Volume 5, issue 1, December 2004
209 articles in this issue
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A database for G proteins and their interaction with GPCRs
Authors (first, second and last of 4)
- Antigoni L Elefsinioti
- Pantelis G Bagos
- Stavros J Hamodrakas
- Content type: Database
- Open Access
- Published: 24 December 2004
- Article: 208
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Clustering under the line graph transformation: application to reaction network
Authors (first, second and last of 5)
- Jose C Nacher
- Nobuhisa Ueda
- Tatsuya Akutsu
- Content type: Research article
- Open Access
- Published: 24 December 2004
- Article: 207
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An empirical analysis of training protocols for probabilistic gene finders
Authors
- William H Majoros
- Steven L Salzberg
- Content type: Research article
- Open Access
- Published: 21 December 2004
- Article: 206
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Predicting binding sites of hydrolase-inhibitor complexes by combining several methods
Authors (first, second and last of 11)
- Taner Z Sen
- Andrzej Kloczkowski
- Drena Dobbs
- Content type: Methodology article
- Open Access
- Published: 17 December 2004
- Article: 205
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An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage
Authors
- Gary W Stuart
- Michael W Berry
- Content type: Research article
- Open Access
- Published: 17 December 2004
- Article: 204
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A power law global error model for the identification of differentially expressed genes in microarray data
Authors (first, second and last of 7)
- Norman Pavelka
- Mattia Pelizzola
- Paola Ricciardi-Castagnoli
- Content type: Methodology article
- Open Access
- Published: 17 December 2004
- Article: 203
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Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations
Authors (first, second and last of 4)
- Rajalakshmi Gurunathan
- Bernard Van Emden
- Sudhir Kumar
- Content type: Software
- Open Access
- Published: 16 December 2004
- Article: 202
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A novel Mixture Model Method for identification of differentially expressed genes from DNA microarray data
Authors (first, second and last of 5)
- Kayvan Najarian
- Maryam Zaheri
- Javad Dargahi
- Content type: Methodology article
- Open Access
- Published: 16 December 2004
- Article: 201
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Analysis of superfamily specific profile-profile recognition accuracy
Authors
- James A Casbon
- Mansoor AS Saqi
- Content type: Research article
- Open Access
- Published: 16 December 2004
- Article: 200
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Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach
Authors
- Hong-Wu Ma
- Jan Buer
- An-Ping Zeng
- Content type: Research article
- Open Access
- Published: 16 December 2004
- Article: 199
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GenomeViz: visualizing microbial genomes
Authors
- Rohit Ghai
- Torsten Hain
- Trinad Chakraborty
- Content type: Software
- Open Access
- Published: 15 December 2004
- Article: 198
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SCOPmap: Automated assignment of protein structures to evolutionary superfamilies
Authors (first, second and last of 5)
- Sara Cheek
- Yuan Qi
- Nick V Grishin
- Content type: Research article
- Open Access
- Published: 14 December 2004
- Article: 197
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A functional hierarchical organization of the protein sequence space
Authors (first, second and last of 4)
- Noam Kaplan
- Moriah Friedlich
- Michal Linial
- Content type: Research article
- Open Access
- Published: 14 December 2004
- Article: 196
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GECKO: a complete large-scale gene expression analysis platform
Authors (first, second and last of 9)
- Joachim Theilhaber
- Anatoly Ulyanov
- Steven Bushnell
- Content type: Software
- Open Access
- Published: 10 December 2004
- Article: 195
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Optimized LOWESS normalization parameter selection for DNA microarray data
Authors (first, second and last of 6)
- John A Berger
- Sampsa Hautaniemi
- Jaakko Astola
- Content type: Methodology article
- Open Access
- Published: 09 December 2004
- Article: 194
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Comparing functional annotation analyses with Catmap
Authors
- Thomas Breslin
- Patrik Edén
- Morten Krogh
- Content type: Methodology article
- Open Access
- Published: 09 December 2004
- Article: 193
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ABC: software for interactive browsing of genomic multiple sequence alignment data
Authors
- Gregory M Cooper
- Senthil AG Singaravelu
- Arend Sidow
- Content type: Software
- Open Access
- Published: 08 December 2004
- Article: 192
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Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information
Authors (first, second and last of 8)
- Yian A Chen
- David J Mckillen
- Jonas S Almeida
- Content type: Research article
- Open Access
- Published: 07 December 2004
- Article: 191
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A two-way interface between limited Systems Biology Markup Language and R
Authors
- Tomas Radivoyevitch
- Content type: Software
- Open Access
- Published: 07 December 2004
- Article: 190
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DEDB: a database of Drosophila melanogaster exons in splicing graph form
Authors
- Bernett TK Lee
- Tin Wee Tan
- Shoba Ranganathan
- Content type: Database
- Open Access
- Published: 07 December 2004
- Article: 189
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Haplotype frequency estimation error analysis in the presence of missing genotype data
Authors
- Enda D Kelly
- Fabian Sievers
- Ross McManus
- Content type: Research article
- Open Access
- Published: 01 December 2004
- Article: 188
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prot4EST: Translating Expressed Sequence Tags from neglected genomes
Authors
- James D Wasmuth
- Mark L Blaxter
- Content type: Software
- Open Access
- Published: 30 November 2004
- Article: 187
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Constraint Logic Programming approach to protein structure prediction
Authors
- Alessandro Dal Palù
- Agostino Dovier
- Federico Fogolari
- Content type: Research article
- Open Access
- Published: 30 November 2004
- Article: 186
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Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer
Authors (first, second and last of 7)
- Virginie M Aris
- Michael J Cody
- Peter P Tolias
- Content type: Methodology article
- Open Access
- Published: 29 November 2004
- Article: 185
