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Bioinformatics, Volume 17
Volume 17, Number 1, January 2001
- Chris Sander:
Bioinformatics - Challenges in 2001. 1-2
- 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
- Richard M. R. Coulson, Anton J. Enright
, Christos A. Ouzounis
:
Transcription-associated protein families are primarily taxon-specific. 95-97
- 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
- Alvis Brazma
:
On the Importance of Standardisation in Life Sciences. 113-114
- Frédéric Achard, Guy Vaysseix, Emmanuel Barillot:
XML, bioinformatics and data integration. 115-125
- 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
- Hiromi Nishida
:
Distribution of genes for lysine biosynthesis through the aminoadipate pathway among prokaryotic genomes. 189-191
- 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
- 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
- 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
- David J. States:
Time to defend what we have won. 299
- 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 S. Eisenberg:
Mining literature for protein-protein interactions. 359-363 - Hubert Hug, Rainer Schuler:
Strategies for the development of a peptide computer. 364-368
- 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
- Martin Vingron:
Bioinformatics needs to adopt statistical thinking - Editorial. 389-390
- Webb Miller:
Comparison of genomic DNA sequences: solved and unsolved problems. 391-397
- 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
- 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
- Win Hide
:
ExScript: An 'EX'-Centric Approach to the Description of Transcript Diversity. 485-486
- 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
- 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
- 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
- David B. Searls
:
Reading the book of life. 579-580
- 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
- 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
- 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 E. 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
- 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