Journal: Bioinformatics

Volume 14, Issue 9

755 -- 763Sean R. Eddy. Profile hidden Markov models
764 -- 771Eileen Kraemer, Thomas E. Ferrin. Molecules to maps: tools for visualization and interaction in support of computational biology
772 -- 782Rachel Karchin, Richard Hughey. Weighting hidden Markov models for maximum discrimination
783 -- 788X. Guan, L. Du. Domain identification by clustering sequence alignments
789 -- 802Katsuhisa Horimoto, M. Suyama, Hiroyuki Toh, Kentaro Mori, Jinya Otsuka. A method for comparing circular genomes from gene locations: application to mitochondrial genomes
803 -- 806L. B. Ellis, S. M. Speedie, R. McLeish. Representing metabolic pathway information: an object-oriented approach
807 -- 814Stuart Pook, Guy Vaysseix, Emmanuel Barillot. Zomit: biological data visualization and browsing
815 -- 816Giovanni Iazzetti, G. Santini, M. Rau, E. Bucci, Raffaele Calogero. VIRTLAB: a virtual molecular biology laboratory
817 -- 818David Posada, Keith A. Crandall. MODELTEST: testing the model of DNA substitution
819 -- 820Roderic D. M. Page. GeneTree: comparing gene and species phylogenies using reconciled trees
821 -- 822M. R. Southern, A. P. Lewis. JavaShade: multiple sequence alignment box-and-shading on the World Wide Web
823 -- 824Matthew R. Pocock, Tim J. P. Hubbard, Ewan Birney. SPEM: a parser for EMBL style flat file database entries
825 -- 826W. Newell, P. Sanseau, J. Riley, A. Lyall. WEBMAP: radiation hybrid mapping on the WWW
827 -- 828Matthias Wjst, Thomas Immervoll. An Internet linkage and mutation database for the complex phenotype asthma

Volume 14, Issue 8

656 -- 664Michael Rebhan, Vered Chalifa-Caspi, J. Prilusky, Doron Lancet. GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support
665 -- 675K. Murakami, T. Takagi. Gene recognition by combination of several gene-finding programs
676 -- 684Salvatore Rampone. Recognition of splice junctions on DNA sequences by BRAIN learning algorithm
685 -- 690M. Yan, Z. S. Lin, C. T. Zhang. A new fourier transform approach for protein coding measure based on the format of the Z curve
691 -- 699Jack E. Tabaska, Robert B. Cary, Harold N. Gabow, Gary D. Stormo. An RNA folding method capable of identifying pseudoknots and base triples
700 -- 706Li Wuju, W. JiaJin. Prediction of RNA secondary structure based on helical regions distribution
707 -- 714Mark Gerstein. Measurement of the effectiveness of transitive sequence comparison, through a third intermediate sequence
715 -- 725Pierre Vincens, L. Buffat, Cécile André, Jean-Paul Chevrolat, Jean-François Boisvieux, Serge A. Hazout. A strategy for finding regions of similarity in complete genome sequences
726 -- 733Pietro Liò, N. Goldman, Jeffrey L. Thorne, David T. Jones. PASSML: combining evolutionary inference and protein secondary structure prediction
734 -- 738Kim Jungfer, Patricia Rodriguez-Tomé. Mapplet: a CORBA-based genome map viewer
739 -- 748J. Boyle. A visual environment for the manipulation and integration of JAVA beans
749 -- 750C. M. Pasquier, Vassilis J. Promponas, N. J. Varvayannis, Stavros J. Hamodrakas. A web server to locate periodicities in a sequence
751 -- 752T. R. Burglin. PPCMatrix: a PowerPC dotmatrix program to compare large genomic sequences against protein sequences

Volume 14, Issue 7

549 -- 550Russ B. Altman. A curriculum for bioinformatics: the time is ripe
551 -- 561Dmitrij Frishman, Klaus Heumann, A. Lesk, Hans-Werner Mewes. Comprehensive, comprehensible, distributed and intelligent databases: current status
562 -- 574Nathan Goodman, Steve Rozen, Lincoln Stein, A. G. Smith. The LabBase system for data management in large scale biology research laboratories
575 -- 582John Macauley, Huajun Wang, Nathan Goodman. A model system for studying the integration of molecular biology databases
583 -- 590Ulf Leser, Hans Lehrach, Hugues Roest Crollius. Issues in developing integrated genomic databases and application to the human X chromosome
591 -- 599Susumu Goto, Takaaki Nishioka, Minoru Kanehisa. LIGAND: chemical database for enzyme reactions
600 -- 607Miguel A. Andrade, Alfonso Valencia. Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families
617 -- 623Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington. JOY: protein sequence-structure representation and analysis
624 -- 631Therese E. Malliavin, Jean-Luc Pons, Marc-André Delsuc. An NMR assignment module implemented in the Gifa NMR processing program
632 -- 653Dean W. Podlich, Mark Cooper. QU-GENE: a simulation platform for quantitative analysis of genetic models

