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Contents: Volume 20, Number 16, November 1 2004   [Index by Author]       Other Issues: Previous Next  
       REVIEW
       DISCOVERY NOTES
       ORIGINAL PAPERS
       APPLICATIONS NOTES
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REVIEW:

Ziv Bar-Joseph
Analyzing time series gene expression data
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2493-2503; doi:10.1093/bioinformatics/bth283 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

DISCOVERY NOTES:

Akira R. Kinjo and Ken Nishikawa
Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2504-2508; doi:10.1093/bioinformatics/bth297 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Dominique Tessier, Benjamin Bardiaux, Colette Larré, and Yves Popineau
Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptor
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2509-2512; doi:10.1093/bioinformatics/bth332 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Sanju Attoor, Edward R. Dougherty, Yidong Chen, Michael L. Bittner, and Jeffrey M. Trent
Which is better for cDNA-microarray-based classification: ratios or direct intensities
Bioinformatics Advance Access published on September 28, 2004
Bioinformatics 2004 20: 2513-2520; doi:10.1093/bioinformatics/bth272 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Delong Liu, Clarice R. Weinberg, and Shyamal D. Peddada
A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2521-2528; doi:10.1093/bioinformatics/bth274 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Xiaoqiu Huang, Liang Ye, Hui-Hsien Chou, I-Hsuan Yang, and Kun-Mao Chao
Efficient combination of multiple word models for improved sequence comparison
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2529-2533; doi:10.1093/bioinformatics/bth279 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jinwook Seo, Marina Bakay, Yi-Wen Chen, Sara Hilmer, Ben Shneiderman, and Eric P Hoffman
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2534-2544; doi:10.1093/bioinformatics/bth280 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Roxana Alexandridis, Shili Lin, and Mark Irwin
Class discovery and classification of tumor samples using mixture modeling of gene expression data—a unified approach
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2545-2552; doi:10.1093/bioinformatics/bth281 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Mahlet G. Tadesse, Marina Vannucci, and Pietro Liò
Identification of DNA regulatory motifs using Bayesian variable selection
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2553-2561; doi:10.1093/bioinformatics/bth282 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Philippe Broët, Alex Lewin, Sylvia Richardson, Cyril Dalmasso, and Henri Magdelenat
A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2562-2571; doi:10.1093/bioinformatics/bth285 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kuo-Bin Li, Praveen Issac, and Arun Krishnan
Predicting allergenic proteins using wavelet transform
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2572-2578; doi:10.1093/bioinformatics/bth286 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

S. Gupta, D. Zink, B. Korn, M. Vingron, and S. A. Haas
Genome wide identification and classification of alternative splicing based on EST data
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2579-2585; doi:10.1093/bioinformatics/bth288 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Chien-Yu Chen, Yen-Jen Oyang, and Hsueh-Fen Juan
Incremental generation of summarized clustering hierarchy for protein family analysis
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2586-2596; doi:10.1093/bioinformatics/bth290 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. J. Schuemie, M. Weeber, B. J. A. Schijvenaars, E. M. van Mulligen, C. C. van der Eijk, R. Jelier, B. Mons, and J. A. Kors
Distribution of information in biomedical abstracts and full-text publications
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2597-2604; doi:10.1093/bioinformatics/bth291 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Feng Luo, Latifur Khan, Farokh Bastani, I-Ling Yen, and Jizhong Zhou
A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2605-2617; doi:10.1093/bioinformatics/bth292 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Marcel Smid and Lambert C. J. Dorssers
GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2618-2625; doi:10.1093/bioinformatics/bth293 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gert R. G. Lanckriet, Tijl De Bie, Nello Cristianini, Michael I. Jordan, and William Stafford Noble
A statistical framework for genomic data fusion
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2626-2635; doi:10.1093/bioinformatics/bth294 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

