Bioinformatics, Volume 20

Volume 20, Number 1, January 2004

Discovery Note

• 
  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

Original Papers

• 
  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
• 
  Mónica Benito, Joel S. 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

Applications Notes

• 
  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

PAG Meeting Preface

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

PAG Meeting Original Papers

• 
  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

PAG Meeting Applications Notes

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

Original Papers

• 
  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, Wiktor 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 M. 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

Applications Notes

• 
  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 J. Pérez-Pulido, Guillermo Thode, Oswaldo Trelles:
  AnaGram: protein function assignment. 291-292

Corrigenda

• 
  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

Original Papers

• 
  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
• 
  Zoltán 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 G. Drake, Ronald H. Schwartz, Jonathan Powell:
  Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypes. 364-373
• 
  Ulisses M. Braga-Neto, Edward R. Dougherty:
  Is cross-validation valid for small-sample microarray classification? 374-380
• 
  Sung Geun Lee, Junguk 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

Applications Notes

• 
  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

Discovery Notes

• 
  Alexey V. Kochetov, Akinori Sarai:
  Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana. 445-447
• 
  Zoltán Gáspári, Csaba P. Ortutay, András Perczel:
  A simple fold with variations: the pacifastin inhibitor family. 448-451

Original Papers

• 
  Elisabetta Manduchi, Gregory R. Grant, H. He, Junmin Liu, Matthew D. Mailman, Angel 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. 452-459
• 
  Yue Huang, Ling Zhang:
  Rapid and sensitive dot-matrix methods for genome analysis. 460-466
• 
  Christina S. Leslie, Eleazar Eskin, Adiel Cohen, Jason Weston, William Stafford Noble:
  Mismatch string kernels for discriminative protein classification. 467-476
• 
  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. 477-486
• 
  Daehee Hwang, George Stephanopoulos, Christina Chan:
  Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function. 487-499
• 
  Tzu-Ming Chu, B. S. Weir, Russell D. Wolfinger:
  Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays. 500-506
• 
  Tatiana V. Karpinets, Brent D. Foy, John M. Frazier:
  Tailored gene array databases: applications in mechanistic toxicology. 507-517
• 
  Neil D. Lawrence, Marta Milo, Mahesan Niranjan, Penny Rashbass, Stephan Soullier:
  Reducing the variability in cDNA microarray image processing by Bayesian inference. 518-526
• 
  Eytan Adar:
  SaRAD: a Simple and Robust Abbreviation Dictionary. 527-533
• 
  Olivier Bastien, Jean-Christophe Aude, Sylvaine Roy, Eric Maréchal:
  Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics. 534-537
• 
  Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita:
  A multi-algorithm, multi-timescale method for cell simulation. 538-546
• 
  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. 547-556
• 
  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. 557-568
• 
  Wen Xue, Jin Wang, Zhirong Shen, Huaiqiu Zhu:
  Enrichment of transcriptional regulatory sites in non-coding genomic region. 569-575

Applications Notes

• 
  Sven Ekdahl, Erik L. L. Sonnhammer:
  ChromoWheel: a new spin on eukaryotic chromosome visualization. 576-577
• 
  Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo:
  FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. 578-580
• 
  Soohyun Lee, Changwon Kang:
  CHOISS for selection of single nucleotide polymorphism markers on interval regularity. 581-582
• 
  Giovanni Lavorgna, Luca Sessa, Alessandro Guffanti, Lelio Lassandro, Giorgio Casari:
  AntiHunter: searching BLAST output for EST antisense transcripts. 583-585
• 
  Paul Pavlidis, Ilan Wapinski, William Stafford Noble:
  Support vector machine classification on the web. 586-587
• 
  Kevin Murphy, Towfique Raj, R. Scott Winters, Peter S. White:
  me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements. 588-590
• 
  Marijke J. van Baren, Peter Heutink:
  The PCR Suite. 591-593
• 
  Kentaro Tomii, Yutaka Akiyama:
  FORTE: a profile-profile comparison tool for protein fold recognition. 594-595
• 
  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. 596-598

Volume 20, Number 5, March 22 2004

Discovery Notes

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

Original Papers

• 
  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
• 
  Rob Lavigne, W. D. Sun, Guido Volckaert:
  PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. 629-635
• 
  Nameeta Y. 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
• 
  Hironori Fujisawa, Shinto Eguchi, Masaru Ushijima, Satoshi Miyata, Yoshio Miki, T. Muto, Masaaki 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, Ulrik 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

Application Notes

• 
  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, Christophe Rusniok, Carmen Buchrieser, Eric 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
• 
  Christa Niederhauser-Wiederkehr, R. Basavaraj, Cyril Sarrauste de Menthière, R. Koch, U. Schlecht, Leandro Hermida, Benjamin Masdoua, Ryohei 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

Original Papers

• 
  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
• 
  Michelle S. Scott, Guoqing Lu, Michael T. Hallett, David Y. Thomas:
  The Hera database and its use in the characterization of endoplasmic reticulum proteins. 937-944
• 
  Morgan N. Price, Eleanor Gilbert 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

Applications Notes

• 
  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 Ehetsham Hasnain:
  AmpliBASE MT^TM: a Mycobacterium tuberculosis diversity knowledgebase. 989-992

Volume 20, Number 7, May 1 2004

Original Papers

• 
  Rajeev K. Azad, Mark Borodovsky:
  Effects of choice of DNA sequence model structure on gene identification accuracy. 993-1005
• 
  Robert J. Clifford, Michael N. 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, Gilberto L. Thomas, Gabor Forgacs, Mark S. Alber, H. George E. Hentschel, Stuart A. Newman, James A. Glazier:
  COMPUCELL, a multi-model framework for simulation of morphogenesis. 1129-1137
• 
  Wan Kyu 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

