Bioinformatics, Volume 19

Volume 19, Number 1, January 2003

Editorial

• 
  Chris Sander:
  Growth in Bioinformatics. 1

Reviews

• 
  Pietro Liò:
  Wavelets in bioinformatics and computational biology: state of art and perspectives. 2-9

Discovery Notes

• 
  K. V. Krishna Mohan, C. D. Atreya:
  Novel organelle-targeting signals in viral proteins. 10-13

Original Papers

• 
  Ji-Hong Zhang, Ling-Yun Wu, Xiang-Sun Zhang:
  Reconstruction of DNA sequencing by hybridization. 14-21
• 
  Hasan H. Otu, Khalid Sayood:
  A divide-and-conquer approach to fragment assembly. 22-29
• 
  João Aires-de-Sousa, Luisa Aires-de-Sousa:
  Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps. 30-36
• 
  C. H. Ooi, Patrick Tan:
  Genetic algorithms applied to multi-class prediction for the analysis of gene expression data. 37-44
• 
  J. M. Deutsch:
  Evolutionary algorithms for finding optimal gene sets in microarray prediction. 45-52
• 
  Lorenz Wernisch, Sharon L. Kendall, Shamit Soneji, Andreas Wietzorrek, Tanya Parish, Jason Hinds, Philip D. Butcher, Neil G. Stoker:
  Analysis of whole-genome microarray replicates using mixed models. 53-61
• 
  Rahul Bijlani, Yinhe Cheng, David A. Pearce, Andrew I. Brooks, Mitsunori Ogihara:
  Prediction of biologically significant components from microarray data: Independently Consistent Expression Discriminator (ICED). 62-70
• 
  Jinyan Li, Huiqing Liu, James R. Downing, Allen Eng-Juh Yeoh, Limsoon Wong:
  Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. 71-78
• 
  Chad Creighton, Samir Hanash:
  Mining gene expression databases for association rules. 79-86
• 
  Richard A. McIndoe, Aaron Lanzen, Kimberly Hurtz:
  MADGE: scalable distributed data management software for cDNA microarrays. 87-89
• 
  Kyeong Eun Lee, Naijun Sha, Edward R. Dougherty, Marina Vannucci, Bani K. Mallick:
  Gene selection: a Bayesian variable selection approach. 90-97
• 
  Sorin Draghici, R. Brian Potter:
  Predicting HIV drug resistance with neural networks. 98-107
• 
  Olivier Perriquet, Hélène Touzet, Max Dauchet:
  Finding the common structure shared by two homologous RNAs. 108-116
• 
  Jacek Leluk, Leszek Konieczny, Irena Roterman:
  Search for structural similarity in proteins. 117-124
• 
  Joel R. Bock, David A. Gough:
  Whole-proteome interaction mining. 125-134
• 
  Robert J. Gaizauskas, George Demetriou, Peter J. Artymiuk, Peter Willett:
  Protein Structures and Information Extraction from Biological Texts: The PASTA System. 135-143
• 
  C. Carleos, F. Rodriguez, H. Lamelas, J. A. Baro:
  Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations. 144-148

Applications Notes

• 
  Shaun Purcell, Stacey S. Cherny, Pak Chung Sham:
  Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. 149-150
• 
  Yaw-Ling Lin, Xiaoqiu Huang, Tao Jiang, Kun-Mao Chao:
  MAVG: locating non-overlapping maximum average segments in a given sequence. 151-152
• 
  T. De Oliveira, R. Miller, M. Tarin, S. Cassol:
  An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences. 153-154
• 
  Jianhua Zhang, Vincent J. Carey, Robert Gentleman:
  An extensible application for assembling annotation for genomic data. 155-156
• 
  Ramswamy Anbazhagan:
  Microarray data assembler. 157-158
• 
  Vivek Gopalan, Tin Wee Tan, Shoba Ranganathan:
  XdomView: protein domain and exon position visualization. 159-160
• 
  Patrick Aloy, Robert B. Russell:
  InterPreTS: protein Interaction Prediction through Tertiary Structure. 161-162
• 
  Fabian Glaser, Tal Pupko, Inbal Paz, Rachel E. Bell, Dalit Bechor-Shental, Eric Martz, Nir Ben-Tal:
  ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information. 163-164
• 
  Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Linda McMahan, Andrej Sali:
  ModView, visualization of multiple protein sequences and structures. 165-166
• 
  Tejasvini Prasad, M. N. Prathima, Nagasuma Chandra:
  Detection of hydrogen-bond signature patterns in protein families. 167-168

Volume 19, Number 2, February 2003

Discovery Notes

• 
  Akhilesh Pandey, Suraj Peri, Colin Thacker, Chery A. Whipple, John J. Collins, Matthias Mann:
  Computational, experimental analysis reveals a novel Src family kinase in the C. elegans genome. 169-172