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Integrating partonomic hierarchies in anatomy ontologies
Authors (first, second and last of 4)
- Albert Burger
- Duncan Davidson
- Richard Baldock
- Content type: Research article
- Open Access
- Published: 26 November 2004
- Article: 184
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Protein family comparison using statistical models and predicted structural information
Authors
- Richard Chung
- Golan Yona
- Content type: Methodology article
- Open Access
- Published: 25 November 2004
- Article: 183
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A new mixture model approach to analyzing allelic-loss data using Bayes factors
Authors
- Manisha Desai
- Mary J Emond
- Content type: Methodology article
- Open Access
- Published: 24 November 2004
- Article: 182
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Discriminative topological features reveal biological network mechanisms
Authors (first, second and last of 9)
- Manuel Middendorf
- Etay Ziv
- Chris Wiggins
- Content type: Research article
- Open Access
- Published: 22 November 2004
- Article: 181
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Performance of a genetic algorithm for mass spectrometry proteomics
Authors
- Neal O Jeffries
- Content type: Research article
- Open Access
- Published: 19 November 2004
- Article: 180
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CLOE: Identification of putative functional relationships among genes by comparison of expression profiles between two species
Authors (first, second and last of 4)
- Maurizio Pellegrino
- Paolo Provero
- Ferdinando Di Cunto
- Content type: Methodology article
- Open Access
- Published: 19 November 2004
- Article: 179
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GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
Authors
- David MA Martin
- Matthew Berriman
- Geoffrey J Barton
- Content type: Methodology article
- Open Access
- Published: 18 November 2004
- Article: 178
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Calibration and assessment of channel-specific biases in microarray data with extended dynamical range
Authors
- Henrik Bengtsson
- Göran Jönsson
- Johan Vallon-Christersson
- Content type: Research article
- Open Access
- Published: 12 November 2004
- Article: 177
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ESTIMA, a tool for EST management in a multi-project environment
Authors (first, second and last of 6)
- Charu G Kumar
- Richard LeDuc
- Lei Liu
- Content type: Software
- Open Access
- Published: 04 November 2004
- Article: 176
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Computation of elementary modes: a unifying framework and the new binary approach
Authors
- Julien Gagneur
- Steffen Klamt
- Content type: Research article
- Open Access
- Published: 04 November 2004
- Article: 175
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The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)
Authors
- Nicolas Le Novère
- Marco Donizelli
- Content type: Database
- Open Access
- Published: 01 November 2004
- Article: 174
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The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison
Authors
- Sierra D Stoneberg Holt
- Jason A Holt
- Content type: Software
- Open Access
- Published: 29 October 2004
- Article: 173
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Incremental genetic K-means algorithm and its application in gene expression data analysis
Authors (first, second and last of 5)
- Yi Lu
- Shiyong Lu
- Susan J Brown
- Content type: Methodology article
- Open Access
- Published: 28 October 2004
- Article: 172
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SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters
Authors
- Chunlin Wang
- Elliot J Lefkowitz
- Content type: Software
- Open Access
- Published: 28 October 2004
- Article: 171
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PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
Authors
- Saurabh Sinha
- Mathieu Blanchette
- Martin Tompa
- Content type: Research article
- Open Access
- Published: 28 October 2004
- Article: 170
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Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites
Authors (first, second and last of 4)
- Peter Meinicke
- Maike Tech
- Rainer Merkl
- Content type: Methodology article
- Open Access
- Published: 28 October 2004
- Article: 169
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d-matrix – database exploration, visualization and analysis
Authors (first, second and last of 6)
- Dominik Seelow
- Raffaello Galli
- Silke Sperling
- Content type: Software
- Open Access
- Published: 28 October 2004
- Article: 168
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Improvement of alignment accuracy utilizing sequentially conserved motifs
Authors (first, second and last of 4)
- Saikat Chakrabarti
- Nitin Bhardwaj
- Ramanathan Sowdhamini
- Content type: Software
- Open Access
- Published: 28 October 2004
- Article: 167
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A probabilistic model for the evolution of RNA structure
Authors
- Ian Holmes
- Content type: Methodology article
- Open Access
- Published: 26 October 2004
- Article: 166
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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
Authors (first, second and last of 5)
- Zhining Wang
- Mark G Lewis
- Maryanne T Vahey
- Content type: Methodology article
- Open Access
- Published: 26 October 2004
- Article: 165
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Multivariate search for differentially expressed gene combinations
Authors (first, second and last of 5)
- Yuanhui Xiao
- Robert Frisina
- Andrei Yakovlev
- Content type: Methodology article
- Open Access
- Published: 26 October 2004
- Article: 164
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TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
Authors (first, second and last of 5)
- Hanno Teeling
- Jost Waldmann
- Frank Oliver Glöckner
- Content type: Software
- Open Access
- Published: 26 October 2004
- Article: 163
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Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing
Authors
- Andreas M Boehm
- Robert P Galvin
- Albert Sickmann
- Content type: Software
- Open Access
- Published: 26 October 2004
- Article: 162
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Implications for domain fusion protein-protein interactions based on structural information
Authors
- Jer-Ming Chia
- Prasanna R Kolatkar
- Content type: Research article
- Open Access
- Published: 26 October 2004
- Article: 161
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Reuse of imputed data in microarray analysis increases imputation efficiency
Authors
- Ki-Yeol Kim
- Byoung-Jin Kim
- Gwan-Su Yi
- Content type: Methodology article
- Open Access
- Published: 26 October 2004
- Article: 160