C. Pasquier, F. Girardot, K. Jevardat de Fombelle, and R. Christen
THEA: ontology-driven analysis of microarray data
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2636-2643; doi:10.1093/bioinformatics/bth295 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Harm van Bakel, Martijn Huynen, and Cisca Wijmenga
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2644-2655; doi:10.1093/bioinformatics/bth298 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Y.-F. Liu and U.-C. Yang
SCA db: spinocerebellar ataxia candidate gene database
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 2656-2661; doi:10.1093/bioinformatics/bth305 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Koji Kyoda, Kotaro Baba, Shuichi Onami, and Hiroaki Kitano
DBRF–MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2662-2675; doi:10.1093/bioinformatics/bth306 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Prudence W. H. Wong, T. W. Lam, N. Lu, H. F. Ting, and S. M. Yiu
An efficient algorithm for optimizing whole genome alignment with noise
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2676-2684; doi:10.1093/bioinformatics/bth308 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Lori E. Dodd, Edward L. Korn, Lisa M. McShane, G.V.R. Chandramouli, and Eric Y. Chuang
Correcting log ratios for signal saturation in cDNA microarrays
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2685-2693; doi:10.1093/bioinformatics/bth309 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

J.G. Liao, Yong Lin, Zachariah E. Selvanayagam, and Weichung Joe Shih
A mixture model for estimating the local false discovery rate in DNA microarray analysis
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2694-2701; doi:10.1093/bioinformatics/bth310 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Arun Krishnan and Francis Tang
Exhaustive whole-genome tandem repeats search
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2702-2710; doi:10.1093/bioinformatics/bth311 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Liping Ji and Kian-Lee Tan
Mining gene expression data for positive and negative co-regulated gene clusters
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2711-2718; doi:10.1093/bioinformatics/bth312 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nicolas Omont and François Képès
Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2719-2725; doi:10.1093/bioinformatics/bth317 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robert Mansourian, David M. Mutch, Nicolas Antille, Jerome Aubert, Paul Fogel, Jean-Marc Le Goff, Julie Moulin, Anton Petrov, Andreas Rytz, Johannes J. Voegel, and Matthew-Alan Roberts
The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2726-2737; doi:10.1093/bioinformatics/bth319 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yonatan H. Grad, Frederick P. Roth, Marc S. Halfon, and George M. Church
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2738-2750; doi:10.1093/bioinformatics/bth320 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Harpreet Kaur and G. P. S. Raghava
A neural network method for prediction of ß-turn types in proteins using evolutionary information
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2751-2758; doi:10.1093/bioinformatics/bth322 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Zheng Rong Yang
Mining gene expression data based on template theory
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2759-2766; doi:10.1093/bioinformatics/bth323 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yimeng Dou, Pierre-François Baisnée, Gianluca Pollastri, Yann Pécout, James Nowick, and Pierre Baldi
ICBS: a database of interactions between protein chains mediated by ß-sheet formation
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2767-2777; doi:10.1093/bioinformatics/bth326 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Karla V. Ballman, Diane E. Grill, Ann L. Oberg, and Terry M. Therneau
Faster cyclic loess: normalizing RNA arrays via linear models
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2778-2786; doi:10.1093/bioinformatics/bth327 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Manuel Martínez-Bueno, Antonio J. Molina-Henares, Eduardo Pareja, Juan L. Ramos, and Raquel Tobes
BacTregulators: a database of transcriptional regulators in bacteria and archaea
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2787-2791; doi:10.1093/bioinformatics/bth330 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Pérez-Enciso and I. Misztal
Qxpak: a versatile mixed model application for genetical genomics and QTL analyses
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2792-2798; doi:10.1093/bioinformatics/bth331 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sündüz Keles, Mark J. van der Laan, and Chris Vulpe
Regulatory motif finding by logic regression
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2799-2811; doi:10.1093/bioinformatics/bth333 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Olivier Delgrange and Eric Rivals
STAR: an algorithm to Search for Tandem Approximate Repeats
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2812-2820; doi:10.1093/bioinformatics/bth335 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Shu-Dong Zhang and Timothy W. Gant
A statistical framework for the design of microarray experiments and effective detection of differential gene expression
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2821-2828; doi:10.1093/bioinformatics/bth336 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Bruce E. Shapiro, Michael Hucka, Andrew Finney, and John Doyle
MathSBML: a package for manipulating SBML-based biological models
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2829-2831; doi:10.1093/bioinformatics/bth271 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Luiz G. P. Almeida, Roger Paixão, Rangel C. Souza, Gisele C. da Costa, Frank J. A. Barrientos, M. Trindade dos Santos, Darcy F. de Almeida, and Ana Tereza R. Vasconcelos
A System for Automated Bacterial (genome) Integrated Annotation—SABIA
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2832-2833; doi:10.1093/bioinformatics/bth273 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robert Friedman, Vikram Ekollu, John R. Rose, and Austin L. Hughes
Dblox: a genome-wide test for ancient segmental duplication
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2834-2835; doi:10.1093/bioinformatics/bth275 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Eisuke Chikayama, Atsushi Kurotani, Yutaka Kuroda, and Shigeyuki Yokoyama
ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences
Bioinformatics Advance Access published on April 22, 2004
Bioinformatics 2004 20: 2836-2838; doi:10.1093/bioinformatics/bth276 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Terry M. Casstevens and Edward S. Buckler
GDPC: connecting researchers with multiple integrated data sources
Bioinformatics Advance Access published on April 22, 2004
Bioinformatics 2004 20: 2839-2840; doi:10.1093/bioinformatics/bth277 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alexander Lüdemann, Daniel Weicht, Joachim Selbig, and Joachim Kopka
PaVESy: Pathway Visualization and Editing System
Bioinformatics Advance Access published on April 22, 2004
Bioinformatics 2004 20: 2841-2844; doi:10.1093/bioinformatics/bth278 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sandra Barth, Markus Fischer, Rolf D. Schmid, and Jürgen Pleiss
The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2845-2847; doi:10.1093/bioinformatics/bth284 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