Applications Notes

• 
  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

Original Papers

• 
  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, Irit 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

Applications Notes

• 
  Pawan Dhar, Tan Chee Meng, Sandeep Somani, Li Ye, Anand Sairam, Mandar A. 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 Stephen 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

Original Papers

• 
  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, Ramakrishna 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

Editorials

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

GCB Conference Papers

• 
  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-Chan 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

Original Papers

• 
  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 S. Grasso, Christopher J. 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 R. Jones, Ela Hunt, Jonathan M. Wastling, Angel D. 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 Carolyn McHardy, Alexander Goesmann, Alfred Pühler, Folker Meyer:
  Development of joint application strategies for two microbial gene finders. 1622-1631

Discovery Notes

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

Applications Notes

• 
  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, Marie-Claude 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
• 
  Robert 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
• 
  Nadav Kashtan, Shalev Itzkovitz, Ron Milo, Uri 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

Applications Notes

• 
  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

Editorials

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

Original Papers

• 
  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

Applications Notes

• 
  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, Fátima Sánchez-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

Original Papers

• 
  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, Engbert 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 J. Pérez-Pulido, 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

Applications Notes

• 
  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

Editorials

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

Discovery Notes

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

Letter to the editors

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

Reply to the letters

• 
  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

Original papers

• 
  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
• 
  Hugh 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. 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, Lianyi Han, Chun Wei Yap, Yuzong 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

Application notes

• 
  Markus Ringnér, Srinivas Veerla, Samuel Andersson, Johan Staaf, Jari Häkkinen:
  ACID: a database for microarray clone information. 2305-2306
• 
  Ricardo 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, Fabio Macciardi, James L. Kennedy:
  PedSplit: pedigree management for stratified analysis. 2315-2316
• 
  Thomas Huber, Geoffrey J. 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

Original Papers

• 
  Brian Marsden, Ruben Abagyan:
  SAD - a normalized structural alignment database: improving sequence-structure alignments. 2333-2344
• 
  Ruxandra I. Dima, D. Thirumalai:
  Proteins associated with diseases show enhanced sequence correlation between charged residues. 2345-2354
• 
  Charles Semple, Philip Daniel, Wim Hordijk, Roderic D. M. Page, Mike A. Steel:
  Supertree algorithms for ancestral divergence dates and nested taxa. 2355-2360
• 
  Neil F. W. Saunders, Paul M. G. Curmi, Ricardo Cavicchioli:
  An online database for the detection of novel archaeal sequences in human ESTs. 2361-2362
• 
  Jukka Corander, Patrik Waldmann, Pekka Marttinen, Mikko J. Sillanpää:
  BAPS 2: enhanced possibilities for the analysis of genetic population structure. 2363-2369
• 
  N. Simonis, Shoshana J. Wodak, G. N. Cohen, Jacques van Helden:
  Combining pattern discovery and discriminant analysis to predict gene co-regulation. 2370-2379
• 
  Ricardo Núñez Miguel:
  Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families. 2380-2389
• 
  Yan Zhang, David A. Eberhard, Gretchen D. Frantz, Patrick Dowd, Thomas D. Wu, Yan Zhou, Colin K. Watanabe, Shiuh-Ming Luoh, Paul Polakis, Kenneth J. Hillan, William I. Wood, Zemin Zhang:
  GEPIS - quantitative gene expression profiling in normal and cancer tissues. 2390-2398
• 
  Paul C. Boutros, Allan B. Okey:
  PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design. 2399-2400
• 
  Jonathan M. Keith, Peter Adams, Darryn E. Bryant, Duncan A. E. Cochran, Gita H. Lala, Keith R. Mitchelson:
  Algorithms for sequence analysis via mutagenesis. 2401-2410
• 
  Jyrki P. Kukkonen:
  Explicit formulation of different receptor-G-protein interactions and effector regulation. 2411-2420
• 
  Yuriy Fofanov, Yi Luo, Charles Katili, Jim Wang, Yuri Belosludtsev, Thomas Powdrill, Chetan Belapurkar, Viacheslav Fofanov, Tong-Bin Li, Sergei Chumakov, B. Montgomery Pettitt:
  How independent are the appearances of n-mers in different genomes? 2421-2428
• 
  Tao Li, Chengliang Zhang, Mitsunori Ogihara:
  A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression. 2429-2437
• 
  Jeroen J. Jansen, Huub C. J. Hoefsloot, Hans F. M. Boelens, Jan van der Greef, Age K. Smilde:
  Analysis of longitudinal metabolomics data. 2438-2446
• 
  Matthias Scholz, S. Gatzek, Alisdair R. Sterling, Oliver Fiehn, Joachim Selbig:
  Metabolite fingerprinting: detecting biological features by independent component analysis. 2447-2454

