Journal: Bioinformatics

Volume 16, Issue 9

749 -- 0Philip E. Bourne, Michael Gribskov. ISMB-2000: Bioinformatics enters a new millennium
750 -- 759Frédéric Plewniak, Julie Dawn Thompson, Olivier Poch. Ballast: Blast post-processing based on locally conserved segments
760 -- 766Pauline C. Ng, Jorja G. Henikoff, Steven Henikoff. PHAT: a transmembrane-specific substitution matrix
767 -- 775Junhyong Kim, Etsuko N. Moriyama, Coral G. Warr, Peter J. Clyne, John R. Carlson. Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties
776 -- 785Naomi Siew, Arne Elofsson, Leszek Rychlewski, Daniel Fischer. MaxSub: an automated measure for the assessment of protein structure prediction quality
786 -- 798Rui Alves, Michael A. Savageau. Extending the method of mathematically controlled comparison to include numerical comparisons
799 -- 807Alexander Zien, Gunnar Rätsch, Sebastian Mika, Bernhard Schölkopf, Thomas Lengauer, Klaus-Robert Müller. Engineering support vector machine kernels that recognize translation initiation sites
808 -- 814Knut Reinert, Jens Stoye, Torsten Will. An iterative method for faster sum-of-pairs multiple sequence alignment
815 -- 824Oliver Kohlbacher, Hans-Peter Lenhof. BALL-rapid software prototyping in computational molecular biology
825 -- 836Robert Küffner, Ralf Zimmer, Thomas Lengauer. Pathway analysis in metabolic databases via differential metabolic display (DMD)
837 -- 838M. M. Soloviev. Detection of a surface-exposed PEST like sequence in the metabotropic glutamate receptor mGluR1
839 -- 842T. V. Gnanasekaran, Suraj Peri, A. Arockiasamy, S. Krishnaswamy. Profiles from structure based sequence alignment of porins can identify ß stranded integral membrane proteins
843 -- 844Michael C. Giddings, Olga V. Matveeva, John F. Atkins, Raymond F. Gesteland. ODNBase-a web database for antisense oligonucleotide effectiveness studies
845 -- 846Martin Prokop, Jirí Damborský, Jaroslav Koca. TRITON: in silico construction of protein mutants and prediction of their activities
847 -- 849Bernhard Haubold, Richard R. Hudson. LIAN 3.0: detecting linkage disequilibrium in multilocus data

Volume 16, Issue 8

663 -- 664Akiyoshi Wada. Bioinformatics-the necessity of the quest for first principles in life
665 -- 677Robert Giegerich. A systematic approach to dynamic programming in bioinformatics
678 -- 684D. Curtis Jamison, James W. Thomas, Eric D. Green. ComboScreen facilitates the multiplex hybridization-based screening of high-density clone arrays
685 -- 698Elisabetta Manduchi, Gregory R. Grant, Steven E. McKenzie, G. Christian Overton, Saul Surrey, Christian J. Stoeckert Jr.. Generation of patterns from gene expression data by assigning confidence to differentially expressed genes
699 -- 706Torbjørn Rognes, Erling Seeberg. Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
707 -- 726Patrik D haeseleer, Shoudan Liang, Roland Somogyi. Genetic network inference: from co-expression clustering to reverse engineering
727 -- 734Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara. Inferring qualitative relations in genetic networks and metabolic pathways
735 -- 738C. A. M. Semple, S. W. Morris, David J. Porteous, Kathryn L. Evans. In silico identification of transcripts and SNPs from a region of 4p linked with bipolar affective disorder
739 -- 740Mukund V. Katti, Meena K. Sakharkar, Prabhakar K. Ranjekar, Vidya S. Gupta. TRES: comparative promoter sequence analysis
741 -- 742Kerstin M. L. Menne, Henning Hermjakob, Rolf Apweiler. A comparison of signal sequence prediction methods using a test set of signal peptides
743 -- 744Josep F. Abril, Roderic Guigó. gff2ps: visualizing genomic annotations
745 -- 746Kevin G. Becker, Shawnte L. White, Jerri Muller, James Engel. BBID: the biological biochemical image database
747 -- 748Alexey Lagunin, Alla Stepanchikova, Dmitrii Filimonov, Vladimir Poroikov. PASS: prediction of activity spectra for biologically active substances