Original Papers

• 
  Dörte Solle, David Geissler, Eckbert Stärk, Thomas Scheper, Bernd Hitzmann:
  Chemometric Modelling based on 2D-Fluorescence Spectra without a Calibration Measurement. 173-177
• 
  Felix Naef, Nicholas D. Socci, Marcelo Magnasco:
  A study of accuracy, precision in oligonucleotide arrays: extracting more signal at large concentrations. 178-184
• 
  Benjamin M. Bolstad, Rafael A. Irizarry, Magnus Åstrand, Terence P. Speed:
  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. 185-193
• 
  Chris A. Glasbey, Peter Ghazal:
  Combinatorial image analysis of DNA microarray features. 194-203
• 
  Igor Dozmorov, Michael Centola:
  An associative analysis of gene expression array data. 204-211
• 
  Neil D. Clarke, Joshua A. Granek:
  Rank order metrics for quantifying the association of sequence features with gene regulation. 212-218
• 
  Jakob Skou Pedersen, Jotun Hein:
  Gene finding with a hidden Markov model of genome structure and evolution. 219-227
• 
  Xiaoqiu Huang, Kun-Mao Chao:
  A generalized global alignment algorithm. 228-233
• 
  Jack Cao, Rosemarie Panetta, Shiyi Yue, Alain Steyaert, Michele Young-Bellido, Sultan Ahmad:
  A naive Bayes model to predict coupling between seven transmembrane domain receptors, and G-proteins. 234-240
• 
  Iwei Yeh, Peter D. Karp, Natalya Fridman Noy, Russ B. Altman:
  Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). 241-248
• 
  Gregory P. Harhay, John W. Keele:
  Positional candidate gene selection from livestock EST databases using Gene Ontology. 249-255
• 
  Myung-Hoon Chung, Chul Koo Kim, Kyun Nahm:
  Fractional populations in multiple gene inheritance. 256-260
• 
  Steffen Klamt, Jörg Stelling, Martin Ginkel, Ernst Dieter Gilles:
  FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. 261-269
• 
  Hongwu Ma, An-Ping Zeng:
  Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. 270-277
• 
  Peter Ernst, Karl-Heinz Glatting, Sándor Suhai:
  A task framework for the web interface W2H. 278-282

Applications Notes

• 
  Felix Kokocinski, Gunnar Wrobel, Meinhard Hahn, Peter Lichter:
  QuickLIMS: facilitating the data management for DNA-microarray fabrication. 283-284
• 
  Ming-Hua Hsieh, Wei-Che Hsu, Sung-Kay Chiu, Chi-Meng Tzeng:
  An efficient algorithm for minimal primer set selection. 285-286
• 
  Xiayi Ke, Lon R. Cardon:
  Efficient selective screening of haplotype tag SNPs. 287-288
• 
  David Posada, Carsten Wiuf:
  Simulating haplotype blocks in the human genome. 289-290
• 
  Jeremy M. R. Martin, Lan J. Mackay, Christopher J. Rawlings:
  Pedstrip: extracting a maximal subset of available, unrelated individuals from a pedigree. 291-292
• 
  Yihua Zhou, Jingdong Liu:
  AVA: visual analysis of gene expression microarray data. 293-294
• 
  Paul Pavlidis, William Stafford Noble:
  Matrix2png: a utility for visualizing matrix data. 295-296
• 
  Lusheng Wang, Ying Xu:
  SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignments. 297-298
• 
  Peter De Rijk, Jan Wuyts, Rupert De Wachter:
  RnaViz 2: an improved representation of RNA secondary structure. 299-300
• 
  Michael J. Sanderson:
  r8s: inferring absolute rates of molecular evolution, divergence times in the absence of a molecular clock. 301-302
• 
  Jack A. M. Leunissen:
  Chimera: construction of chimeric sequences for phylogenetic analysis. 303-304
• 
  Kazuharu Arakawa, Koya Mori, Katsuhiko Ikeda, Tatekimi Matsuzaki, Yusuke Kobayashi, Masaru Tomita:
  G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. 305-306
• 
  Zemin Zhang, William I. Wood:
  A profile hidden Markov model for signal peptides generated by HMMER. 307-308
• 
  Kunde Ramamoorthy Govindarajan, Pandjassarame Kangueane, Tin Wee Tan, Shoba Ranganathan:
  MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. 309-310
• 
  Charles S. Bond:
  TopDraw: a sketchpad for protein structure topology cartoons. 311-321
• 
  Alessandro Pintar, Oliviero Carugo, Sándor Pongor:
  DPX: for the analysis of the protein core. 313-314
• 
  Jens P. Linge, Michael Habeck, Wolfgang Rieping, Michael Nilges:
  ARIA: automated NOE assignment and NMR structure calculation. 315-316
• 
  Byong-Hyon Ju, Byungkyu Park, Jong H. Park, Kyungsook Han:
  Visualization and analysis of protein interactions. 317-318

