Bioinformatics, Volume 17

Volume 17, Number 1, January 2001

Ditorial

• 
  Chris Sander:
  Bioinformatics - Challenges in 2001. 1-2

Original Papers

• 
  Ekaterina M. Myasnikova, Anastassia Samsonova, Konstantin Kozlov, Maria Samsonova, John Reinitz:
  Registration of the expression patterns of Drosophila segmentation genes by two independent methods. 3-12
• 
  Andrey A. Mironov, Pavel S. Novichkov, Mikhail S. Gelfand:
  Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. 13-15
• 
  Prasith Baccam, Robert J. Thompson, Olivier Fedrigo, Susan Carpenter, James L. Cornette:
  PAQ: Partition Analysis of Quasispecies. 16-22
• 
  Gill Bejerano, Golan Yona:
  Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. 23-43
• 
  Dmitrij Frishman, Kaj Albermann, Jean Hani, Klaus Heumann, Agnes Metanomski, Alfred Zollner, Hans-Werner Mewes:
  Functional and structural genomics using PEDANT. 44-57
• 
  Salvatore Lanzavecchia, Francesca Cantele, Pier Luigi Bellon:
  Alignment of 3D structures of macromolecular assemblies. 58-62
• 
  Liam J. McGuffin, Kevin Bryson, David T. Jones:
  What are the baselines for protein fold recognition? 63-72
• 
  Catherine Letondal:
  A Web interface generator for molecular biology programs in Unix. 73-82
• 
  Adam C. Siepel, Andrew D. Farmer, Andrew N. Tolopko, Mingzhe Zhuang, Pedro Mendes, William D. Beavis, Bruno W. S. Sobral:
  ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. 83-94

Discovery Notes

• 
  Richard M. R. Coulson, Anton J. Enright, Christos A. Ouzounis:
  Transcription-associated protein families are primarily taxon-specific. 95-97

Applications Notes

• 
  Günter Raddatz, Michaela Dehio, Thomas F. Meyer, Christoph Dehio:
  PrimeArray: genome-scale primer design for DNA-microarray construction. 98-99
• 
  William C. Ray, Charles J. Daniels:
  The PACRAT system: an extensible WWW-based system for correlated sequence retrieval, storage and analysis. 100-104
• 
  J. N. Selley, J. Swift, Terri K. Attwood:
  EASY-an Expert Analysis SYstem for interpreting database search outputs. 105-106
• 
  Christoph Helma, Ross D. King, Stefan Kramer, Ashwin Srinivasan:
  The Predictive Toxicology Challenge 2000-2001. 107-108

Volume 17, Numer 2, February

Editorial

• 
  Alvis Brazma:
  On the Importance of Standardisation in Life Sciences. 113-114

Reviews

• 
  Frédéric Achard, Guy Vaysseix, Emmanuel Barillot:
  XML, bioinformatics and data integration. 115-125

Original Papers

• 
  Javier Herrero, Alfonso Valencia, Joaquín Dopazo:
  A hierarchical unsupervised growing neural network for clustering gene expression patterns. 126-136
• 
  Bruce A. Shapiro, Jin Chu Wu, David Bengali, Mark J. Potts:
  The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation. 137-148
• 
  Ming Li, Jonathan H. Badger, Xin Chen, Sam Kwong, Paul E. Kearney, Haoyong Zhang:
  An information-based sequence distance and its application to whole mitochondrial genome phylogeny. 149-154
• 
  Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, Toshihisa Takagi:
  Automated extraction of information on protein-protein interactions from the biological literature. 155-161
• 
  Raja Mazumder, Ashok S. Kolaskar, Donald Seto:
  GeneOrder: comparing the order of genes in small genomes. 162-166
• 
  Hideaki Mizuno, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai:
  ORI-GENE: gene classification based on the evolutionary tree. 167-173
• 
  Frédéric Tores, Emmanuel Barillot:
  The art of pedigree drawing: algorithmic aspects. 174-179
• 
  Robert Stevens, Carole A. Goble, Patricia G. Baker, Andy Brass:
  A classification of tasks in bioinformatics. 180-188