Volume 16, Issue 7

571 -- 572Aleksandar Milosavljevic. The Economic Value of Bioinformation
573 -- 582Mark J. Gibbs, John S. Armstrong, Adrian J. Gibbs. Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
583 -- 605Elena Rivas, Sean R. Eddy. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs
606 -- 612Fabien Campagne. Clustalnet: the joining of Clustal and CORBA
613 -- 618S. J. Wheelan, Aron Marchler-Bauer, Stephen H. Bryant. Domain size distributions can predict domain boundaries
619 -- 627Chantal Korostensky, Gaston H. Gonnet. Using traveling salesman problem algorithms for evolutionary tree construction
628 -- 638Chenna Ramu, Christine Gemünd, Toby J. Gibson. Object-oriented parsing of biological databases with Python
639 -- 649David L. Steffen, Alan E. Levine, S. Yarus, R. A. Baasiri, D. A. Wheeler. Digital reviews in molecular biology: approaches to structured digital publication
650 -- 651Elliott H. Margulies, Jeffrey W. Innis. eSAGE: managing and analysing data generated with Serial Analysis of Gene Expression (SAGE)
652 -- 653Hugh-G. Patterton, Steven Graves. DNAssist: the integrated editing and analysis of molecular biology sequences in Windows
654 -- 655Gina Cannarozzi, Michael T. Hallett, J. Norberg, Xianghong Zhou. A cross-comparison of a large dataset of genes
656 -- 657Luis Sánchez-Pulido, Yan P. Yuan, Miguel A. Andrade, Peer Bork. NAIL-Network Analysis Interface for Linking HMMER results
658 -- 659Stephen A. Cammer. SChiSM: creating interactive web page annotations of molecular structure models using Chime
660 -- 661Jonathan Bingham, Sucha Sudarsanam. Visualizing large hierarchical clusters in hyperbolic space

Volume 16, Issue 6

491 -- 493Rainer Fuchs. Analyse This...Or: Intelligent Help for The Rest of Us
494 -- 500Ting Chen, Steven Skiena. A case study in genome-level fragment assembly
501 -- 512Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo. Phylogenetically enhanced statistical tools for RNA structure prediction
513 -- 519David F. Burke, Charlotte M. Deane, Tom L. Blundell. Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure
520 -- 526Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando, Hideo Matsuda, Yutaka Akiyama. Quick selection of representative protein chain sets based on customizable requirements
527 -- 533Rui Alves, Michael A. Savageau. Comparing systemic properties of ensembles of biological networks by graphical and statistical methods
534 -- 547Rui Alves, Michael A. Savageau. Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways
548 -- 557Norman W. Paton, Shakeel A. Khan, Andrew Hayes, Fouzia Moussouni, Andy Brass, Karen Eilbeck, Carole A. Goble, Simon J. Hubbard, Stephen G. Oliver. Conceptual modelling of genomic information
558 -- 559Denis Milan, Rachel Hawken, Cédric Cabau, Sophie Leroux, Carine Genet, Yvette Lahbib, Gwenola Tosser, Annie Robic, Francois Hatey, Lee Alexander, Craig Beattie, Larry Schook, Martine Yerle, Joël Gellin. IMpRH Server: an RH mapping server available on the Web
560 -- 561A. C. Frank, J. R. Lobry. Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes
562 -- 563Darren Martin, Ed Rybicki. RDP: detection of recombination amongst aligned sequences
564 -- 565Raphaël Clifford, Aaron J. Mackey. Disperse: a simple and efficient approach to parallel database searching
566 -- 567Liisa Holm, Jong Park. DaliLite workbench for protein structure comparison
568 -- 569Miquel de Càceres, Jordi Villà, Juan J. Lozano, Ferran Sanz. MIPSIM: similarity analysis of molecular interaction potentials

