Jelle J. Goeman:
  Enhancing scatterplots with smoothed densities. 623-628
  
• R. Lavigne, W. D. Sun, G. Volckaert:
  PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. 629-635
  
• Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak:
  Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. 636-643
  
• Alexey V. Antonov, Igor V. Tetko, Michael T. Mader, Jan Budczies, Hans-Werner Mewes:
  Optimization models for cancer classification: extracting gene interaction information from microarray expression data. 644-652
  
• Alessandro Vullo, Paolo Frasconi:
  Disulfide connectivity prediction using recursive neural networks and evolutionary information. 653-659
  
• Blythe Durbin, David M. Rocke:
  Variance-stabilizing transformations for two-color microarrays. 660-667
  
• Jonathan D. Wren:
  404 not found: the stability and persistence of URLs published in MEDLINE. 668-672
  
• Feng Gao, Chun-Ting Zhang:
  Comparison of various algorithms for recognizing short coding sequences of human genes. 673-681
  
• David R. Bickel:
  Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes. 682-688
  
• Michael A. Gilchrist, Laura A. Salter, Andreas Wagner:
  A statistical framework for combining and interpreting proteomic datasets. 689-700
  
• Akito Taneda:
  Adplot: detection and visualization of repetitive patterns in complete genomes. 701-708
  
• Pedro Romero, Peter D. Karp:
  Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. 709-717
  
• H. Fujisawa, S. Eguchi, M. Ushijima, S. Miyata, Y. Miki, T. Muto, M. Matsuura:
  Genotyping of single nucleotide polymorphism using model-based clustering. 718-726
  
• Hao Sun, Ramana V. Davuluri:
  Java-based application framework for visualization of gene regulatory region annotations. 727-734
  
• Zheng Rong Yang, Kuo-Chen Chou:
  Bio-support vector machines for computational proteomics. 735-741
  
• Lap Kun Yeung, Lap Keung Szeto, Alan Wee-Chung Liew, Hong Yan:
  Dominant spectral component analysis for transcriptional regulations using microarray time-series data. 742-749
  
• Tu Minh Phuong, Doheon Lee, Kwang Hyung Lee:
  Regression trees for regulatory element identification. 750-757
  
• Yinon Shafrir, H. Robert Guy:
  STAM: simple Transmembrane Alignment Method. 758-769
  
• Ingolf Sommer, Jörg Rahnenführer, Francisco S. Domingues, U. de Lichtenberg, Thomas Lengauer:
  Predicting protein structure classes from function predictions. 770-776
  
• Keith A. Baggerly, Jeffrey S. Morris, Kevin R. Coombes:
  Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. 777-785
  

• Jakob C. Mueller, Christophe Andreoli:
  Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity. 786-787
  
• Gill Bejerano:
  Algorithms for variable length Markov chain modeling. 788-789
  
• L. Frangeul, Philippe Glaser, C. Rusniok, C. Buchrieser, E. Duchaud, P. Dehoux, Frank Kunst:
  CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projects. 790-797
  
• Joseba Bikandi, Rosario San Millán, Aitor Rementeria, Javier Garaizar:
  In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction. 798-799
  
• Andre R. O. Cavalcanti, Laura F. Landweber:
  Gene Unscrambler for detangling scrambled genes in ciliates. 800-802
  
• Martti T. Tammi, Erik Arner, Ellen Kindlund, Björn Andersson:
  ReDiT: Repeat Discrepancy Tagger-a shotgun assembly finishing aid. 803-804
  
• Gernot Stocker, Dietmar Rieder, Zlatko Trajanoski:
  ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster. 805-807
  
• C. Wiederkehr, R. Basavaraj, Cyril Sarrauste de Menthière, R. Koch, U. Schlecht, Leandro Hermida, Benjamin Masdoua, R. Ishii, V. Cassen, M. Yamamoto, Christopher Lane, J. Michael Cherry, N. Lamb, Michael Primig:
  Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation. 808-811
  

Volume 20, Number 6, April 12 2004

• Deepak Grover, Mitali Mukerji, Pankaj Bhatnagar, Krishnamoorthy Kannan, Samir K. Brahmachari:
  Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. 813-817
  

• Ruslan Sadreyev, Nick V. Grishin:
  Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. 818-828
  
• Chun Tang, Aidong Zhang, Murali Ramanathan:
  ESPD: a pattern detection model underlying gene expression profiles. 829-838
  
• Yoseph Barash, Elinor Dehan, Meir Krupsky, Wilbur Franklin, Marc Geraci, Nir Friedman, Naftali Kaminski:
  Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. 839-846
  
• R. B. Vilim, R. M. Cunningham, B. Lu, P. Kheradpour, Fred J. Stevens:
  Fold-specific substitution matrices for protein classification. 847-853
  
• Dung-Tsa Chen, Sue-Hwa Lin, Seng-jaw Soong:
  Gene selection for oligonucleotide array: an approach using PM probe level data. 854-862
  