Discovery Notes

• 
  Hiromi Nishida:
  Distribution of genes for lysine biosynthesis through the aminoadipate pathway among prokaryotic genomes. 189-191

Applications Notes

• 
  Matej Lexa, J. Horak, Bretislav Brzobohaty:
  Virtual PCR. 192-193
• 
  Kevin P. Micallef, Mark Cooper, Dean W. Podlich:
  Using clusters of computers for large QU-GENE simulation experiments. 194-195
• 
  Cécile André, Pierre Vincens, Jean-François Boisvieux, Serge A. Hazout:
  MOSAIC: segmenting multiple aligned DNA sequences. 196-197
• 
  P. M. Stothard:
  COMBOSA3D: combining sequence alignments with three-dimensional structures. 198-199
• 
  Asim S. Siddiqui, Uwe Dengler, Geoffrey J. Barton:
  3Dee: a database of protein structural domains. 200-201
• 
  Piero Fariselli, Rita Casadio:
  RCNPRED: prediction of the residue co-ordination numbers in proteins. 202-204

Volume 17, Number 3, March 2001

Original Papers

• 
  David Hall, Suchendra M. Bhandarkar, Jonathan P. Arnold, Tongzhang Jiang:
  Physical mapping with automatic capture of hybridization data. 205-213
• 
  Thomas Kämpke, Markus Kieninger, Michael Mecklenburg:
  Efficient primer design algorithms. 214-225
• 
  Siu-wai Leung, Chris Mellish, Dave Robertson:
  Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences. 226-236
• 
  Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen:
  Flexibility of the genetic code with respect to DNA structure. 237-248
• 
  Kevin A. T. Silverstein, Elizabeth Shoop, James E. Johnson, Ernest F. Retzel:
  MetaFam: a unified classification of protein families. I. Overview and statistics. 249-261
• 
  Elizabeth Shoop, Kevin A. T. Silverstein, James E. Johnson, Ernest F. Retzel:
  MetaFam: a unified classification of protein families. II. Schema and query capabilities. 262-271
• 
  Andreas Heger, Liisa Holm:
  Picasso: generating a covering set of protein family profiles. 272-279

Applications Notes

• 
  T. Andrew Ronneberg, Stephen J. Freeland, Laura F. Landweber:
  Genview and Gencode: a pair of programs to test theories of genetic code evolution. 280-281
• 
  Weizhong Li, Lukasz Jaroszewski, Adam Godzik:
  Clustering of highly homologous sequences to reduce the size of large protein databases. 282-283
• 
  Kurt S. Thorn, Andrew A. Bogan:
  ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. 284-285
• 
  Neema Jamshidi, Jeremy S. Edwards, Tom Fahland, George M. Church, Bernhard O. Palsson:
  Dynamic simulation of the human red blood cell metabolic network. 286-287
• 
  Pedro Mendes, Douglas B. Kell:
  MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. 288-289

Volume 17, Number 4, April 2001

Editorial

• 
  David J. States:
  Time to defend what we have won. 299

Original Papers

• 
  Christian J. Stoeckert Jr., Angel D. Pizarro, Elisabetta Manduchi, M. Gibson, Brian P. Brunk, Jonathan Crabtree, Jonathan Schug, Shai Shen-Orr, G. Christian Overton:
  A relational schema for both array-based and SAGE gene expression experiments. 300-308
• 
  Ka Yee Yeung, David R. Haynor, Walter L. Ruzzo:
  Validating clustering for gene expression data. 309-318
• 
  Daniel R. Masys, John B. Welsh, J. Lynn Fink, Michael Gribskov, Igor Klacansky, Jacques Corbeil:
  Use of keyword hierarchies to interpret gene expression patterns. 319-326
• 
  Abdullah N. Arslan, Ömer Egecioglu, Pavel A. Pevzner:
  A new approach to sequence comparison: normalized sequence alignment. 327-337
• 
  Rainer Spang, Martin Vingron:
  Limits of homology detection by pairwise sequence comparison. 338-342
• 
  Christian E. V. Storm, Erik L. L. Sonnhammer:
  NIFAS: visual analysis of domain evolution in proteins. 343-348
• 
  Chris H. Q. Ding, Inna Dubchak:
  Multi-class protein fold recognition using support vector machines and neural networks. 349-358
• 
  Edward M. Marcotte, Ioannis Xenarios, David Eisenberg:
  Mining literature for protein-protein interactions. 359-363
• 
  Hubert Hug, Rainer Schuler:
  Strategies for the development of a peptide computer. 364-368