Volume 19, Number 3, February 2003

Jobim Papers

• 
  Arnaud Lefebvre, Thierry Lecroq, Hélène Dauchel, Joël Alexandre:
  FORRepeats: detects repeats on entire chromosomes and between genomes. 319-326
• 
  Michaël Bekaert, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen, Jean-Paul Forest, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset, Michel Termier:
  Towards a computational model for -1 eukaryotic frameshifting sites. 327-335
• 
  Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page:
  Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. 336-344
• 
  Alexandre G. de Brevern, Serge A. Hazout:
  'Hybrid Protein Model' for optimally defining 3D protein structure fragments. 345-353

Original Papers:

• 
  Shu-Yun Le, Jih-Hsiang Chen, Danielle Konings, Jacob V. Maizel:
  Discovering well-ordered folding patterns in nucleotide sequences. 354-361
• 
  Eugene M. McCarthy, John F. McDonald:
  LTR_STRUC: a novel search and identification program for LTR retrotransposons. 362-367
• 
  Anat Reiner, Daniel Yekutieli, Yoav Benjamini:
  Identifying differentially expressed genes using false discovery rate controlling procedures. 368-375
• 
  Lance W. Hahn, Marylyn D. Ritchie, Jason H. Moore:
  Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. 376-382
• 
  Blaz Zupan, Janez Demsar, Ivan Bratko, Peter Juvan, John A. Halter, Adam Kuspa, Gad Shaulsky:
  GenePath: a system for automated construction of genetic networks from mutant data. 383-389
• 
  John Parkinson, Mark L. Blaxter:
  SimiTri-visualizing similarity relationships for groups of sequences. 390-395
• 
  Soumya Raychaudhuri, Russ B. Altman:
  A literature-based method for assessing the functional coherence of a gene group. 396-401
• 
  William H. Majoros, G. M. Subramanian, Mark Yandell:
  Identification of key concepts in biomedical literature using a modified Markov heuristic. 402-407
• 
  Sudhir Sivakumaran, Sridhar Hariharaputran, Jyoti Mishra, Upinder S. Bhalla:
  The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. 408-415

Applications Notes

• 
  Zhiwei Fang, Mary L. Polacco, Su-Shing Chen, Steven G. Schroeder, D. Hancock, Hector Sanchez-Villeda, Edward H. Coe:
  cMap: the comparative genetic map viewer. 416-417
• 
  William W. L. Hsiao, Ivan Wan, Steven J. Jones, Fiona S. L. Brinkman:
  IslandPath: aiding detection of genomic islands in prokaryotes. 418-420
• 
  Gary Barker, Jacqueline Batley, Helen O'Sullivan, Keith J. Edwards, David Edwards:
  Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. 421-422
• 
  Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai:
  MELINA: motif extraction from promoter regions of potentially co-regulated genes. 423-424
• 
  Burkhard Morgenstern, Sachin Goel, Alexander Sczyrba, Andreas W. M. Dress:
  AltAVisT: Comparing alternative multiple sequence alignments. 425-426
• 
  Jimin Pei, Ruslan Sadreyev, Nick V. Grishin:
  PCMA: fast and accurate multiple sequence alignment based on profile consistency. 427-428
• 
  Nickolai Alexandrov, Ilya N. Shindyalov:
  PDP: protein domain parser. 429-430
• 
  E. Minch, M. de Rinaldis, S. Weiss:
  pathSCOUTTM: exploration and analysis of biochemical pathways. 431-432
• 
  Tetsuro Toyoda, Akihiko Konagaya:
  KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. 433-434
• 
  Lingchong You, Apirak Hoonlor, John Yin:
  Modeling biological systems using Dynetica-a simulator of dynamic networks. 435-436
• 
  Tetsuro Toyoda, Yoshiki Mochizuki, Akihiko Konagaya:
  GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs. 437-438
• 
  Björn M. Ursing:
  WiGID: wireless genome information database. 439-440
• 
  Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, Daniel R. Caffrey:
  Wrapping up BLAST and other applications for use on Unix clusters. 441-442