Volume 16, Issue 5

411 -- 0François Rechenmann. From data to knowledge
412 -- 424Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen. Assessing the accuracy of prediction algorithms for classification: an overview
425 -- 438Peter M. Hooper, Haiyan Zhang, David S. Wishart. Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment
439 -- 450Graziano Pesole, Sabino Liuni, Mark D Souza. PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
451 -- 457Anton J. Enright, Christos A. Ouzounis. GeneRAGE: a robust algorithm for sequence clustering and domain detection
458 -- 464Jong Park, Liisa Holm, Andreas Heger, Cyrus Chothia. RSDB: representative protein sequence databases have high information content
465 -- 477Gary D. Bader, Christopher W. V. Hogue. BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways
478 -- 481Chang Zhu, Kevin Karplus, Leslie Grate, Philip Coffino. A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiae
482 -- 483Gustavo Glusman, Doron Lancet. GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses
484 -- 485David Hiscock, Chris Upton. Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes
486 -- 487Joseph L. Thorley, Roderic D. M. Page. RadCon: phylogenetic tree comparison and consensus
488 -- 489Timothy L. Bailey, Michael Gribskov. Concerning the accuracy of MAST E-values

Volume 16, Issue 4

301 -- 312Abdelkrim Rachedi, Michael Rebhan, Hong Xue. GABAagent: a system for integrating data on GABA receptors
313 -- 325J. D. Parsons, Patricia Rodriguez-Tomé. JESAM: CORBA software components to create and publish EST alignments and clusters
326 -- 333Lars Juhl Jensen, Steen Knudsen. Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
334 -- 340Elena Rivas, Sean R. Eddy. The language of RNA: a formal grammar that includes pseudoknots
341 -- 357Andrea Califano. SPLASH: structural pattern localization analysis by sequential histograms
358 -- 366Alexander G. Bachinsky, Anatoly S. Frolov, Andrey N. Naumochkin, Lily Ph. Nizolenko, Andrey A. Yarigin. PROF_ PAT 1.3: Updated database of patterns used to detect local similarities
367 -- 371Pierre Baldi. On the convergence of a clustering algorithm for protein-coding regions in microbial genomes
376 -- 382Pietro Liò, Marina Vannucci. Wavelet change-point prediction of transmembrane proteins
383 -- 394Marty J. Wolf, Simon Easteal, Margaret Kahn, Brendan D. McKay, Lars S. Jermiin. TrExML: a maximum-likelihood approach for extensive tree-space exploration
395 -- 399Andrew Rambaut. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
400 -- 401Patrick P. Rose, Bette T. Korber. Detecting hypermutations in viral sequences with an emphasis on G A hypermutation
402 -- 403Matthew R. Pocock, Tim J. P. Hubbard. A browser for expression data
404 -- 405Liam J. McGuffin, Kevin Bryson, David T. Jones. The PSIPRED protein structure prediction server
406 -- 407R. Gilmour. Taxonomic markup language: applying XML to systematic data
408 -- 410Kenneth F. Manly. Mathematica packages for simulation of experimental genetics