Application notes

• 
  José María Fernández, Alfonso Valencia:
  YAdumper: extracting and translating large information volumes from relational databases to structured flat files. 2455-2457
• 
  Jan K. Rainey, M. Cynthia Goh:
  An interactive triple-helical collagen builder. 2458-2459
• 
  Aleksey A. Porollo, Rafal Adamczak, Jaroslaw Meller:
  POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins. 2460-2462
• 
  Kevin L. Garwood, Chris F. Taylor, Kai J. Runte, Andy Brass, Stephen G. Oliver, Norman W. Paton:
  Pedro: a configurable data entry tool for XML. 2463-2465
• 
  Kyungsook Han, Byungkyu Park, Hyongguen Kim, Jinsun Hong, Jong-Chan Park:
  HPID: The Human Protein Interaction Database. 2466-2470
• 
  Owen J. Marshall:
  PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. 2471-2472
• 
  Jiren Wang, Kuo-Bin Li, Wing-Kin Sung:
  G-PRIMER: greedy algorithm for selecting minimal primer set. 2473-2475
• 
  Seán I. O'Donoghue, Joachim E. W. Meyer, Andrea Schafferhans, Karsten Fries:
  The SRS 3D module: integrating structures, sequences and features. 2476-2478
• 
  Eibe Frank, Mark A. Hall, Leonard E. Trigg, Geoffrey Holmes, Ian H. Witten:
  Data mining in bioinformatics using Weka. 2479-2481
• 
  Daniel Fischer, Jakub Pas, Leszek Rychlewski:
  The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries. 2482-2484
• 
  Guillaume Laval, Laurent Excoffier:
  SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. 2485-2487
• 
  Alistair M. Chalk, Martin Wennerberg, Erik L. L. Sonnhammer:
  Sfixem - graphical sequence feature display in Java. 2488-2490
• 
  Alexander G. Williams, Robert W. Williams:
  GenomeMixer: a complex genetic cross simulator. 2491-2492

Volume 20, Number 16, November 2004

Review

• 
  Ziv Bar-Joseph:
  Analyzing time series gene expression data. 2493-2503

Discovery notes

• 
  Akira R. Kinjo, Ken Nishikawa:
  Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. 2504-2508
• 
  Dominique Tessier, Benjamin Bardiaux, Colette Larré, Yves Popineau:
  Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptor. 2509-2512

Original papers

• 
  Sanju Attoor, Edward R. Dougherty, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent:
  Which is better for cDNA-microarray-based classification: ratios or direct intensities. 2513-2520
• 
  Delong Liu, Clarice R. Weinberg, Shyamal D. Peddada:
  A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions. 2521-2528
• 
  Xiaoqiu Huang, Liang Ye, Hui-Hsien Chou, I-Hsuan Yang, Kun-Mao Chao:
  Efficient combination of multiple word models for improved sequence comparison. 2529-2533
• 
  Jinwook Seo, Marina Bakay, Yi-Wen Chen, Sara Hilmer, Ben Shneiderman, Eric P. Hoffman:
  Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. 2534-2544
• 
  Roxana Alexandridis, Shili Lin, Mark Irwin:
  Class discovery and classification of tumor samples using mixture modeling of gene expression data - a unified approach. 2545-2552
• 
  Mahlet G. Tadesse, Marina Vannucci, Pietro Liò:
  Identification of DNA regulatory motifs using Bayesian variable selection. 2553-2561
• 
  Philippe Broët, Alex Lewin, Sylvia Richardson, Cyril Dalmasso, Henri Magdelenat:
  A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments. 2562-2571
• 
  Kuo-Bin Li, Praveen Issac, Arun Krishnan:
  Predicting allergenic proteins using wavelet transform. 2572-2578
• 
  Shobhit Gupta, Dorothea Zink, Bernhard Korn, Martin Vingron, Stefan A. Haas:
  Genome wide identification and classification of alternative splicing based on EST data. 2579-2585
• 
  Chien-Yu Chen, Yen-Jen Oyang, Hsueh-Fen Juan:
  Incremental generation of summarized clustering hierarchy for protein family analysis. 2586-2596
• 
  Martijn J. Schuemie, Marc Weeber, Bob J. A. Schijvenaars, Erik M. van Mulligen, C. Christiaan van der Eijk, Rob Jelier, Barend Mons, Jan A. Kors:
  Distribution of information in biomedical abstracts and full-text publications. 2597-2604
• 
  Feng Luo, Latifur Khan, Farokh B. Bastani, I-Ling Yen, Jizhong Zhou:
  A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles. 2605-2617
• 
  Marcel Smid, Lambert C. J. Dorssers:
  GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. 2618-2625
• 
  Gert R. G. Lanckriet, Tijl De Bie, Nello Cristianini, Michael I. Jordan, William Stafford Noble:
  A statistical framework for genomic data fusion. 2626-2635
• 
  Claude Pasquier, Fabrice Girardot, K. Jevardat de Fombelle, Richard Christen:
  THEA: ontology-driven analysis of microarray data. 2636-2643
• 
  Harm van Bakel, Martijn A. Huynen, Cisca Wijmenga:
  Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway. 2644-2655
• 
  Y.-F. Liu, Ueng-Cheng Yang:
  SCA db: spinocerebellar ataxia candidate gene database. 2656-2661
• 
  Koji Kyoda, Kotaro Baba, Shuichi Onami, Hiroaki Kitano:
  DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants. 2662-2675
• 
  Prudence W. H. Wong, Tak Wah Lam, N. Lu, Hing-Fung Ting, Siu-Ming Yiu:
  An efficient algorithm for optimizing whole genome alignment with noise. 2676-2684
• 
  Lori E. Dodd, Edward L. Korn, Lisa M. McShane, G. V. R. Chandramouli, Eric Y. Chuang:
  Correcting log ratios for signal saturation in cDNA microarrays. 2685-2693
• 
  J. G. Liao, Yong Lin, Zachariah E. Selvanayagam, Weichung Joe Shih:
  A mixture model for estimating the local false discovery rate in DNA microarray analysis. 2694-2701
• 
  Arun Krishnan, Francis Tang:
  Exhaustive whole-genome tandem repeats search. 2702-2710
• 
  Liping Ji, Kian-Lee Tan:
  Mining gene expression data for positive and negative co-regulated gene clusters. 2711-2718
• 
  Nicolas Omont, François Képès:
  Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication. 2719-2725
• 
  Robert Mansourian, David M. Mutch, Nicolas Antille, Jerome Aubert, Paul Fogel, Jean-Marc Le Goff, Julie Moulin, Anton Petrov, Andreas Rytz, Johannes J. Voegel, Matthew-Alan Roberts:
  The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data. 2726-2737
• 
  Yonatan H. Grad, Frederick P. Roth, Marc S. Halfon, George M. Church:
  Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. 2738-2750
• 
  Harpreet Kaur, G. P. S. Raghava:
  A neural network method for prediction of ?-turn types in proteins using evolutionary information. 2751-2758
• 
  Zheng Rong Yang:
  Mining gene expression data based on template theory. 2759-2766
• 
  Yimeng Dou, Pierre-François Baisnée, Gianluca Pollastri, Yann Pécout, James Nowick, Pierre Baldi:
  ICBS: a database of interactions between protein chains mediated by ?-sheet formation. 2767-2777
• 
  Karla V. Ballman, Diane E. Grill, Ann L. Oberg, Terry M. Therneau:
  Faster cyclic loess: normalizing RNA arrays via linear models. 2778-2786
• 
  Manuel Martínez-Bueno, Antonio J. Molina-Henares, Eduardo Pareja, Juan L. Ramos, Raquel Tobes:
  BacTregulators: a database of transcriptional regulators in bacteria and archaea. 2787-2791
• 
  Miguel Pérez-Enciso, Ignacy Misztal:
  Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. 2792-2798
• 
  Sündüz Keles, Mark J. van der Laan, Chris Vulpe:
  Regulatory motif finding by logic regression. 2799-2811
• 
  Olivier Delgrange, Eric Rivals:
  STAR: an algorithm to Search for Tandem Approximate Repeats. 2812-2820
• 
  Shu-Dong Zhang, Timothy W. Gant:
  A statistical framework for the design of microarray experiments and effective detection of differential gene expression. 2821-2828