• Yuichiro Hourai, Tatsuya Akutsu, Yutaka Akiyama:
  Optimizing substitution matrices by separating score distributions. 863-873
  
• Jens Nilsson, Thoas Fioretos, Mattias Höglund, Magnus Fontes:
  Approximate geodesic distances reveal biologically relevant structures in microarray data. 874-880
  
• Florian Frommlet, Andreas Futschik, Malgorzata Bogdan:
  On the significance of sequence alignments when using multiple scoring matrices. 881-887
  
• Xiaohong Huang, Wei Pan, Soon J. Park, Xinqiang Han, Leslie W. Miller, Jennifer Hall:
  Modeling the relationship between LVAD support time and gene expression changes in the human heart by penalized partial least squares. 888-894
  
• Minghua Deng, Zhidong Tu, Fengzhu Sun, Ting Chen:
  Mapping gene ontology to proteins based on protein-protein interaction data. 895-902
  
• Zheng Rong Yang, Kuo-Chen Chou:
  Predicting the linkage sites in glycoproteins using bio-basis function neural network. 903-908
  
• Qing Zhou, Jun S. Liu:
  Modeling within-motif dependence for transcription factor binding site predictions. 909-916
  
• Ming Ouyang, William J. Welsh, Panos Georgopoulos:
  Gaussian mixture clustering and imputation of microarray data. 917-923
  
• Aniruddha Datta, Ashish Choudhary, Michael L. Bittner, Edward R. Dougherty:
  External control in Markovian genetic regulatory networks: the imperfect information case. 924-930
  
• Martin Dugas, Sylvia Merk, S. Breit, P. Dirschedl:
  mdclust-exploratory microarray analysis by multidimensional clustering. 931-936
  
• M. Scott, Guoqing Lu, Michael T. Hallett, David Thomas:
  The Hera database and its use in the characterization of endoplasmic reticulum proteins. 937-944
  
• Morgan N. Price, Eleanor G. Rieffel:
  Finding coexpressed genes in counts-based data: an improved measure with validation experiments. 945-952
  
• Michael E. Smoot, Stephanie A. Guerlain, William R. Pearson:
  Visualization of near-optimal sequence alignments. 953-958
  
• Kyongbum Lee, Daehee Hwang, Tadaaki Yokoyama, George Stephanopoulos, Gregory Stephanopoulos, Martin L. Yarmush:
  Identification of optimal classification functions for biological sample and state discrimination from metabolic profiling data. 959-969
  
• Xing Han, Wenjun Kang:
  Sequence analysis and membrane partitioning energies of -helical antimicrobial peptides. 970-973
  

• Michael L. Tress, Osvaldo Graña, Alfonso Valencia:
  SQUARE-determining reliable regions in sequence alignments. 974-975
  
• Nelson Young, Zhan Chang, David S. Wishart:
  GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images. 976-978
  
• Peter N. Robinson, Andreas Wollstein, Ulrike Böhme, Bradley J. Beattie:
  Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology. 979-981
  
• Ross Hall, Linda Stern:
  A rapid method for illustrating features in both coding and non-coding regions of a genome. 982-983
  
• Kishore R. Sakharkar, Vincent T. K. Chow:
  Exploring genome architecture through GOV: a WWW-based gene order visualizer. 984-985
  
• Andrew C. R. Martin:
  PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt. 986-988
  
• Ahmed A. Majeed, Niyaz Ahmed, K. Rajender Rao, S. Ghousunnissa, Farhana Kauser, Buddhaditta Bose, Hampapathalu A. Nagarajaram, V. M. Katoch, Debby V. Cousins, Leonardo A. Sechi, Robert H. Gilman, Seyed E. Hasnain:
  AmpliBASE MT^TM: a Mycobacterium tuberculosis diversity knowledgebase. 989-992
  

Volume 20, Number 7, May 1 2004

• Rajeev K. Azad, Mark Borodovsky:
  Effects of choice of DNA sequence model structure on gene identification accuracy. 993-1005
  
• Robert J. Clifford, Michael Edmonson, Cu Nguyen, Kenneth H. Buetow:
  Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. 1006-1014
  
• Natalio Krasnogor, David A. Pelta:
  Measuring the similarity of protein structures by means of the universal similarity metric. 1015-1021
  
• Adele A. Mitchell, Michael E. Zwick, Aravinda Chakravarti, David J. Cutler:
  Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns. 1022-1032
  
• Jorge Lepre, John Jeremy Rice, Yuhai Tu, Gustavo Stolovitzky:
  Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data. 1033-1044
  
• Zeyar Aung, Kian-Lee Tan:
  Rapid 3D protein structure database searching using information retrieval techniques. 1045-1052
  
• Kwok Pui Choi, Fanfan Zeng, Louxin Zhang:
  Good spaced seeds for homology search. 1053-1059
  
• Andrew C. James, Jim G. Veitch, Ali R. Zareh, Timothy Triche:
  Sensitivity and specificity of five abundance estimators for high-density oligonucleotide microarrays. 1060-1065
  