Applications Notes

• 
  B. Dysvik, Inge Jonassen:
  J-Express: exploring gene expression data using Java. 369-370
• 
  J. L. Lessem, Stacey S. Cherny:
  DeFries-Fulker multiple regression analysis of sibship QTL data: a SAS®macro. 371-372
• 
  Cédric Notredame:
  Mocca: semi-automatic method for domain hunting. 373-374
• 
  S. Sujatha, S. Balaji, Narayanaswamy Srinivasan:
  PALI: a database of alignments and phylogeny of homologous protein structures. 375-376
• 
  Christoph Gille, Cornelius Frömmel:
  STRAP: editor for STRuctural Alignments of Proteins. 377-378
• 
  Kim Lan Sim, Tomoyuki Uchida, Satoru Miyano:
  ProDDO: a database of disordered proteins from the Protein Data Bank (PDB). 379-380
• 
  Eran Eyal, Rafael Najmanovich, Vladimir Sobolev, Marvin Edelman:
  MutaProt: a web interface for structural analysis of point mutations. 381-382
• 
  Christian M. Zmasek, Sean R. Eddy:
  ATV: display and manipulation of annotated phylogenetic. 383-384
• 
  Fiona S. L. Brinkman, Ivan Wan, Robert E. W. Hancock, Ann M. Rose, Steven J. M. Jones:
  PhyloBLAST: facilitating phylogenetic analysis of BLAST results. 385-387

Volume 17, Number 5, May 2001

Editorial

• 
  Martin Vingron:
  Bioinformatics needs to adopt statistical thinking - Editorial. 389-390

Reviews

• 
  Webb Miller:
  Comparison of genomic DNA sequences: solved and unsolved problems. 391-397

Original Papers

• 
  Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak, Marcin Jaroszewski, Wojciech T. Markiewicz:
  Construction of DNA restriction maps based on a simplified experiment. 398-404
• 
  Alexander V. Lukashin, Rainer Fuchs:
  Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters. 405-414
• 
  Brian Gaschen, Carla Kuiken, Bette T. Korber, Brian T. Foley:
  Retrieval and on-the-fly alignment of sequence fragments from the HIV database. 415-418
• 
  Jeremy Buhler:
  Efficient large-scale sequence comparison by locality-sensitive hashing. 419-428
• 
  Jonas S. Almeida, João A. Carriço, António Maretzek, Peter A. Noble, Madilyn Fletcher:
  Analysis of genomic sequences by Chaos Game Representation. 429-437
• 
  Tony Y. T. Chan:
  Unsupervised classification of noisy chromosomes. 438-444
• 
  Ross D. King, Andreas Karwath, Amanda Clare, Luc Dehaspe:
  The utility of different representations of protein sequence for predicting functional class. 445-454
• 
  Joel R. Bock, David A. Gough:
  Predicting protein-protein interactions from primary structure. 455-460
• 
  Moritz Y. Becker, Isabel Rojas:
  A graph layout algorithm for drawing metabolic pathways. 461-467
• 
  Yury V. Bukhman, Jeffrey Skolnick:
  BioMolQuest: integrated database-based retrieval of protein structural and functional information. 468-478