Volume 14, Issue 6

472 -- 478Toshitsugu Okayama, Takuro Tamura, Takashi Gojobori, Yoshio Tateno, Kazuho Ikeo, Satoru Miyazaki, Kaoru Fukami-Kobayashi, Hideaki Sugawara. Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library
486 -- 497Kei-Hoi Cheung, Prakash M. Nadkarni, Dong-Guk Shin. A metadata approach to query interoperation between molecular biology databases
498 -- 507Eivind Coward, Finn Drabløs. Detecting periodic patterns in biological sequences
508 -- 515Pierre Nicodème. SSMAL: similarity searching with alignment graphs
516 -- 522Xavier Pennec, Nicholas Ayache. A geometric algorithm to find small but highly similar 3D substructures in proteins
523 -- 528R. Rodriguez, G. Chinea, N. Lopez, T. Pons, Gert Vriend. Homology modeling, model and software evaluation: three related resources
529 -- 537F. A. Kolpakov, Elena A. Ananko, G. B. Kolesov, Nikolay A. Kolchanov. GeneNet: a gene network database and its automated visualization
538 -- 539Carol Soderlund, Timun Lau, Panos Deloukas. Z extensions to the RHMAPPER package
540 -- 541Foo-Tim Chau, Tsz-Pun Chan, Jing Wang. TLCQA: quantitative study of thin-layer chromatography
542 -- 543Javier Tamames, Christos A. Ouzounis, Georg Casari, Chris Sander, Alfonso Valencia. EUCLID: automatic classification of proteins in functional classes by their database annotations
544 -- 545Oswaldo Trelles, C. Ceron, Huaichun Wang, Joaquín Dopazo, José María Carazo. New phylogenetic venues opened by a novel implementation of the DNAml algorithm
546 -- 547V. N. Serov, Alexander V. Spirov, Maria Samsonova. Graphical interface to the genetic network database GeNet

Volume 14, Issue 5

384 -- 390Asaf A. Salamov, Tetsuo Nishikawa, Mark B. Swindells. Assessing protein coding region integrity in cDNA sequencing projects
391 -- 400Denis Thieffry, Heladia Salgado, Araceli M. Huerta, Julio Collado-Vides. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12
401 -- 406C. Tarnas, Richard Hughey. Reduced space hidden Markov model training
407 -- 422Cédric Notredame, Liisa Holm, Desmond G. Higgins. COFFEE: an objective function for multiple sequence alignments
423 -- 429Liisa Holm, Chris Sander. Removing near-neighbour redundancy from large protein sequence collections
430 -- 438Antje Krause, Martin Vingron. A set-theoretic approach to database searching and clustering
439 -- 451Oswaldo Trelles, Miguel A. Andrade, Alfonso Valencia, Emilio L. Zapata, José María Carazo. Computational space reduction and parallelization of a new clustering approach for large groups of sequences
452 -- 457Martin Senger, T. Flores, Karl-Heinz Glatting, Peter Ernst, Agnes Hotz-Wagenblatt, Sándor Suhai. W2H: WWW interface to the GCG sequence analysis package
458 -- 464Jochen Hampe, T. Wienker, Stefan Schreiber, P. Nurnberg. POPSIM: a general population simulation program
465 -- 466Pierre Lindenbaum. CloneIt: finding cloning strategies, in-frame deletions and frameshifts
467 -- 468V. Proutski, E. Holmes. SWAN: sliding window analysis of nucleotide sequence variability
469 -- 470Patricia Rodriguez-Tomé. The BioCatalog