• Werner G. Krebs, Philip E. Bourne:
  Statistically rigorous automated protein annotation. 1066-1073
  
• Ramakant Sharma, Jitendra Kumar Maheshwari, Tulika Prakash, Debasis Dash, Samir K. Brahmachari:
  Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus. 1074-1080
  
• Lida Zhang, Dejun Yuan, Shunwu Yu, Zhugang Li, Youfang Cao, Zhiqi Miao, Hongmei Qian, Kexuan Tang:
  Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. 1081-1086
  
• Adrian K. Arakaki, Yang Zhang, Jeffrey Skolnick:
  Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. 1087-1096
  
• Yohei Minakuchi, Masahiro Ito, Yuji Kohara:
  SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis. 1097-1109
  
• Ross D. King, Paul H. Wise, Amanda Clare:
  Confirmation of data mining based predictions of protein function. 1110-1118
  
• Goro Terai, Toshihisa Takagi:
  Predicting rules on organization of cis-regulatory elements, taking the order of elements into account. 1119-1128
  
• Jesús A. Izaguirre, Rajiv Chaturvedi, Chengbang Huang, Trevor M. Cickovski, J. Coffland, G. Thomas, Gabor Forgacs, Mark S. Alber, G. Hentschel, Stuart A. Newman, James A. Glazier:
  COMPUCELL, a multi-model framework for simulation of morphogenesis. 1129-1137
  
• Wan K. Kim, Dan M. Bolser, Jong H. Park:
  Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). 1138-1150
  
• Yu-Dong Cai, Kuo-Chen Chou:
  Predicting subcellular localization of proteins in a hybridization space. 1151-1156
  
• Volker Brendel, Liqun Xing, Wei Zhu:
  Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. 1157-1169
  
• Yong Wang, Frederick C. C. Leung:
  An evaluation of new criteria for CpG islands in the human genome as gene markers. 1170-1177
  
• Guodong Zhou, Jie Zhang, Jian Su, Dan Shen, Chew Lim Tan:
  Recognizing names in biomedical texts: a machine learning approach. 1178-1190
  

• Jihoon Kim, Hee-Joon Chung, Chan Hee Park, Woong-Yang Park, Ju Han Kim:
  ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics. 1191-1192
  
• Justin Ebedes, Amitava Datta:
  Multiple sequence alignment in parallel on a workstation cluster. 1193-1195
  
• N. H. Shah, Nina V. Fedoroff:
  CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology. 1196-1197
  
• Han Yu, Andrew S. Yoo, Iva Greenwald:
  Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites. 1198-1200
  
• Nigel I. Kirby, Eugene F. DeRose, Robert E. London, Geoffrey A. Mueller:
  NvAssign: protein NMR spectral assignment with NMRView. 1201-1203
  

Volume 20, Number 8, May 22 2004

• Ivan Iossifov, Michael Krauthammer, Carol Friedman, Vasileios Hatzivassiloglou, Joel S. Bader, Kevin P. White, Andrey Rzhetsky:
  Probabilistic inference of molecular networks from noisy data sources. 1205-1213
  
• Weijia Xu, Daniel P. Miranker:
  A metric model of amino acid substitution. 1214-1221
  
• Mario Medvedovic, Ka Yee Yeung, Roger Eugene Bumgarner:
  Bayesian mixture model based clustering of replicated microarray data. 1222-1232
  
• Ming Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb, Wing Hung Wong, Cheng Li:
  dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. 1233-1240
  
• Ronaldo Fumio Hashimoto, Seungchan Kim, Ilya Shmulevich, Wei Zhang, Michael L. Bittner, Edward R. Dougherty:
  Growing genetic regulatory networks from seed genes. 1241-1247
  
• Hagay Shmuely, E. Dinitz, I. Dahan, Jerry Eichler, D. Fischer, Boaz Shaanan:
  Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins. 1248-1253
  
• Viatcheslav R. Akmaev, Clarence J. Wang:
  Correction of sequence-based artifacts in serial analysis of gene expression. 1254-1263
  
• Stephane Flibotte, Readman Chiu, Chris Fjell, Martin Krzywinski, Jacqueline E. Schein, Heesun Shin, Marco A. Marra:
  Automated ordering of fingerprinted clones. 1264-1271
  
• R. Keira Curtis, Martin D. Brand:
  Analysing microarray data using modular regulation analysis. 1272-1284
  
• Hin Hark Gan, Daniela Fera, Julie Zorn, Nahum Shiffeldrim, Michael Tang, Uri Laserson, Namhee Kim, Tamar Schlick:
  RAG: RNA-As-Graphs database-concepts, analysis, features. 1285-1291
  
• Yu-Dong Cai, Andrew J. Doig:
  Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition. 1292-1300
  
• Robert C. Edgar, Kimmen Sjölander:
  A comparison of scoring functions for protein sequence profile alignment. 1301-1308
  
• Robert C. Edgar, Kimmen Sjölander:
  COACH: profile-profile alignment of protein families using hidden Markov models. 1309-1318
  