Applications Notes

• 
  Gráinne McGuire, Michael C. Denham, David J. Balding:
  MAC5: Bayesian inference of phylogenetic trees from DNA sequences incorporating gaps. 479-480
• 
  Louxin Zhang, Chew-Kiat Heng, Tin Wee Tan:
  Cladogramer: incorporating haplotype frequency into cladogram analysis. 481-482
• 
  Kazuhisa Ichikawa:
  A-Cell: graphical user interface for the construction of biochemical reaction models. 483-484

Volume 17, Number 6, June 2001

Editorial

• 
  Win Hide:
  ExScript: An 'EX'-Centric Approach to the Description of Transcript Diversity. 485-486

Original Papers

• 
  Eric Harley, Anthony J. Bonner, Nathan Goodman:
  Uniform integration of genome mapping data using intersection graphs. 487-494
• 
  John Aach, George M. Church:
  Aligning gene expression time series with time warping algorithms. 495-508
• 
  Pierre Baldi, Anthony D. Long:
  A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. 509-519
• 
  Olga G. Troyanskaya, Michael N. Cantor, Gavin Sherlock, Patrick O. Brown, Trevor Hastie, Robert Tibshirani, David Botstein, Russ B. Altman:
  Missing value estimation methods for DNA microarrays. 520-525
• 
  Peter D. Karp, Suzanne M. Paley, Jingchun Zhu:
  Database verification studies of SWISS-PROT and GenBank. 526-532
• 
  Rolf Apweiler, Paul J. Kersey, Vivien Junker, Amos Bairoch:
  Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al. 533-534
• 
  Ingrid B. Jakobsen, Jennifer A. Saleeba, Michael Poidinger, Timothy G. Littlejohn:
  TreeGeneBrowser: phylogenetic data mining of gene sequences from public databases. 535-540
• 
  Charlotte M. Deane, Quentin Kaas, Tom L. Blundell:
  SCORE: predicting the core of protein models. 541-550
• 
  Robert Garian:
  Prediction of quaternary structure from primary structure. 551-556

Discovery Notes

• 
  Dong Qi, A. Jamie Cuticchia:
  Compositional symmetries in complete genomes. 557-559
• 
  John M. Ward:
  Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana. 560-563

Applications Notes

• 
  Pierre R. Bushel, Hisham Hamadeh, Lee Bennett, Stella Sieber, Karla Martin, Emile F. Nuwaysir, Kate Johnson, Kelli Reynolds, Richard S. Paules, Cynthia A. Afshari:
  MAPS: a microarray project system for gene expression experiment information and data validation. 564-565
• 
  Michael E. Wall, Patricia A. Dyck, Thomas S. Brettin:
  SVDMAN-singular value decomposition analysis of microarray data. 566-568
• 
  Xuhua Xia, Zheng Xie:
  AMADA: analysis of microarray data. 569-570
• 
  Birgitta Geier, Gabi Kastenmüller, Matthias Fellenberg, Hans-Werner Mewes, Burkhard Morgenstern:
  The HIB database of annotated UniGene clusters. 571-572
• 
  Ari Löytynoja, Michel C. Milinkovitch:
  SOAP, cleaning multiple alignments from unstable blocks. 573-574
• 
  Nicolas Le Novère, Thomas Simon Shimizu:
  STOCHSIM: modelling of stochastic biomolecular processes. 575-576
• 
  Malay Kumar Basu:
  SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services. 577-578

Volume 17, Supplement, June 2001

• 
  Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, July 21-25, 2001, Copenhagen, Denmark. 2001 [contents]