Volume 14, Issue 4

310 -- 316Prakash M. Nadkarni. Mapmerge: merge genomic maps
317 -- 325Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai, Kenta Nakai. Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences
326 -- 331M. Dlakic, R. E. Harrington. DIAMOD: display and modeling of DNA bending
332 -- 341Emmet A. O Brien, Cédric Notredame, Desmond G. Higgins. Optimization of ribosomal RNA profile alignments
342 -- 348Frédéric Achard, Christophe Cussat-Blanc, Eric Viara, Emmanuel Barillot. The new Virgil database: a service of rich links
349 -- 356I. Anderson, A. Brass. Searching DNA databases for similarities to DNA sequences: when is a match significant?
357 -- 366P. Briffeuil, G. Baudoux, Christophe G. Lambert, Xavier De Bolle, C. Vinals, Ernest Feytmans, Eric Depiereux. Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions
367 -- 371N. P. Brown, Chris Sander, Peer Bork. Frame: detection of genomic sequencing errors
372 -- 373James O. McInerney. GCUA: general codon usage analysis
374 -- 375S. Levin, B. H. Satir. POLINA: detection and evaluation of single amino acid substitutions in protein superfamilies
376 -- 377Huaichun Wang, Joaquín Dopazo, José María Carazo. Self-organizing tree growing network for classifying amino acids
378 -- 379Takatsugu Hirokawa, S. Boon-Chieng, Shigeki Mitaku. SOSUI: classification and secondary structure prediction system for membrane proteins
380 -- 381N. P. Brown, Christophe Leroy, Chris Sander. MView: a web-compatible database search or multiple alignment viewer

Volume 14, Issue 3

232 -- 243Jürgen Kleffe, Klaus Hermann, W. Vahrson, Burghardt Wittig, Volker Brendel. GeneGenerator - a flexible algorithm for gene prediction and its application to maize sequences
244 -- 251L. Pickert, Ingmar Reuter, Frank Klawonn, Edgar Wingender. Transcription regulatory region analysis using signal detection and fuzzy clustering
252 -- 258Andrei Grigoriev, Alexander Levin, Hans Lehrach. A distributed environment for physical map construction
259 -- 270Alexander E. Kel, Andrey A. Ptitsyn, Vladimir N. Babenko, Sebastian Meier-Ewert, Hans Lehrach. A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily
271 -- 278Thomas Dandekar, Katrin Beyer, Peer Bork, Mary-Rose Kenealy, Kostas Pantopoulos, Mathias Hentze, Vera Sonntag-Buck, Gilles Flouriot, Frank Gannon, Sonja Schreiber. Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches
279 -- 284Rainer Spang, Martin Vingron. Statistics of large-scale sequence searching
285 -- 289Yan P. Yuan, Oliver Eulenstein, Martin Vingron, Peer Bork. Towards detection of orthologues in sequence databases
290 -- 294Burkhard Morgenstern, Kornelie Frech, Andreas W. M. Dress, Thomas Werner. DIALIGN: finding local similarities by multiple sequence alignment
295 -- 308Ralf Zimmer, Marko Wöhler, Ralf Thiele. New scoring schemes for protein fold recognition based on Voronoi contacts