F. Lazzarato, G. Franceschinis, M. Botta, F. Cordero, and R. A. Calogero
RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2848-2850; doi:10.1093/bioinformatics/bth287 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Boris Adryan and Reinhard Schuh
Gene-Ontology-based clustering of gene expression data
Bioinformatics Advance Access published on April 29, 2004
Bioinformatics 2004 20: 2851-2852; doi:10.1093/bioinformatics/bth289 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sachiyo Aburatani, Kousuke Goto, Shigeru Saito, Masaki Fumoto, Akira Imaizumi, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Sato, Hiroyuki Toh, and Katsuhisa Horimoto
ASIAN: a website for network inference
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2853-2856; doi:10.1093/bioinformatics/bth296 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Stephen C. Grubb, Gary A. Churchill, and Molly A. Bogue
A collaborative database of inbred mouse strain characteristics
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2857-2859; doi:10.1093/bioinformatics/bth299 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Li Chen, Rose Oughtred, Helen M. Berman, and John Westbrook
TargetDB: a target registration database for structural genomics projects
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2860-2862; doi:10.1093/bioinformatics/bth300 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

W. H. Lee and V. B. Vega
Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2863-2864; doi:10.1093/bioinformatics/bth301 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Song Li and Hui-Hsien Chou
LUCY2: an interactive DNA sequence quality trimming and vector removal tool
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2865-2866; doi:10.1093/bioinformatics/bth302 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Mario A. Fares
SWAPSC: sliding window analysis procedure to detect selective constraints
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2867-2868; doi:10.1093/bioinformatics/bth303 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ghislain Bidaut and Michael F. Ochs
ClutrFree: cluster tree visualization and interpretation
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2869-2871; doi:10.1093/bioinformatics/bth307 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

D. Chen, O. Eulenstein, and D. Fernández-Baca
Rainbow: a toolbox for phylogenetic supertree construction and analysis
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2872-2873; doi:10.1093/bioinformatics/bth313 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robert N. Goldberg, Yadu B. Tewari, and Talapady N. Bhat
Thermodynamics of enzyme-catalyzed reactions—a database for quantitative biochemistry
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2874-2877; doi:10.1093/bioinformatics/bth314 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

W. H. Majoros, M. Pertea, and S. L. Salzberg
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2878-2879; doi:10.1093/bioinformatics/bth315 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Fang Liu, Tor-Kristian Jenssen, Vegard Nygaard, John Sack, and Eivind Hovig
FigSearch: a figure legend indexing and classification system
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2880-2882; doi:10.1093/bioinformatics/bth316 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

P. D'Addabbo, L. Lenzi, F. Facchin, R. Casadei, S. Canaider, L. Vitale, F. Frabetti, P. Carinci, M. Zannotti, and P. Strippoli
GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2883-2885; doi:10.1093/bioinformatics/bth321 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tulika Prakash, Mamta Khandelwal, Dipayan Dasgupta, Debasis Dash, and Samir K. Brahmachari
CoPS: Comprehensive Peptide Signature Database
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2886-2888; doi:10.1093/bioinformatics/bth325 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andreas M. Boehm, Florian Grosse-Coosmann, and Albert Sickmann
Command line tool for calculating theoretical MS spectra for given sequences
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2004 20: 2889-2891; doi:10.1093/bioinformatics/bth328 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.