Volume 16, Issue 3

187 -- 189Christos A. Ouzounis. Two or three myths about bioinformatics
190 -- 202Osamu Gotoh. Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps
203 -- 211Jonathan Usuka, Wei Zhu, Volker Brendel. Optimal spliced alignment of homologous cDNA to a genomic DNA template
212 -- 221Dorothy M. Lang. Net Nearest Neighbor Analysis (NNNA) summarizes non-compensated dinucleotides within gene sequences
222 -- 232Yuh-Jyh Hu, Suzanne B. Sandmeyer, Calvin McLaughlin, Dennis F. Kibler. Combinatorial motif analysis and hypothesis generation on a genomic scale
233 -- 244Thomas D. Wu, Craig G. Nevill-Manning, Douglas L. Brutlag. Fast probabilistic analysis of sequence function using scoring matrices
245 -- 250B. Jagla, Johannes Schuchhardt. Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites
251 -- 256András Fiser, István Simon. Predicting the oxidation state of cysteines by multiple sequence alignment
269 -- 285Dong Xu, Michael A. Unseren, Ying Xu, Edward C. Uberbacher. Sequence-structure specificity of a knowledge based energy function at the secondary structure level
269 -- 285Peter D. Karp. An ontology for biological function based on molecular interactions
286 -- 287Christophe Blanchet, Christophe Combet, Christophe Geourjon, Gilbert Deléage. MPSA: integrated system for multiple protein sequence analysis with client/server capabilities
288 -- 289Guochun Xie, Reynold DeMarco, Richard Blevins, Yuhong Wang. Storing biological sequence databases in relational form
290 -- 291Peter B. McGarvey, Hongzhan Huang, Winona C. Barker, Bruce C. Orcutt, John S. Garavelli, Geetha Y. Srinivasarao, Lai-Su L. Yeh, Chunlin Xiao, Cathy H. Wu. PIR: a new resource for bioinformatics
292 -- 293Angelo M. Facchiano. HELM: searching for helix motifs within protein sequences
294 -- 295Tim Massingham, Nick Goldman. EDIBLE: experimental design and information calculations in phylogenetics
296 -- 297Marc Robinson-Rechavi, Dorothée Huchon. RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree

Volume 16, Issue 2

77 -- 78Andy Brass. Bioinformatics Education-A UK perspective
79 -- 95Marcella A. McClure. The complexities of genome analysis, the Retroid agent perspective
96 -- 100Sorinel Adrian Oprisan, Aurel Ardelean, Petre T. Frangopol. Self-organization and competition in the immune response to cancer invasion: a phase-orientated computational model of oncogenesis
101 -- 103Gaston H. Gonnet, Michael T. Hallett, Chantal Korostensky, Laurent Bernardin. Darwin v. 2.0: an interpreted computer language for the biosciences
104 -- 110Jong Park, Liisa Holm, Cyrus Chothia. Sequence search algorithm assessment and testing toolkit (SAT)
111 -- 116James A. Cuff, Ewan Birney, Michele E. Clamp, Geoffrey J. Barton. ProtEST: protein multiple sequence alignments from expressed sequence tags
117 -- 124Sarah A. Teichmann, Cyrus Chothia, George M. Church, Jong Park. Fast assignment of protein structures to sequences using the Intermediate Sequence Library PDB-ISL
125 -- 129Robert M. MacCallum, Lawrence A. Kelley, Michael J. E. Sternberg. SAWTED: Structure Assignment With Text Description-Enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons
130 -- 134Gráinne McGuire, Frank Wright. TOPAL 2.0: improved detection of mosaic sequences within multiple alignments
140 -- 151Paul Walton Purdom Jr., Phillip G. Bradford, Koichiro Tamura, Sudhir Kumar. Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees
152 -- 158Deyou Cai, Arthur L. Delcher, Ben Kao, Simon Kasif. Modeling splice sites with Bayes networks
159 -- 168John D. Westbrook, Philip E. Bourne. STAR/mmCIF: An ontology for macromolecular structure
169 -- 175Mikio Yoshida, Ken-ichiro Fukuda, Toshihisa Takagi. PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary
176 -- 177John Bouck, Michael P. McLeod, Kim Worley, Richard A. Gibbs. The Human Transcript Database: a catalogue of full length cDNA inserts
178 -- 179Thomas Junier, Marco Pagni. Dotlet: diagonal plots in a Web browser
180 -- 181Naoki Sato. SISEQ: manipulation of multiple sequence and large database files for common platforms
182 -- 183Gonçalo R. Abecasis, W. O. C. Cookson. GOLD-Graphical Overview of Linkage Disequilibrium
184 -- 186Robert Stevens, Patricia G. Baker, Sean Bechhofer, Gary Ng, Alex Jacoby, Norman W. Paton, Carole A. Goble, Andy Brass. TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources

Volume 16, Issue 12

1059 -- 1061C. Victor Jongeneel. The need for a human gene index
1062 -- 1072Wooyoung Choe, Okan K. Ersoy, Minou Bina. Neural network schemes for detecting rare events in human genomic DNA
1073 -- 1081Dimitris Anastassiou. Frequency-domain analysis of biomolecular sequences
1082 -- 1090Raymond Wheeler, Richard Hughey. Optimizing reduced-space sequence analysis
1091 -- 1104Ying Xu, Dong Xu, Harold N. Gabow. Protein domain decomposition using a graph-theoretic approach
1105 -- 1110Weizhong Li, Frederic Pio, Krzysztof Pawlowski, Adam Godzik. Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology
1111 -- 1119Kenji Mizuguchi, Tom L. Blundell. Analysis of conservation and substitutions of secondary structure elements within protein superfamilies
1120 -- 1128Andrey Rzhetsky, Tomohiro Koike, Sergey Kalachikov, Shawn M. Gomez, Michael Krauthammer, Sabina H. Kaplan, Pauline Kra, James J. Russo, Carol Friedman. A knowledge model for analysis and simulation of regulatory networks
1129 -- 1144Toni Kazic. Semiotes: a semantics for sharing
1145 -- 1150Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov. InterPro-an integrated documentation resource for protein families, domains and functional sites
1151 -- 1152Meena K. Sakharkar, Pandjassarame Kangueane, Tong W. Woon, Tin Wee Tan, Prasanna R. Kolatkar, Manyuan Long, Sandro J. de Souza. IE-Kb: intron exon knowledge base
1153 -- 1154Xavier Serra-Hartmann, Xavier Rebordosa, Jaume Piñol, Enrique Querol, Marc A. Martí-Renom. ASAP: analysis of peptide composition
1155 -- 1156János Murvai, Kristian Vlahovicek, Sándor Pongor. A simple probabilistic scoring method for protein domain identification
1157 -- 1158Kevin A. T. Silverstein, Alan Kilian, John L. Freeman, James E. Johnson, Ihab A. Awad, Ernest F. Retzel. PANAL: an integrated resource for Protein sequence ANALysis
1159 -- 1160Steffen Möller, Evgenia V. Kriventseva, Rolf Apweiler. A collection of well characterised integral membrane proteins

Volume 16, Issue 11

953 -- 959Michael Z. Man, Xuning Wang, Yixin Wang. POWER_SAGE: comparing statistical tests for SAGE experiments
960 -- 967Tetsuo Nishikawa, Toshio Ota, Takao Isogai. Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences
968 -- 977Ana Tereza R. Vasconcelos, Marco A. Grivet Mattoso Maia, Darcy F. de Almeida. Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidis
978 -- 987Jong Park, Sabine Dietmann, Andreas Heger, Liisa Holm. Estimating the significance of sequence order in protein secondary structure and prediction
988 -- 1002Anders Wallqvist, Yoshifumi Fukunishi, Lynne Reed Murphy, Addi Fadel, Ronald M. Levy. Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases
1003 -- 1009Derek A. Ruths, Edward S. Chen, Leland Ellis. Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions
1010 -- 1013Simon P. Blomberg. Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertainty
1014 -- 1022Tim Beißbarth, Kurt Fellenberg, Benedikt Brors, R. Arribas-Prat, J. M. Boer, Nicole C. Hauser, Marcel Scheideler, Jörg D. Hoheisel, G. Schütz, Annemarie Poustka, Martin Vingron. Processing and quality control of DNA array hybridization data
1023 -- 1037Eberhard O. Voit, Tomas Radivoyevitch. Biochemical systems analysis of genome-wide expression data
1038 -- 1039Christopher M. L. S. Bouton, Jonathan Pevsner. DRAGON: Database Referencing of Array Genes Online
1040 -- 1041Joseph A. Bedell, Ian Korf, Warren Gish. MaskerAid : a performance enhancement to RepeatMasker
1042 -- 1043Roderic D. M. Page. Circles: automating the comparative analysis of RNA secondary structure
1044 -- 1045Kristian Vlahovicek, Sándor Pongor. model.it : building three dimensional DNA models from sequence data
1046 -- 1047Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak. VISTA : visualizing global DNA sequence alignments of arbitrary length
1048 -- 1049Paul Kersey, Henning Hermjakob, Rolf Apweiler. VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL
1052 -- 1053Ian Korf, Warren Gish. MPBLAST : improved BLAST performance with multiplexed queries
1054 -- 1055Matthew Boone, Chris Upton. BLAST Search Updater: a notification system for new database matches
1056 -- 1058Jeong-Hyeon Choi, Ho-Youl Jung, Hye Sun Kim, Hwan-Gue Cho. PhyloDraw: a phylogenetic tree drawing system