Applications notes

• 
  Bruce E. Shapiro, Michael Hucka, Andrew Finney, John Doyle:
  MathSBML: a package for manipulating SBML-based biological models. 2829-2831
• 
  Luiz G. P. Almeida, Roger F. C. Paixão, Rangel C. Souza, Gisele C. da Costa, Frank J. A. Barrientos, Marcelo Trindade dos Santos, Darcy F. de Almeida, Ana Tereza Ribeiro de Vasconcelos:
  A System for Automated Bacterial (genome) Integrated Annotation - SABIA. 2832-2833
• 
  Robert Friedman, Vikram Ekollu, John R. Rose, Austin L. Hughes:
  Dblox: a genome-wide test for ancient segmental duplication. 2834-2835
• 
  Eisuke Chikayama, Atsushi Kurotani, Yutaka Kuroda, Shigeyuki Yokoyama:
  ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences. 2836-2838
• 
  Terry M. Casstevens, Edward S. Buckler:
  GDPC: connecting researchers with multiple integrated data sources. 2839-2840
• 
  Alexander Lüdemann, Daniel Weicht, Joachim Selbig, Joachim Kopka:
  PaVESy: Pathway Visualization and Editing System. 2841-2844
• 
  Sandra Barth, Markus Fischer, Rolf D. Schmid, Jürgen Pleiss:
  The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions. 2845-2847
• 
  Fulvio Lazzarato, Giuliana Franceschinis, Marco Botta, Francesca Cordero, Raffaele A. Calogero:
  RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets. 2848-2850
• 
  Boris Adryan, Reinhard Schuh:
  Gene-Ontology-based clustering of gene expression data. 2851-2852
• 
  Sachiyo Aburatani, Kousuke Goto, Shigeru Saito, Masaki Fumoto, Akira Imaizumi, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Sato, Hiroyuki Toh, Katsuhisa Horimoto:
  ASIAN: a website for network inference. 2853-2856
• 
  Stephen C. Grubb, Gary A. Churchill, Molly A. Bogue:
  A collaborative database of inbred mouse strain characteristics. 2857-2859
• 
  Li Chen, Rose Oughtred, Helen M. Berman, John D. Westbrook:
  TargetDB: a target registration database for structural genomics projects. 2860-2862
• 
  W. H. Lee, V. B. Vega:
  Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies. 2863-2864
• 
  Song Li, Hui-Hsien Chou:
  LUCY2: an interactive DNA sequence quality trimming and vector removal tool. 2865-2866
• 
  Mario A. Fares:
  SWAPSC: sliding window analysis procedure to detect selective constraints. 2867-2868
• 
  Ghislain Bidaut, Michael F. Ochs:
  ClutrFree: cluster tree visualization and interpretation. 2869-2871
• 
  Duhong Chen, Oliver Eulenstein, David Fernández-Baca:
  Rainbow: a toolbox for phylogenetic supertree construction and analysis. 2872-2873
• 
  Robert N. Goldberg, Yadu B. Tewari, Talapady N. Bhat:
  Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistry. 2874-2877
• 
  William H. Majoros, Mihaela Pertea, Steven Salzberg:
  TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. 2878-2879
• 
  Fang Liu, Tor-Kristian Jenssen, Vegard Nygaard, John Sack, Eivind Hovig:
  FigSearch: a figure legend indexing and classification system. 2880-2882
• 
  Pietro D'Addabbo, Luca Lenzi, Federica Facchin, Raffaella Casadei, Silvia Canaider, Lorenza Vitale, Flavia Frabetti, Paolo Carinci, Maria Zannotti, Pierluigi Strippoli:
  GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers. 2883-2885
• 
  Tulika Prakash, Mamta Khandelwal, Dipayan Dasgupta, Debasis Dash, Samir K. Brahmachari:
  CoPS: Comprehensive Peptide Signature Database. 2886-2888
• 
  Andreas M. Boehm, Florian Grosse-Coosmann, Albert Sickmann:
  Command line tool for calculating theoretical MS spectra for given sequences. 2889-2891

