Bioinformatics, Volume 14

Volume 14, Number 1, February 1998

• Barbara 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. 2-13
  
• Sing-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. 14-19
  
• Frédéric Achard, Philippe Dessen:
  GenXref. VI: Automatic generation of links between two heterogeneous databases. 20-24
  
• Jun Zhu, Jun S. Liu, Charles E. Lawrence:
  Bayesian adaptive sequence alignment algorithms. 25-39
  
• Pankaj Agarwal, David J. States:
  Comparative accuracy of methods for protein sequence similarity search. 40-47
  
• Timothy L. Bailey, Michael Gribskov:
  Combining evidence using p-values: application to sequence homology searches. 48-54
  
• Isidore Rigoutsos, Aris Floratos:
  Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm [published erratum appears in Bioinformatics 1998;14(2): 229]. 55-67
  
• Daniel H. Huson:
  SplitsTree: analyzing and visualizing evolutionary data. 68-73
  
• Samuel Levy, L. Compagnoni, Eugene W. Myers, Gary D. Stormo:
  Xlandscape: the graphical display of word frequencies in sequences. 74-80
  
• Karsten R. Heidtke, Steffen Schulze-Kremer:
  Design and implementation of a qualitative simulation model of lambda phage infection. 81-91
  
• Richard Mott:
  Trace alignment and some of its applications. 92-97
  
• Michael A. Charleston:
  Spectrum: spectral analysis of phylogenetic data. 98-99
  

Volume 14, Number 2, March 1998

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

Volume 14, Number 3, April 1998

• Jürgen Kleffe, Klaus Hermann, W. Vahrson, Burghardt Wittig, Volker Brendel:
  GeneGenerator - a flexible algorithm for gene prediction and its application to maize sequences. 232-243
  
• L. Pickert, Ingmar Reuter, Frank Klawonn, Edgar Wingender:
  Transcription regulatory region analysis using signal detection and fuzzy clustering. 244-251
  
• Andrei Grigoriev, Alexander Levin, Hans Lehrach:
  A distributed environment for physical map construction. 252-258
  
• Alexander 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. 259-270
  
• Thomas Dandekar, Katrin Beyer, Peer Bork, Mary-Rose Kenealy, Kostas Pantopoulos, Matthias W. 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. 271-278
  
• Rainer Spang, Martin Vingron:
  Statistics of large-scale sequence searching. 279-284
  
• Yan P. Yuan, Oliver Eulenstein, Martin Vingron, Peer Bork:
  Towards detection of orthologues in sequence databases. 285-289
  
• Burkhard Morgenstern, Kornelie Frech, Andreas W. M. Dress, Thomas Werner:
  DIALIGN: finding local similarities by multiple sequence alignment. 290-294
  
• Ralf Zimmer, Marko Wöhler, Ralf Thiele:
  New scoring schemes for protein fold recognition based on Voronoi contacts. 295-308
  

Volume 14, Number 4, May 1998

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

Volume 14, Number 5, June 1998

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

Volume 14, Number 6, July 1998

• Toshitsugu 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. 472-478
  
• S. Z. Maltchenko:
  The bio-objects project. Part I: the object data model core elements. 479-485
  
• Kei-Hoi Cheung, Prakash M. Nadkarni, Dong-Guk Shin:
  A metadata approach to query interoperation between molecular biology databases. 486-497
  
• Eivind Coward, Finn Drabløs:
  Detecting periodic patterns in biological sequences. 498-507
  
• Pierre Nicodème:
  SSMAL: similarity searching with alignment graphs. 508-515
  
• Xavier Pennec, Nicholas Ayache:
  A geometric algorithm to find small but highly similar 3D substructures in proteins. 516-522
  
• R. Rodriguez, G. Chinea, N. Lopez, T. Pons, Gert Vriend:
  Homology modeling, model and software evaluation: three related resources. 523-528
  
• F. A. Kolpakov, Elena A. Ananko, G. B. Kolesov, Nikolay A. Kolchanov:
  GeneNet: a gene network database and its automated visualization. 529-537
  
• Carol Soderlund, Timun Lau, Panos Deloukas:
  Z extensions to the RHMAPPER package. 538-539
  
• Foo-Tim Chau, Tsz-Pun Chan, Jing Wang:
  TLCQA: quantitative study of thin-layer chromatography. 540-541
  
• Javier Tamames, Christos A. Ouzounis, Georg Casari, Chris Sander, Alfonso Valencia:
  EUCLID: automatic classification of proteins in functional classes by their database annotations. 542-543
  
• Oswaldo Trelles, C. Ceron, Huaichun Wang, Joaquín Dopazo, José María Carazo:
  New phylogenetic venues opened by a novel implementation of the DNAml algorithm. 544-545
  
• V. N. Serov, Alexander V. Spirov, Maria Samsonova:
  Graphical interface to the genetic network database GeNet. 546-547
  