Volume 16, Issue 10

849 -- 850Timothy G. Littlejohn. Bioinformatics in Australia
851 -- 864Kirill Degtyarenko. Bioinorganic motifs: towards functional classification of metalloproteins
865 -- 889Pierre Baldi, Pierre-François Baisnée. Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths
890 -- 898Ralf Herwig, Armin O. Schmitt, Matthias Steinfath, John O Brien, Henrik Seidel, Sebastian Meier-Ewert, Hans Lehrach, Uwe Radelof. Information theoretical probe selection for hybridisation experiments
899 -- 905Antoine H. C. van Kampen, B. D. C. van Schaik, E. Pauws, E. M. C. Michiels, J. M. Ruijter, H. N. Caron, R. Versteeg, S. H. Heisterkamp, Jack A. M. Leunissen, F. Baas, M. van der Mee. USAGE: a web-based approach towards the analysis of SAGE data
906 -- 914Terrence S. Furey, Nello Cristianini, Nigel Duffy, David W. Bednarski, Michèl Schummer, David Haussler. Support vector machine classification and validation of cancer tissue samples using microarray expression data
915 -- 922Vassilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy, Stavros J. Hamodrakas, Chris Sander, Christos A. Ouzounis. CAST: an iterative algorithm for the complexity analysis of sequence tracts
923 -- 931Federico M. Stefanini, A. Camussi. The reduction of large molecular profiles to informative components using a Genetic Algorithm
932 -- 940Pietro Liò, Marina Vannucci. Finding pathogenicity islands and gene transfer events in genome data
941 -- 943George Johnson, Tai Te Wu. Matching amino acid and nucleotide sequences of mouse rheumatoid factor CDRH3-FRH4 segments to other mouse antibodies with known specificities
944 -- 945Kim Rutherford, Julian Parkhill, James Crook, Terry Horsnell, Peter Rice, Marie-Adèle Rajandream, Bart Barrell. Artemis: sequence visualization and annotation
946 -- 947Birong Liao, Walker Hale, Charles B. Epstein, Ronald A. Butow, Harold R. Garner. MAD: a suite of tools for microarray data management and processing
948 -- 949Burkhard Morgenstern. A space-efficient algorithm for aligning large genomic sequences
950 -- 951H. Zhu, Catherine H. Schein, Werner Braun. MASIA: recognition of common patterns and properties in multiple aligned protein sequences

Volume 16, Issue 1

2 -- 4Richard J. Roberts. The early days of bioinformatics publishing
5 -- 9Edward N. Trifonov. Earliest pages of bioinformatics
10 -- 15T. Charles Hodgman. A historical perspective on gene/protein functional assignment
16 -- 23Gary D. Stormo. DNA binding sites: representation and discovery
24 -- 33Russell F. Doolittle. On the trail of protein sequences
34 -- 40Keith F. Tipton, Sinéad Boyce. History of the enzyme nomenclature system
41 -- 47David Sankoff. The early introduction of dynamic programming into computational biology
48 -- 64Amos Bairoch. Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!
65 -- 75Antoine Danchin. A brief history of genome research and bioinformatics in France