Volume 19, Number 4, March 2003

Original Papers

• 
  Michael D. Stern, Sergey V. Anisimov, Kenneth R. Boheler:
  Can transcriptome size be estimated from SAGE catalogs? 443-448
• 
  Jyotsna Kasturi, Raj Acharya, Murali Ramanathan:
  An information theoretic approach for analyzing temporal patterns of gene expression. 449-458
• 
  Susmita Datta, Somnath Datta:
  Comparisons and validation of statistical clustering techniques for microarray gene expression data. 459-466
• 
  Daniel Johansson, Petter Lindgren, Anders Berglund:
  A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription. 467-473
• 
  Yihui Luan, Hongzhe Li:
  Clustering of time-course gene expression data using a mixed-effects model with B-splines. 474-482
• 
  Lee Makowski, Alexei Soares:
  Estimating the diversity of peptide populations from limited sequence data. 483-489
• 
  Dirk Metzler:
  Statistical alignment based on fragment insertion and deletion models. 490-499
• 
  Piero Fariselli, Michele Finelli, Davide Marchignoli, Pier Luigi Martelli, Ivan Rossi, Rita Casadio:
  MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. 500-505
• 
  Mounir Errami, Christophe Geourjon, Gilbert Deléage:
  Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures. 506-512
• 
  Susana Vinga, Jonas S. Almeida:
  Alignment-free sequence comparison-a review. 513-523
• 
  Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, D. Bray, A. Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, J. H. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul M. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang:
  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. 524-531
• 
  Petter Holme, Mikael Huss, Hawoong Jeong:
  Subnetwork hierarchies of biochemical pathways. 532-538

Applications Notes

• 
  Stephen Wooding:
  PopHist: inferring population history from the spectrum of allele frequencies. 539-540
• 
  Steven P. Bennett, Craig G. Nevill-Manning, Douglas L. Brutlag:
  3MOTIF: visualizing conserved protein sequence motifs in the protein structure database. 541-542
• 
  Endre Barta, László Kaján, Sándor Pongor:
  IS: a web-site for intron statistics. 543
• 
  Jason M. Johnson, Keith Mason, Ciamac Cyrus Moallemi, Hualin Xi, Shyamal Somaroo, Enoch S. Huang:
  Protein family annotation in a multiple alignment viewer. 544-545
• 
  Rodrigo Lopez, Stephen Robinson, Asif Kibria, Nicola Harte, Gulam Patel, Rob Harper, Emmanuel Quevillon, Ville Silventoinen, Kimmo Kallio, Petteri Jokinen:
  The European Bioinformatics Institute web site: a new view. 546-547

Volume 19, Number 5, March 2003

Discovery Notes

• 
  Subbaya Subramanian, Vamsi M. Madgula, Ranjan George, Rakesh K. Mishra, Madhusudhan W. Pandit, Chanderashekar S. Kumar, Lalji Singh:
  Triplet repeats in human genome: distribution and their association with genes and other genomic regions. 549-552

Original Papers

• 
  Jesús Angulo, Jean Serra:
  Automatic analysis of DNA microarray images using mathematical morphology. 553-562
• 
  Anestis Antoniadis, Sophie Lambert-Lacroix, Frédérique Leblanc:
  Effective dimension reduction methods for tumor classification using gene expression data. 563-570
• 
  Silvio Bicciato, A. Luchini, Carlo Di Bello:
  PCA disjoint models for multiclass cancer analysis using gene expression data. 571-578
• 
  Gernot G. Presting:
  Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome. 579-586
• 
  Angela Torres, Juan J. Nieto:
  The fuzzy polynucleotide space: basic properties. 587-592
• 
  Chun-Ting Zhang, Ren Zhang, Hong-Yu Ou:
  The Z curve database: a graphic representation of genome sequences. 593-599
• 
  David Stephen Horner, Graziano Pesole:
  The estimation of relative site variability among aligned homologous protein sequences. 600-606
• 
  Konstantinos Blekas, Dimitrios I. Fotiadis, Aristidis Likas:
  Greedy mixture learning for multiple motif discovery in biological sequences. 607-617
• 
  Stéphane Aris-Brosou:
  How Bayes tests of molecular phylogenies compare with frequentist approaches. 618-624
• 
  Andrew I. Jewett, Conrad C. Huang, Thomas E. Ferrin:
  MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. 625-634
• 
  Lars Juhl Jensen, Ramneek Gupta, Hans Henrik Stærfeldt, Søren Brunak:
  Prediction of human protein function according to Gene Ontology categories. 635-642
• 
  Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Katsutoshi Takahashi, Masaru Tomita:
  Dynamic modeling of genetic networks using genetic algorithm and S-system. 643-650

Applications Notes

• 
  Geo Pertea, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush:
  TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. 651-652
• 
  Jianxin Wang, Ping Liang:
  DigiNorthern, digital expression analysis of query genes based on ESTs. 653-654
• 
  Javier Herrero, Ramón Díaz-Uriarte, Joaquín Dopazo:
  Gene expression data preprocessing. 655-656
•