Volume 14, Number 7, August 1998

• Russ B. Altman:
  A curriculum for bioinformatics: the time is ripe. 549-550
  

• Dmitrij Frishman, Klaus Heumann, A. Lesk, Hans-Werner Mewes:
  Comprehensive, comprehensible, distributed and intelligent databases: current status. 551-561
  
• Nathan Goodman, Steve Rozen, Lincoln Stein, A. G. Smith:
  The LabBase system for data management in large scale biology research laboratories. 562-574
  
• John Macauley, Huajun Wang, Nathan Goodman:
  A model system for studying the integration of molecular biology databases. 575-582
  
• Ulf Leser, Hans Lehrach, Hugues Roest Crollius:
  Issues in developing integrated genomic databases and application to the human X chromosome. 583-590
  
• Susumu Goto, Takaaki Nishioka, Minoru Kanehisa:
  LIGAND: chemical database for enzyme reactions. 591-599
  
• Miguel A. Andrade, Alfonso Valencia:
  Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. 600-607
  
• P. H. Sneath:
  The effect of evenly spaced constant sites on the distribution of the random division of a molecular sequence. 608-616
  
• Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington:
  JOY: protein sequence-structure representation and analysis. 617-623
  
• Therese E. Malliavin, Jean-Luc Pons, Marc-André Delsuc:
  An NMR assignment module implemented in the Gifa NMR processing program. 624-631
  
• Dean W. Podlich, Mark Cooper:
  QU-GENE: a simulation platform for quantitative analysis of genetic models. 632-653
  

Volume 14, Number 8, September 1998

• Michael Rebhan, Vered Chalifa-Caspi, J. Prilusky, Doron Lancet:
  GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. 656-664
  
• K. Murakami, T. Takagi:
  Gene recognition by combination of several gene-finding programs. 665-675
  
• Salvatore Rampone:
  Recognition of splice junctions on DNA sequences by BRAIN learning algorithm. 676-684
  
• M. Yan, Z. S. Lin, C. T. Zhang:
  A new fourier transform approach for protein coding measure based on the format of the Z curve. 685-690
  
• Jack E. Tabaska, Robert B. Cary, Harold N. Gabow, Gary D. Stormo:
  An RNA folding method capable of identifying pseudoknots and base triples. 691-699
  
• Li Wuju, W. JiaJin:
  Prediction of RNA secondary structure based on helical regions distribution. 700-706
  
• Mark Gerstein:
  Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. 707-714
  
• Pierre 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. 715-725
  
• Pietro Liò, N. Goldman, Jeffrey L. Thorne, David T. Jones:
  PASSML: combining evolutionary inference and protein secondary structure prediction. 726-733
  
• Kim Jungfer, Patricia Rodriguez-Tomé:
  Mapplet: a CORBA-based genome map viewer. 734-738
  
• J. Boyle:
  A visual environment for the manipulation and integration of JAVA beans. 739-748
  
• C. M. Pasquier, Vassilis J. Promponas, N. J. Varvayannis, Stavros J. Hamodrakas:
  A web server to locate periodicities in a sequence. 749-750
  
• T. R. Burglin:
  PPCMatrix: a PowerPC dotmatrix program to compare large genomic sequences against protein sequences. 751-752
  

Volume 14, Number 9, October 1998

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

Volume 14, Number 10, November 1998

• Emmet A. O'Brien, Desmond G. Higgins:
  Empirical estimation of the reliability of ribosomal RNA alignments. 830-838
  
• Torbjørn Rognes, Erling Seeberg:
  SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments. 839-845
  
• Kevin Karplus, Christian Barrett, Richard Hughey:
  Hidden Markov models for detecting remote protein homologies. 846-856
  
• C. T. Zhang, R. Zhang:
  A new criterion to classify globular proteins based on their secondary structure contents. 857-865
  
• W. J. Lin, M. J. Hwang:
  VHMPT: a graphical viewer and editor for helical membrane protein topologies. 866-868
  
• Pedro Mendes, Douglas B. Kell:
  Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. 869-883
  
• L. W. Ju, L. H. Xing, P. W. Hong, W. J. Jin:
  GeneDn: for high-level expression design of heterologous genes in a prokaryotic system. 884-885
  
• C. P. Goujon, V. M. Schneider, C. Jacomet, J. C. Nicolas:
  HIV-1 genotypic resistance: automated sequence analysis and interpretation. 886-887
  
• M. Rimer, Michael O'Connell:
  BioABACUS: a database of abbreviations and acronyms in biotechnology and computer science. 888-889
  
• K. C. Worley, P. Culpepper, B. A. Wiese, R. F. Smith:
  BEAUTY-X: enhanced BLAST searches for DNA queries. 890-891
  
• James A. Cuff, Michele E. Clamp, Asim S. Siddiqui, M. Finlay, Geoffrey J. Barton:
  JPred: a consensus secondary structure prediction server. 892-893
  

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