Volume 17, Number 7, July 2001

Editorial

• 
  David B. Searls:
  Reading the book of life. 579-580

Original Papers

• 
  Xiayi Ke, William Tapper, Andrew Collins:
  LDB2000: sequence-based integrated maps of the human genome. 581-586
• 
  Barbara A. Eckman, Anthony Kosky, Leonardo A. Laroco Jr.:
  Extending traditional query-based integration approaches for functional characterization of post-genomic data. 587-601
• 
  Jack E. Tabaska, Ramana V. Davuluri, Michael Q. Zhang:
  Identifying the 3'-terminal exon in human DNA. 602-607
• 
  Debraj Guha Thakurta, Gary D. Stormo:
  Identifying target sites for cooperatively binding factors. 608-621
• 
  Rongxiang Liu, Thomas W. Blackwell, David J. States:
  Conformational model for binding site recognition by the E.coli MetJ transcription factor. 622-633
• 
  Matthias Steinfath, Wasco Wruck, Henrik Seidel, Hans Lehrach, Uwe Radelof, John O'Brien:
  Automated image analysis for array hybridization experiments. 634-641
• 
  Jan Gorodkin, Christian Zwieb, Bjarne Knudsen:
  Semi-automated update and cleanup of structural RNA alignment databases. 642-645
• 
  Steffen Möller, Michael D. R. Croning, Rolf Apweiler:
  Evaluation of methods for the prediction of membrane spanning regions. 646-653

Applications Notes

• 
  Jochen Hampe, Andreas Wollstein, Timothy Lu, Hans-Jürgen Frevel, Marcus Will, Carl Manaster, Stefan Schreiber:
  An integrated system for high throughput TaqManTM based SNP genotyping. 654-655
• 
  Raf M. Podowski, Erik L. L. Sonnhammer:
  MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs. 656-657
• 
  Rob M. Ewing, J. Michael Cherry:
  Visualization of expression clusters using Sammon's non-linear mapping. 658-659
• 
  Yoshiyuki Suzuki, Takashi Gojobori, Masatoshi Nei:
  ADAPTSITE: detecting natural selection at single amino acid sites. 660-661
• 
  Alexei J. Drummond, Korbinian Strimmer:
  PAL: an object-oriented programming library for molecular evolution and phylogenetics. 662-663
• 
  Vladimir Makarenkov:
  T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. 664-668
• 
  Ralf Mrowka:
  A Java applet for visualizing protein-protein interaction. 669-671

Volume 17, Number 8, August 2001

Original Papers

• 
  Meena K. Sakharkar, Tin Wee Tan, Sandro J. de Souza:
  Generation of a database containing discordant intron positions in eukaryotic genes (MIDB). 671-675
• 
  Avril Coghlan, Dónall A. Mac Dónaill, Nigel H. Buttimore:
  Representation of amino acids as five-bit or three-bit patterns for filtering protein databases. 676-685
• 
  Zsuzsanna Dosztányi, Andrew Ernest Torda:
  Amino acid similarity matrices based on force fields. 686-699
• 
  Jimin Pei, Nick V. Grishin:
  AL2CO: calculation of positional conservation in a protein sequence alignment. 700-712
• 
  Kevin Karplus, Birong Hu:
  Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. 713-720
• 
  Sujun Hua, Zhirong Sun:
  Support vector machine approach for protein subcellular localization prediction. 721-728
• 
  William R. Pitt, Mark A. Williams, M. Steven, B. Sweeney, Alan J. Bleasby, David S. Moss:
  The Bioinformatics Template Library-generic components for biocomputing. 729-737

Applications Notes

• 
  David G. Cox, Federico Canzian:
  Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis. 738-739
• 
  Yang He, Xiangming Xu, Kenneth R. Tobutt, Martin S. Ridout:
  Polylink: to support two-point linkage analysis in autotetraploids. 740-741
• 
  Gonçalo R. Abecasis, Stacey S. Cherny, W. O. C. Cookson, Lon R. Cardon:
  GRR: graphical representation of relationship errors. 742-743
• 
  Liqun Xing, Volker Brendel:
  Multi-query sequence BLAST output examination with MuSeqBox. 744-745
• 
  Marc A. Martí-Renom, Valentin A. Ilyin, Andrej Sali:
  DBAli: a database of protein structure alignments. 746-747
• 
  Paul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, Jiye Shi, Hiroki Shirai, Tom L. Blundell:
  HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. 748-749
• 
  Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski:
  Structure prediction meta server. 750-751
• 
  Dominique Douguet, Gilles Labesse:
  Easier threading through web-based comparisons and cross-validations. 752-753
• 
  John P. Huelsenbeck, Fredrik Ronquist:
  MRBAYES: Bayesian inference of phylogenetic trees. 754-755
• 
  Chenna Ramu:
  SIR: a simple indexing and retrieval system for biological flat file databases. 756-758

