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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Tim Sands PhD
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| | BMC Bioinformatics, Volume 5 |
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Research article
 
Analysis of oligonucleotide array experiments with repeated measures using mixed models
Hao Li, Constance L Wood, Thomas V Getchell, Marilyn L Getchell, Arnold J Stromberg
BMC Bioinformatics 2004, 5:209 (30December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
A database for G proteins and their interaction with GPCRs
Antigoni L Elefsinioti, Pantelis G Bagos, Ioannis C Spyropoulos, Stavros J Hamodrakas
BMC Bioinformatics 2004, 5:208 (24December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Clustering under the line graph transformation: application to reaction network
Jose C Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu
BMC Bioinformatics 2004, 5:207 (24December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
An empirical analysis of training protocols for probabilistic gene finders
William H Majoros, Steven L Salzberg
BMC Bioinformatics 2004, 5:206 (21December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods
Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan, Changhui Yan, Vasant Honavar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs
BMC Bioinformatics 2004, 5:205 (17December2004)
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Research article
An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage
Gary W Stuart, Michael W Berry
BMC Bioinformatics 2004, 5:204 (17December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
A power law global error model for the identification of differentially expressed genes in microarray data
Norman Pavelka, Mattia Pelizzola, Caterina Vizzardelli, Monica Capozzoli, Andrea Splendiani, Francesca Granucci, Paola Ricciardi-Castagnoli
BMC Bioinformatics 2004, 5:203 (17December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations
Rajalakshmi Gurunathan, Bernard Van Emden, Sethuraman Panchanathan, Sudhir Kumar
BMC Bioinformatics 2004, 5:202 (16December2004)
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Methodology article
A novel Mixture Model Method for identification of differentially expressed genes from DNA microarray data
Kayvan Najarian, Maryam Zaheri, Ali A Rad, Siamak Najarian, Javad Dargahi
BMC Bioinformatics 2004, 5:201 (16December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Analysis of superfamily specific profile-profile recognition accuracy
James A Casbon, Mansoor AS Saqi
BMC Bioinformatics 2004, 5:200 (16December2004)
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Research article
Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach
Hong-Wu Ma, Jan Buer, An-Ping Zeng
BMC Bioinformatics 2004, 5:199 (16December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
GenomeViz: visualizing microbial genomes
Rohit Ghai, Torsten Hain, Trinad Chakraborty
BMC Bioinformatics 2004, 5:198 (15December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
SCOPmap: Automated assignment of protein structures to evolutionary superfamilies
Sara Cheek, Yuan Qi, S Sri Krishna, Lisa N Kinch, Nick V Grishin
BMC Bioinformatics 2004, 5:197 (14December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A functional hierarchical organization of the protein sequence space
Noam Kaplan, Moriah Friedlich, Menachem Fromer, Michal Linial
BMC Bioinformatics 2004, 5:196 (14December2004)
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Software
GECKO: a complete large-scale gene expression analysis platform
Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel, Steven Bushnell
BMC Bioinformatics 2004, 5:195 (10December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Optimized LOWESS normalization parameter selection for DNA microarray data
John A Berger, Sampsa Hautaniemi, Anna-Kaarina J rvinen, Henrik Edgren, Sanjit K Mitra, Jaakko Astola
BMC Bioinformatics 2004, 5:194 (9December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Comparing functional annotation analyses with Catmap
Thomas Breslin, Patrik Ed n, Morten Krogh
BMC Bioinformatics 2004, 5:193 (9December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
ABC: software for interactive browsing of genomic multiple sequence alignment data
Gregory M Cooper, Senthil AG Singaravelu, Arend Sidow
BMC Bioinformatics 2004, 5:192 (8December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information
Yian A Chen, David J Mckillen, Shuyuan Wu, Matthew J Jenny, Robert Chapman, Paul S Gross, Gregory W Warr, Jonas S Almeida
BMC Bioinformatics 2004, 5:191 (7December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
A two-way interface between limited Systems Biology Markup Language and R
Tomas Radivoyevitch
BMC Bioinformatics 2004, 5:190 (7December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
DEDB: a database of Drosophila melanogaster exons in splicing graph form
Bernett TK Lee, Tin Wee Tan, Shoba Ranganathan
BMC Bioinformatics 2004, 5:189 (7December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Haplotype frequency estimation error analysis in the presence of missing genotype data
Enda D Kelly, Fabian Sievers, Ross McManus
BMC Bioinformatics 2004, 5:188 (1December2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
prot4EST: Translating Expressed Sequence Tags from neglected genomes
James D Wasmuth, Mark L Blaxter
BMC Bioinformatics 2004, 5:187 (30November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Constraint Logic Programming approach to protein structure prediction
Alessandro Dal Pal , Agostino Dovier, Federico Fogolari
