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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Maria Kowalczuk
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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)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
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)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
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)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
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)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
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]
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)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
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)
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