• Pawan Dhar, Tan Chee Meng, Sandeep Somani, Li Ye, Anand Sairam, Mandar Chitre, Hao Zhu, Kishore R. Sakharkar:
  Cellware-a multi-algorithmic software for computational systems biology. 1319-1321
  
• Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal:
  ConSeq: the identification of functionally and structurally important residues in protein sequences. 1322-1324
  
• Jing Hua Zhao:
  2LD, GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis. 1325-1326
  
• Line Olsen, Morten Hansen, Claus Thorn Ekstrøm, Jesper T. Troelsen, Jørgen Olsen:
  CVD: the intestinal crypt/villus in situ hybridization database. 1327-1328
  
• Kengo Kinoshita, Haruki Nakamura:
  eF-site and PDBjViewer: database and viewer for protein functional sites. 1329-1330
  
• Flavio Mignone, David S. Horner, Graziano Pesole:
  WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments. 1331-1333
  

Volume 20, Number 9, June 12 2004

• Niranjan Nagarajan, Golan Yona:
  Automatic prediction of protein domains from sequence information using a hybrid learning system. 1335-1360
  
• Claudia Rangel, John Angus, Zoubin Ghahramani, Maria Lioumi, Elizabeth Sotheran, Alessia Gaiba, David L. Wild, Francesco Falciani:
  Modeling T-cell activation using gene expression profiling and state-space models. 1361-1372
  
• Claudia Andreini, Ivano Bertini, Antonio Rosato:
  A hint to search for metalloproteins in gene banks. 1373-1380
  
• Gerhard Kauer, Helmut Blöcker:
  Analysis of disturbed images. 1381-1387
  
• Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund:
  Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. 1388-1397
  
• John Parkinson, Alasdair Anthony, James Wasmuth, Ralf Schmid, Ann Hedley, Mark L. Blaxter:
  PartiGene-constructing partial genomes. 1398-1404
  
• Deepak Sharma, Biju Issac, G. P. S. Raghava, R. Ramaswamy:
  Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. 1405-1412
  
• Phuong-Van Luc, Paul Tempst:
  PINdb: a database of nuclear protein complexes from human and yeast. 1413-1415
  
• Jeffrey Yuan, Bruce Bush, Alex Elbrecht, Yuan Liu, Theresa Zhang, Wenqing Zhao, Richard Blevins:
  Enhanced homology searching through genome reading frame predetermination. 1416-1427
  
• Ivo Van Walle, Ignace Lasters, Lode Wyns:
  Align-m-a new algorithm for multiple alignment of highly divergent sequences. 1428-1435
  
• James J. Chen, Robert R. Delongchamp, Chen-An Tsai, Huey-miin Hsueh, Frank Sistare, Karol L. Thompson, Varsha G. Desai, James C. Fuscoe:
  Analysis of variance components in gene expression data. 1436-1446
  
• R. Henrik Nilsson, Karl-Henrik Larsson, Björn M. Ursing:
  galaxie-CGI scripts for sequence identification through automated phylogenetic analysis. 1447-1452
  

Volume 20, Number 10, July 1 2004

• Hans-Werner Mewes:
  German Conference on Bioinformatics 2003 (GCB'03). 1481
  

• Peter F. Arndt, Terence Hwa:
  Regional and time-resolved mutation patterns of the human genome. 1482-1485
  
• Panos Dafas, Dan M. Bolser, Jacek Gomoluch, Jong Park, Michael Schroeder:
  Using convex hulls to extract interaction interfaces from known structures. 1486-1490
  
• André Flöter, Jacques Nicolas, Torsten Schaub, Joachim Selbig:
  Threshold extraction in metabolite concentration data. 1491-1494
  
• Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits:
  Conserved RNA secondary structures in viral genomes: a survey. 1495-1499
  
• Rainer König, Roland Eils:
  Gene expression analysis on biochemical networks using the Potts spin model. 1500-1505
  
• Maciej Swat, Alexander E. Kel, Hanspeter Herzel:
  Bifurcation analysis of the regulatory modules of the mammalian G1/S transition. 1506-1511
  
• Alexander E. Kel, Yuri Tikunov, Nico Voss, Edgar Wingender:
  Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods. 1512-1516
  
• Florian Sohler, Daniel Hanisch, Ralf Zimmer:
  New methods for joint analysis of biological networks and expression data. 1517-1521
  
• Nils Weskamp, Daniel Kuhn, Eyke Hüllermeier, Gerhard Klebe:
  Efficient similarity search in protein structure databases by k-clique hashing. 1522-1526
  

• Michael C. Wendl, Shiaw-Pyng Yang:
  Gap statistics for whole genome shotgun DNA sequencing projects. 1527-1534
  
• A. Fazel Famili, Ganming Liu, Ziying Liu:
  Evaluation and optimization of clustering in gene expression data analysis. 1535-1545
  
• Catherine Grasso, Christopher Lee:
  Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. 1546-1556
  
• Shane T. Jensen, Jun S. Liu:
  BioOptimizer: a Bayesian scoring function approach to motif discovery. 1557-1564
  