Volume 20, Number 17, November 2004

Editorials

• 
  Hui-Hsien Chou, An-Ping Hsia, Denise L. Mooney, Patrick S. Schnable:
  Picky: oligo microarray design for large genomes. 2893-2902

Letter To The Editors

• 
  Lisa M. Schilling, Jonathan D. Wren, Robert P. Dellavalle:
  Letter to the Editor. 2903

Discovery Notes

• 
  Neeraj Pandey, Mythily Ganapathi, Kaushal Kumar, Dipayan Dasgupta, Sushanta Kumar Das Sutar, Debasis Dash:
  Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins. 2904-2910
• 
  Eric Bonnet, Jan Wuyts, Pierre Rouzé, Yves Van de Peer:
  Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. 2911-2917

Original Papers

• 
  Xiaobo Zhou, Xiaodong Wang, Ranadip Pal, Ivan Ivanov, Michael L. Bittner, Edward R. Dougherty:
  A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks. 2918-2927
• 
  Sven Rahmann, Christine Gräfe:
  Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions. 2928-2933
• 
  Iosifina Pournara, Lorenz Wernisch:
  Reconstruction of gene networks using Bayesian learning and manipulation experiments. 2934-2942
• 
  Madhuchhanda Bhattacharjee, Colin C. Pritchard, Peter S. Nelson, Elja Arjas:
  Bayesian integrated functional analysis of microarray data. 2943-2953
• 
  Wenqing He:
  A spline function approach for detecting differentially expressed genes in microarray data analysis. 2954-2963
• 
  Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon:
  Transmembrane proteins in the Protein Data Bank: identification and classification. 2964-2972
• 
  Ji-Ping Z. Wang, Bruce G. Lindsay, James H. Leebens-Mack, Liying Cui, P. Kerr Wall, Webb Colby Miller, Claude W. dePamphilis:
  EST clustering error evaluation and correction. 2973-2984
• 
  Christian Baumgartner, Christian Böhm, Daniela Baumgartner, G. Marini, Klaus Weinberger, B. Olgemöller, B. Liebl, A. A. Roscher:
  Supervised machine learning techniques for the classification of metabolic disorders in newborns. 2985-2996
• 
  Cynthia Sims Parr, Bongshin Lee, Dana Campbell, Benjamin B. Bederson:
  Visualizations for taxonomic and phylogenetic trees. 2997-3004
• 
  Jörn Lewin, Armin Otto Schmitt, Péter Adorján, Thomas Hildmann, Christian Piepenbrock:
  Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates. 3005-3012
• 
  Andrew D. King, Natasa Przulj, Igor Jurisica:
  Protein complex prediction via cost-based clustering. 3013-3020
• 
  Mark A. Girolami, Rainer Breitling:
  Biologically valid linear factor models of gene expression. 3021-3033
• 
  Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, Scott G. Soltys, Gongyi Shi, Albert C. Koong, Quynh-Thu Le:
  Sample classification from protein mass spectrometry, by 'peak probability contrasts'. 3034-3044
• 
  Thomas M. Oinn, Matthew Addis, Justin Ferris, Darren Marvin, Martin Senger, Robert Mark Greenwood, Tim Carver, Kevin Glover, Matthew R. Pocock, Anil Wipat, Peter Li:
  Taverna: a tool for the composition and enactment of bioinformatics workflows. 3045-3054
• 
  Pål Sætrom:
  Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. 3055-3063
• 
  Trees-Juen Chuang, Feng-Chi Chen, Meng-Yuan Chou:
  A comparative method for identification of gene structures and alternatively spliced variants. 3064-3079
• 
  Changyu Hu II, Xiang Li, Jie Liang:
  Developing optimal non-linear scoring function for protein design. 3080-3098
• 
  Yan Liu, Jaime G. Carbonell, Judith Klein-Seetharaman, Vanathi Gopalakrishnan:
  Comparison of probabilistic combination methods for protein secondary structure prediction. 3099-3107
• 
  Albert Hsiao, D. S. Worrall, Jerrold M. Olefsky, Shankar Subramaniam:
  Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes. 3108-3127
• 
  Glen A. Satten, Somnath Datta, Hercules Moura, Adrian R. Woolfitt, Maria da G. Carvalho, George M. Carlone, Barun K. De, Antonis Pavlopoulos, John R. Barr:
  Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens. 3128-3136
• 
  Jun Sese, Yukinori Kurokawa, Morito Monden, Kikuya Kato, Shinichi Morishita:
  Constrained clusters of gene expression profiles with pathological features. 3137-3145
• 
  Yinglei Lai, Baolin Wu, Liang Chen, Hongyu Zhao:
  A statistical method for identifying differential gene-gene co-expression patterns. 3146-3155
• 
  Ben-Yang Liao, Yu-Jung Chang, Jan-Ming Ho, Ming-Jing Hwang:
  The UniMarker (UM) method for synteny mapping of large genomes. 3156-3165
• 
  Jing Wang, Kevin R. Coombes, W. Edward Highsmith, Michael J. Keating, Lynne V. Abruzzo:
  Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. 3166-3178
• 
  Jong-Hun Kim, Juyoung Lee, Bermseok Oh, Kuchan Kimm, InSong Koh:
  Prediction of phosphorylation sites using SVMs. 3179-3184
• 
  Nathalie Pochet, Frank De Smet, Johan A. K. Suykens, Bart De Moor:
  Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. 3185-3195
• 
  David Baird, Peter Johnstone, Theresa Wilson:
  Normalization of microarray data using a spatial mixed model analysis which includes splines. 3196-3205
• 
  David P. A. Corney, Bernard F. Buxton, William B. Langdon, David T. Jones:
  BioRAT: extracting biological information from full-length papers. 3206-3213
• 
  Ralf Bundschuh:
  Computational prediction of RNA editing sites. 3214-3220
• 
  Reuben Thomas, Sanjay Mehrotra, Eleftherios T. Papoutsakis, Vassily Hatzimanikatis:
  A model-based optimization framework for the inference on gene regulatory networks from DNA array data. 3221-3235

