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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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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last updated on 2013-06-18T214307 by the dblp team