• John P. Dekker, Anthony Fodor, Richard W. Aldrich, Gary Yellen:
  A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. 1565-1572
  
• Björn Voss, Carsten Meyer, Robert Giegerich:
  Evaluating the predictability of conformational switching in RNA. 1573-1582
  
• Andrew Jones, Ela Hunt, Jonathan M. Wastling, Angel Pizarro, Christian J. Stoeckert Jr.:
  An object model and database for functional genomics. 1583-1590
  
• Yongmei Ji, Xing Xu, Gary D. Stormo:
  A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. 1603-1611
  
• Rui Kuang, Christina S. Leslie, An-Suei Yang:
  Protein backbone angle prediction with machine learning approaches. 1612-1621
  
• Alice C. McHardy, Alexander Goesmann, Alfred Pühler, Folker Meyer:
  Development of joint application strategies for two microbial gene finders. 1622-1631
  

• Aubrey Hill, Eric Sorscher:
  Common structural patterns in human genes. 1632-1635
  

• Thomas Mailund, Christian N. S. Pedersen:
  QDist-quartet distance between evolutionary trees. 1636-1637
  
• Leping Li, David M. Umbach, Paul Terry, Jack A. Taylor:
  Application of the GA/KNN method to SELDI proteomics data. 1638-1640
  
• G. Golfier, M. Tran Dang, L. Dauphinot, E. Graison, J. Rossier, M.-C. Potier:
  VARAN: a web server for Variability Analysis of DNA microarray experiments. 1641-1643
  
• Simon N. Jarman:
  Amplicon: software for designing PCR primers on aligned DNA sequences. 1644-1645
  
• Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya:
  OBIYagns: a grid-based biochemical simulator with a parameter estimator. 1646-1648
  
• John Boyle:
  SeqExpress: desktop analysis and visualization tool for gene expression experiments. 1649-1650
  
• Wolfgang Huber, Robert Gentleman:
  matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements. 1651-1652
  

Volume 20, Number 11, July 22 2004

• Luciano da Fontoura Costa, M. S. Barbosa, Edson Tadeu Monteiro Manoel, Johannes Streicher, Gerd B. Müller:
  Mathematical characterization of three-dimensional gene expression patterns. 1653-1662
  
• Debashis Ghosh:
  Mixture models for assessing differential expression in complex tissues using microarray data. 1663-1669
  
• Eberhard O. Voit, Jonas S. Almeida:
  Decoupling dynamical systems for pathway identification from metabolic profiles. 1670-1681
  
• Hiroto Saigo, Jean-Philippe Vert, Nobuhisa Ueda, Tatsuya Akutsu:
  Protein homology detection using string alignment kernels. 1682-1689
  
• Nabil Belacel, Miroslava Cuperlovic-Culf, Mark Laflamme, Rodney Ouellette:
  Fuzzy J-Means and VNS methods for clustering genes from microarray data. 1690-1701
  
• Thorsteinn S. Rögnvaldsson, Liwen You:
  Why neural networks should not be used for HIV-1 protease cleavage site prediction. 1702-1709
  
• Jain-Shing Wu, Chungnan Lee, Chien-Chang Wu, Yow-Ling Shiue:
  Primer design using genetic algorithm. 1710-1717
  
• Audrius Meskauskas, Frank Lehmann-Horn, Karin Jurkat-Rott:
  Sight: automating genomic data-mining without programming skills. 1718-1720
  
• R. S. Anderssen, Y. Wu, R. Dolferus, I. Saunders:
  An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments. 1721-1727
  
• Mia Hubert, Sanne Engelen:
  Robust PCA and classification in biosciences. 1728-1736
  
• Stan Pounds, Cheng Cheng:
  Improving false discovery rate estimation. 1737-1745
  
• N. Kashtan, S. Itzkovitz, R. Milo, U. Alon:
  Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. 1746-1758
  
• Tetsuro Toyoda, Akiyoshi Wada:
  Omic space: coordinate-based integration and analysis of genomic phenomic interactions. 1759-1765
  
• Fenghai Duan, Heping Zhang:
  Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weights. 1766-1771
  
• Radka Stoyanova, Troy D. Querec, Truman R. Brown, Christos Patriotis:
  Normalization of single-channel DNA array data by principal component analysis. 1772-1784
  
• Chittibabu Guda, Eoin Fahy, Shankar Subramaniam:
  MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. 1785-1794
  
• Michael Reich, K. Ohm, Michael Angelo, Pablo Tamayo, Jill P. Mesirov:
  GeneCluster 2.0: an advanced toolset for bioarray analysis. 1797-1798
  

• Katsuyuki Yugi, Masaru Tomita:
  A general computational model of mitochondrial metabolism in a whole organelle scale. 1795-1796
  
• Xinglai Ji, Yuan Yuan, Jesse Li-Ling, Yanda Li, Zhirong Sun:
  HMMGEP: clustering gene expression data using hidden Markov models. 1799-1800
  