Applications Notes

• 
  Rasko Leinonen, Federico Garcia Diez, David Binns, Wolfgang Fleischmann, Rodrigo Lopez, Rolf Apweiler:
  UniProt archive. 3236-3237
• 
  Don Gilbert, Yoshihiro Ugawa, Markus Buchhorn, Tin Wee Tan, Akira Mizushima, Hyunchul Kim, Kilnam Chon, Seyeon Weon, Juncai Ma, Yoshihiro Ichiyanagi, Der-Ming Liou, Somnuk Keretho, Suhaimi Napis:
  Bio-Mirror project for public bio-data distribution. 3238-3240
• 
  Fredrik Pettersson, Oskar Jonsson, Lon R. Cardon:
  GOLDsurfer: three dimensional display of linkage disequilibrium. 3241-3243
• 
  Jaime R. Robles, Edwin J. C. G. van den Oord:
  lga972: a cross-platform application for optimizing LD studies using a genetic algorithm. 3244-3245
• 
  Alok J. Saldanha:
  Java Treeview - extensible visualization of microarray data. 3246-3248
• 
  Ryan T. McDonald, R. Scott Winters, Mark A. Mandel, Yang Jin, Peter S. White, Fernando C. N. Pereira:
  An entity tagger for recognizing acquired genomic variations in cancer literature. 3249-3251
• 
  Stacia K. Wyman, Robert K. Jansen, Jeffrey L. Boore:
  Automatic annotation of organellar genomes with DOGMA. 3252-3255
• 
  Wangsen Feng, Lusheng Wang, Daming Zhu:
  CTRD: a fast applet for computing signed translocation distance between genomes. 3256-3257
• 
  Ioannis C. Spyropoulos, Theodore Liakopoulos, Pantelis G. Bagos, Stavros J. Hamodrakas:
  TMRPres2D: high quality visual representation of transmembrane protein models. 3258-3260
• 
  Thomas Mailund, Christian N. S. Pedersen:
  QuickJoin - fast neighbour-joining tree reconstruction. 3261-3262
• 
  Tianhua Niu, Zhenjun Hu:
  SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays. 3263-3265
• 
  Eugen C. Buehler, Jeffrey R. Sachs, Kui Shao, Ansuman Bagchi, Lyle H. Ungar:
  The CRASSS plug-in for integrating annotation data with hierarchical clustering results. 3266-3269
• 
  Bo Kyeng Hou, Jin Sik Kim, Ji Hoon Jun, Dong-Yup Lee, Yong Wook Kim, Sujin Chae, Mira Roh, Yong-Ho In, Sang Yup Lee:
  BioSilico: an integrated metabolic database system. 3270-3272
• 
  Tao-Wei Huang, An-Chi Tien, Wen-Shien Huang, Yuan-Chii G. Lee, Chin-Lin Peng, Huei-Hun Tseng, Cheng-Yan Kao, Chi-Ying F. Huang:
  POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. 3273-3276
• 
  Patrick May, Stefan Barthel, Ina Koch:
  PTGL - a web-based database application for protein topologies. 3277-3279
• 
  Melanie Bahlo, Lei Xing, C. R. Wilkinson:
  HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers. 3280-3283
• 
  Alexey V. Antonov, Igor V. Tetko, Volodymyr V. Prokopenko, Denis Kosykh, Hans-Werner Mewes:
  A web portal for classification of expression data using maximal margin linear programming. 3284-3285
• 
  Jose-Roman Bilbao-Castro, Carlos Oscar Sánchez Sorzano, Inmaculada García, José-Jesús Fernández:
  Phan3D: design of biological phantoms in 3D electron microscopy. 3286-3288
• 
  Michael L. Blinov, James R. Faeder, Byron Goldstein, William S. Hlavacek:
  BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. 3289-3291

Volume 20, Number 18, December 2004

Discovery Notes

• 
  Maria Carmela Accardo, Ennio Giordano, Sara Riccardo, Filomena Anna Digilio, Giovanni Iazzetti, Raffaele A. Calogero, Maria Furia:
  A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome. 3293-3301
• 
  André Catic, Cal T. Collins, George M. Church, Hidde L. Ploegh:
  Preferred in vivo ubiquitination sites. 3302-3307

