Bioinformatics, Volume 16

Volume 16, Number 1, January 2000

Articles

• 
  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

Articles

• 
  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

Articles

• 
  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

Articles

• 
  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

Articles

• 
  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

Editorial

• 
  Rainer Fuchs:
  Analyse This...Or: Intelligent Help for The Rest of Us. 491-493

Original Papers

• 
  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

Applications Notes

• 
  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

Editorial

• 
  Aleksandar Milosavljevic:
  The Economic Value of Bioinformation. 571-572

Original Papers

• 
  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

Applications Notes

• 
  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

Editorial

• 
  Akiyoshi Wada:
  Bioinformatics-the necessity of the quest for 'first principles' in life. 663-664

REVIEWS:

• 
  Robert Giegerich:
  A systematic approach to dynamic programming in bioinformatics. 665-677

Original Papers

• 
  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

Computing with Genetic Networks

• 
  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

Discovery Notes

• 
  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

Applications Notes

• 
  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

Volume 16, Number 9, September 2000

Editorial

• 
  Philip E. Bourne, Michael Gribskov:
  ISMB-2000: Bioinformatics enters a new millennium. 749

Original Papers

• 
  Frédéric Plewniak, Julie Dawn Thompson, Olivier Poch:
  Ballast: Blast post-processing based on locally conserved segments. 750-759
• 
  Pauline C. Ng, Jorja G. Henikoff, Steven Henikoff:
  PHAT: a transmembrane-specific substitution matrix. 760-766
• 
  Junhyong Kim, Etsuko N. Moriyama, Coral G. Warr, Peter J. Clyne, John R. Carlson:
  Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties. 767-775
• 
  Naomi Siew, Arne Elofsson, Leszek Rychlewski, Daniel Fischer:
  MaxSub: an automated measure for the assessment of protein structure prediction quality. 776-785
• 
  Rui Alves, Michael A. Savageau:
  Extending the method of mathematically controlled comparison to include numerical comparisons. 786-798

GCB'99 Papers Presented at the German Conference on Bioinformactics, 1999, Hanover

• 
  Alexander Zien, Gunnar Rätsch, Sebastian Mika, Bernhard Schölkopf, Thomas Lengauer, Klaus-Robert Müller:
  Engineering support vector machine kernels that recognize translation initiation sites. 799-807
• 
  Knut Reinert, Jens Stoye, Torsten Will:
  An iterative method for faster sum-of-pairs multiple sequence alignment. 808-814
• 
  Oliver Kohlbacher, Hans-Peter Lenhof:
  BALL-rapid software prototyping in computational molecular biology. 815-824
• 
  Robert Küffner, Ralf Zimmer, Thomas Lengauer:
  Pathway analysis in metabolic databases via differential metabolic display (DMD). 825-836

Discovery Notes

• 
  M. M. Soloviev:
  Detection of a surface-exposed PEST like sequence in the metabotropic glutamate receptor mGluR1. 837-838
• 
  T. V. Gnanasekaran, Suraj Peri, A. Arockiasamy, S. Krishnaswamy:
  Profiles from structure based sequence alignment of porins can identify ß stranded integral membrane proteins. 839-842

Applications Notes

• 
  Michael C. Giddings, Olga V. Matveeva, John F. Atkins, Raymond F. Gesteland:
  ODNBase-a web database for antisense oligonucleotide effectiveness studies. 843-844
• 
  Martin Prokop, Jirí Damborský, Jaroslav Koca:
  TRITON: in silico construction of protein mutants and prediction of their activities. 845-846
• 
  Bernhard Haubold, Richard R. Hudson:
  LIAN 3.0: detecting linkage disequilibrium in multilocus data. 847-849

Volume 16, Number 10, October 2000

Editorial

• 
  Timothy G. Littlejohn:
  Bioinformatics in Australia. 849-850

Reviews

• 
  Kirill Degtyarenko:
  Bioinorganic motifs: towards functional classification of metalloproteins. 851-864