• Chesley M. Leslin, Alexej Abyzov, Valentin A. Ilyin:
  Structural exon database, SEDB, mapping exon boundaries on multiple protein structures. 1801-1803
  
• Wei Wu, William Stafford Noble:
  Genomic data visualization on the Web. 1804-1805
  
• Iain Milne, Frank Wright, Glenn Rowe, David F. Marshall, Dirk Husmeier, Gráinne McGuire:
  TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. 1806-1807
  
• Chang-Xing Ma, Rongling Wu, George Casella:
  FunMap: functional mapping of complex traits. 1808-1811
  
• Robert Kerkhoven, Frank H. J. van Enckevort, Jos Boekhorst, Douwe Molenaar, Roland J. Siezen:
  Visualization for genomics: the Microbial Genome Viewer. 1812-1814
  
• Peter M. Haverty, Zhiping Weng:
  CisML: an XML-based format for sequence motif detection software. 1815-1817
  
• Luquan Wang, Forest Y. Mu:
  A Web-based design center for vector-based siRNA and siRNA cassette. 1818-1820
  

Volume 20, Number 12, August 12 2004

• Alex Bateman, Alfonso Valencia:
  New Leadership for Bioinformatics. 1821
  

• Thijs Beuming, Harel Weinstein:
  A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. 1822-1835
  
• Nadia El-Mabrouk, Damian Labuda:
  Haplotypes histories as pathways of recombinations. 1836-1841
  
• Eran Halperin, Eleazar Eskin:
  Haplotype reconstruction from genotype data using Imperfect Phylogeny. 1842-1849
  
• Jon D. McAuliffe, Lior Pachter, Michael I. Jordan:
  Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. 1850-1860
  
• Danny Barash:
  Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation. 1861-1869
  
• Hongwu Ma, Xue-Ming Zhao, Ying-Jin Yuan, An-Ping Zeng:
  Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. 1870-1876
  
• Eduardo D. Sontag, Anatoly Kiyatkin, Boris N. Kholodenko:
  Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. 1877-1886
  
• Kajsa Ljungberg, Sverker Holmgren, Örjan Carlborg:
  Simultaneous search for multiple QTL using the global optimization algorithm DIRECT. 1887-1895
  
• Kimberly D. Siegmund, Peter W. Laird, Ite A. Laird-Offringa:
  A comparison of cluster analysis methods using DNA methylation data. 1896-1904
  
• Yi Qu, Shizhong Xu:
  Supervised cluster analysis for microarray data based on multivariate Gaussian mixture. 1905-1913
  
• Hong-Chu Chen, Hsiao-Ching Lee, Tsai-Yun Lin, Wen-Hsiung Li, Bor-Sen Chen:
  Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. 1914-1927
  
• Dirk Steinhauser, Björn H. Junker, Alexander Lüdemann, Joachim Selbig, Joachim Kopka:
  Hypothesis-driven approach to predict transcriptional units from gene expression data. 1928-1939
  
• Dmitry Pekurovsky, Ilya N. Shindyalov, Philip E. Bourne:
  A case study of high-throughput biological data processing on parallel platforms. 1940-1947
  
• Yan Fu, Qiang Yang, Ruixiang Sun, Dequan Li, Rong Zeng, Charles X. Ling, Wen Gao:
  Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. 1948-1954
  
• Troy D. Querec, Radka Stoyanova, Eric Ross, Christos Patriotis:
  A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays. 1955-1961
  

• Urban Liebel, Bjoern Kindler, Rainer Pepperkok:
  ??Harvester??: a fast meta search engine of human protein resources. 1962-1963
  
• Jomuna V. Choudhuri, Chris Schleiermacher, Stefan Kurtz, Robert Giegerich:
  GenAlyzer: interactive visualization of sequence similarities between entire genomes. 1964-1965
  
• Claudia Voigt, Steffen Möller, Saleh M. Ibrahim, Pablo Serrano-Fernández:
  Non-linear conversion between genetic and physical chromosomal distances. 1966-1967
  
• Mikita Suyama, David Torrents, Peer Bork:
  BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. 1968-1970
  
• Roland Pieler, Fatima Sanchez-Cabo, Hubert Hackl, Gerhard G. Thallinger, Zlatko Trajanoski:
  ArrayNorm: comprehensive normalization and analysis of microarray data. 1971-1973
  
• Stein Aerts, Peter Van Loo, Yves Moreau, Bart De Moor:
  A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes. 1974-1976
  
• Carolyn J. Lawrence, Christian M. Zmasek, R. Kelly Dawe, Russell L. Malmberg:
  LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference. 1977-1979
  
• Maksym Korotkiy, Rutger Middelburg, Henk Dekker, Frank van Harmelen, Jan Lankelma:
  A tool for gene expression based PubMed search through combining data sources. 1980-1982
  
• Roberto H. Higa, Arnaldo J. Montagner, Roberto C. Togawa, Paula R. Kuser, Michel E. B. Yamagishi, Adauto L. Mancini, Georgios Joannis Pappas Jr., Ronald T. Miura, Luiz G. Horita, Goran Neshich:
  ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure. 1983-1985
  
