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ORCIDBioinformatics, Volume 19
Volume 19, Number 1, January 2003
- Chris Sander:
Growth in Bioinformatics. 1
- Pietro Liò:
Wavelets in bioinformatics and computational biology: state of art and perspectives. 2-9
- K. V. Krishna Mohan, C. D. Atreya:
Novel organelle-targeting signals in viral proteins. 10-13
- Ji-Hong Zhang, Ling-Yun Wu, Xiang-Sun Zhang:
Reconstruction of DNA sequencing by hybridization. 14-21 - Hasan H. Otu
, Khalid Sayood:
A divide-and-conquer approach to fragment assembly. 22-29 - João Aires-de-Sousa, Luisa Aires-de-Sousa:
Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps. 30-36 - Chia Huey Ooi, Patrick Tan:
Genetic algorithms applied to multi-class prediction for the analysis of gene expression data. 37-44 - J. M. Deutsch:
Evolutionary algorithms for finding optimal gene sets in microarray prediction. 45-52 - Lorenz Wernisch, Sharon L. Kendall, Shamit Soneji, Andreas Wietzorrek, Tanya Parish, Jason Hinds, Philip D. Butcher, Neil G. Stoker:
Analysis of whole-genome microarray replicates using mixed models. 53-61 - Rahul Bijlani, Yinhe Cheng, David A. Pearce, Andrew I. Brooks, Mitsunori Ogihara:
Prediction of biologically significant components from microarray data: Independently Consistent Expression Discriminator (ICED). 62-70 - Jinyan Li, Huiqing Liu, James R. Downing, Allen Eng-Juh Yeoh, Limsoon Wong:
Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. 71-78 - Chad Creighton, Samir Hanash:
Mining gene expression databases for association rules. 79-86 - Richard A. McIndoe, Aaron Lanzen, Kimberly Hurtz:
MADGE: scalable distributed data management software for cDNA microarrays. 87-89 - Kyeong Eun Lee, Naijun Sha, Edward R. Dougherty, Marina Vannucci, Bani K. Mallick:
Gene selection: a Bayesian variable selection approach. 90-97 - Sorin Draghici, R. Brian Potter:
Predicting HIV drug resistance with neural networks. 98-107 - Olivier Perriquet, Hélène Touzet, Max Dauchet:
Finding the common structure shared by two homologous RNAs. 108-116 - Jacek Leluk, Leszek Konieczny, Irena Roterman:
Search for structural similarity in proteins. 117-124 - Joel R. Bock, David A. Gough:
Whole-proteome interaction mining. 125-134 - Robert J. Gaizauskas, George Demetriou, Peter J. Artymiuk, Peter Willett:
Protein Structures and Information Extraction from Biological Texts: The PASTA System. 135-143 - C. Carleos, F. Rodriguez, H. Lamelas, Jesus A. Baro:
Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations. 144-148
- Shaun Purcell, Stacey S. Cherny, Pak Chung Sham:
Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. 149-150 - Yaw-Ling Lin, Xiaoqiu Huang, Tao Jiang, Kun-Mao Chao:
MAVG: locating non-overlapping maximum average segments in a given sequence. 151-152 - T. De Oliveira, R. Miller, M. Tarin, S. Cassol:
An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences. 153-154 - Jianhua Zhang, Vincent J. Carey, Robert Gentleman:
An extensible application for assembling annotation for genomic data. 155-156 - Ramswamy Anbazhagan:
Microarray data assembler. 157-158 - Vivek Gopalan, Tin Wee Tan, Shoba Ranganathan:
XdomView: protein domain and exon position visualization. 159-160 - Patrick Aloy, Robert B. Russell:
InterPreTS: protein Interaction Prediction through Tertiary Structure. 161-162 - Fabian Glaser, Tal Pupko, Inbal Paz, Rachel E. Bell, Dalit Bechor-Shental, Eric Martz, Nir Ben-Tal:
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information. 163-164 - Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Linda McMahan, Andrej Sali:
ModView, visualization of multiple protein sequences and structures. 165-166 - Tejasvini Prasad, M. N. Prathima, Nagasuma Chandra:
Detection of hydrogen-bond signature patterns in protein families. 167-168
Volume 19, Number 2, February 2003
- Akhilesh Pandey, Suraj Peri, Colin Thacker, Chery A. Whipple, John J. Collins, Matthias Mann:
Computational, experimental analysis reveals a novel Src family kinase in the C. elegans genome. 169-172
- Dörte Solle, David Geissler, Eckbert Stärk, Thomas Scheper, Bernd Hitzmann:
Chemometric Modelling based on 2D-Fluorescence Spectra without a Calibration Measurement. 173-177 - Felix Naef, Nicholas D. Socci, Marcelo Magnasco:
A study of accuracy, precision in oligonucleotide arrays: extracting more signal at large concentrations. 178-184 - Benjamin M. Bolstad, Rafael A. Irizarry, Magnus Åstrand, Terence P. Speed:
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. 185-193 - Chris A. Glasbey, Peter Ghazal:
Combinatorial image analysis of DNA microarray features. 194-203 - Igor Dozmorov, Michael Centola:
An associative analysis of gene expression array data. 204-211 - Neil D. Clarke, Joshua A. Granek:
Rank order metrics for quantifying the association of sequence features with gene regulation. 212-218 - Jakob Skou Pedersen, Jotun Hein:
Gene finding with a hidden Markov model of genome structure and evolution. 219-227 - Xiaoqiu Huang, Kun-Mao Chao:
A generalized global alignment algorithm. 228-233 - Jack Cao, Rosemarie Panetta, Shiyi Yue, Alain Steyaert, Michele Young-Bellido, Sultan Ahmad:
A naive Bayes model to predict coupling between seven transmembrane domain receptors, and G-proteins. 234-240 - Iwei Yeh, Peter D. Karp, Natalya Fridman Noy, Russ B. Altman:
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). 241-248 - Gregory P. Harhay, John W. Keele:
Positional candidate gene selection from livestock EST databases using Gene Ontology. 249-255 - Myung-Hoon Chung, Chul Koo Kim, Kyun Nahm:
Fractional populations in multiple gene inheritance. 256-260 - Steffen Klamt, Jörg Stelling, Martin Ginkel, Ernst Dieter Gilles:
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. 261-269 - Hongwu Ma, An-Ping Zeng:
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. 270-277 - Peter Ernst, Karl-Heinz Glatting, Sándor Suhai:
A task framework for the web interface W2H. 278-282
- Felix Kokocinski, Gunnar Wrobel, Meinhard Hahn, Peter Lichter:
QuickLIMS: facilitating the data management for DNA-microarray fabrication. 283-284 - Ming-Hua Hsieh, Wei-Che Hsu, Sung-Kay Chiu, Chi-Meng Tzeng:
An efficient algorithm for minimal primer set selection. 285-286 - Xiayi Ke, Lon R. Cardon:
Efficient selective screening of haplotype tag SNPs. 287-288 - David Posada, Carsten Wiuf:
Simulating haplotype blocks in the human genome. 289-290 - Jeremy M. R. Martin, Lan J. Mackay, Christopher J. Rawlings:
Pedstrip: extracting a maximal subset of available, unrelated individuals from a pedigree. 291-292 - Yihua Zhou, Jingdong Liu:
AVA: visual analysis of gene expression microarray data. 293-294 - Paul Pavlidis, William Stafford Noble:
Matrix2png: a utility for visualizing matrix data. 295-296 - Lusheng Wang, Ying Xu:
SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignments. 297-298 - Peter De Rijk, Jan Wuyts, Rupert De Wachter:
RnaViz 2: an improved representation of RNA secondary structure. 299-300 - Michael J. Sanderson:
r8s: inferring absolute rates of molecular evolution, divergence times in the absence of a molecular clock. 301-302 - Jack A. M. Leunissen:
Chimera: construction of chimeric sequences for phylogenetic analysis. 303-304 - Kazuharu Arakawa, Koya Mori, Katsuhiko Ikeda, Tatekimi Matsuzaki, Yusuke Kobayashi, Masaru Tomita:
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. 305-306 - Zemin Zhang, William I. Wood:
A profile hidden Markov model for signal peptides generated by HMMER. 307-308 - Kunde Ramamoorthy Govindarajan, Pandjassarame Kangueane, Tin Wee Tan, Shoba Ranganathan:
MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. 309-310 - Charles S. Bond:
TopDraw: a sketchpad for protein structure topology cartoons. 311-321 - Alessandro Pintar, Oliviero Carugo, Sándor Pongor:
DPX: for the analysis of the protein core. 313-314 - Jens P. Linge, Michael Habeck, Wolfgang Rieping, Michael Nilges:
ARIA: automated NOE assignment and NMR structure calculation. 315-316 - Byong-Hyon Ju, Byungkyu Park, Jong H. Park, Kyungsook Han:
Visualization and analysis of protein interactions. 317-318
Volume 19, Number 3, February 2003
- Arnaud Lefebvre, Thierry Lecroq, Hélène Dauchel, Joël Alexandre:
FORRepeats: detects repeats on entire chromosomes and between genomes. 319-326 - Michaël Bekaert, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen, Jean-Paul Forest, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset, Michel Termier:
Towards a computational model for -1 eukaryotic frameshifting sites. 327-335 - Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page:
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. 336-344 - Alexandre G. de Brevern, Serge A. Hazout:
'Hybrid Protein Model' for optimally defining 3D protein structure fragments. 345-353
- Shu-Yun Le, Jih-Hsiang Chen, Danielle Konings, Jacob V. Maizel:
Discovering well-ordered folding patterns in nucleotide sequences. 354-361 - Eugene M. McCarthy, John F. McDonald:
LTR_STRUC: a novel search and identification program for LTR retrotransposons. 362-367 - Anat Reiner, Daniel Yekutieli, Yoav Benjamini:
Identifying differentially expressed genes using false discovery rate controlling procedures. 368-375 - Lance W. Hahn, Marylyn D. Ritchie, Jason H. Moore:
Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. 376-382 - Blaz Zupan, Janez Demsar, Ivan Bratko, Peter Juvan, John A. Halter, Adam Kuspa, Gad Shaulsky:
GenePath: a system for automated construction of genetic networks from mutant data. 383-389 - John Parkinson, Mark L. Blaxter:
SimiTri-visualizing similarity relationships for groups of sequences. 390-395 - Soumya Raychaudhuri, Russ B. Altman:
A literature-based method for assessing the functional coherence of a gene group. 396-401 - William H. Majoros, G. M. Subramanian, Mark Yandell:
Identification of key concepts in biomedical literature using a modified Markov heuristic. 402-407 - Sudhir Sivakumaran, Sridhar Hariharaputran, Jyoti Mishra, Upinder S. Bhalla:
The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. 408-415
- Zhiwei Fang, Mary L. Polacco, Su-Shing Chen, Steven G. Schroeder, D. Hancock, Hector Sanchez-Villeda, Edward H. Coe:
cMap: the comparative genetic map viewer. 416-417 - William W. L. Hsiao, Ivan Wan, Steven J. M. Jones, Fiona S. L. Brinkman:
IslandPath: aiding detection of genomic islands in prokaryotes. 418-420 - Gary Barker, Jacqueline Batley, Helen O'Sullivan, Keith J. Edwards, David Edwards:
Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. 421-422 - Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai:
MELINA: motif extraction from promoter regions of potentially co-regulated genes. 423-424 - Burkhard Morgenstern, Sachin Goel, Alexander Sczyrba, Andreas W. M. Dress:
AltAVisT: Comparing alternative multiple sequence alignments. 425-426 - Jimin Pei, Ruslan Sadreyev, Nick V. Grishin:
PCMA: fast and accurate multiple sequence alignment based on profile consistency. 427-428 - Nickolai Alexandrov, Ilya N. Shindyalov:
PDP: protein domain parser. 429-430 - E. Minch, M. de Rinaldis, S. Weiss:
pathSCOUTTM: exploration and analysis of biochemical pathways. 431-432 - Tetsuro Toyoda, Akihiko Konagaya:
KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. 433-434 - Lingchong You, Apirak Hoonlor, John Yin:
Modeling biological systems using Dynetica-a simulator of dynamic networks. 435-436 - Tetsuro Toyoda, Yoshiki Mochizuki, Akihiko Konagaya:
GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs. 437-438 - Björn M. Ursing:
WiGID: wireless genome information database. 439-440 - Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, Daniel R. Caffrey:
Wrapping up BLAST and other applications for use on Unix clusters. 441-442
Volume 19, Number 4, March 2003
- Michael D. Stern, Sergey V. Anisimov, Kenneth R. Boheler:
Can transcriptome size be estimated from SAGE catalogs? 443-448 - Jyotsna Kasturi, Raj Acharya, Murali Ramanathan:
An information theoretic approach for analyzing temporal patterns of gene expression. 449-458 - Susmita Datta, Somnath Datta:
Comparisons and validation of statistical clustering techniques for microarray gene expression data. 459-466 - Daniel Johansson, Petter Lindgren, Anders Berglund:
A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription. 467-473 - Yihui Luan, Hongzhe Li:
Clustering of time-course gene expression data using a mixed-effects model with B-splines. 474-482 - Lee Makowski, Alexei Soares:
Estimating the diversity of peptide populations from limited sequence data. 483-489 - Dirk Metzler:
Statistical alignment based on fragment insertion and deletion models. 490-499 - Piero Fariselli, Michele Finelli, Davide Marchignoli, Pier Luigi Martelli, Ivan Rossi, Rita Casadio:
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. 500-505 - Mounir Errami, Christophe Geourjon, Gilbert Deléage:
Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures. 506-512 - Susana Vinga, Jonas S. Almeida:
Alignment-free sequence comparison-a review. 513-523 - Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, Dennis Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, Jan-Hendrik S. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul M. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang:
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. 524-531 - Petter Holme, Mikael Huss, Hawoong Jeong:
Subnetwork hierarchies of biochemical pathways. 532-538
- Stephen Wooding:
PopHist: inferring population history from the spectrum of allele frequencies. 539-540 - Steven P. Bennett, Craig G. Nevill-Manning, Douglas L. Brutlag:
3MOTIF: visualizing conserved protein sequence motifs in the protein structure database. 541-542 - Endre Barta, László Kaján, Sándor Pongor:
IS: a web-site for intron statistics. 543 - Jason M. Johnson, Keith Mason, Ciamac Cyrus Moallemi, Hualin Xi, Shyamal Somaroo, Enoch S. Huang:
Protein family annotation in a multiple alignment viewer. 544-545 - Rodrigo Lopez, Stephen Robinson, Asif Kibria, Nicola Harte, Gulam Patel, Rob Harper, Emmanuel Quevillon, Ville Silventoinen, Kimmo Kallio, Petteri Jokinen:
The European Bioinformatics Institute web site: a new view. 546-547
Volume 19, Number 5, March 2003
- Subbaya Subramanian, Vamsi M. Madgula, Ranjan George, Rakesh K. Mishra, Madhusudhan W. Pandit, Chanderashekar S. Kumar, Lalji Singh:
Triplet repeats in human genome: distribution and their association with genes and other genomic regions. 549-552
- Jesús Angulo, Jean Serra:
Automatic analysis of DNA microarray images using mathematical morphology. 553-562 - Anestis Antoniadis, Sophie Lambert-Lacroix, Frédérique Leblanc:
Effective dimension reduction methods for tumor classification using gene expression data. 563-570 - Silvio Bicciato, Alessandra Luchini, Carlo Di Bello:
PCA disjoint models for multiclass cancer analysis using gene expression data. 571-578 - Gernot G. Presting:
Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome. 579-586 - Angela Torres, Juan J. Nieto:
The fuzzy polynucleotide space: basic properties. 587-592 - Chun-Ting Zhang, Ren Zhang, Hong-Yu Ou:
The Z curve database: a graphic representation of genome sequences. 593-599 - David Stephen Horner, Graziano Pesole:
The estimation of relative site variability among aligned homologous protein sequences. 600-606 - Konstantinos Blekas, Dimitrios I. Fotiadis, Aristidis Likas:
Greedy mixture learning for multiple motif discovery in biological sequences. 607-617 - Stéphane Aris-Brosou:
How Bayes tests of molecular phylogenies compare with frequentist approaches. 618-624 - Andrew I. Jewett, Conrad C. Huang, Thomas E. Ferrin:
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. 625-634 - Lars Juhl Jensen, Ramneek Gupta, Hans Henrik Stærfeldt, Søren Brunak:
Prediction of human protein function according to Gene Ontology categories. 635-642 - Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Katsutoshi Takahashi, Masaru Tomita:
Dynamic modeling of genetic networks using genetic algorithm and S-system. 643-650
- Geo Pertea, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush:
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. 651-652 - Jianxin Wang, Ping Liang:
DigiNorthern, digital expression analysis of query genes based on ESTs. 653-654 - Javier Herrero, Ramón Díaz-Uriarte, Joaquín Dopazo:
Gene expression data preprocessing. 655-656 - Jorge García de la Nava, Daniel Franco Santaella, Jesús Cuenca Alba, José María Carazo, Oswaldo Trelles, Alberto D. Pascual-Montano:
Engene: the processing and exploratory analysis of gene expression data. 657-658 - David Venet:
MatArray: a Matlab toolbox for microarray data. 659-660 - Stefano Toppo, Nicola Cannata, Paolo Fontana, Chiara Romualdi, Paolo Laveder, Emanuela Bertocco, Gerolamo Lanfranchi, Giorgio Valle:
TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts. 661-662 - K. Livingstone, Loren H. Rieseberg:
MENDB: a database of polymorphic loci from natural populations. 663-664 - Manoj Bhasin, Harpreet Singh, G. P. S. Raghava:
MHCBN: a comprehensive database of MHC binding and non-binding peptides. 665-666 - Ron Shigeta, Melissa S. Cline, Guoying Liu, Michael A. Siani-Rose:
GPCR-GRAPA-LIB-a refined library of hidden Markov Models for annotating GPCRs. 667-668 - Gianmaria Mancosu, Giuseppe Ledda, Paola M. Melis:
PedNavigator: a pedigree drawing servlet for large and inbred populations. 669-670 - Steve Woolley, Justin Johnson, Matthew J. Smith, Keith A. Crandall, David A. McClellan:
TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees. 671-672 - Mikita Suyama, Osamu Ohara:
DomCut: prediction of inter-domain linker regions in amino acid sequences. 673-674 - Andrew V. Kossenkov, Frank J. Manion, Eugene V. Korotkov, Thomas D. Moloshok, Michael F. Ochs:
ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database. 675-676 - Bruce E. Shapiro, Andre Levchenko, Elliot M. Meyerowitz, Barbara J. Wold, Eric Mjolsness:
Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. 677-678
Volume 19, Number 6, April 2003
- D. Curtis Jamison:
Open Bioinformatics. 679-680
- Subbaya Subramanian, Rakesh K. Mishra, Lalji Singh:
Genome-wide analysis of Bkm sequences (GATA repeats): predominant association with sex chromosomes and potential role in higher order chromatin organization and function. 681-685
- Michael LeBlanc, Charles L. Kooperberg, Thomas M. Grogan, Thomas P. Miller:
Directed indices for exploring gene expression data. 686-693 - Taesung Park, Sung-Gon Yi, Seungmook Lee, Seung Yeoun Lee, Dong-Hyun Yoo, Jun-Ik Ahn, Yong-Sung Lee:
Statistical tests for identifying differentially expressed genes in time-course microarray experiments. 694-703 - Atsushi Kajita, Masayuki Yamamura, Yuji Kohara:
Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans. 704-716 - Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, Anton J. Enright, Mark Carroll, Patrick Poullet, Vasilis J. Promponas, Theodore Liakopoulos, Giorgos Palaios, Claude Pasquier, Stavros J. Hamodrakas, Javier Tamames, Asutosh T. Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David M. A. Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A. Ouzounis:
Evaluation of annotation strategies using an entire genome sequence. 717-726 - Michael I. Sadowski, John Howard Parish:
Automated generation and refinement of protein signatures: case study with G-protein coupled receptors. 727-734 - Edward S. C. Shih, Ming-Jing Hwang:
Protein structure comparison by probability-based matching of secondary structure elements. 735-741 - Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, Adam Godzik:
A segment alignment approach to protein comparison. 742-749 - Elisabeth R. M. Tillier, Thomas W. H. Lui:
Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. 750-755 - Rintaro Saito, Harukazu Suzuki, Yoshihide Hayashizaki:
Construction of reliable protein-protein interaction networks with a new interaction generality measure. 756-763 - Jason Weston, Fernando Pérez-Cruz, Olivier Bousquet, Olivier Chapelle, André Elisseeff, Bernhard Schölkopf:
Feature selection and transduction for prediction of molecular bioactivity for drug design. 764-771
- Alexander Sturn, Bernhard Mlecnik, Roland Pieler, Johannes Rainer, Thomas Truskaller, Zlatko Trajanoski:
Client-Server environment for high-performance gene expression data analysis. 772-773 - Marco Masseroli, Pietro Cerveri, Pier Giuseppe Pelicci, Myriam Alcalay:
GAAS: Gene Array Analyzer Software for management, analysis and visualization of gene expression data. 774-775 - Stephane Rombauts, Yves Van de Peer, Pierre Rouzé:
AFLPinSilico, simulating AFLP fingerprints. 776-777 - Kyungjoon Lee, Isaac S. Kohane, Atul J. Butte:
PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applications. 778-779 - Ren Hua Chung, Dan Gusfield:
Perfect phylogeny haplotyper: haplotype inferral using a tree model. 780-781 - Philip Wong, Grigory Kolesov, Dmitrij Frishman, Walid A. Houry:
Phylogenetic Web Profiler. 782-783 - Klaus Reichard, Michael Kaufmann:
EPPS: mining the COG database by an extended phylogenetic patterns search. 784-785 - Elmar Trost, Hubert Hackl, Michael Maurer, Zlatko Trajanoski:
Java editor for biological pathways. 786-787 - Gabriel F. Berriz, James V. White, Oliver D. King, Frederick P. Roth:
GoFish finds genes with combinations of Gene Ontology attributes. 788-789 - Polixeni Dimitropoulou, Chris Cannings:
RECSIM and INDSTATS: probabilities of identity in general genealogies. 790-791 - Rune Matthiesen, M. Lundsgaard, Karen G. Welinder, G. Bauw:
Interpreting peptide mass spectra by VEMS. 792-793
Volume 19, Number 7, May 2003
- Alfonso Valencia:
Meta, Metan and Cyber Servers. 795
- Xiaowei Wang, Brian Seed:
Selection of Oligonucleotide Probes for Protein Coding Sequences. 796-802 - Kevin Dobbin, Joanna H. Shih, Richard Simon:
Statistical Design of Reverse Dye Microarrays. 803-810 - Wuju Li, Ming Fan, Momiao Xiong:
SamCluster: An Integrated Scheme for Automatic Discovery of Sample Classes Using Gene Expression Profile. 811-817 - David R. Bickel:
Robust Cluster Analysis of Microarray Gene Expression Data with the Number of Clusters Determined Biologically. 818-824 - David Edwards:
Non-linear Normalization and Background Correction in One-channel CDNA Microarray Studies. 825-833 - Shyamal D. Peddada, Edward K. Lobenhofer, Leping Li, Cynthia A. Afshari, Clarice R. Weinberg, David M. Umbach:
Gene Selection and Clustering for Time-course and Dose-response Microarray Experiments Using Order-restricted Inference. 834-841 - Paul M. Magwene, Paul Lizardi, Junhyong Kim:
Reconstructing the Temporal Ordering of Biological Samples Using Microarray Data. 842-850 - Volker Braun, Ricardo B. R. Azevedo, Markus Gumbel, Paul-Michael Agapow, Armand M. Leroi, Hans-Peter Meinzer:
ALES: Cell Lineage Analysis and Mapping of Developmental Events. 851-858 - Mark Hoebeke, Pierre Nicolas, Philippe Bessières:
MuGeN: Simultaneous Exploration of Multiple Genomes and Computer Analysis Results. 859-864 - Sverker Edvardsson, Paul P. Gardner, Anthony M. Poole, Michael D. Hendy, David Penny, Vincent Moulton:
A Search for H/ACA SnoRNAs in Yeast Using MFE Secondary Structure Prediction. 865-873 - Liam J. McGuffin, David T. Jones:
Improvement of the GenTHREADER Method for Genomic Fold Recognition. 874-881 - Oscar Sverud, Robert M. MacCallum:
Towards Optimal Views of Proteins. 882-888
- Karl W. Broman, Hao Wu, Saunak Sen, Gary A. Churchill:
R/qtl: QTL Mapping in Experimental Crosses. 889-890 - Cristian I. Castillo-Davis, Daniel L. Hartl:
GeneMerge - Post-genomic Analysis, Data Mining, and Hypothesis Testing. 891-892 - Kristof Engelen, Bert Coessens, Kathleen Marchal, Bart De Moor:
MARAN: Normalizing Micro-array Data. 893-894 - Antonio Gómez Moruno, Núria Domedel-Puig, Juan Cedano, Jaume Piñol, Enrique Querol:
Do Current Sequence Analysis Algorithms Disclose Multifunctional (moonlighting) Proteins?. 895-896 - Peng Yang, Paul A. Craig, David S. Goodsell, Philip E. Bourne:
BioEditor - Simplifying Macromolecular Structure Annotation. 897-898 - Zsuzsanna Dosztányi, Csaba Magyar, Gábor E. Tusnády, István Simon:
SCide: Identification of Stabilization Centers in Proteins. 899-900 - James M. Brundege, Christopher Dubay:
BioQuery: An Object Framework for Building Queries to Biomedical Databases. 901-902 - Nicolas Goffard, Virginie Garcia, Florian Iragne, Alexis Groppi, Antoine de Daruvar:
IPPRED: Server for Proteins Interactions Inference. 903-904
Volume 19, Number 8, May 2003
- Andrew Tae-Jun Kwon, Holger H. Hoos, Raymond T. Ng:
Inference of Transcriptional Regulation Relationships from Gene Expression Data. 905-912 - Tolga Can, Yujun Wang, Yuan-Fang Wang, Jianwen Su:
FPV: Fast Protein Visualization Using Java 3DTM. 913-922 - See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan:
Integrative Approach for Computationally Inferring Protein Domain Interactions. 923-929 - Larkshmi Krishnamurthy, Joseph H. Nadeau, Gultekin Özsoyoglu, Z. Meral Özsoyoglu, Greg Schaeffer, Murat Tasan, Wanhong Xu:
Pathways Database System: An Integrated System for Biological Pathways. 930-937 - Goran Nenadic, Irena Spasic, Sophia Ananiadou:
Terminology-driven Mining of Biomedical Literature. 938-943
- Marcel Brun, David Sabbagh, Seungchan Kim, Edward R. Dougherty:
Corrected Small-sample Estimation of the Bayes Error. 944-951 - Howard H. Yang, Ying Hu, Michael N. Edmonson, Kenneth H. Buetow, Maxwell P. Lee:
Computation Method to Identify Differential Allelic Gene Expression and Novel Imprinted Genes. 952-955 - Yudong D. He, Hongyue Dai, Eric E. Schadt, Guy Cavet, Stephen W. Edwards, Sergey B. Stepaniants, Sven Duenwald, Robert Kleinhanz, Allan R. Jones, Daniel D. Shoemaker, Roland B. Stoughton:
Microarray Standard Data Set and Figures of Merit for Comparing Data Processing Methods and Experiment Designs. 956-965 - David M. Rocke, Blythe Durbin:
Approximate Variance-stabilizing Transformations for Gene-expression Microarray Data. 966-972 - Doulaye Dembélé, Philippe Kastner:
Fuzzy C-means Method for Clustering Microarray Data. 973-980 - Sorin Draghici, Frank M. Graziano, Samira Y. Kettoola, Ishwar K. Sethi, George Towfic:
Mining HIV Dynamics Using Independent Component Analysis. 981-986 - Svetlana Boycheva, Georgi Chkodrov, Ivan Ivanov:
Codon Pairs in the Genome of Escherichia Coli. 987-998 - Christopher J. Lee:
Generating Consensus Sequences from Partial Order Multiple Sequence Alignment Graphs. 999-1008 - Harpreet Singh, G. P. S. Raghava:
ProPred1: Prediction of Promiscuous MHC Class-I Binding Sites. 1009-1014 - Krzysztof Ginalski, Arne Elofsson, Daniel Fischer, Leszek Rychlewski:
3D-Jury: A Simple Approach to Improve Protein Structure Predictions. 1015-1018 - Ralph E. Steuer, Jürgen Kurths, Oliver Fiehn, Wolfram Weckwerth:
Observing and Interpreting Correlations in Metabolic Networks. 1019-1026 - Julien Gagneur, David B. Jackson, Georg Casari:
Hierarchical Analysis of Dependency in Metabolic Networks. 1027-1034
- Apuã C. M. Paquola, Abimael A. Machado, Eduardo M. Reis, Aline Maria da Silva, Sergio Verjovski-Almeida:
Zerg: A Very Fast BLAST Parser Library. 1035-1036 - David M. A. Martin, Pamela Hill, Geoffrey J. Barton, Andrew J. Flavell:
Visual Representation of Database Search Results: The RHIMS Plot. 1037-1038 - Tao Xie, Leroy E. Hood:
ACGT - A Comparative Genomics Tool. 1039-1040 - Marcin von Grotthuss, Jakub Pas, Leszek Rychlewski:
Ligand-Info, Searching for Similar Small Compounds Using Index Profiles. 1041-1042 - S. S. Sheik, Prasanna Sundararajan, V. Shanthi, Krishna Sekar:
CAP: Conformation Angles Package - Displaying the Conformation Angles of Side Chains in Proteins. 1043-1044
Volume 19, Number 9, June 2003
- Colin Campbell:
New Analytical Techniques for the Interpretation of Microarray Data. 1045 - Yanli Zhao, Wei Pan:
Modified Nonparametric Approaches to Detecting Differentially Expressed Genes in Replicated Microarray Experiments. 1046-1054 - Ernst Wit, John McClure:
Statistical Adjustment of Signal Censoring in Gene Expression Experiments. 1055-1060 - Marcel Dettling, Peter Bühlmann:
Boosting for Tumor Classification with Gene Expression Data. 1061-1069 - Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angèle M. Hamel, Tommi S. Jaakkola:
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. 1070-1078 - Gad Getz, Hilah Gal, Itai Kela, Daniel A. Notterman, Eytan Domany:
Coupled Two-way Clustering Analysis of Breast Cancer and Colon Cancer Gene Expression Data. 1079-1089 - Sandrine Dudoit, Jane Fridlyand:
Bagging to Improve the Accuracy of A Clustering Procedure. 1090-1099 - Rebecka Jörnsten, Bin Yu:
Simultaneous Gene Clustering and Subset Selection for Sample Classification Via MDL. 1100-1109 - David Horn, Inon Axel:
Novel Clustering Algorithm for Microarray Expression Data in A Truncated SVD Space. 1110-1115 - Torgeir R. Hvidsten, Astrid Lægreid, Henryk Jan Komorowski:
Learning Rule-based Models of Biological Process from Gene Expression Time Profiles Using Gene Ontology. 1116-1123 - Hiroyuki Nakahara, Shin-ichi Nishimura, Masato Inoue, Gen Hori, Shun-ichi Amari:
Gene Interaction in DNA Microarray Data Is Decomposed by Information Geometric Measure. 1124-113 - Yoonkyung Lee, Cheol-Koo Lee:
Classification of Multiple Cancer Types by Multicategory Support Vector Machines Using Gene Expression Data. 1132-1139 - Dennis J. Michaud, Adam G. Marsh, Prasad S. Dhurjati:
eXPatGen: Generating Dynamic Expression Patterns for the Systematic Evaluation of Analytical Methods. 1140-1146 - Tianjiao Chu, Clark Glymour, Richard Scheines, Peter Spirtes:
A Statistical Problem for Inference to Regulatory Structure from Associations of Gene Expression Measurements with Microarrays. 1147-1152
- Gad Getz, Eytan Domany:
Coupled Two-way Clustering Server. 1153-1154
- Julie Dawn Thompson, Jean-Claude Thierry, Olivier Poch:
RASCAL: Rapid Scanning and Correction of Multiple Sequence Alignments. 1155-1161 - William H. Piel, Michael J. Sanderson, Michael J. Donoghue:
The Small-world Dynamics of Tree Networks and Data Mining in Phyloinformatics. 1162-1168 - Martin Ginkel, Andreas Kremling, Torsten Nutsch, R. Rehner, Ernst Dieter Gilles:
Modular Modeling of Cellular Systems with ProMoT/Diva. 1169-1176
- Alexander K. Hudek, Joseph Cheung, Andrew P. Boright, Stephen W. Scherer:
Genescript: DNA Sequence Annotation Pipeline. 1177-1178
Volume 19, Number 10, July 2003
- Christoph Helma, Stefan Kramer:
A Survey of the Predictive Toxicology Challenge 2000-2001. 1179-1182 - Hannu Toivonen, Ashwin Srinivasan, Ross D. King, Stefan Kramer, Christoph Helma:
Statistical Evaluation of the Predictive Toxicology Challenge 2000-2001. 1183-1193 - Romualdo Benigni, Alessandro Giuliani:
Putting the Predictive Toxicology Challenge Into Perspective: Reflections on the Results. 1194-1200 - V. G. Blinova, D. A. Dobrynin, Victor K. Finn, Sergei O. Kuznetsov, E. S. Pankratova:
Toxicology Analysis by Means of the JSM-method. 1201-1207 - Takashi Okada:
Characteristic Substructures and Properties in Chemical Carcinogens Studied by the Cascade Model. 1208-1215
- Mario Albrecht, Thomas Lengauer:
Pyranose Oxidase Identified as A Member of the GMC Oxidoreductase Family. 1216-1220
- Ketil Malde, Eivind Coward, Inge Jonassen:
Fast Sequence Clustering Using A Suffix Array Algorithm. 1221-1226 - Joseph Bockhorst, Mark W. Craven, David Page, Jude W. Shavlik, Jeremy D. Glasner:
A Bayesian Network Approach to Operon Prediction. 1227-1235 - Stan Pounds, Stephan W. Morris:
Estimating the Occurrence of False Positives and False Negatives in Microarray Studies by Approximating and Partitioning the Empirical Distribution of P-values. 1236-1242 - Minghe Sun, Momiao Xiong:
A Mathematical Programming Approach for Gene Selection and Tissue Classification. 1243-1251 - Efstathia Bura, Ruth M. Pfeiffer:
Graphical Methods for Class Prediction Using Dimension Reduction Techniques on DNA Microarray Data. 1252-1258 - Chris H. Q. Ding:
Unsupervised Feature Selection Via Two-way Ordering in Gene Expression Analysis. 1259-1266 - An-Suei Yang, Lu-Yong Wang:
Local Structure Prediction with Local Structure-based Sequence Profiles. 1267-1274 - Phillip W. Lord, Robert D. Stevens, Andy Brass, Carole A. Goble:
Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation. 1275-1283 - Ronghui Xu, Xiaochun Li:
A Comparison of Parametric Versus Permutation Methods with Applications to General and Temporal Microarray Gene Expression Data. 1284-1289
- Richard A. Lee, Moe Razaz, Steven Hayward:
The DynDom Database of Protein Domain Motions. 1290-1291 - James E. Johnson, Martina V. Stromvik, Kevin A. T. Silverstein, John A. Crow, Elizabeth Shoop, Ernest F. Retzel:
TableView: Portable Genomic Data Visualization. 1292-1293 - Lloyd Allison:
Longest Biased Interval and Longest Non-negative Sum Interval. 1294-1295 - Sohrab P. Shah, Graham P. McVicker, Alan K. Mackworth, Sanja Rogic, B. F. Francis Ouellette:
GeneComber: Combining Outputs of Gene Prediction Programs for Improved Results. 1296-1297 - James A. R. Dalton, Ioannis Michalopoulos, David R. Westhead:
Calculation of Helix Packing Angles in Protein Structures. 1298-1299 - Kun Zhang, Li Jin:
HaploBlockFinder: Haplotype Block Analyses. 1300-1301
Volume 19, Number 11, July 2003
- Jinling Huang, Suchendra M. Bhandarkar:
A Comparison of Physical Mapping Algorithms Based on the Maximum Likelihood Model. 1303-1310 - Pei-chin Chang, Konan Peck:
Design and Assessment of A Fast Algorithm for Identifying Specific Probes for Human and Mouse Genes. 1311-1317 - Todd E. Scheetz, Nishank Trivedi, Chad A. Roberts, Tamara Kucaba, Brian Berger, Natalie L. Robinson, Clayton L. Birkett, Allen J. Gavin, Brian O'Leary, Terry A. Braun, Maria F. Bonaldo, John P. Robinson, Val C. Sheffield, Marcelo Bento Soares, Thomas L. Casavant:
ESTprep: Preprocessing CDNA Sequence Reads. 1318-1324 - Dale L. Wilson, Michael J. Buckley, Chris A. Helliwell, I. W. Wilson:
New Normalization Methods for CDNA Microarray Data. 1325-1332 - Wei Pan:
On the Use of Permutation in and the Performance of A Class of Nonparametric Methods to Detect Differential Gene Expression. 1333-1340 - Xujing Wang, Martin J. Hessner, Yan Wu, Nirupma Pati, Soumitra Ghosh:
Quantitative Quality Control in Microarray Experiments and the Application in Data Filtering, Normalization and False Positive Rate Prediction. 1341-1347 - Sorin Draghici, Olga Kulaeva, Bruce Hoff, Anton Petrov, Soheil Shams, Michael A. Tainsky:
Noise Sampling Method: An ANOVA Approach Allowing Robust Selection of Differentially Regulated Genes Measured by DNA Microarrays. 1348-1359 - Blythe Durbin, David M. Rocke:
Estimation of Transformation Parameters for Microarray Data. 1360-1367 - Mark Spencer:
Exact Significance Levels for the Maximum 2 Method of Detecting Recombination. 1368-1370 - Misaki Sato, Hitomi Umeki, Rintaro Saito, Akio Kanai, Masaru Tomita:
Computational Analysis of Stop Codon Readthrough in D.melanogaster. 1371-1380 - Venkatarajan S. Mathura, Catherine H. Schein, Werner Braun:
Identifying Property Based Sequence Motifs in Protein Families and Superfamilies: Application to DNase-1 Related Endonucleases. 1381-1390 - Hongyu Zhang:
Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithm. 1391-1396 - Caleb Webber, Geoffrey J. Barton:
Increased Coverage Obtained by Combination of Methods for Protein Sequence Database Searching. 1397-1403 - Robert C. Edgar, Kimmen Sjölander:
SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models. 1404-1411 - Victor Kunin, Christos A. Ouzounis:
GeneTRACE - Reconstruction of Gene Content of Ancestral Species. 1412-1416 - Jung-Hsien Chiang, Hsu-Chun Yu:
MeKE: Discovering the Functions of Gene Products from Biomedical Literature Via Sentence Alignment. 1417-1422 - Hongwu Ma, An-Ping Zeng:
The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks. 1423-1430 - Artem L. Ponomarev, Ronald L. Davis:
An Adjustable-threshold Algorithm for the Identification of Objects in Three-dimensional Images. 1431-1435
- Michael A. Banks, Will Eichert, Jeffrey B. Olsen:
Which Genetic Loci Have Greater Population Assignment Power? 1436-1438 - Perikles Simon:
Q-Gene: Processing Quantitative Real-time RT-PCR Data. 1439-1440 - Yong Li, Mario G. Rosso, Nicolai Strizhov, Prisca Viehoever, Bernd Weisshaar:
GABI-Kat SimpleSearch: A Flanking Sequence Tag (FST) Database for the Identification of T-DNA Insertion Mutants in Arabidopsis Thaliana. 1441-1442 - J. Lynn Fink, Scott Drewes, Hiren Patel, John B. Welsh, Daniel R. Masys, Jacques Corbeil, Michael Gribskov:
2HAPI: A Microarray Data Analysis System. 1443-1445 - Catherine S. Grasso, Michael Quist, Kevin Ke, Christopher J. Lee:
POAVIZ: A Partial Order Multiple Sequence Alignment Visualizer. 1446-1448 - René Gibson, Douglas R. Smith:
Genome Visualization Made Fast and Simple. 1449-1450 - Paul J. Janssen, Anton J. Enright, Benjamin Audit, Ildefonso Cases, Leon Goldovsky, Nicola Harte, Victor Kunin, Christos A. Ouzounis:
COmplete GENome Tracking (COGENT): A Flexible Data Environment for Computational Genomics. 1451-1452 - Tiffany B. Fischer, K. V. Arunachalam, D. Bailey, V. Mangual, S. Bakhru, R. Russo, D. Huang, M. Paczkowski, V. Lalchandani, C. Ramachandra, B. Ellison, S. Galer, J. Shapley, E. Fuentes, Jerry Tsai:
The Binding Interface Database (BID): A Compilation of Amino Acid Hot Spots in Protein Interfaces. 1453-1454
Volume 19, Number 12, August 2003
- Christian Weinel, Maria D. Ermolaeva, Christos A. Ouzounis:
PseuRECA: genome annotation and gene context analysis for Pseudomonas aeruginosa PAO1. 1457-1460
- T. Z. DeSantis Jr., I. Dubosarskiy, S. R. Murray, Gary L. Andersen:
Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. 1461-1468 - Dilip Rajagopalan:
A comparison of statistical methods for analysis of high density oligonucleotide array data. 1469-1476 - Keith A. Baggerly, Li Deng, Jeffrey S. Morris, C. Marcelo Aldaz:
Differential expression in SAGE: accounting for normal between-library variation. 1477-1483 - Ray L. Somorjai, B. Dolenko, Richard Baumgartner:
Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions. 1484-1491 - Ian Korf:
Serial BLAST searching. 1492-1496 - Louxin Zhang, Bin Ma, Lusheng Wang, Ying Xu:
Greedy method for inferring tandem duplication history. 1497-1504 - Ari Löytynoja, Michel C. Milinkovitch:
A hidden Markov model for progressive multiple alignment. 1505-1513 - Yoshiharu Hayashi, Katsuyoshi Sakaguchi, Mime Kobayashi, Masaki Kobayashi, Yo Kikuchi, Eiichiro Ichiishi:
Molecular evaluation using in silico protein interaction profiles. 1514-1523 - Jie Wu, Simon Kasif, Charles DeLisi:
Identification of functional links between genes using phylogenetic profiles. 1524-1530 - David Mittelman, Ruslan Sadreyev, Nick V. Grishin:
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. 1531-1539 - Bala Krishnamoorthy, Alexander Tropsha:
Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. 1540-1548 - Homayoun Valafar, James H. Prestegard:
Rapid classification of a protein fold family using a statistical analysis of dipolar couplings. 1549-1555 - Simon Whelan, Paul I. W. de Bakker, Nick Goldman:
Pandit: a database of protein and associated nucleotide domains with inferred trees. 1556-1563 - Patrick Lambrix, Manal Habbouche, Marta Pérez:
Evaluation of ontology development tools for bioinformatics. 1564-1571
- Fredrik Ronquist, John P. Huelsenbeck:
MrBayes 3: Bayesian phylogenetic inference under mixed models. 1572-1574 - Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern:
AGenDA: homology-based gene prediction. 1575-1577 - Yang Su, T. M. Murali, Vladimir Pavlovic, Michael Schaffer, Simon Kasif:
RankGene: identification of diagnostic genes based on expression data. 1578-1579 - Sacha A. F. T. van Hijum, Anne de Jong, Girbe Buist, Jan Kok, Oscar P. Kuipers:
UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. 1580-1582 - Naoki Sato, Shigeki Ehira:
GenoMap, a circular genome data viewer. 1583-1584 - Kuo-Bin Li:
ClustalW-MPI: ClustalW analysis using distributed and parallel computing. 1585-1586 - Apuã C. M. Paquola, Milton Y. Nishyiama Jr., Eduardo M. Reis, Aline Maria da Silva, Sergio Verjovski-Almeida:
ESTWeb: bioinformatics services for EST sequencing projects. 1587-1588 - Guoli Wang, Roland L. Dunbrack Jr.:
PISCES: a protein sequence culling server. 1589-1591 - Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen:
Digital extractor: analysis of digital differential display output. Bioinform. 19(12): 1592-1593 (2003) - Stephen F. Madden, Barry O'Donovan, Simon J. Furney, Hugh R. Brady, Guenole C. M. Silvestre, Peter P. Doran:
Digital extractor: analysis of digital differential display output. 1594-1595
Volume 19, Number 13, September 2003
- Shuyu Li, Gene Cutler, Jane Jijun Liu, Timothy Hoey, Liangbiao Chen, Peter G. Schultz, Jia yu Liao, Xuefeng Bruce Ling:
A comparative analysis of HGSC and Celera human genome assemblies and gene sets. 1597-1605 - Diego di Bernardo, Thomas A. Down, Tim J. P. Hubbard:
ddbRNA: detection of conserved secondary structures in multiple alignments. 1606-1611 - Inderjit S. Dhillon, Edward M. Marcotte, Usman Roshan:
Diametrical clustering for identifying anti-correlated gene clusters. 1612-1619 - Paul Pavlidis, Qinghong Li, William Stafford Noble:
The effect of replication on gene expression microarray experiments. 1620-1627 - Xu Guo, Huilin Qi, Catherine M. Verfaillie, Wei Pan:
Statistical significance analysis of longitudinal gene expression data. 1628-1635 - Baolin Wu, Tom Abbott, David Fishman, Walter McMurray, Gil Mor, Kathryn L. Stone, David Ward, Kenneth R. Williams, Hongyu Zhao:
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. 1636-1643 - Jonathan A. Barker, Janet M. Thornton:
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. 1644-1649 - Jonathan J. Ward, Liam J. McGuffin, Bernard F. Buxton, David T. Jones:
Secondary structure prediction with support vector machines. 1650-1655 - Keun-Joon Park, Minoru Kanehisa:
Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. 1656-1663 - Alex L. Mitchell, Jacqueline Renée Reich, Terri K. Attwood:
PRECIS: Protein reports engineered from concise information in SWISS-PROT. 1664-1671 - David P. Kreil, Christos A. Ouzounis:
Comparison of sequence masking algorithms and the detection of biased protein sequence regions. 1672-1681 - Jahnavi C. Prasad, Stephen R. Comeau, Sandor Vajda, Carlos J. Camacho:
Consensus alignment for reliable framework prediction in homology modeling. 1682-1691 - Daniel C. McShan, S. Rao, Imran Shah:
PathMiner: predicting metabolic pathways by heuristic search. 1692-1698 - Svetlana Novichkova, Sergei Egorov, Nikolai Daraselia:
MedScan, a natural language processing engine for MEDLINE abstracts. 1699-1706
- Christophe Pichon, Brice Felden:
Intergenic sequence inspector: searching and identifying bacterial RNAs. 1707-1709 - Dennis P. Wall, H. B. Fraser, A. E. Hirsh:
Detecting putative orthologs. 1710-1711 - Jian Wang, Eileen T. Kraemer:
GFPE: gene-finding program evaluation. 1712-1713 - Reija Autio, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi:
CGH-Plotter: MATLAB toolbox for CGH-data analysis. 1714-1715 - Richard J. Laws, Tracy L. Bergemann, Filemon Quiaoit, Lue Ping Zhao:
SignalViewer: analyzing microarray images. 1716-1717 - Robert J. Blick, Andrew T. Revel, Eric J. Hansen:
FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis. 1718-1719 - Chunhong Mao, John C. Cushman, Gregory D. May, Jennifer W. Weller:
ESTAP-an automated system for the analysis of EST data. 1720-1722 - Razif R. Gabdoulline, René Hoffmann, Florian Leitner, Rebecca C. Wade:
ProSAT: functional annotation of protein 3D structures. 1723-1725 - C. J. Creevey, James O. McInerney:
CRANN: detecting adaptive evolution in protein-coding DNA sequences. 1726 - Koichi Takahashi, Naota Ishikawa, Yasuhiro Sadamoto, Hiroyuki Sasamoto, Seiji Ohta, Akira Shiozawa, Fumihiko Miyoshi, Yasuhiro Naito, Yoichi Nakayama, Masaru Tomita:
E-Cell 2: Multi-platform E-Cell simulation system. 1727-1729 - Sinan Güler, Andreas Eberhart, Isabel Rojas:
Web-based exchange of biochemical information. 1730-1731
Volume 19, Number 14, September 2003
- Valerio Parisi, Valeria De Fonzo, Filippo Aluffi-Pentini:
STRING: finding tandem repeats in DNA sequences. 1733-1738 - Alessandro Marongiu, Paolo Palazzari, Vittorio Rosato:
Designing hardware for protein sequence analysis. 1739-1740
- Rebecca Thomson, T. Charles Hodgman, Zheng Rong Yang, Austin K. Doyle:
Characterizing proteolytic cleavage site activity using bio-basis function neural networks. 1741-1747 - Andrew P. Harrison, Frances M. G. Pearl, Ian Sillitoe, Tim Slidel, Richard Mott, Janet M. Thornton, Christine A. Orengo:
Recognizing the fold of a protein structure. 1748-1759 - A. Vinayagam, Jiye Shi, Ganesan Pugalenthi, B. Meenakshi, Tom L. Blundell, Ramanathan Sowdhamini:
DDBASE2.0: updated domain database with improved identification of structural domains. 1760-1764 - Björn Peters, Weiwei Tong, John Sidney, Alessandro Sette, Zhiping Weng:
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. 1765-1772 - Lusheng Wang, Ying Xu:
Haplotype inference by maximum parsimony. 1773-1780 - Gábor Firneisz, Idit Zehavi, Csaba Vermes, Anita Hanyecz, Joshua A. Frieman, Tibor T. Glant:
Identification and quantification of disease-related gene clusters. 1781-1786 - Roded Sharan, Adi Maron-Katz, Ron Shamir:
CLICK and EXPANDER: a system for clustering and visualizing gene expression data. 1787-1799 - Adil M. Bagirov, Brent Ferguson, Sasha Ivkovic, G. Saunders, John Yearwood:
New algorithms for multi-class cancer diagnosis using tumor gene expression signatures. 1800-1807 - Sue C. Geller, Jeff P. Gregg, Paul Hagerman, David M. Rocke:
Transformation and normalization of oligonucleotide microarray data. 1817-1823 - Vitaly L. Galinsky:
Automatic registration of microarray images. I. Rectangular grid. 1824-1831 - Vitaly L. Galinsky:
Automatic registration of microarray images. II. Hexagonal grid. 1832-1836 - Tim Carver, Alan J. Bleasby:
The design of Jemboss: a graphical user interface to EMBOSS. 1837-1843
- Donny Tjandra, Stephen T. C. Wong, Weimin Shen, Brian Pulliam, Elaine Yu, Laura Esserman:
An XML message broker framework for exchange and integration of microarray data. 1844-1845 - N. H. Shah, D. C. King, P. N. Shah, Nina V. Fedoroff:
A tool-kit for cDNA microarray and promoter analysis. 1846-1848 - Shandar Ahmad, M. Michael Gromiha, Akinori Sarai:
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences. 1849-1851 - Alan A. Dombkowski:
Disulfide by DesignTM: a computational method for the rational design of disulfide bonds in proteins. 1852-1853 - Fabien Campagne, Emmanuel Bettler, Gert Vriend, Harel Weinstein:
Batch mode generation of residue-based diagrams of proteins. 1854-1855 - Dushyanthan Puvanendrampillai, John B. O. Mitchell:
Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. 1856-1857 - Sean D. Mooney, Russ B. Altman:
MutDB: annotating human variation with functionally relevant data. 1858-1860 - Rasko Leinonen, Francesco Nardone, Olalekan Oyewole, Nicole Redaschi, Peter Stoehr:
The EMBL sequence version archive. 1861-1862 - Jiren Wang, Qing Mu:
Soap-HT-BLAST: high throughput BLAST based on Web services. 1863-1864 - David R. Mathog:
Parallel BLAST on split databases. 1865-1866
Volume 19, Number 15, October 2003
- The Fourth Georgia Tech-University of Georgia International Conference in Bioinformatics: in silico Biology, Biological Networks, from Genomics to Epidemiology (November 13-16, 2003, Atlanta, Georgia, USA). Bioinform. 19(15): 1867-1868 (2003)
- Joel S. Bader:
Greedily building protein networks with confidence. 1869-1874 - Shawn M. Gomez, William Stafford Noble, Andrey Rzhetsky:
Learning to predict protein-protein interactions from protein sequences. 1875-1881 - Kyungsook Han, Byong-Hyon Ju:
A fast layout algorithm for protein interaction networks. 1882-1888 - Georgy P. Karev, Yuri I. Wolf, Eugene V. Koonin:
Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve? 1889-1900 - Roland Krause, Christian von Mering, Peer Bork:
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens. 1901-1908 - Alexander V. Lukashin, Matvey E. Lukashev, Rainer Fuchs:
Topology of gene expression networks as revealed by data mining and modeling. 1909-1916 - Jiang Qian, C. Jimmy Lin, Nicholas M. Luscombe, Haiyuan Yu, Mark Gerstein:
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. 1917-1926 - Daniel Rocco, Terence Critchlow:
Automatic discovery and classification of bioinformatics Web sources. 1927-1933
- Jeff Shrager:
The fiction of function. 1934-1936
- Xueli Liu, Hans-Georg Müller:
Modes and clustering for time-warped gene expression profile data. 1937-1944 - Nitin Jain, Jayant Thatte, Thomas Braciale, Klaus Ley, Michael O'Connell, Jae K. Lee:
Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. 1945-1951 - Chandrasegaran Narasimhan, Philip F. LoCascio, Edward C. Uberbacher:
Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection. 1952-1963 - Leo Gordon, Alexey Ya. Chervonenkis, Alex J. Gammerman, Ilham A. Shahmuradov, Victor V. Solovyev:
Sequence alignment kernel for recognition of promoter regions. 1964-1971 - Yonghong Wang, Jinwei Liu, Tongju Zhao, Qing Ji:
Recognizing translation initiation sites of eukaryotic genes based on the cooperatively scanning model. 1972-1977 - Yingdong Zhao, Clemencia Pinilla, Danila Valmori, Roland Martin, Richard M. Simon:
Application of support vector machines for T-cell epitopes prediction. 1978-1984 - Manesh J. Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip F. LoCascio, Dong Xu, Ying Xu:
A computational pipeline for protein structure prediction and analysis at genome scale. 1985-1996
- Scott C.-H. Pegg, Walter R. P. Novak, Patricia C. Babbitt:
Intersect: identification and visualization of overlaps in database search results. 1997-1999 - W. P. H. de Boer, J. J. Oudejans, C. J. L. M. Meijer, Jan Lankelma:
Analysing gene expressions with GRANK. 2000-2001 - Alun Thomas:
GCHap: fast MLEs for haplotype frequencies by gene counting. 2002-2003
Volume 19, Number 16, November 2003
- Alessandra Carbone, Andrei Yu. Zinovyev, François Képès:
Codon adaptation index as a measure of dominating codon bias. 2005-2015 - Gerhard Kauer, Helmut Blöcker:
Applying signal theory to the analysis of biomolecules. 2016-2021 - Hector Sanchez-Villeda, Steven G. Schroeder, Mary L. Polacco, Michael D. McMullen, Seth A. Havermann, Georgia L. Davis, Irie Vroh-Bi, Karen C. Cone, Natasha Sharopova, Young-Sun Yim, Linda Schultz, Ngozi A. Duru, Theresa A. Musket, Kate Houchins, Zhiwei Fang, Jack M. Gardiner, Edward H. Coe:
Development of an integrated laboratory information management system for the maize mapping project. 2022-2030 - Sampsa Hautaniemi, Henrik Edgren, Petri Vesanen, Maija Wolf, Anna-Kaarina Järvinen, Olli Yli-Harja, Jaakko Astola, Olli-P. Kallioniemi, Outi Monni:
A novel strategy for microarray quality control using Bayesian networks. 2031-2038 - Jason Gertz, Georgiy Elfond, Anna Shustrova, Matt Weisinger, Matteo Pellegrini, Shawn Cokus, Bruce Rothschild:
Inferring protein interactions from phylogenetic distance matrices. 2039-2045 - Joshua M. Temkin, Mark R. Gilder:
Extraction of protein interaction information from unstructured text using a context-free grammar. 2046-2053 - S. P. Mielke, V. V. Krishnan:
Protein structural class identification directly from NMR spectra using averaged chemical shifts. 2054-2064 - Marcel Smid, Lambert C. J. Dorssers, Guido Jenster:
Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes. 2065-2071 - Xiaohong Huang, Wei Pan:
Linear regression and two-class classification with gene expression data. 2072-2078 - Humberto González Díaz, Ronal Ramos de Armas, Reinaldo Molina Ruiz:
Markovian negentropies in bioinformatics. 1. A picture of footprints after the interaction of the HIV-1 -RNA packaging region with drugs. 2079-2087 - Shigeyuki Oba, Masa-aki Sato, Ichiro Takemasa, Morito Monden, Ken-ichi Matsubara, Shin Ishii:
A Bayesian missing value estimation method for gene expression profile data. 2088-2096 - Jie Qin, Darrin P. Lewis, William Stafford Noble:
Kernel hierarchical gene clustering from microarray expression data. 2097-2104 - Zhiwei Fang, Karen C. Cone, Hector Sanchez-Villeda, Mary L. Polacco, Michael D. McMullen, Steven G. Schroeder, Jack M. Gardiner, Georgia L. Davis, Seth A. Havermann, Young-Sun Yim, Irie Vroh-Bi, Edward H. Coe:
iMap: a database-driven utility to integrate and access the genetic and physical maps of maize. 2105-2111 - Kristian Rother, Robert Preissner, Andrean Goede, Cornelius Frömmel:
Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. 2112-2121 - Hasan H. Otu, Khalid Sayood:
A new sequence distance measure for phylogenetic tree construction. 2122-2130 - Arthur L. Hsu, Sen-Lin Tang, Saman K. Halgamuge:
An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data. 2131-2140
- Mark Harris, Jeremy M. R. Martin, John F. Peden, Christopher J. Rawlings:
SNP cherry picker: maximizing the chance of finding an association with a disease SNP. 2141-2143 - Dong-Yup Lee, Hongseok Yun, Sunwon Park, Sang Yup Lee:
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. 2144-2146 - Keyue Ding, Kaixin Zhou, Fuchu He, Yan Shen:
LDA - a java-based linkage disequilibrium analyzer. 2147-2148 - Aubrey E. Hill, Helen Kim:
The UAB Proteomics Database. 2149-2151 - Kamyar Farahi, William B. Whitman, Eileen T. Kraemer:
RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events. 2152-2154 - Alexander Nikitin, Sergei Egorov, Nikolai Daraselia, Ilya Mazo:
Pathway studio - the analysis and navigation of molecular networks. 2155-2157 - Luis A. Martínez-Cruz, Angel Rubio, María L. Martínez-Chantar, Alberto Labarga, Isabel Barrio, Adam Podhorski, Victor Segura, José L. Sevilla Campo, Matías A. Avila, José M. Mato:
GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data. 2158-2160 - Bairong Shen, Mauno Vihinen:
RankViaContact: ranking and visualization of amino acid contacts. 2161-2162 - Gianluigi Cardinali, Francesco Maraziti, Sabrina Selvi:
Electrophoretic data classification for phylogenetics and biostatistics. 2163-2165
Volume 19, Number 17, November 2003
- Alexander E. Vinogradov:
Silent DNA: speaking RNA language? 2167-2170 - Mario Albrecht, Thomas Lengauer, Stefan Schreiber:
Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence. 2171-2175
- Christos A. Ouzounis, Alfonso Valencia:
Early bioinformatics: the birth of a discipline - a personal view. 2176-2190
- Vincent Thareau, Patrice Déhais, Carine Serizet, Pierre Hilson, Pierre Rouzé, Sébastien Aubourg:
Automatic design of gene-specific sequence tags for genome-wide functional studies. 2191-2198 - Vidhya Gomathi Krishnan, David R. Westhead:
A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. 2199-2209 - Junbai Wang, Ola Myklebost, Eivind Hovig:
MGraph: graphical models for microarray data analysis. 2210-2211 - Anders Wallqvist, Alfred A. Rabow, Robert H. Shoemaker, Edward A. Sausville, David G. Covell:
Linking the growth inhibition response from the National Cancer Institute's anticancer screen to gene expression levels and other molecular target data. 2212-2224 - Ivan Erill, Marcos Escribano, Susana Campoy, Jordi Barbé:
In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon. 2225-2236 - Lusheng Wang, Jianyun Zhao:
Parametric alignment of ordered trees. 2237-2245 - Shirish K. Shevade, S. Sathiya Keerthi:
A simple and efficient algorithm for gene selection using sparse logistic regression. 2246-2253 - Peter J. Giles, David Kipling:
Normality of oligonucleotide microarray data and implications for parametric statistical analyses. 2254-2262 - Irini A. Doytchinova, Darren R. Flower:
Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction. 2263-2270 - Dirk Husmeier:
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. 2271-2282 - Anthony L. Duran, Jian Yang, Liangjiang Wang, Lloyd W. Sumner:
Metabolomics spectral formatting, alignment and conversion tools (MSFACTs). 2283-2293 - Yuna Hou, Wynne Hsu, Mong-Li Lee, Chris Bystroff:
Efficient remote homology detection using local structure. 2294-2301 - Xiaobo Zhou, Xiaodong Wang, Edward R. Dougherty:
Missing-value estimation using linear and non-linear regression with Bayesian gene selection. 2302-2307
- Thomas Hamelryck, Bernard Manderick:
PDB file parser and structure class implemented in Python. 2308-2310 - Yanming Yang, Li M. Fu:
TSGDB: a database system for tumor suppressor genes. 2311-2312 - Kim Carter, Matthew I. Bellgard:
MASV - Multiple (BLAST) Annotation System Viewer. 2313-2315 - Jason S. Iacovoni:
GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome. 2316-2318 - Mads Wichmann Matthiessen:
BioWareDB: the biomedical software and database search engine. 2319-2320 - Gabriel S. Eichler, Sui Huang, Donald E. Ingber:
Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles. 2321-2322 - Hao Wang, Beng Chin Ooi, Kian-Lee Tan, Twee-Hee Ong, Lei Zhou:
BLAST++: BLASTing queries in batches. 2323-2324 - Kevin R. Thornton:
libsequence: a C++ class library for evolutionary genetic analysis. 2325-2327 - Jorge García de la Nava, Sacha A. F. T. van Hijum, Oswaldo Trelles:
PreP: gene expression data pre-processing. 2328-2329 - Paul O. Lewis:
NCL: a C++ class library for interpreting data files in NEXUS format. 2330-2331 - Carsten O. Daub, Sebastian Kloska, Joachim Selbig:
MetaGeneAlyse: analysis of integrated transcriptional and metabolite data. 2332-2333
Volume 19, Number 18, December 2003
- Johannes Hüsing, Michael Zeschnigk, Tanja Boes, Karl-Heinz Jöckel:
Combining DNA expression with positional information to detect functional silencing of chromosomal regions. 2335-2342 - Igor Landais, M. Ogliastro, Kazuei Mita, Junko Nohata, Miguel López-Ferber, Martine Duonor-Cérutti, Toru Shimada, Philippe Fournier, Gérard Devauchelle:
Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias. 2343-2350 - Yihua Huang, Tianyun Ni, Lei Zhou, Stanley Y. W. Su:
JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration. 2351-2358 - Virpi Ahola, Tero Aittokallio, Esa Uusipaikka, Mauno Vihinen:
Efficient estimation of emission probabilities in profile hidden Markov models. 2359-2368 - Ting Wang, Gary D. Stormo:
Combining phylogenetic data with co-regulated genes to identify regulatory motifs. 2369-2380 - Irit Gat-Viks, Roded Sharan, Ron Shamir:
Scoring clustering solutions by their biological relevance. 2381-2389 - Shao-Wu Zhang, Quan Pan, Hongcai Zhang, Yun-Long Zhang, Hai-Yu Wang:
Classification of protein quaternary structure with support vector machine. 2390-2396 - Wei-Min Liu, Xiaojun Di, Geoffrey Yang, Hajime Matsuzaki, Jing Huang, Rui Mei, Thomas B. Ryder, Teresa A. Webster, Shoulian Dong, Guoying Liu, Keith W. Jones, Giulia C. Kennedy, David Kulp:
Algorithms for large-scale genotyping microarrays. 2397-2403 - Peter A. Covitz, Frank W. Hartel, Carl F. Schaefer, Sherri de Coronado, Gilberto Fragoso, Himanso Sahni, Scott Gustafson, Kenneth H. Buetow:
caCORE: A common infrastructure for cancer informatics. 2404-2412 - Chen-Shan Chin, Manoj Pratim Samanta:
Global snapshot of a protein interaction network - a percolation based approach. 2413-2419 - Jacob Köhler, Stephan Philippi, Matthias Lange:
SEMEDA: ontology based semantic integration of biological databases. 2420-2427 - Antonio S. Torralba:
Susceptibility of non-linear systems as an approach to metabolic responses. 2428-2435 - Igor Rojdestvenski:
Metabolic pathways in three dimensions. 2436-2441 - Cornelius Frömmel, Christoph Gille, Andrean Goede, Clemens Gröpl, Stefan Hougardy, Till Nierhoff, Robert Preissner, Martin Thimm:
Accelerating screening of 3D protein data with a graph theoretical approach. 2442-2447 - George W. Wright, Richard Simon:
A random variance model for detection of differential gene expression in small microarray experiments. 2448-2455 - Zhuoran Chen:
Assessing sequence comparison methods with the average precision criterion. 2456-2460 - Ricardo Z. N. Vêncio, Helena Paula Brentani, Carlos A. de B. Pereira:
Using credibility intervals instead of hypothesis tests in SAGE analysis. 2461-2464 - Anne-Laure Boulesteix, Gerhard Tutz, Korbinian Strimmer:
A CART-based approach to discover emerging patterns in microarray data. 2465-2472
- Gary L. Argraves, Jeremy L. Barth, W. Scott Argraves:
The MUSC DNA Microarray Database. 2473-2474 - Roman Roset, Juan A. Subirana, Xavier Messeguer:
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences. 2475-2476 - Josep F. Abril, Roderic Guigó, Thomas Wiehe:
gff2aplot: Plotting sequence comparisons. 2477-2479 - Kim Brügger, Peter Redder, Marie Skovgaard:
MUTAGEN: Multi-User Tool for Annotating GENomes. 2480-2481 - Thomas Lütteke, Peter Krieg, Gerhard Fürstenberger, Claus-Wilhelm von der Lieth:
LOX-DB - a database on lipoxygenases. 2482-2483 - Salim Khan, Gang Situ, Keith Decker, Carl J. Schmidt:
GoFigure: Automated Gene OntologyTM annotation. 2484-2485 - Matej Lexa, Giorgio Valle:
PRIMEX: rapid identification of oligonucleotide matches in whole genomes. 2486-2488 - Christoph Gille, Stephan Lorenzen, Elke Michalsky, Cornelius Frömmel:
KISS for STRAP: user extensions for a protein alignment editor. 2489-2491 - Daniel Aguilar, Baldomero Oliva, Francesc X. Avilés, Enrique Querol:
SNOW: Standard NOmenclature Wizard to help searching for (bio) chemical standardized names. 2492-2493 - Nadia Bolshakova, Francisco Azuaje:
Machaon CVE: cluster validation for gene expression data. 2494-2495 - Julio Rozas, Juan C. Sánchez-DelBarrio, Xavier Messeguer, Ricardo Rozas:
DnaSP, DNA polymorphism analyses by the coalescent and other methods. 2496-2497 - Piero Fariselli, Giacomo Finocchiaro, Rita Casadio:
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. 2498-2499 - András Fiser, Andrej Sali:
ModLoop: automated modeling of loops in protein structures. 2500-2501 - Gabriel F. Berriz, Oliver D. King, Barbara Bryant, Chris Sander, Frederick P. Roth:
Characterizing gene sets with FuncAssociate. 2502-2504
Supplements
- Proceedings of the European Conference on Computational Biology (ECCB 2003), September 27-30, 2003, Paris, France. 2003 [contents]
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