Volume 6, issue 1, December 2005
310 articles in this issue
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Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function
Authors (first, second and last of 9)
- Markey C McNutt
- Ron Tongbai
- Kevin Gardner
- Content type: Research article
- Open Access
- Published: 18 October 2005
- Article: 259
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Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification
Authors (first, second and last of 4)
- Li-Hsieh Lin
- Hsiao-Ching Lee
- Bor-Sen Chen
- Content type: Methodology article
- Open Access
- Published: 18 October 2005
- Article: 258
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Statistical distributions of optimal global alignment scores of random protein sequences
Authors (first, second and last of 4)
- Hongxia Pang
- Jiaowei Tang
- Shiheng Tao
- Content type: Research article
- Open Access
- Published: 15 October 2005
- Article: 257
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Evaluating eukaryotic secreted protein prediction
Authors
- Eric W Klee
- Lynda BM Ellis
- Content type: Research article
- Open Access
- Published: 14 October 2005
- Article: 256
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The modeled structure of the RNA dependent RNA polymerase of GBV-C Virus suggests a role for motif E in Flaviviridae RNA polymerases
Authors (first, second and last of 4)
- François Ferron
- Cécile Bussetta
- Bruno Canard
- Content type: Research article
- Open Access
- Published: 14 October 2005
- Article: 255
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Prediction of β-barrel membrane proteins by searching for restricted domains
Authors
- Oliver Mirus
- Enrico Schleiff
- Content type: Research article
- Open Access
- Published: 14 October 2005
- Article: 254
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ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins
Authors
- Tomas Ohlson
- Arne Elofsson
- Content type: Research article
- Open Access
- Published: 14 October 2005
- Article: 253
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CoaSim: A flexible environment for simulating genetic data under coalescent models
Authors (first, second and last of 6)
- Thomas Mailund
- Mikkel H Schierup
- Leif Schauser
- Content type: Software
- Open Access
- Published: 14 October 2005
- Article: 252
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Differentiation of regions with atypical oligonucleotide composition in bacterial genomes
Authors
- Oleg N Reva
- Burkhard Tümmler
- Content type: Research article
- Open Access
- Published: 14 October 2005
- Article: 251
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MASQOT: a method for cDNA microarray spot quality control
Authors (first, second and last of 7)
- Max Bylesjö
- Daniel Eriksson
- Johan Trygg
- Content type: Methodology article
- Open Access
- Published: 13 October 2005
- Article: 250
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SPdb – a signal peptide database
Authors
- Khar Heng Choo
- Tin Wee Tan
- Shoba Ranganathan
- Content type: Database
- Open Access
- Published: 13 October 2005
- Article: 249
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Better prediction of protein contact number using a support vector regression analysis of amino acid sequence
Authors
- Zheng Yuan
- Content type: Research article
- Open Access
- Published: 13 October 2005
- Article: 248
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Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis
Authors
- François Enault
- Karsten Suhre
- Jean-Michel Claverie
- Content type: Software
- Open Access
- Published: 12 October 2005
- Article: 247
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T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory
Authors (first, second and last of 4)
- Stéphanie Monnier
- David G Cox
- Federico Canzian
- Content type: Software
- Open Access
- Published: 12 October 2005
- Article: 246
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Extension of Lander-Waterman theory for sequencing filtered DNA libraries
Authors
- Michael C Wendl
- W Brad Barbazuk
- Content type: Research article
- Open Access
- Published: 10 October 2005
- Article: 245
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ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences
Authors
- Paola Bonizzoni
- Raffaella Rizzi
- Graziano Pesole
- Content type: Software
- Open Access
- Published: 05 October 2005
- Article: 244
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Phylogenetic detection of conserved gene clusters in microbial genomes
Authors (first, second and last of 4)
- Yu Zheng
- Brian P Anton
- Simon Kasif
- Content type: Research article
- Open Access
- Published: 03 October 2005
- Article: 243
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Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks
Authors (first, second and last of 5)
- Qicheng Ma
- Gung-Wei Chirn
- NR Nirmala
- Content type: Methodology article
- Open Access
- Published: 03 October 2005
- Article: 242
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A comparison of RNA folding measures
Authors
- Eva Freyhult
- Paul P Gardner
- Vincent Moulton
- Content type: Research article
- Open Access
- Published: 03 October 2005
- Article: 241
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Sequence variation in ligand binding sites in proteins
Authors
- Thomas J Magliery
- Lynne Regan
- Content type: Research article
- Open Access
- Published: 30 September 2005
- Article: 240
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Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data
Authors (first, second and last of 5)
- Florent Baty
- Michel P Bihl
- Martin H Brutsche
- Content type: Methodology article
- Open Access
- Published: 28 September 2005
- Article: 239
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Mathematical design of prokaryotic clone-based microarrays
Authors (first, second and last of 4)
- Bart Pieterse
- Elisabeth J Quirijns
- Mariët J van der Werf
- Content type: Methodology article
- Open Access
- Published: 28 September 2005
- Article: 238
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Measuring similarities between transcription factor binding sites
Authors
- Szymon M Kielbasa
- Didier Gonze
