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ORCIDBioinformatics, Volume 16
Volume 16, Number 1, January 2000
- Richard J. Roberts
:
The early days of bioinformatics publishing. 2-4 - Edward N. Trifonov:
Earliest pages of bioinformatics. 5-9 - T. Charles Hodgman:
A historical perspective on gene/protein functional assignment. 10-15 - Gary D. Stormo:
DNA binding sites: representation and discovery. 16-23 - Russell F. Doolittle:
On the trail of protein sequences. 24-33 - Keith F. Tipton, Sinéad Boyce:
History of the enzyme nomenclature system. 34-40 - David Sankoff:
The early introduction of dynamic programming into computational biology. 41-47 - Amos Bairoch:
Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!. 48-64 - Antoine Danchin:
A brief history of genome research and bioinformatics in France. 65-75
Volume 16, Number 2, February 2000
- Andy Brass:
Bioinformatics Education-A UK perspective. 77-78 - Marcella A. McClure:
The complexities of genome analysis, the Retroid agent perspective. 79-95 - Sorinel Adrian Oprisan, Aurel Ardelean, Petre T. Frangopol:
Self-organization and competition in the immune response to cancer invasion: a phase-orientated computational model of oncogenesis. 96-100 - Gaston H. Gonnet, Michael T. Hallett, Chantal Korostensky, Laurent Bernardin:
Darwin v. 2.0: an interpreted computer language for the biosciences. 101-103 - Jong-Chan Park, Liisa Holm, Cyrus Chothia:
Sequence search algorithm assessment and testing toolkit (SAT). 104-110 - James A. Cuff, Ewan Birney, Michele E. Clamp, Geoffrey J. Barton:
ProtEST: protein multiple sequence alignments from expressed sequence tags. 111-116 - Sarah A. Teichmann, Cyrus Chothia, George M. Church, Jong-Chan Park:
Fast assignment of protein structures to sequences using the Intermediate Sequence Library PDB-ISL. 117-124 - Robert M. MacCallum, Lawrence A. Kelley, Michael J. E. Sternberg:
SAWTED: Structure Assignment With Text Description-Enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons. 125-129 - Gráinne McGuire, Frank Wright:
TOPAL 2.0: improved detection of mosaic sequences within multiple alignments. 130-134 - Eric Beitz:
TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e. 135-139 - Paul Walton Purdom Jr., Phillip G. Bradford, Koichiro Tamura, Sudhir Kumar:
Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees. 140-151 - Deyou Cai, Arthur L. Delcher, Ben Kao, Simon Kasif:
Modeling splice sites with Bayes networks. 152-158 - John D. Westbrook, Philip E. Bourne:
STAR/mmCIF: An ontology for macromolecular structure. 159-168 - Mikio Yoshida, Ken-ichiro Fukuda, Toshihisa Takagi:
PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary. 169-175 - John Bouck, Michael P. McLeod, Kim Worley, Richard A. Gibbs:
The Human Transcript Database: a catalogue of full length cDNA inserts. 176-177 - Thomas Junier, Marco Pagni:
Dotlet: diagonal plots in a Web browser. 178-179 - Naoki Sato:
SISEQ: manipulation of multiple sequence and large database files for common platforms. 180-181 - Gonçalo R. Abecasis, W. O. C. Cookson:
GOLD-Graphical Overview of Linkage Disequilibrium. 182-183 - Robert Stevens, Patricia G. Baker, Sean Bechhofer, Gary Ng, Alex Jacoby, Norman W. Paton, Carole A. Goble, Andy Brass:
TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources. 184-186
Volume 16, Number 3, March 2000
- Christos A. Ouzounis:
Two or three myths about bioinformatics. 187-189 - Osamu Gotoh:
Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps. 190-202 - Jonathan Usuka, Wei Zhu, Volker Brendel:
Optimal spliced alignment of homologous cDNA to a genomic DNA template. 203-211 - Dorothy M. Lang:
Net Nearest Neighbor Analysis (NNNA) summarizes non-compensated dinucleotides within gene sequences. 212-221 - Yuh-Jyh Hu, Suzanne B. Sandmeyer, Calvin McLaughlin, Dennis F. Kibler:
Combinatorial motif analysis and hypothesis generation on a genomic scale. 222-232 - Thomas D. Wu, Craig G. Nevill-Manning, Douglas L. Brutlag:
Fast probabilistic analysis of sequence function using scoring matrices. 233-244 - B. Jagla, Johannes Schuchhardt:
Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites. 245-250 - András Fiser, István Simon:
Predicting the oxidation state of cysteines by multiple sequence alignment. 251-256 - Dong Xu, Michael A. Unseren, Ying Xu, Edward C. Uberbacher:
Sequence-structure specificity of a knowledge based energy function at the secondary structure level. 269-285 - Peter D. Karp:
An ontology for biological function based on molecular interactions. 269-285 - Christophe Blanchet, Christophe Combet, Christophe Geourjon, Gilbert Deléage:
MPSA: integrated system for multiple protein sequence analysis with client/server capabilities. 286-287 - Guochun Xie, Reynold DeMarco, Richard Blevins, Yuhong Wang:
Storing biological sequence databases in relational form. 288-289 - Peter B. McGarvey, Hongzhan Huang, Winona C. Barker, Bruce C. Orcutt, John S. Garavelli, Geetha Y. Srinivasarao, Lai-Su L. Yeh, Chunlin Xiao, Cathy H. Wu:
PIR: a new resource for bioinformatics. 290-291 - Angelo M. Facchiano:
HELM: searching for helix motifs within protein sequences. 292-293 - Tim Massingham, Nick Goldman:
EDIBLE: experimental design and information calculations in phylogenetics. 294-295 - Marc Robinson-Rechavi, Dorothée Huchon:
RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree. 296-297 - Stephen Wooding:
PRoMT: inferring demographic history from DNA sequences. 298-299
Volume 16, Number 4, April 2000
- Abdelkrim Rachedi, Michael Rebhan, Hong Xue:
GABAagent: a system for integrating data on GABA receptors. 301-312 - J. D. Parsons, Patricia Rodriguez-Tomé:
JESAM: CORBA software components to create and publish EST alignments and clusters. 313-325 - Lars Juhl Jensen, Steen Knudsen:
Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. 326-333 - Elena Rivas, Sean R. Eddy:
The language of RNA: a formal grammar that includes pseudoknots. 334-340 - Andrea Califano:
SPLASH: structural pattern localization analysis by sequential histograms. 341-357 - Alexander G. Bachinsky, Anatoly S. Frolov, Andrey N. Naumochkin, Lily Ph. Nizolenko, Andrey A. Yarigin:
PROF_ PAT 1.3: Updated database of patterns used to detect local similarities. 358-366 - Pierre Baldi:
On the convergence of a clustering algorithm for protein-coding regions in microbial genomes. 367-371 - Kunchur Guruprasad, Maheshuni S. Prasad, Gundu R. Kumar:
Database of Structural Motifs in Proteins. 372-375 - Pietro Liò, Marina Vannucci:
Wavelet change-point prediction of transmembrane proteins. 376-382 - Marty J. Wolf, Simon Easteal, Margaret Kahn, Brendan D. McKay, Lars S. Jermiin:
TrExML: a maximum-likelihood approach for extensive tree-space exploration. 383-394 - Andrew Rambaut:
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. 395-399 - Patrick P. Rose, Bette T. Korber:
Detecting hypermutations in viral sequences with an emphasis on G A hypermutation. 400-401 - Matthew R. Pocock, Tim J. P. Hubbard:
A browser for expression data. 402-403 - Liam J. McGuffin, Kevin Bryson, David T. Jones:
The PSIPRED protein structure prediction server. 404-405 - R. Gilmour:
Taxonomic markup language: applying XML to systematic data. 406-407 - Kenneth F. Manly:
Mathematica packages for simulation of experimental genetics. 408-410
Volume 16, Number 5, May 2000
- François Rechenmann:
From data to knowledge. 411 - Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen:
Assessing the accuracy of prediction algorithms for classification: an overview. 412-424 - Peter M. Hooper, Haiyan Zhang, David S. Wishart:
Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment. 425-438 - Graziano Pesole, Sabino Liuni, Mark D'Souza:
PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. 439-450 - Anton J. Enright, Christos A. Ouzounis:
GeneRAGE: a robust algorithm for sequence clustering and domain detection. 451-457 - Jong-Chan Park, Liisa Holm, Andreas Heger, Cyrus Chothia:
RSDB: representative protein sequence databases have high information content. 458-464 - Gary D. Bader, Christopher W. V. Hogue:
BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. 465-477 - Chang Zhu, Kevin Karplus, Leslie Grate, Philip Coffino:
A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiae. 478-481 - Gustavo Glusman, Doron Lancet:
GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses. 482-483 - David Hiscock, Chris Upton:
Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes. 484-485 - Joseph L. Thorley, Roderic D. M. Page:
RadCon: phylogenetic tree comparison and consensus. 486-487 - Timothy L. Bailey, Michael Gribskov:
Concerning the accuracy of MAST E-values. 488-489
Volume 16, Number 6, June 2000
- Rainer Fuchs:
Analyse This...Or: Intelligent Help for The Rest of Us. 491-493
- Ting Chen, Steven Skiena:
A case study in genome-level fragment assembly. 494-500 - Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo:
Phylogenetically enhanced statistical tools for RNA structure prediction. 501-512 - David F. Burke, Charlotte M. Deane, Tom L. Blundell:
Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure. 513-519 - Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando, Hideo Matsuda, Yutaka Akiyama:
Quick selection of representative protein chain sets based on customizable requirements. 520-526 - Rui Alves, Michael A. Savageau:
Comparing systemic properties of ensembles of biological networks by graphical and statistical methods. 527-533 - Rui Alves, Michael A. Savageau:
Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways. 534-547 - Norman W. Paton, Shakeel A. Khan, Andrew Hayes, Fouzia Moussouni, Andy Brass, Karen Eilbeck, Carole A. Goble, Simon J. Hubbard, Stephen G. Oliver:
Conceptual modelling of genomic information. 548-557
- Denis Milan, Rachel Hawken, Cédric Cabau, Sophie Leroux, Carine Genet, Yvette Lahbib, Gwenola Tosser, Annie Robic, Francois Hatey, Lee Alexander, Craig Beattie, Larry Schook, Martine Yerle, Joël Gellin:
IMpRH Server: an RH mapping server available on the Web. 558-559 - A. C. Frank, J. R. Lobry:
Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. 560-561 - Darren Martin, Ed Rybicki:
RDP: detection of recombination amongst aligned sequences. 562-563 - Raphaël Clifford, Aaron J. Mackey:
Disperse: a simple and efficient approach to parallel database searching. 564-565 - Liisa Holm, Jong-Chan Park:
DaliLite workbench for protein structure comparison. 566-567 - Miquel de Cáceres, Jordi Villá, Juan José Lozano, Ferran Sanz:
MIPSIM: similarity analysis of molecular interaction potentials. 568-569
Volume 16, Number 7, July 2000
- Aleksandar Milosavljevic:
The Economic Value of Bioinformation. 571-572
- Mark J. Gibbs, John S. Armstrong, Adrian J. Gibbs:
Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. 573-582 - Elena Rivas, Sean R. Eddy:
Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. 583-605 - Fabien Campagne:
Clustalnet: the joining of Clustal and CORBA. 606-612 - Sarah J. Wheelan, Aron Marchler-Bauer, Stephen H. Bryant:
Domain size distributions can predict domain boundaries. 613-618 - Chantal Korostensky, Gaston H. Gonnet:
Using traveling salesman problem algorithms for evolutionary tree construction. 619-627 - Chenna Ramu, Christine Gemünd, Toby J. Gibson:
Object-oriented parsing of biological databases with Python. 628-638 - David L. Steffen, Alan E. Levine, S. Yarus, R. A. Baasiri, D. A. Wheeler:
Digital reviews in molecular biology: approaches to structured digital publication. 639-649
- Elliott H. Margulies, Jeffrey W. Innis:
eSAGE: managing and analysing data generated with Serial Analysis of Gene Expression (SAGE). 650-651 - Hugh-George Patterton, Steven Graves:
DNAssist: the integrated editing and analysis of molecular biology sequences in Windows. 652-653 - Gina Cannarozzi, Michael T. Hallett, J. Norberg, Xianghong Zhou:
A cross-comparison of a large dataset of genes. 654-655 - Luis Sánchez-Pulido, Yan P. Yuan, Miguel A. Andrade, Peer Bork:
NAIL-Network Analysis Interface for Linking HMMER results. 656-657 - Stephen A. Cammer:
SChiSM: creating interactive web page annotations of molecular structure models using Chime. 658-659 - Jonathan Bingham, Sucha Sudarsanam:
Visualizing large hierarchical clusters in hyperbolic space. 660-661
Volume 16, Number 8, August 2000
- Akiyoshi Wada:
Bioinformatics-the necessity of the quest for 'first principles' in life. 663-664
- Robert Giegerich:
A systematic approach to dynamic programming in bioinformatics. 665-677
- D. Curtis Jamison, James W. Thomas, Eric D. Green:
ComboScreen facilitates the multiplex hybridization-based screening of high-density clone arrays. 678-684 - Elisabetta Manduchi, Gregory R. Grant, Steven E. McKenzie, G. Christian Overton, Saul Surrey, Christian J. Stoeckert Jr.:
Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. 685-698 - Torbjørn Rognes, Erling Seeberg:
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. 699-706
- Patrik D'haeseleer, Shoudan Liang, Roland Somogyi:
Genetic network inference: from co-expression clustering to reverse engineering. 707-726 - Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
Inferring qualitative relations in genetic networks and metabolic pathways. 727-734
- C. A. M. Semple, S. W. Morris, David J. Porteous, Kathryn L. Evans:
In silico identification of transcripts and SNPs from a region of 4p linked with bipolar affective disorder. 735-738
- Mukund V. Katti, Meena K. Sakharkar, Prabhakar K. Ranjekar, Vidya S. Gupta:
TRES: comparative promoter sequence analysis. 739-740 - Kerstin M. L. Menne, Henning Hermjakob, Rolf Apweiler:
A comparison of signal sequence prediction methods using a test set of signal peptides. 741-742 - Josep F. Abril, Roderic Guigó:
gff2ps: visualizing genomic annotations. 743-744 - Kevin G. Becker, Shawnte L. White, Jerri Muller, James Engel:
BBID: the biological biochemical image database. 745-746 - Alexey Lagunin, Alla Stepanchikova, Dmitrii Filimonov, Vladimir Poroikov:
PASS: prediction of activity spectra for biologically active substances. 747-748