Original Papers

• 
  Huaiqiu Zhu, Gang-Qing Hu, Zheng-Qing Ouyang, Jin Wang, Zhen-Su She:
  Accuracy improvement for identifying translation initiation sites in microbial genomes. 3308-3317
• 
  Joanna H. Shih, Aleksandra M. Michalowska, Kevin Dobbin, Yumei Ye, Ting Hu Qiu, Jeffrey E. Green:
  Effects of pooling mRNA in microarray class comparisons. 3318-3325
• 
  Marco Masseroli, Andrea Stella, Natalia Meani, Myriam Alcalay, Francesco Pinciroli:
  MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanks. 3326-3335
• 
  Yong Wang, Frederick C. C. Leung:
  DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria. 3336-3345
• 
  István Albert, Réka Albert:
  Conserved network motifs allow protein-protein interaction prediction. 3346-3352
• 
  Raji Balasubramanian, Thomas LaFramboise, Denise Scholtens, Robert Gentleman:
  A graph-theoretic approach to testing associations between disparate sources of functional genomics data. 3353-3362
• 
  Michael Roberts, Wayne B. Hayes, Brian R. Hunt, Stephen M. Mount, James A. Yorke:
  Reducing storage requirements for biological sequence comparison. 3363-3369
• 
  Daniel McDonald, Hsinchun Chen, Hua Su, Byron Marshall:
  Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser. 3370-3378
• 
  Mehmet Bilgen, Mehmet Karaca, A. Naci Onus, Ayse Gül Ince:
  A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences. 3379-3386
• 
  Vitaly A. Selivanov, Joaquim Puigjaner, Antonio Sillero, Josep J. Centelles, Antonio Ramos-Montoya, Paul W.-N. Lee, Marta Cascante:
  An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites. 3387-3397
• 
  Zheng Rong Yang, Andrew R. Dalby, Jing Qiu:
  Mining HIV protease cleavage data using genetic programming with a sum-product function. 3398-3405
• 
  Lexin Li, Hongzhe Li:
  Dimension reduction methods for microarrays with application to censored survival data. 3406-3412
• 
  Philippe Hupé, Nicolas Stransky, Jean-Paul Thiery, François Radvanyi, Emmanuel Barillot:
  Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. 3413-3422
• 
  Kyounghwa Bae, Bani K. Mallick:
  Gene selection using a two-level hierarchical Bayesian model. 3423-3430
• 
  Peter M. Haverty, Li-Li Hsiao, Steven R. Gullans, Ulla Hansen, Zhiping Weng:
  Limited agreement among three global gene expression methods highlights the requirement for non-global validation. 3431-3441
• 
  Elizabeth Shoop, Paulo Casaes, Getiria Onsongo, Lisa Lesnett, Erla Osk Petursdottir, Edward Kofi Yeboah Donkor, Dennis Tkach, Michael Cosimini:
  Data exploration tools for the Gene Ontology database. 3442-3454
• 
  Tuan D. Pham, Johannes Zuegg:
  A probabilistic measure for alignment-free sequence comparison. 3455-3461
• 
  Jeffrey A. Rosenfeld, Indra Neil Sarkar, Paul J. Planet, David H. Figurski, Robert DeSalle:
  ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms. 3462-3465
• 
  Joyce Phui Yee Siew, Asif M. Khan, Paul T. J. Tan, Judice L. Y. Koh, Seng Hong Seah, Chuay Yeng Koo, Siaw Ching Chai, Arunmozhiarasi Armugam, Vladimir Brusic, Kandiah Jeyaseelan:
  Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach. 3466-3480
• 
  Diane J. Rodi, Suneeta Mandava, Lee Makowski:
  DIVAA: analysis of amino acid diversity in multiple aligned protein sequences. 3481-3489
• 
  Kodangattil R. Sreekumar, You-Ping Huang, Mark H. Pausch, Kamalakar Gulukota:
  Predicting GPCR-G-protein coupling using hidden Markov models. 3490-3499
• 
  Soojin Lee, Min-Kyu Cho, Jin-Won Jung, Jai-Hoon Kim, Weontae Lee:
  Exploring protein fold space by secondary structure prediction using data distribution method on Grid platform. 3500-3507
• 
  Natasa Przulj, Derek G. Corneil, Igor Jurisica:
  Modeling interactome: scale-free or geometric?. 3508-3515
• 
  Robert Osada, Elena Zaslavsky, Mona Singh:
  Comparative analysis of methods for representing and searching for transcription factor binding sites. 3516-3525
• 
  Anton Yuryev, Jianping Huang, Kathryn E. Scott, Jennifer Kuebler, Miriam Donaldson, Michael S. Phillips, Mark Pohl, Michael T. Boyce-Jacino:
  Primer Design and Marker Clustering for Multiplex SNP-IT Primer Extension Genotyping Assay using Statistical Modeling. 3526-3532
• 
  Chad L. Myers, Maitreya J. Dunham, Sun-Yuan Kung, Olga G. Troyanskaya:
  Accurate detection of aneuploidies in array CGH and gene expression microarray data. 3533-3543
• 
  Roland Linder, Dawn Dew, Holger Sudhoff, Dirk Theegarten, Klaus Remberger, Siegfried J. Pöppl, Mathias Wagner II:
  The 'subsequent artificial neural network' (SANN) approach might bring more classificatory power to ANN-based DNA microarray analyses. 3544-3552
• 
  Markus Neuhäuser, Roswitha Senske:
  The Baumgartner-Wei?-Schindler test for the detection of differentially expressed genes in replicated microarray experiments. 3553-3564
• 
  Alberto de la Fuente, Nan Bing, Ina Hoeschele, Pedro Mendes:
  Discovery of meaningful associations in genomic data using partial correlation coefficients. 3565-3574
• 
  Markus Anderle II, Sushmita Roy, Hua Lin, Christopher Becker, Keith Joho:
  Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum. 3575-3582
• 
  Marcel Dettling:
  BagBoosting for tumor classification with gene expression data. 3583-3593
• 
  Jing Yu, V. Anne Smith, Paul P. Wang, Alexander J. Hartemink, Erich D. Jarvis:
  Advances to Bayesian network inference for generating causal networks from observational biological data. 3594-3603
• 
  Minlie Huang, Xiaoyan Zhu, Hao Yu, Donald G. Payan, Kunbin Qu, Ming Li:
  Discovering patterns to extract protein-protein interactions from full texts. 3604-3612
• 
  Kyoung-Jae Won, Adam Prügel-Bennett, Anders Krogh:
  Training HMM structure with genetic algorithm for biological sequence analysis. 3613-3619
• 
  Matthias Koenig, Niels Grabe:
  Highly specific prediction of phosphorylation sites in proteins. 3620-3627
• 
  Jim Samuelsson, Daniel Dalevi, Fredrik Levander, Thorsteinn S. Rögnvaldsson:
  Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting. 3628-3635