Volume 14, Issue 2

101 -- 111J. A. Inglehart, P. C. Nelson, Y. Zou. Mapper: an intelligent restriction mapping tool
112 -- 120Jian Hu, Chris Mungall, David Nicholson, Alan L. Archibald. Design and implementation of a CORBA-based genome mapping system prototype
121 -- 130Vladimir Brusic, George B. Rudy, G. Honeyman, Jürgen Hammer, Leonard C. Harrison. Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network
131 -- 138Rupali V. Parbhane, Sanjeev S. Tambe, Bhaskar D. Kulkarni. Analysis of DNA curvature using artificial neural networks
139 -- 143Nadia A. Chuzhanova, Antonia J. Jones, Steve Margetts. Feature selection for genetic sequence classification
144 -- 150Jong Park, Sarah A. Teichmann. DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins
151 -- 156D. K. Smith, H. Xue. A major component approach to presenting consensus sequences
157 -- 163Jens Stoye, Dirk Evers, Folker Meyer. Rose: generating sequence families
164 -- 173Jérôme Gracy, P. Argos. Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment
174 -- 187Jérôme Gracy, P. Argos. Automated protein sequence database classification. II. Delineation Of domain boundaries from sequence similarities
188 -- 195Jianghong An, T. Nakama, Y. Kubota, Akinori Sarai. 3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules
196 -- 205Friedrich Ackermann, Grit Herrmann, Stefan Posch, Gerhard Sagerer. Estimation and filtering of potential protein-protein docking positions
206 -- 211Gilles Labesse, J. P. Mornon. Incremental threading optimization (TITO) to help alignment and modelling of remote homologues
212 -- 216Salvatore Lanzavecchia, Pier Luigi Bellon. Fast computation of 3D radon transform via a direct Fourier method
217 -- 218S. Taylor, T. Charles Hodgman, C. B. Littler, Roger A. Sayle, R. W. Gill, M. D. Oxer, C. H. O Donnell, Andrew Lyall. Automated management of gene discovery projects
219 -- 220Gráinne McGuire, Frank Wright. TOPAL: recombination detection in DNA and protein sequences
221 -- 222Giovanni Iazzetti, M. L. Chiusano, Raffaele Calogero. STRIRED: graphical analysis of string repeats
223 -- 224Cathy H. Wu, Sailaja Shivakumar, Chittari V. Shivakumar, Sheng-Chih Chen. GeneFIND web server for protein family identification and information retrieval
225 -- 226B. V. B. Reddy, P. Ramesh, S. Tiwari. MEICPS: substitution mutations to engineer intracellular protein stability
227 -- 228A. Hernandez, M. T. Ruiz. An EXCEL template for calculation of enzyme kinetic parameters by non-linear regression

Volume 14, Issue 10

830 -- 838Emmet A. O Brien, Desmond G. Higgins. Empirical estimation of the reliability of ribosomal RNA alignments
839 -- 845Torbjørn Rognes, Erling Seeberg. SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments
846 -- 856Kevin Karplus, Christian Barrett, Richard Hughey. Hidden Markov models for detecting remote protein homologies
857 -- 865C. T. Zhang, R. Zhang. A new criterion to classify globular proteins based on their secondary structure contents
866 -- 868W. J. Lin, M. J. Hwang. VHMPT: a graphical viewer and editor for helical membrane protein topologies
869 -- 883Pedro Mendes, Douglas B. Kell. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation
884 -- 885. GeneDn: for high-level expression design of heterologous genes in a prokaryotic system
888 -- 889M. Rimer, Michael O Connell. BioABACUS: a database of abbreviations and acronyms in biotechnology and computer science
890 -- 891K. C. Worley, P. Culpepper, B. A. Wiese, R. F. Smith. BEAUTY-X: enhanced BLAST searches for DNA queries
892 -- 893James A. Cuff, Michele E. Clamp, Asim S. Siddiqui, M. Finlay, Geoffrey J. Barton. JPred: a consensus secondary structure prediction server

Volume 14, Issue 1

2 -- 13Barbara A. Eckman, Jeffery S. Aaronson, J. A. Borkowski, W. J. Bailey, K. O. Elliston, A. R. Williamson, R. A. Blevins. The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining
14 -- 19Sing-Hoi Sze, Mikhail A. Roytberg, Mikhail S. Gelfand, Andrey A. Mironov, Tatiana V. Astakhova, Pavel A. Pevzner. Algorithms and software for support of gene identification experiments
20 -- 24Frédéric Achard, Philippe Dessen. GenXref. VI: Automatic generation of links between two heterogeneous databases
25 -- 39Jun Zhu, Jun S. Liu, Charles E. Lawrence. Bayesian adaptive sequence alignment algorithms
40 -- 47Pankaj Agarwal, David J. States. Comparative accuracy of methods for protein sequence similarity search
48 -- 54Timothy L. Bailey, Michael Gribskov. Combining evidence using p-values: application to sequence homology searches
55 -- 67Isidore Rigoutsos, Aris Floratos. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm [published erratum appears in Bioinformatics 1998;14(2): 229]
68 -- 73Daniel H. Huson. SplitsTree: analyzing and visualizing evolutionary data
74 -- 80Samuel Levy, L. Compagnoni, Eugene W. Myers, Gary D. Stormo. Xlandscape: the graphical display of word frequencies in sequences
81 -- 91Karsten R. Heidtke, Steffen Schulze-Kremer. Design and implementation of a qualitative simulation model of lambda phage infection
92 -- 97Richard Mott. Trace alignment and some of its applications
98 -- 99Michael A. Charleston. Spectrum: spectral analysis of phylogenetic data