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ORCIDBioinformatics, Volume 14
Volume 14, Number 1, February 1998
- Barbara A. Eckman, Jeffery S. Aaronson, Joseph A. Borkowski, Wendy J. Bailey, Keith O. Elliston
, Alan R. Williamson, Richard 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
- James A. Inglehart, Peter C. Nelson, Yibo 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-Chan Park, Sarah A. Teichmann:
DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. 144-150 - David 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 - Steve Taylor, T. Charles Hodgman, Chris B. Littler, Roger A. Sayle, Robert W. Gill, Marcus 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, Maria Luisa Chiusano, Raffaele A. 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 - Agustín Hernández, María Teresa 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, Wolfgang 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 B. 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 - Mensur 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 - Isobel Anderson, Andy Brass:
Searching DNA databases for similarities to DNA sequences: when is a match significant? 349-356 - Pascal Briffeuil, Guy Baudoux, Christophe G. Lambert, Xavier De Bolle, Carla Vinals, Ernest Feytmans, Eric Depiereux:
Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions. 357-366 - Nigel P. Brown, Chris Sander, Peer Bork:
Frame: detection of genomic sequencing errors. 367-371 - James O. McInerney:
GCUA: general codon usage analysis. 372-373 - Sergei Levin, Birgit 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, Seah Boon-Chieng, Shigeki Mitaku:
SOSUI: classification and secondary structure prediction system for membrane proteins. 378-379 - Nigel 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, Thomas F. Wienker, Stefan Schreiber, Peter Nürnberg:
POPSIM: a general population simulation program. 458-464 - Pierre Lindenbaum:
CloneIt: finding cloning strategies, in-frame deletions and frameshifts. 465-466 - Vitali Proutski, Edward C. 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 - Rolando Rodríguez, Glay Chinea, Nelia Lopez, Tirso Pons, Gert Vriend:
Homology modeling, model and software evaluation: three related resources. 523-528 - Fedor 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 - Vassili 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, Arthur M. 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, Jaime Prilusky, Doron Lancet:
GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. 656-664 - Katsuhiko Murakami, Toshihisa 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 - Wuju Li, 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, Vasilis 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 T. 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, Mikita 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, Stuart 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 A. 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, Alan 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 - William Newell, Philippe Sanseau, John Riley, Andrew 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 - Li Wu Ju, Lei Hong Xing, Pei Wu Hong, Wu Jia 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 - Mendell Rimer, Mary 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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