Original Papers

• 
  Pierre Baldi, Pierre-François Baisnée:
  Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. 865-889
• 
  Ralf Herwig, Armin Otto Schmitt, Matthias Steinfath, John O'Brien, Henrik Seidel, Sebastian Meier-Ewert, Hans Lehrach, Uwe Radelof:
  Information theoretical probe selection for hybridisation experiments. 890-898
• 
  Antoine H. C. van Kampen, Barbera D. C. van Schaik, Erwin Pauws, E. M. C. Michiels, J. M. Ruijter, H. N. Caron, Rogier Versteeg, S. H. Heisterkamp, Jack A. M. Leunissen, Frank Baas, M. van der Mee:
  USAGE: a web-based approach towards the analysis of SAGE data. 899-905
• 
  Terrence S. Furey, Nello Cristianini, Nigel Duffy, David W. Bednarski, Michèl Schummer, David Haussler:
  Support vector machine classification and validation of cancer tissue samples using microarray expression data. 906-914
• 
  Vasilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy, Stavros J. Hamodrakas, Chris Sander, Christos A. Ouzounis:
  CAST: an iterative algorithm for the complexity analysis of sequence tracts. 915-922
• 
  Federico M. Stefanini, A. Camussi:
  The reduction of large molecular profiles to informative components using a Genetic Algorithm. 923-931
• 
  Pietro Liò, Marina Vannucci:
  Finding pathogenicity islands and gene transfer events in genome data. 932-940

Discovery Notes

• 
  George Johnson, Tai Te Wu:
  Matching amino acid and nucleotide sequences of mouse rheumatoid factor CDRH3-FRH4 segments to other mouse antibodies with known specificities. 941-943

Applications Notes

• 
  Kim Rutherford, Julian Parkhill, James Crook, Terry Horsnell, Peter Rice, Marie-Adèle Rajandream, Bart Barrell:
  Artemis: sequence visualization and annotation. 944-945
• 
  Birong Liao, Walker Hale, Charles B. Epstein, Ronald A. Butow, Harold R. Garner:
  MAD: a suite of tools for microarray data management and processing. 946-947
• 
  Burkhard Morgenstern:
  A space-efficient algorithm for aligning large genomic sequences. 948-949
• 
  Hongyao Zhu, Catherine H. Schein, Werner Braun:
  MASIA: recognition of common patterns and properties in multiple aligned protein sequences. 950-951

Volume 16, Number 11, November 2000

Original Papers

• 
  Michael Z. Man, Xuning Wang, Yixin Wang:
  POWER_SAGE: comparing statistical tests for SAGE experiments. 953-959
• 
  Tetsuo Nishikawa, Toshio Ota, Takao Isogai:
  Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences. 960-967
• 
  Ana Tereza Ribeiro de Vasconcelos, Marco A. Grivet Mattoso Maia, Darcy F. de Almeida:
  Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidis. 968-977
• 
  Jong-Chan Park, Sabine Dietmann, Andreas Heger, Liisa Holm:
  Estimating the significance of sequence order in protein secondary structure and prediction. 978-987
• 
  Anders Wallqvist, Yoshifumi Fukunishi, Lynne Reed Murphy, Addi Fadel, Ronald M. Levy:
  Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. 988-1002
• 
  Derek A. Ruths, Edward S. Chen, Leland Ellis:
  Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions. 1003-1009
• 
  Simon P. Blomberg:
  Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertainty. 1010-1013

Computing with Genetic Networks

• 
  Tim Beißbarth, Kurt Fellenberg, Benedikt Brors, Rosa Arribas-Prat, Judith M. Boer, Nicole C. Hauser, Marcel Scheideler, Jörg D. Hoheisel, Günther Schütz, Annemarie Poustka, Martin Vingron:
  Processing and quality control of DNA array hybridization data. 1014-1022
• 
  Eberhard O. Voit, Tomas Radivoyevitch:
  Biochemical systems analysis of genome-wide expression data. 1023-1037