• David H. Ardell:
  SCANMS: adjusting for multiple comparisons in sliding window neutrality tests. 1986-1988
  
• Roberto H. Higa, Adilton G. Oliveira, Luiz G. Horita, Ronald T. Miura, Marcus K. Inoue, Paula R. Kuser, Adauto L. Mancini, Michel E. B. Yamagishi, Roberto C. Togawa, Goran Neshich:
  Defining 3D residue environment in protein structures using SCORPION and FORMIGA. 1989-1991
  

Volume 20, Number 13, September 1 2004

• Jan Ihmels, Sven Bergmann, Naama Barkai:
  Defining transcription modules using large-scale gene expression data. 1993-2003
  
• Sandhya Xirasagar, Scott F. Gustafson, B. Alex Merrick, Kenneth B. Tomer, Stanley Stasiewicz, Denny D. Chan, Kenneth J. Yost III, John R. Yates III, Susan Sumner, Nianqing Xiao, Michael D. Waters:
  CEBS object model for systems biology data, SysBio-OM. 2004-2015
  
• HyungJun Cho, Jae K. Lee:
  Bayesian hierarchical error model for analysis of gene expression data. 2016-2025
  
• David P. Kreil, Natasha A. Karp, Kathryn S. Lilley:
  DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results. 2026-2034
  
• Hiroshi Wako, Masaki Kato, Shigeru Endo:
  ProMode: a database of normal mode analyses on protein molecules with a full-atom model. 2035-2043
  
• Daniel H. Huson, Mike A. Steel:
  Phylogenetic trees based on gene content. 2044-2049
  
• Andrew B. Horne, T. Charles Hodgman, Hugh D. Spence, Andrew R. Dalby:
  Constructing an enzyme-centric view of metabolism. 2050-2055
  
• Momiao Xiong, Jinying Zhao, Hao Xiong:
  Network-based regulatory pathways analysis. 2056-2066
  
• Mark Chaisson, Pavel A. Pevzner, Haixu Tang:
  Fragment assembly with short reads. 2067-2074
  
• Morris A. Swertz, E. O. de Brock, Sacha A. F. T. van Hijum, Anne de Jong, Girbe Buist, Richard J. S. Baerends, Jan Kok, Oscar P. Kuipers, Ritsert C. Jansen:
  Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. 2075-2083
  
• Antonio Jesús Pérez, Carolina Perez-Iratxeta, Peer Bork, Guillermo Thode, Miguel A. Andrade:
  Gene annotation from scientific literature using mappings between keyword systems. 2084-2091
  
• Monica Chagoyen, M. Erdem Kurul, Pedro A. de Alarcón, José María Carazo, Amarnath Gupta:
  Designing and executing scientific workflows with a programmable integrator. 2092-2100
  
• Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi:
  Efficient selection of unique and popular oligos for large EST databases. 2101-2112
  
• Vladimir Makarenkov, François-Joseph Lapointe:
  A weighted least-squares approach for inferring phylogenies from incomplete distance matrices. 2113-2121
  
• Tamer Kahveci, Vebjorn Ljosa, Ambuj K. Singh:
  Speeding up whole-genome alignment by indexing frequency vectors. 2122-2134
  

• Liting Wen, Jin-An Feng:
  Repair-FunMap: a functional database of proteins of the DNA repair systems. 2135-2137
  
• Jonathan J. Ward, Liam J. McGuffin, Kevin Bryson, Bernard F. Buxton, David T. Jones:
  The DISOPRED server for the prediction of protein disorder. 2138-2139
  
• Nikola Stojanovic, Ken Dewar:
  Identifying multiple alignment regions satisfying simple formulas and patterns. 2140-2142
  
• Brett G. Olivier, Jacky L. Snoep:
  Web-based kinetic modelling using JWS Online. 2143-2144
  
• Adauto L. Mancini, Roberto H. Higa, Adilton G. Oliveira, Fabiana Dominiquini, Paula R. Kuser, Michel E. B. Yamagishi, Roberto C. Togawa, Goran Neshich:
  STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces. 2145-2147
  
• Andrés Moreira, Alejandro Maass:
  TIP: protein backtranslation aided by genetic algorithms. 2148-2149
  
• Gad Getz, Alina Starovolsky, Eytan Domany:
  F2CS: FSSP to CATH and SCOP prediction server. 2150-2152
  
• Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, John D. Westbrook:
  Ligand Depot: a data warehouse for ligands bound to macromolecules. 2153-2155
  
• Ritu Pandey, Raghavendra K. Guru, David W. Mount:
  Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. 2156-2158
  

Volume 20, Number 14, September 2004

• Pavel A. Pevzner:
  Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians. 2159-2161
  

• Katherine A. Kantardjieff, Bernhard Rupp:
  Protein isoelectric point as a predictor for increased crystallization screening efficiency. 2162-2168
  

• Thomas Huber, Bostjan Kobe:
  Comment on 'Protein isoelectric point as a predictor for increased crystallization screening efficiency'. 2169-2170
  

