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ORCIDBioinformatics, Volume 15
Volume 15, Number 1, January 1999
- Claudine Médigue, François Rechenmann, Antoine Danchin
, Alain Viari:
Imagene: an integrated computer environment for sequence annotation and analysis. 2-15 - Wojciech Kasprzak, Bruce A. Shapiro:
Stem Trace: an interactive visual tool for comparative RNA structure analysis. 16-31 - Dirk Evers, Robert Giegerich:
RNA movies: visualizing RNA secondary structure spaces. 32-37 - Jun S. Liu, Charles E. Lawrence:
Bayesian inference on biopolymer models. 38-52 - Cheng Che Chen, Jaswinder Pal Singh, Russ B. Altman:
Using imperfect secondary structure predictions to improve molecular structure computations. 53-65 - Oakley H. Crawford:
A fast, stochastic threading algorithm for proteins. 66-71 - Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Thomas Simon Shimizu, Yuri Matsuzaki, Fumihiko Miyoshi, Kanako Saito, Sakura Tanida, Katsuyuki Yugi, J. Craig Venter, Clyde A. Hutchison III:
E-CELL: software environment for whole-cell simulation. 72-84 - John S. Conery, Michael Lynch:
Genetic Simulation Library. 85-86 - Julie Dawn Thompson, Frédéric Plewniak, Olivier Poch:
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. 87-88 - Mark J. Forster, Alan B. Heath, Muhammad A. Afzal:
Application of distance geometry to 3D visualization of sequence relationships. 89-90
Volume 15, Number 2, February 1999
- G. Giacomo Consalez, Andrea Cabibbo, Anna Corradi, Cristina Alli, Milena Sardella, Roberto Sitia, Riccardo Fesce:
A computer-driven approach to PCR-based differential screening, alternative to differential display. 93-105 - G. A. Seluja, Andrew D. Farmer, Mia McLeod, Carol Harger, Peter A. Schad:
Establishing a method of vector contamination identification in database sequences. 106-110 - Crispin J. Miller, J. Gurd, Andy Brass:
A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases. 111-121 - K. Bucka-Lassen, O. Caprani, J. Hein:
Combining many multiple alignments in one improved alignment. 122-130 - Valentina Di Francesco, Peter J. Munson, Jean Garnier:
FORESST: fold recognition from secondary structure predictions of proteins. 131-140 - Hideki Hirakawa, S. Muta, Satoru Kuhara:
The hydrophobic cores of proteins predicted by wavelet analysis. 141-148 - Yang Zhong, Y. Luo, Sakti Pramanik, John H. Beaman:
HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees. 149-156 - Emmanuel Barillot, Ulf Leser, Philip Lijnzaad, Christophe Cussat-Blanc, Kim Jungfer, Frédéric Guyon, Guy Vaysseix, Carsten Helgesen, Patricia Rodriguez-Tomé:
A proposal for a standard CORBA interface for genome maps. 157-169 - M. E. Mangan, K. S. Frazer:
An extensive list of genes that produce alternative transcripts in the mouse. 170-171 - Giovanni Lavorgna, Alessandro Guffanti, G. Borsani, Andrea Ballabio, E. Boncinelli:
TargetFinder: searching annotated sequence databases for target genes of transcription factors. 172-173 - Julio Rozas, Ricardo Rozas:
DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. 174-175 - Marie-Hélène Mucchielli-Giorgi, Serge A. Hazout, Pierre Tufféry:
PredAcc: prediction of solvent accessibility. 176-177
Volume 15, Number 3, March 1999
- Andreas Klingenhoff, Kornelie Frech, Kerstin Quandt, Thomas Werner:
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. 180-186 - Hanspeter Herzel, Olaf Weiss, Edward N. Trifonov:
10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. 187-193 - Jean-Stéphane Varré, Jean-Paul Delahaye, Eric Rivals:
Transformation distances: a family of dissimilarity measures based on movements of segments. 194-202 - Hans-Peter Lenhof, Burkhard Morgenstern, Knut Reinert:
An exact solution for the segment-to-segment multiple sequence alignment problem. 203-210 - Burkhard Morgenstern:
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. 211-218 - Steffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler:
EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation. 219-227 - Wolfgang Fleischmann, Steffen Möller, Alain Gateau, Rolf Apweiler:
A novel method for automatic functional annotation of proteins. 228-233 - Rolf Backofen, Sebastian Will, Erich Bornberg-Bauer:
Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets. 234-242 - Matthias Rarey, Bernd Kramer, Thomas Lengauer:
Docking of hydrophobic ligands with interaction-based matching algorithms. 243-250 - Thomas Pfeiffer, Ignacio Sánchez-Valdenebro, Juan Carlos Nuño, Francisco Montero, Stefan Schuster:
METATOOL: for studying metabolic networks. 251-257 - Claire O'Donovan, Maria Jesus Martin, Eric Glémet, Jean-Jacques Codani, Rolf Apweiler:
Removing redundancy in SWISS-PROT and TrEMBL. 258-259 - Yvonne Kallberg, Bengt Persson:
KIND-a non-redundant protein database. 260-261 - Antje Krause, Pierre Nicodème, Erich Bornberg-Bauer, Marc Rehmsmeier, Martin Vingron:
WWW access to the SYSTERS protein sequence cluster set. 262-263
Volume 15, Number 4, April 1999
- R. F. Lascaris, W. H. Mager, J. Planta:
DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences. 267-277 - Eric Harley, Anthony J. Bonner, Nathan Goodman:
Revealing hidden interval graph structure in STS-content data. 278-285 - Kyungsook Han, Dohyung Kim, Hong-Jin Kim:
A vector-based method for drawing RNA secondary structure. 286-297 - Kun-Mao Chao:
Calign: aligning sequences with restricted affine gap penalties. 298-304 - Patrice Gouet, Emmanuel Courcelle, D. I. Stuart, F. Metoz:
ESPript: analysis of multiple sequence alignments in PostScript. 305-308 - Jesse Bentz, Albion Baucom, Marc Hansen, Lydia M. Gregoret:
DINAMO: interactive protein alignment and model building. 309-316 - David R. Gilbert, David R. Westhead, Nozomi Nagano, Janet M. Thornton:
Motif-based searching in TOPS protein topology databases. 317-326 - Vladimir Sobolev, Anatoly A. Sorokin, Jaime Prilusky, Enrique E. Abola, Marvin Edelman:
Automated analysis of interatomic contacts in proteins. 327-332 - Thierry Coupaye:
Wrapping SRS with CORBA: from textual data to distributed objects. 333-338 - David Fenyö:
The Biopolymer Markup Language. 339-340 - Patricia Thébault, Pierre Monestie, Annette McGrath, Desmond G. Higgins:
MIAH: automatic alignment of eukaryotic SSU rRNAs. 341-342 - János Murvai, Kristian Vlahovicek, Endre Barta, Subbiah Parthasarathy, Hedvig Hegyi, Friedhelm Pfeiffer, Sándor Pongor:
The domain-server: direct prediction of protein domain-homologies from BLAST search. 343-344 - L. Brun-Samarcq, Sophie Gallina, A. Philippi, Florence Demenais, Guy Vaysseix, Emmanuel Barillot:
CoPE: a collaborative pedigree drawing environment. 345-346
Volume 15, Number 5, May 1999
- Steven Bushnell, J. Budde, T. Catino, Jack Cole, A. Derti, R. Kelso, M. L. Collins, G. Molino, P. Sheridan, J. Monahan, M. Urdea:
ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays. 348-355 - Steen Knudsen:
Promoter2.0: for the recognition of PolII promoter sequences. 356-361 - Uwe Ohler, Stefan Harbeck, Heinrich Niemann, Elmar Nöth, Martin G. Reese:
Interpolated markov chains for eukaryotic promoter recognition. 362-369 - Richard D. Blake, Jeff W. Bizzaro, Jonathan D. Blake, G. R. Day, S. G. Delcourt, J. Knowles, Kenneth A. Marx, J. SantaLucia Jr.:
Statistical mechanical simulation of polymeric DNA melting with MELTSIM. 370-375 - Amanda Chou, John Burke:
CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences. 376-381 - Geetha Y. Srinivasarao, Lai-Su L. Yeh, Christopher R. Marzec, Bruce C. Orcutt, Winona C. Barker:
PIR-ALN: a database of protein sequence alignments. 382-390 - Miguel A. Andrade, Nigel P. Brown, Christophe Leroy, S. Hörsch, Antoine de Daruvar, C. Reich, Angelo Franchini, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis, Chris Sander:
Automated genome sequence analysis and annotation. 391-412 - Yann Guermeur, Christophe Geourjon, Patrick Gallinari, Gilbert Deléage:
Improved performance in protein secondary structure prediction by inhomogeneous score combination. 413-421 - Prakash S. Ferlanti, Joseph F. Ryan, Izabela Makalowska, Andreas D. Baxevanis:
WebBLAST 2.0: an integrated solution for organizing and analyzing sequence data. 422-423 - Isabelle Gonçalves, Marc Robinson-Rechavi, Guy Perrière, Dominique Mouchiroud:
JaDis: computing distances between nucleic acid sequences. 424-425 - Stefan Kurtz, Chris Schleiermacher:
REPuter: fast computation of maximal repeats in complete genomes. 426-427
Volume 15, Number 6, June 1999
- R. R. Mallios:
Class II MHC quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminant analysis meta- algorithm. 432-439 - Rune B. Lyngsø, Michael Zuker, Christian N. S. Pedersen:
Fast evaluation of internal loops in RNA secondary structure prediction. 440-445 - Bjarne Knudsen, Jotun Hein:
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. 446-454 - Richard Mott:
Local sequence alignments with monotonic gap penalties. 455-462 - William Noble Grundy, Timothy L. Bailey:
Family pairwise search with embedded motif models. 463-470 - Steven Henikoff, Jorja G. Henikoff, Shmuel Pietrokovski:
Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations. 471-479 - Arne Elofsson, Erik L. L. Sonnhammer:
A comparison of sequence and structure protein domain families as a basis for structural genomics. 480-500 - Finn Drabløs:
Clustering of non-polar contacts in proteins. 501-509 - Patricia G. Baker, Carole A. Goble, Sean Bechhofer, Norman W. Paton, Robert Stevens, Andy Brass:
An ontology for bioinformatics applications. 510-520 - Mansoor A. S. Saqi, David L. Wild, M. J. Hartshorn:
Protein analyst - a distributed object environment for protein sequence and structure analysis. 521-522 - W. Wright, Philip Scordis, Terri K. Attwood:
BLAST PRINTS - alternative perspectives on sequence similarity. 523-524 - Oleg Shats, Iosif I. Vaisman, A. Shats, Simon Sherman:
SECOST: sequence-conformation-structure database for amino acid residues in proteins. 525-526
Volume 15, Number 7/8, July 1999
- Frank Eisenhaber, Peer Bork:
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries. 528-535 - Tatiana A. Tatusova, Ilene Karsch-Mizrachi, James Ostell:
Complete genomes in WWW Entrez: data representation and analysis. 536-543 - Kotoko Nakata, T. Takai, Tsuguchika Kaminuma:
Development of the receptor database (RDB): application to the endocrine disruptor problem. 544-552 - Vladimir B. Berikov, Igor B. Rogozin:
Regression trees for analysis of mutational spectra in nucleotide sequences. 553-562 - G. Z. Hertz, Gary D. Stormo:
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. 563-577 - Y. Osada, Rintaro Saito, Masaru Tomita:
Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes. 578-581 - Victor G. Levitsky, Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay A. Kolchanov:
Nucleosomal DNA property database. 582-592 - Luis Mendoza, Denis Thieffry, Elena R. Álvarez-Buylla:
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. 593-606 - Jian Zhu, Michael Q. Zhang:
SCPD: a promoter database of the yeast Saccharomyces cerevisiae. 607-611 - Luciano Milanesi, D. D'Angelo, Igor B. Rogozin:
GeneBuilder: interactive in silico prediction of gene structure. 612-621 - Tatsuhiko Tsunoda, Toshihisa Takagi:
Estimating transcription factor bindability on DNA. 622-630 - Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Olga A. Podkolodnaya, Denis G. Vorobiev, Nikolay A. Kolchanov, G. Christian Overton:
Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. 631-643 - Vladimir N. Babenko, P. S. Kosarev, Oleg V. Vishnevsky, Victor G. Levitsky, V. V. Basin, Anatoly S. Frolov:
Investigating extended regulatory regions of genomic DNA sequences. 644-653 - Julia V. Ponomarenko, Mikhail P. Ponomarenko, Anatoly S. Frolov, Denis G. Vorobiev, G. Christian Overton, Nikolay A. Kolchanov:
Conformational and physicochemical DNA features specific for transcription factor binding sites. 654-668 - Nikolay A. Kolchanov, Mikhail P. Ponomarenko, Anatoly S. Frolov, Elena A. Ananko, Fedor A. Kolpakov, Elena V. Ignatieva, Olga A. Podkolodnaya, T. N. Goryachkovskaya, Irina L. Stepanenko, Tatyana I. Merkulova, V. V. Babenko, Y. V. Ponomarenko, Alexey V. Kochetov, Nikolay L. Podkolodny, Denis G. Vorobiev, Sergey V. Lavryushev, Dmitry A. Grigorovich, Yury V. Kondrakhin, Luciano Milanesi, Edgar Wingender, Victor V. Solovyev, G. Christian Overton:
Integrated databases and computer systems for studying eukaryotic gene expression. 669-686 - Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay L. Podkolodny, Ludmila K. Savinkova, Nikolay A. Kolchanov, G. Christian Overton:
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. 687-703 - Alexey V. Kochetov, Mikhail P. Ponomarenko, Anatoly S. Frolov, L. L. Kisselev, Nikolay A. Kolchanov:
Prediction of eukaryotic mRNA translational properties. 704-712 - Fedor A. Kolpakov, Elena A. Ananko:
Interactive data input into the GeneNet database. 713-714
Volume 15, Number 9, September 1999
- L. B. Ellis, D. Kalumbi:
Financing a future for public biological data. 717-722 - Carolyn F. Allex, Jude W. Shavlik, Frederick R. Blattner:
Neural network input representations that produce accurate consensus sequences from DNA fragment assemblies. 723-728 - Scott C.-H. Pegg, Patricia C. Babbitt:
Shotgun: getting more from sequence similarity searches. 729-740 - Jens Hanke, Gerrit Lehmann, Peer Bork, Jens G. Reich:
Associative database of protein sequences. 741-748 - Igor Goryanin, T. Charles Hodgman, Evgeni Selkov:
Mathematical simulation and analysis of cellular metabolism and regulation. 749-758 - Daniel Fischer, David S. Eisenberg:
Finding families for genomic ORFans. 759-762 - Josep M. Comeron:
K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals. 763-764 - T. Wei, Michael O'Connell:
TargetDB: a database of peptides targeting proteins to subcellular locations. 765-766 - Andreas Bohne, Elke Lang, Claus-Wilhelm von der Lieth:
SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides. 767-768 - Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak:
MatrixPlot: visualizing sequence constraints. 769-770 - Henning Hermjakob, Wolfgang Fleischmann, Rolf Apweiler:
Swissknife - 'lazy parsing' of SWISS-PROT entries. 771-772 - Nikos Kyrpides:
Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. 773-774
Volume 15, Number 10, October 1999
- Thomas Lengauer:
Editorial. The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99). 775 - Andreas Wagner:
Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. 776-784 - Dominique Bouthinon, Henry Soldano:
A new method to predict the consensus secondary structure of a set of unaligned RNA sequences. 785-798 - Philip Scordis, Darren R. Flower, Terri K. Attwood:
FingerPRINTScan: intelligent searching of the PRINTS motif database. 799-806 - Helge Weissig, Philip E. Bourne:
An analysis of the Protein Data Bank in search of temporal and global trends. 807-831 - Robert Preissner, Andrean Goede, Cornelius Frömmel:
Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP). 832-836 - Steve Fischer, Jonathan Crabtree, Brian P. Brunk, M. Gibson, G. Christian Overton:
bioWidgets: data interaction components for genomics. 837-846 - Matthew I. Bellgard, Hong Liang Hiew, Adam Hunter, Michael Wiebrands:
ORBIT: an integrated environment for user-customized bioinformatics tools. 847-851 - Pentti Riikonen, Mauno Vihinen:
MUTbase: maintenance and analysis of distributed mutation databases. 852-859 - Gavin H. Thomas:
Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequence. 860-861 - Jeffrey Yuan, Angela Amend, Joseph A. Borkowski, Reynold DelMarco, Wendy Bailey, Yuan Liu, Guochun Xie, Richard Blevins:
MULTICLUSTAL: a systematic method for surveying Clustal W alignment parameters. 862-863 - Daniel Fischer, David S. Eisenberg:
Erratum. Finding families for genomic ORFans. 864
Volume 15, Number 11, November 1999
- Chris Burge, Andrej Sali, Mark Borodovsky:
The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA). 865-866 - Eran Halperin, Simchon Faigler, Raveh Gill-More:
FramePlus: aligning DNA to protein sequences. 867-873 - Anton M. Shmatkov, Arik A. Melikyan, Felix L. Chernousko, Mark Borodovsky:
Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes. 874-886 - Nathalie Pavy, Stephane Rombauts, Patrice Déhais, Catherine Mathé, Ramana V. Davuluri, Philippe Leroy, Pierre Rouzé:
Evaluation of gene prediction software using a genomic data set: application to <$O_SSF>Arabidopsis thaliana<$C_SSF>sequences. 887-899 - Arvind K. Bansal:
An automated comparative analysis of 17 complete microbial genomes. 900-908 - David Sankoff:
Genome rearrangement with gene families. 909-917 - Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen:
Structural basis for triplet repeat disorders: a computational analysis. 918-929 - S. Uliel, A. Fliess, Amihood Amir, Ron Unger:
A simple algorithm for detecting circular permutations in proteins. 930-936 - Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri:
Exploiting the past and the future in protein secondary structure prediction. 937-946 - Alexander V. Lukashin, Joseph J. Rosa:
Local multiple sequence alignment using dead-end elimination. 947-953
Volume 15, Number 12, December 1999
- Bioinformatics and the Y2K Problem. Bioinform. 15(12): 955-956 (1999)
- Artem L. Ponomarev, Rainer K. Sachs:
Polymer chromosome models and Monte Carlo simulations of radiation breaking DNA. 957-964 - Michael Cariaso, P. Folta, M. Wagner, Tom Kuczmarski, Greg Lennon:
IMAGEne I: clustering and ranking of I.M.A.G.E. cDNA clones corresponding to known genes. 965-973 - José L. Oliver, Ramón Román-Roldán, Javier Pérez, Pedro Bernaola-Galván:
SEGMENT: identifying compositional domains in DNA sequences. 974-979 - Leonid Peshkin, Mikhail S. Gelfand:
Segmentation of yeast DNA using hidden Markov models. 980-986 - Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Kenta Nakai:
Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov models. 987-993 - Vladimir D. Gusev, Lubov A. Nemytikova, Nadia A. Chuzhanova:
On the complexity measures of genetic sequences. 994-999 - Alejandro A. Schäffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul:
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. 1000-1011 - Zheng Zhang, Piotr Berman, Thomas Wiehe, Webb Miller:
Post-processing long pairwise alignments. 1012-1019 - Florence Corpet, Jérôme Gouzy, Daniel Kahn:
Browsing protein families via the 'Rich Family Description' format. 1020-1027 - Istvan Ladunga:
PHYSEAN: PHYsical SEquence ANalysis for the identification of protein domains on the basis of physical and chemical properties of amino acids. 1028-1038 - Joachim Selbig, Heinz-Theodor Mevissen, Thomas Lengauer:
Decision tree-based formation of consensus protein secondary structure prediction. 1039-1046 - Véronique Giudicelli, Marie-Paule Lefranc:
Ontology for immunogenetics: the IMGT-ONTOLOGY. 1047-1054 - V. S. Reddy, A. S. N. Reddy:
A plant calmodulin-binding motor is part kinesin and part myosin. 1055-1057 - Eivind Coward:
Shufflet: shuffling sequences while conserving the k-let counts. 1058-1059 - Roberto Sánchez:
ModBase: A database of comparative protein structure models. 1060-1061 - Florencio Pazos, Burkhard Rost, Alfonso Valencia:
A platform for integrating threading results with protein family analyses. 1062-1063 - Thomas Huber, Anthony J. Russell, Daniel Ayers, Andrew E. Torda:
Sausage: protein threading with flexible force fields. 1064-1065 - Vivien L. Junker, Rolf Apweiler, Amos Bairoch:
Representation of functional information in the SWISS-PROT Data Bank. 1066-1067 - Allison Lim, Louxin Zhang:
WebPHYLIP: a web interface to PHYLIP. 1068-1069
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