Volume 17, Number 9, September 2001

Editorial

• 
  William R. Pearson:
  Training for bioinformatics and computational biology. 761-762

Original Papers

• 
  Ka Yee Yeung, Walter L. Ruzzo:
  Principal component analysis for clustering gene expression data. 763-774
• 
  Jeanne Kowalski:
  A non-parametric approach to translating gene region heterogeneity associated with phenotype into location heterogeneity. 775-790
• 
  Katsuhisa Horimoto, Satoshi Fukuchi, Kentaro Mori:
  Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes. 791-802
• 
  Ian Holmes, William J. Bruno:
  Evolutionary HMMs: a Bayesian approach to multiple alignment. 803-820
• 
  Christian M. Zmasek, Sean R. Eddy:
  A simple algorithm to infer gene duplication and speciation events on a gene tree. 821-828
• 
  Ken-ichiro Fukuda, Toshihisa Takagi:
  Knowledge representation of signal transduction pathways. 829-837

Applications Notes

• 
  Xiayi Ke, Andrew Collins, Shu Ye:
  PIRA PCR designer for restriction analysis of single nucleotide polymorphisms. 838-839
• 
  Jacques Colinge, Georg Feger:
  Detecting the impact of sequencing errors on SAGE data. 840-842
• 
  Izabela Makalowska, Joseph F. Ryan, Andreas D. Baxevanis:
  GeneMachine: gene prediction and sequence annotation. 843-844
• 
  Leo Goodstadt, Chris P. Ponting:
  CHROMA: consensus-based colouring of multiple alignments for publication. 845-846
• 
  Evgeni M. Zdobnov, Rolf Apweiler:
  InterProScan - an integration platform for the signature-recognition methods in InterPro. 847-848
• 
  Gábor E. Tusnády, István Simon:
  The HMMTOP transmembrane topology prediction server. 849-850
• 
  John J. Salama, Howard J. Feldman, Christopher W. V. Hogue:
  VISTRAJ: exploring protein conformational space. 851-852
• 
  Anton J. Enright, Christos A. Ouzounis:
  BioLayout-an automatic graph layout algorithm for similarity visualization. 853-854
• 
  Pentti Riikonen, Jorma Boberg, Tapio Salakoski, Mauno Vihinen:
  BioWAP, mobile Internet service for bioinformatics. 855-856
• 
  Kimberly F. Johnson, Simon M. Lin:
  Critical Assessment of Microarray Data Analysis: the 2001 challenge. 857-858

Volume 17, Number 10, October 2001

Editorial

• 
  Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin:
  The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). 859-861