BMC Bioinformatics 2004, 5:186 (30November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer
Virginie M Aris, Michael J Cody, Jeff Cheng, James J Dermody, Patricia Soteropoulos, Michael Recce, Peter P Tolias
BMC Bioinformatics 2004, 5:185 (29November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Integrating partonomic hierarchies in anatomy ontologies
Albert Burger, Duncan Davidson, Yiya Yang, Richard Baldock
BMC Bioinformatics 2004, 5:184 (26November2004)
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Methodology article
Protein family comparison using statistical models and predicted structural information
Richard Chung, Golan Yona
BMC Bioinformatics 2004, 5:183 (25November2004)
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Methodology article
A new mixture model approach to analyzing allelic-loss data using Bayes factors
Manisha Desai, Mary J Emond
BMC Bioinformatics 2004, 5:182 (24November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Discriminative topological features reveal biological network mechanisms
Manuel Middendorf, Etay Ziv, Carter Adams, Jen Hom, Robin Koytcheff, Chaya Levovitz, Gregory Woods, Linda Chen, Chris Wiggins
BMC Bioinformatics 2004, 5:181 (22November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Performance of a genetic algorithm for mass spectrometry proteomics
Neal O Jeffries
BMC Bioinformatics 2004, 5:180 (19November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
CLOE: Identification of putative functional relationships among genes by comparison of expression profiles between two species
Maurizio Pellegrino, Paolo Provero, Lorenzo Silengo, Ferdinando Di Cunto
BMC Bioinformatics 2004, 5:179 (19November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
David MA Martin, Matthew Berriman, Geoffrey J Barton
BMC Bioinformatics 2004, 5:178 (18November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Calibration and assessment of channel-specific biases in microarray data with extended dynamical range
Henrik Bengtsson, G ran Jnsson, Johan Vallon-Christersson
BMC Bioinformatics 2004, 5:177 (12November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
ESTIMA, a tool for EST management in a multi-project environment
Charu G Kumar, Richard LeDuc, George Gong, Levan Roinishivili, Harris A Lewin, Lei Liu
BMC Bioinformatics 2004, 5:176 (4November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Computation of elementary modes: a unifying framework and the new binary approach
Julien Gagneur, Steffen Klamt
BMC Bioinformatics 2004, 5:175 (4November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)
Nicolas Le Nov re, Marco Donizelli
BMC Bioinformatics 2004, 5:174 (1November2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison
Sierra D Stoneberg Holt, Jason A Holt
BMC Bioinformatics 2004, 5:173 (29October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Incremental genetic K-means algorithm and its application in gene expression data analysis
Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J Brown
BMC Bioinformatics 2004, 5:172 (28October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters
Chunlin Wang, Elliot J Lefkowitz
BMC Bioinformatics 2004, 5:171 (28October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
Saurabh Sinha, Mathieu Blanchette, Martin Tompa
BMC Bioinformatics 2004, 5:170 (28October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites
Peter Meinicke, Maike Tech, Burkhard Morgenstern, Rainer Merkl
BMC Bioinformatics 2004, 5:169 (28October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
d-matrix  database exploration, visualization and analysis
Dominik Seelow, Raffaello Galli, Siegrun Mebus, Hans-Peter Sperling, Hans Lehrach, Silke Sperling
BMC Bioinformatics 2004, 5:168 (28October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Improvement of alignment accuracy utilizing sequentially conserved motifs
Saikat Chakrabarti, Nitin Bhardwaj, Prem A Anand, Ramanathan Sowdhamini
BMC Bioinformatics 2004, 5:167 (28October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A probabilistic model for the evolution of RNA structure
Ian Holmes
BMC Bioinformatics 2004, 5:166 (26October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples
Zhining Wang, Mark G Lewis, Martin E Nau, Alma Arnold, Maryanne T Vahey
BMC Bioinformatics 2004, 5:165 (26October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Multivariate search for differentially expressed gene combinations
Yuanhui Xiao, Robert Frisina, Alexander Gordon, Lev Klebanov, Andrei Yakovlev
BMC Bioinformatics 2004, 5:164 (26October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
Hanno Teeling, Jost Waldmann, Thierry Lombardot, Margarete Bauer, Frank Oliver Glckner
BMC Bioinformatics 2004, 5:163 (26October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing
Andreas M Boehm, Robert P Galvin, Albert Sickmann
BMC Bioinformatics 2004, 5:162 (26October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Implications for domain fusion protein-protein interactions based on structural information
Jer-Ming Chia, Prasanna R Kolatkar
BMC Bioinformatics 2004, 5:161 (26October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Reuse of imputed data in microarray analysis increases imputation efficiency
Ki-Yeol Kim, Byoung-Jin Kim, Gwan-Su Yi
BMC Bioinformatics 2004, 5:160 (26October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Combining gene expression data from different generations of oligonucleotide arrays
Kyu-Baek Hwang, Sek Won Kong, Steve A Greenberg, Peter J Park
BMC Bioinformatics 2004, 5:159 (25October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A computational approach for ordering signal transduction pathway components from genomics and proteomics Data