Applications Notes

• 
  Christopher M. L. S. Bouton, Jonathan Pevsner:
  DRAGON: Database Referencing of Array Genes Online. 1038-1039
• 
  Joseph A. Bedell, Ian Korf, Warren Gish:
  MaskerAid : a performance enhancement to RepeatMasker. 1040-1041
• 
  Roderic D. M. Page:
  Circles: automating the comparative analysis of RNA secondary structure. 1042-1043
• 
  Kristian Vlahovicek, Sándor Pongor:
  model.it : building three dimensional DNA models from sequence data. 1044-1045
• 
  Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak:
  VISTA : visualizing global DNA sequence alignments of arbitrary length. 1046-1047
• 
  Paul J. Kersey, Henning Hermjakob, Rolf Apweiler:
  VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL. 1048-1049
• 
  Eric Beitz:
  TEXtopo: shaded membrane protein topology plots in LATEX2. 1050-1051
• 
  Ian Korf, Warren Gish:
  MPBLAST : improved BLAST performance with multiplexed queries. 1052-1053
• 
  Matthew Boone, Chris Upton:
  BLAST Search Updater: a notification system for new database matches. 1054-1055
• 
  Jeong-Hyeon Choi, Ho-Youl Jung, Hye-Sun Kim, Hwan-Gue Cho:
  PhyloDraw: a phylogenetic tree drawing system. 1056-1058

Volume 16, Number 12, December 2000

Editorial

• 
  C. Victor Jongeneel:
  The need for a human gene index. 1059-1061

Original Papers

• 
  Wooyoung Choe, Okan K. Ersoy, Minou Bina:
  Neural network schemes for detecting rare events in human genomic DNA. 1062-1072
• 
  Dimitris Anastassiou:
  Frequency-domain analysis of biomolecular sequences. 1073-1081
• 
  Raymond Wheeler, Richard Hughey:
  Optimizing reduced-space sequence analysis. 1082-1090
• 
  Ying Xu, Dong Xu, Harold N. Gabow:
  Protein domain decomposition using a graph-theoretic approach. 1091-1104
• 
  Weizhong Li, Frederic Pio, Krzysztof Pawlowski, Adam Godzik:
  Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. 1105-1110
• 
  Kenji Mizuguchi, Tom L. Blundell:
  Analysis of conservation and substitutions of secondary structure elements within protein superfamilies. 1111-1119

Ontology

• 
  Andrey Rzhetsky, Tomohiro Koike, Sergey Kalachikov, Shawn M. Gomez, Michael Krauthammer, Sabina H. Kaplan, Pauline Kra, James J. Russo, Carol Friedman:
  A knowledge model for analysis and simulation of regulatory networks. 1120-1128
• 
  Toni Kazic:
  Semiotes: a semantics for sharing. 1129-1144

Database Development

• 
  Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov:
  InterPro-an integrated documentation resource for protein families, domains and functional sites. 1145-1150

Applications Notes

• 
  Meena K. Sakharkar, Pandjassarame Kangueane, Tong W. Woon, Tin Wee Tan, Prasanna R. Kolatkar, Manyuan Long, Sandro J. de Souza:
  IE-Kb: intron exon knowledge base. 1151-1152
• 
  Xavier Serra-Hartmann, Xavier Rebordosa, Jaume Piñol, Enrique Querol, Marc A. Martí-Renom:
  ASAP: analysis of peptide composition. 1153-1154
• 
  János Murvai, Kristian Vlahovicek, Sándor Pongor:
  A simple probabilistic scoring method for protein domain identification. 1155-1156
• 
  Kevin A. T. Silverstein, Alan Kilian, John L. Freeman, James E. Johnson, Ihab A. Awad, Ernest F. Retzel:
  PANAL: an integrated resource for Protein sequence ANALysis. 1157-1158
• 
  Steffen Möller, Evgenia V. Kriventseva, Rolf Apweiler:
  A collection of well characterised integral membrane proteins. 1159-1160