Original Papers

• 
  Vinhthuy T. Phan, Steven Skiena:
  Dealing with errors in interactive sequencing by hybridization. 862-870
• 
  Samuel Levy, Sridhar Hannenhalli, Christopher T. Workman:
  Enrichment of regulatory signals in conserved non-coding genomic sequence. 871-877
• 
  Martin C. Frith, Ulla Hansen, Zhiping Weng:
  Detection of cis -element clusters in higher eukaryotic DNA. 878-889
• 
  Igor B. Rogozin, Alexey V. Kochetov, Fyodor A. Kondrashov, Eugene V. Koonin, Luciano Milanesi:
  Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. 890-900
• 
  Eileen T. Kraemer, Jian Wang, Jinhua Guo, Samuel Hopkins, Jonathan P. Arnold:
  An analysis of gene-finding programs for Neurospora crassa. 901-912
• 
  Artemis G. Hatzigeorgiou, Petko Fiziev, Martin Reczko:
  DIANA-EST: a statistical analysis. 913-919
• 
  Ernst Kretschmann, Wolfgang Fleischmann, Rolf Apweiler:
  Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT. 920-926
• 
  Gill Bejerano, Yevgeny Seldin, Hanah Margalit, Naftali Tishby:
  Markovian domain fingerprinting: statistical segmentation of protein sequences. 927-934
• 
  Eva Bolten, Alexander Schliep, Sebastian Schneckener, Dietmar Schomburg, Rainer Schrader:
  Clustering protein sequences-structure prediction by transitive homology. 935-941
• 
  R. R. Mallios:
  Predicting class II MHC/peptide multi-level binding with an iterative stepwise discriminant analysis meta-algorithm. 942-948
• 
  Jerry Tsai, Neil Voss, Mark Gerstein:
  Determining the minimum number of types necessary to represent the sizes of protein atoms. 949-956
• 
  Piero Fariselli, Rita Casadio:
  Prediction of disulfide connectivity in proteins. 957-964
• 
  I. King Jordan, G. Reid Bishop, Daniel S. Gonzalez:
  Sequence and structural aspects of functional diversification in class I-mannosidase evolution. 965-976
• 
  Ka Yee Yeung, Chris Fraley, Alejandro Murua, Adrian E. Raftery, Walter L. Ruzzo:
  Model-based clustering and data transformations for gene expression data. 977-987
• 
  Andrey Rzhetsky, Shawn M. Gomez:
  Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. 988-996

Volume 17, Number 11, November 2001

Editorial

• 
  Nikolay A. Kolchanov, Charlie Hodgman:
  The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000. 997

BGRS Papers

• 
  Victor G. Levitsky, Olga A. Podkolodnaya, Nikolay A. Kolchanov, Nikolay L. Podkolodny:
  Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. 998-1010
• 
  Pavel S. Novichkov, Mikhail S. Gelfand, Andrey A. Mironov:
  Gene recognition in eukaryotic DNA by comparison of genomic sequences. 1011-1018
• 
  Szymon M. Kielbasa, Jan O. Korbel, Dieter Beule, Johannes Schuchhardt, Hanspeter Herzel:
  Combining frequency and positional information to predict transcription factor binding sites. 1019-1026
• 
  Ponraj Prabakaran, Jianghong An, M. Michael Gromiha, Samuel Selvaraj, Hatsuho Uedaira, Hidetoshi Kono, Akinori Sarai:
  Thermodynamic database for protein-nucleic acid interactions (ProNIT). 1027-1034
• 
  Dmitry A. Afonnikov, Dmitry Yu. Oshchepkov, Nikolay A. Kolchanov:
  Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. 1035-1046
• 
  Eugenia Migliavacca, Alexei A. Adzhubei, Manuel C. Peitsch:
  MDB: a database system utilizing automatic construction of modules and STAR-derived universal language. 1047-1052
• 
  Frank Schacherer, Claudia Choi, Ulrike Götze, Mathias Krull, Susanne Pistor, Edgar Wingender:
  The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. 1053-1057
• 
  Rosel Kretschmer-Kazemi Far, Wolfgang Nedbal, Georg Sczakiel:
  Concepts to automate the theoretical design of effective antisense oligonucleotides. 1058-1061

Discovery Notes

• 
  Victor G. Levitsky, Olga A. Podkolodnaya, Nikolay A. Kolchanov, Nikolay L. Podkolodny:
  Nucleosome formation potential of exons, introns, and Alu repeats. 1062-1064

Applications Notes

• 
  Vasily Ramensky, Vsevolod J. Makeev, Mikhail A. Roytberg, Vladimir G. Tumanyan:
  Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software. 1065-1066

Original Papers

• 
  Fugen Li, Gary D. Stormo:
  Selection of optimal DNA oligos for gene expression arrays. 1067-1076
• 
  Man-Suen Chan, Martin C. J. Maiden, Brian G. Spratt:
  Database-driven Multi Locus Sequence Typing (MLST) of bacterial pathogens. 1077-1083
• 
  P. S. Umesh Adiga, A. Bhomra, Maria Grazia Turri, A. Nicod, S. R. Datta, Peter Jeavons, Richard Mott, Jonathan Flint:
  Automatic analysis of agarose gel images. 1084-1089