Yin Liu, Hongyu Zhao
BMC Bioinformatics 2004, 5:158 (25October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model
Andrew F Neuwald, Jun S Liu
BMC Bioinformatics 2004, 5:157 (25October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Modeling of cell signaling pathways in macrophages by semantic networks
Michael Hsing, Joel L Bellenson, Conor Shankey, Artem Cherkasov
BMC Bioinformatics 2004, 5:156 (19October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
PASBio: predicate-argument structures for event extraction in molecular biology
Tuangthong Wattarujeekrit, Parantu K Shah, Nigel Collier
BMC Bioinformatics 2004, 5:155 (19October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Information assessment on predicting protein-protein interactions
Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao
BMC Bioinformatics 2004, 5:154 (18October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Inter-residue distances derived from fold contact propensities correlate with evolutionary substitution costs
Gareth Williams, Patrick Doherty
BMC Bioinformatics 2004, 5:153 (18October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology]
Methodology article
Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)
Sergey V Anisimov, Alexei A Sharov
BMC Bioinformatics 2004, 5:152 (18October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Caryoscope: An Open Source Java application for viewing microarray data in a genomic context
Ihab AB Awad, Christian A Rees, Tina Hernandez-Boussard, Catherine A Ball, Gavin Sherlock
BMC Bioinformatics 2004, 5:151 (15October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms
Florian Meereis, Michael Kaufmann
BMC Bioinformatics 2004, 5:150 (15October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Improved hit criteria for DNA local alignment
Laurent No, Gregory Kucherov
BMC Bioinformatics 2004, 5:149 (14October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data
Dietmar E Martin, Philippe Demougin, Michael N Hall, Michel Bellis
BMC Bioinformatics 2004, 5:148 (11October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Content-rich biological network constructed by mining PubMed abstracts
Hao Chen, Burt M Sharp
BMC Bioinformatics 2004, 5:147 (8October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Tools for loading MEDLINE into a local relational database
Diane E Oliver, Gaurav Bhalotia, Ariel S Schwartz, Russ B Altman, Marti A Hearst
BMC Bioinformatics 2004, 5:146 (7October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Extending the mutual information measure to rank inferred literature relationships
Jonathan D Wren
BMC Bioinformatics 2004, 5:145 (7October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Overdispersed logistic regression for SAGE: Modelling multiple groups and covariates
Keith A Baggerly, Li Deng, Jeffrey S Morris, C Marcelo Aldaz
BMC Bioinformatics 2004, 5:144 (6October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries
Cline Keime, Francesca Damiola, Dominique Mouchiroud, Laurent Duret, Olivier Gandrillon
BMC Bioinformatics 2004, 5:143 (6October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
ArrayD: A general purpose software for Microarray design
Anu Sharma, Gyan Prakash Srivastava, Vineet K Sharma, Srinivasan Ramachandran
BMC Bioinformatics 2004, 5:142 (2October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
GeneXplorer: an interactive web application for microarray data visualization and analysis
Christian A Rees, Janos Demeter, John C Matese, David Botstein, Gavin Sherlock
BMC Bioinformatics 2004, 5:141 (1October2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A comprehensive comparison of comparative RNA structure prediction approaches
Paul P Gardner, Robert Giegerich
BMC Bioinformatics 2004, 5:140 (30September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Research article
A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions
Neil R Smalheiser, Vetle I Torvik
BMC Bioinformatics 2004, 5:139 (28September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
cuticleDB: a relational database of Arthropod cuticular proteins
Christiana K Magkrioti, Ioannis C Spyropoulos, Vassiliki A Iconomidou, Judith H Willis, Stavros J Hamodrakas
BMC Bioinformatics 2004, 5:138 (28September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis
Michael P Cummings, Mark R Segal
BMC Bioinformatics 2004, 5:137 (28September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A combinational feature selection and ensemble neural network method for classification of gene expression data
Bing Liu, Qinghua Cui, Tianzi Jiang, Songde Ma
BMC Bioinformatics 2004, 5:136 (27September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Profiled support vector machines for antisense oligonucleotide efficacy prediction
Gustavo Camps-Valls, Alistair M Chalk, Antonio J Serrano-L pez, Jos D Mart n-Guerrero, Erik LL Sonnhammer
BMC Bioinformatics 2004, 5:135 (22September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability
Yanlin Huang, David Kowalski
BMC Bioinformatics 2004, 5:134 (21September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
Allermatch , a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines
Mark WEJ Fiers, Gijs A Kleter, Herman Nijland, Ad ACM Peijnenburg, Jan Peter Nap, Roeland CHJ van Ham
BMC Bioinformatics 2004, 5:133 (16September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA
Michael P Cummings, Daniel S Myers
BMC Bioinformatics 2004, 5:132 (16September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
What can we learn from noncoding regions of similarity between genomes?