• Katherine A. Kantardjieff, Mortaza Jamshidian, Bernhard Rupp:
  Distributions of pI versus pH provide prior information for the design of crystallization screening experiments: response to comment on 'Protein isoelectric point as a predictor for increased crystallization screening efficiency'. 2171-2174
  

• Bin Qian, Richard A. Goldstein:
  Performance of an iterated T-HMM for homology detection. 2175-2180
  
• Takaho A. Endo:
  Probabilistic nucleotide assembling method for sequencing by hybridization. 2181-2188
  
• Tuan D. Pham, Denis I. Crane, Tuan H. Tran, Tam H. Nguyen:
  Extraction of fluorescent cell puncta by adaptive fuzzy segmentation. 2189-2196
  
• H. P. Shanahan, Janet M. Thornton:
  An examination of the conservation of surface patch polarity for proteins. 2197-2204
  
• Guillaume Koum, Augustin Yekel, Bengyella Ndifon, Frédéric Simard:
  Design and implementation of a mosquito database through an entomological ontology. 2205-2211
  
• Ekaterina Poustelnikova, Andrei Pisarev, Maxim Blagov, Maria Samsonova, John Reinitz:
  A database for management of gene expression data in situ. 2212-2221
  
• Ivo L. Hofacker, Stephan H. F. Bernhart, Peter F. Stadler:
  Alignment of RNA base pairing probability matrices. 2222-2227
  
• Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer, Thomas Lengauer:
  Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. 2228-2235
  
• C. J. Zheng, H. Zhou, B. Xie, L. Y. Han, Chun Wei Yap, Yu Zong Chen:
  TRMP: a database of therapeutically relevant multiple pathways. 2236-2241
  
• Scott L. Carter, Christian M. Brechbühler, Michael Griffin, Andrew T. Bond:
  Gene co-expression network topology provides a framework for molecular characterization of cellular state. 2242-2250
  
• Dawn J. Brooks, Jacques R. Fresco, Mona Singh:
  A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor. 2251-2257
  
• Linyong Mao, Haluk Resat:
  Probabilistic representation of gene regulatory networks. 2258-2269
  
• Claus Thorn Ekstrøm, Søren Bak, Charlotte Kristensen, Mats Rudemo:
  Spot shape modelling and data transformations for microarrays. 2270-2278
  
• Edward Susko, Andrew J. Roger:
  Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys. 2279-2287
  
• James E. Bray, Russell L. Marsden, Stuart C. G. Rison, Alexei Savchenko, Aled M. Edwards, Janet M. Thornton, Christine A. Orengo:
  A practical and robust sequence search strategy for structural genomics target selection. 2288-2295
  
• Alejandro Heredia-Langner, William R. Cannon, Kenneth D. Jarman, Kristin H. Jarman:
  Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data. 2296-2304
  

• Markus Ringnér, Srinivas Veerla, Samuel Andersson, Johan Staaf, Jari Häkkinen:
  ACID: a database for microarray clone information. 2305-2306
  
• R. Ciria, Cei Abreu-Goodger, Enrique Morett, Enrique Merino:
  GeConT: gene context analysis. 2307-2308
  
• Yin-Te Tsai, Yen Pin Huang, Ching Ta Yu, Chin Lung Lu:
  MuSiC: a tool for multiple sequence alignment with constraints. 2309-2311
  
• Todd J. Dolinsky, P. M. J. Burgers, Kevin Karplus, Nathan A. Baker:
  SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome. 2312-2314
  
• M. B. Lanktree, L. VanderBeek, F. M. Macciardi, J. L. Kennedy:
  PedSplit: pedigree management for stratified analysis. 2315-2316
  
• Thomas Huber, Geoffrey Faulkner, Philip Hugenholtz:
  Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. 2317-2319
  
• Lawrence H. Smith, Thomas C. Rindflesch, W. John Wilbur:
  MedPost: a part-of-speech tagger for bioMedical text. 2320-2321
  
• George Savva, Jenn Conn, Jo L. Dicks:
  Drawing phylogenetic trees in LATEX and Microsoft Word. 2322-2323
  
• Anne Arcade, Aymeric Labourdette, Matthieu Falque, Brigitte Mangin, Fabien Chardon, Alain Charcosset, Johann Joets:
  BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. 2324-2326
  
• Frank Dudbridge, Tim Carver, Gary W. Williams:
  Pelican: pedigree editor for linkage computer analysis. 2327-2328
  
• Fran Supek, Kristian Vlahovicek:
  INCA: synonymous codon usage analysis and clustering by means of self-organizing map. 2329-2330
  
• Florian Iragne, Aurélien Barré, Nicolas Goffard, Antoine de Daruvar:
  AliasServer: a web server to handle multiple aliases used to refer to proteins. 2331-2332
  

Volume 20, Number 15, October 2004

• Brian Marsden, Ruben Abagyan:
  SAD - a normalized structural alignment database: improving sequence-structure alignments. 2333-2344