Volume 17, Number 12, December 2001

Editorial

• 
  Masaru Tomita:
  Towards Computer Aided Design (CAD) of Useful Microorganisms. 1091-1092

Original Papers

• 
  Hui-Hsien Chou, Michael H. Holmes:
  DNA sequence quality trimming and vector removal. 1093-1104
• 
  William C. Ray, Robert S. Munson Jr., Charles J. Daniels:
  Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features. 1105-1112
• 
  Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau:
  A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. 1113-1122
• 
  Baris E. Suzek, Maria D. Ermolaeva, Mark J. Schreiber, Steven Salzberg:
  A probabilistic method for identifying start codons in bacterial genomes. 1123-1130
• 
  Leping Li, Clarice R. Weinberg, Thomas A. Darden, Lee G. Pedersen:
  Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. 1131-1142
• 
  Katsuhisa Horimoto, Hiroyuki Toh:
  Statistical estimation of cluster boundaries in gene expression profile data. 1143-1151
• 
  Stefania Bortoluzzi, Fabio d'Alessi, Chiara Romualdi, Gian Antonio Danieli:
  Differential expression of genes coding for ribosomal proteins in different human tissues. 1152-1157
• 
  Caleb Webber, Geoffrey J. Barton:
  Estimation of P-values for global alignments of protein sequences. 1158-1167
• 
  Georg Fuellen, Johann-Wolfgang Wägele, Robert Giegerich:
  Minimum conflict: a divide-and-conquer approach to phylogeny estimation. 1168-1178
• 
  Michael Wildpaner, Georg Schneider, Alexander Schleiffer, Frank Eisenhaber:
  Taxonomy workbench. 1179-1182
• 
  Andreas Wagner:
  How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps. 1183-1197
• 
  Frank Kose, Wolfram Weckwerth, Thomas Linke, Oliver Fiehn:
  Visualizing plant metabolomic correlation networks using clique-metabolite matrices. 1198-1208
• 
  Mark Hoebeke, Hélène Chiapello, Philippe Noirot, Philippe Bessières:
  SPiD: a subtilis protein interaction database. 1209-1212
• 
  Michael V. Boland, Robert F. Murphy:
  A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. 1213-1223

Discovery Notes

• 
  Hiromi Nishida:
  Evolution of amino acid biosynthesis and enzymes with broad substrate specificity. 1224-1225

Applications Notes

• 
  Nicolas Le Novère:
  MELTING, computing the melting temperature of nucleic acid duplex. 1226-1227
• 
  Michael Baudis, Michael L. Cleary:
  Progenetix.net: an online repository for molecular cytogenetic aberration data. 1228-1229
• 
  Keith A. Jolley, E. J. Feil, Man-Suen Chan, Martin C. J. Maiden:
  Sequence type analysis and recombinational tests (START). 1230-1231
• 
  Theresa Zhang, Michael Q. Zhang:
  Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes. 1232-1233
• 
  Thomas Junier, Marco Pagni, Philipp Bucher:
  mmsearch: a motif arrangement language and search program. 1234-1235
• 
  Harpreet Singh, G. P. S. Raghava:
  ProPred: prediction of HLA-DR binding sites. 1236-1237
• 
  Roberto C. Togawa, John F. Antoniw, Jonathan G. L. Mullins:
  TMCompare: transmembrane region sequence and structure. 1238-1239
• 
  Leszek Rychlewski:
  ToolShop: prerelease inspections for protein structure prediction servers. 1240-1241
• 
  Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost:
  EVA: continuous automatic evaluation of protein structure prediction servers. 1242-1243
• 
  Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen, Masatoshi Nei:
  MEGA2: molecular evolutionary genetics analysis software. 1244-1245
• 
  Hidetoshi Shimodaira, Masami Hasegawa:
  CONSEL: for assessing the confidence of phylogenetic tree selection. 1246-1247