Thomas A Down, Tim JP Hubbard
BMC Bioinformatics 2004, 5:131 (15September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research
Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen Ficklin, Ilhyung Cho, Albert Abbott, Jeffrey Tomkins, Dorrie Main
BMC Bioinformatics 2004, 5:130 (9September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
Saurabh Sinha, Mark D Schroeder, Ulrich Unnerstall, Ulrike Gaul, Eric D Siggia
BMC Bioinformatics 2004, 5:129 (9September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Software
DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors
Martin Schmollinger, Kay Nieselt, Michael Kaufmann, Burkhard Morgenstern
BMC Bioinformatics 2004, 5:128 (9September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Functionally specified protein signatures distinctive for each of the different blue copper proteins
Anuradha Vivekanandan Giri, Sharmila Anishetty, Pennathur Gautam
BMC Bioinformatics 2004, 5:127 (9September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Iterative class discovery and feature selection using Minimal Spanning Trees
Sudhir Varma, Richard Simon
BMC Bioinformatics 2004, 5:126 (8September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Determination of the differentially expressed genes in microarray experiments using local FDR
J Aubert, A Bar-Hen, J-J Daudin, S Robin
BMC Bioinformatics 2004, 5:125 (6September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Handling multiple testing while interpreting microarrays with the Gene Ontology Database
Michael V Osier, Hongyu Zhao, Kei-Hoi Cheung
BMC Bioinformatics 2004, 5:124 (6September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
GASP: Gapped Ancestral Sequence Prediction for proteins
Richard J Edwards, Denis C Shields
BMC Bioinformatics 2004, 5:123 (6September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Automatic annotation of protein motif function with Gene Ontology terms
Xinghua Lu, Chengxiang Zhai, Vanathi Gopalakrishnan, Bruce G Buchanan
BMC Bioinformatics 2004, 5:122 (2September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
SED, a normalization free method for DNA microarray data analysis
Huajun Wang, Hui Huang
BMC Bioinformatics 2004, 5:121 (2September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Artificial neural network approach for selection of susceptible single nucleotide polymorphisms and construction of prediction model on childhood allergic asthma
Yasuyuki Tomita, Shuta Tomida, Yuko Hasegawa, Yoichi Suzuki, Taro Shirakawa, Takeshi Kobayashi, Hiroyuki Honda
BMC Bioinformatics 2004, 5:120 (1September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)
Ricardo ZN V ncio, Helena Brentani, Diogo FC Patr o, Carlos AB Pereira
BMC Bioinformatics 2004, 5:119 (31August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Estimating mutual information using B-spline functions an improved similarity measure for analysing gene expression data
Carsten O Daub, Ralf Steuer, Joachim Selbig, Sebastian Kloska
BMC Bioinformatics 2004, 5:118 (31August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Software
XHM: A system for detection of potential cross hybridizations in DNA microarrays
Kristian Flikka, Fekadu Yadetie, Astrid Laegreid, Inge Jonassen
BMC Bioinformatics 2004, 5:117 (27August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Applying Support Vector Machines for Gene ontology based gene function prediction
Arunachalam Vinayagam, Rainer Knig, Jutta Moormann, Falk Schubert, Roland Eils, Karl-Heinz Glatting, S ndor Suhai
BMC Bioinformatics 2004, 5:116 (26August2004)
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An imaging system for standardized quantitative analysis of C. elegans behavior
Zhaoyang Feng, Christopher J Cronin, John H Wittig Jr, Paul W Sternberg, William R Schafer
BMC Bioinformatics 2004, 5:115 (26August2004)
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Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering
Alexandre G de Brevern, Serge Hazout, Alain Malpertuy
BMC Bioinformatics 2004, 5:114 (23August2004)
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MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Robert C Edgar
BMC Bioinformatics 2004, 5:113 (19August2004)
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IdentiCS Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence
Jibin Sun, An-Ping Zeng
BMC Bioinformatics 2004, 5:112 (16August2004)
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Alternative mapping of probes to genes for Affymetrix chips
Laurent Gautier, Morten M ller, Lennart Friis-Hansen, Steen Knudsen
BMC Bioinformatics 2004, 5:111 (14August2004)
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Tests for finding complex patterns of differential expression in cancers: towards individualized medicine
James Lyons-Weiler, Satish Patel, Michael J Becich, Tony E Godfrey
BMC Bioinformatics 2004, 5:110 (12August2004)
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