Applications Notes

• 
  Kees Jong, Elena Marchiori, Gerrit Meijer, Aad van der Vaart, Bauke Ylstra:
  Breakpoint identification and smoothing of array comparative genomic hybridization data. 3636-3637
• 
  O. J. Shaw, Colin Harwood, L. Jason Steggles, Anil Wipat:
  SARGE: a tool for creation of putative genetic networks. 3638-3640
• 
  Steffen Durinck, Joke Allemeersch, Vincent Carey, Yves Moreau, Bart De Moor:
  Importing MAGE-ML format microarray data into BioConductor. 3641-3642
• 
  Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman, Steven Salzberg:
  DAGchainer: a tool for mining segmental genome duplications and synteny. 3643-3646
• 
  Dirk Steinhauser, Björn Usadel, Alexander Lüdemann, Oliver Thimm, Joachim Kopka:
  CSB.DB: a comprehensive systems-biology database. 3647-3651
• 
  Paolo Di Giovine:
  PLPMDB: Pyridoxal-5'-phosphate dependent enzymes mutants database. 3652-3653
• 
  Kristoffer Forslund, Daniel H. Huson, Vincent Moulton:
  VisRD--visual recombination detection. 3654-3655
• 
  Juan M. Vaquerizas, Joaquín Dopazo, Ramón Díaz-Uriarte:
  DNMAD: web-based diagnosis and normalization for microarray data. 3656-3658
• 
  Simon M. Lin, Patrick McConnell, Kimberly F. Johnson, Jennifer Shoemaker:
  MedlineR: an open source library in R for Medline literature data mining. 3659-3661
• 
  Aaron Kaluszka, Cynthia Gibas:
  Interactive gene-order comparison for multiple small genomes. 3662-3664
• 
  Christophe Hitte, Thomas Derrien, Catherine André, Elaine A. Ostrander, Francis Galibert:
  CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome. 3665-3667
• 
  Shaolin Liu, Nicholas A. Tinker, Stephen J. Molnar, Diane E. Mather:
  EC_oligos: automated and whole-genome primer design for exons within one or between two genomes. 3668-3669
• 
  Giacomo Finocchiaro, Paola Parise, Simone P. Minardi, Myriam Alcalay, Heiko Müller:
  GenePicker: replicate analysis of Affymetrix gene expression microarrays. 3670-3672
• 
  Chris C. A. Spencer, Graham Coop:
  SelSim: a program to simulate population genetic data with natural selection and recombination. 3673-3675
• 
  Andreas Gisel, Maria Panetta, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Cecilia Saccone, Graziano Pesole:
  DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions. 3676-3679
• 
  Marc Vass, Nicholas A. Allen, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson:
  The JigCell Model Builder and Run Manager. 3680-3681
• 
  Peter F. Hallin, David Ussery:
  CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. 3682-3686
• 
  Nicholas Knowlton, Igor Dozmorov, Michael Centola:
  Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. 3687-3690
• 
  Chia-Chin Wu, Hsuan-Cheng Huang, Hsueh-Fen Juan, Shui-Tein Chen:
  GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. 3691-3693
• 
  Vincent Catherinot, Gilles Labesse:
  ViTO: tool for refinement of protein sequence-structure alignments. 3694-3696
• 
  Yuan Qi, Nick V. Grishin:
  PCOAT: positional correlation analysis using multiple methods. 3697-3699
• 
  Peter E. Midford:
  Ontologies for Behavior. 3700-3701
• 
  Tancred Frickey, Andrei N. Lupas:
  CLANS: a Java application for visualizing protein families based on pairwise similarity. 3702-3704
• 
  James M. Wettenhall, Gordon K. Smyth:
  limmaGUI: A graphical user interface for linear modeling of microarray data. 3705-3706
• 
  Jean-Luc Pons, Therese E. Malliavin, Dominique Tramesel, Marc-André Delsuc:
  NMRb: a web-site repository for raw NMR datasets. 3707-3709
• 
  Elizabeth I. Boyle, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein, J. Michael Cherry, Gavin Sherlock:
  GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. 3710-3715

Errata

• 
  Weijia Xu, Daniel P. Miranker:
  A metric model of amino acid substitution. 3716

Volume 20, Supplement August 2004

• 
  Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, Glasgow, UK, July 31-August 4, 2004. 2004 [contents]