Volume 14,
Number 1,
February 1998
Articles
- 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
Articles
- 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
Articles
- 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, 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.
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
Articles
- 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
Articles
- 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
Articles
- 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
Editorials
- Russ B. Altman:
A curriculum for bioinformatics: the time is ripe.
549-550
Articles
- 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
Articles
- 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
Articles:
- 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
- M. 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
Articles
- 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
Copyright © Thu Nov 26 19:38:31 2009
by Michael Ley (ley@uni-trier.de)