- Hanspeter Herzel
- Content type: Software
- Open Access
- Published: 28 September 2005
- Article: 237
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SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
Authors (first, second and last of 4)
- Andy Pang
- Andrew D Smith
- Elisabeth RM Tillier
- Content type: Software
- Open Access
- Published: 27 September 2005
- Article: 236
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An analysis of extensible modelling for functional genomics data
Authors
- Andrew R Jones
- Norman W Paton
- Content type: Methodology article
- Open Access
- Published: 27 September 2005
- Article: 235
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Quality determination and the repair of poor quality spots in array experiments
Authors (first, second and last of 4)
- Brian DM Tom
- Walter R Gilks
- James W Ajioka
- Content type: Methodology article
- Open Access
- Published: 26 September 2005
- Article: 234
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GeneRank: Using search engine technology for the analysis of microarray experiments
Authors (first, second and last of 4)
- Julie L Morrison
- Rainer Breitling
- David R Gilbert
- Content type: Research article
- Open Access
- Published: 21 September 2005
- Article: 233
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EXPANDER – an integrative program suite for microarray data analysis
Authors (first, second and last of 8)
- Ron Shamir
- Adi Maron-Katz
- Ran Elkon
- Content type: Software
- Open Access
- Published: 21 September 2005
- Article: 232
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A linear memory algorithm for Baum-Welch training
Authors
- István Miklós
- Irmtraud M Meyer
- Content type: Research article
- Open Access
- Published: 19 September 2005
- Article: 231
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Chromosomal clustering of a human transcriptome reveals regulatory background
Authors (first, second and last of 4)
- Jan H Vogel
- Anja von Heydebreck
- Silke Sperling
- Content type: Research article
- Open Access
- Published: 19 September 2005
- Article: 230
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ProbeMaker: an extensible framework for design of sets of oligonucleotide probes
Authors
- Johan Stenberg
- Mats Nilsson
- Ulf Landegren
- Content type: Software
- Open Access
- Published: 19 September 2005
- Article: 229
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Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software
Authors (first, second and last of 6)
- Hédi Soula
- Céline Robardet
- Olivier Gandrillon
- Content type: Software
- Open Access
- Published: 19 September 2005
- Article: 228
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Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
Authors
- Cecily J Wolfe
- Isaac S Kohane
- Atul J Butte
- Content type: Research article
- Open Access
- Published: 14 September 2005
- Article: 227
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Assessing local structural perturbations in proteins
Authors
- Martin A Lema
- Julian Echave
- Content type: Software
- Open Access
- Published: 13 September 2005
- Article: 226
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Pathway level analysis of gene expression using singular value decomposition
Authors
- John Tomfohr
- Jun Lu
- Thomas B Kepler
- Content type: Methodology article
- Open Access
- Published: 12 September 2005
- Article: 225
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Versatile and declarative dynamic programming using pair algebras
Authors
- Peter Steffen
- Robert Giegerich
- Content type: Methodology article
- Open Access
- Published: 12 September 2005
- Article: 224
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SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design
Authors
- Andrean Goede
- Ines S Jaeger
- Robert Preissner
- Content type: Software
- Open Access
- Published: 09 September 2005
- Article: 223
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Micro-Mar: a database for dynamic representation of marine microbial biodiversity
Authors (first, second and last of 4)
- Ravindra Pushker
- Giuseppe D'Auria
- Francisco RodrÃguez-Valera
- Content type: Database
- Open Access
- Published: 09 September 2005
- Article: 222
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GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures
Authors
- Daron M Standley
- Hiroyuki Toh
- Haruki Nakamura
- Content type: Software
- Open Access
- Published: 08 September 2005
- Article: 221
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A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage
Authors
- Jianmin Wang
- Xiaoqiu Huang
- Content type: Methodology article
- Open Access
- Published: 07 September 2005
- Article: 220
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Generalizations of Markov model to characterize biological sequences
Authors
- Junwen Wang
- Sridhar Hannenhalli
- Content type: Software
- Open Access
- Published: 06 September 2005
- Article: 219
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TmaDB: a repository for tissue microarray data
Authors
- Archana Sharma-Oates
- Philip Quirke
- David R Westhead
- Content type: Database
- Open Access
- Published: 01 September 2005
- Article: 218
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Automation of gene assignments to metabolic pathways using high-throughput expression data
Authors
- Liviu Popescu
- Golan Yona
- Content type: Methodology article
- Open Access
- Published: 31 August 2005
- Article: 217
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JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture
Authors
- Peter Sperisen
- Marco Pagni
- Content type: Methodology article
- Open Access
- Published: 31 August 2005
- Article: 216
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Dynamic covariation between gene expression and proteome characteristics
Authors (first, second and last of 4)
- Mansour Taghavi Azar Sharabiani
- Markku Siermala
- Mauno Vihinen
- Content type: Research article
- Open Access
- Published: 30 August 2005
- Article: 215
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Sources of variation in Affymetrix microarray experiments
Authors (first, second and last of 9)
- Stanislav O Zakharkin
- Kyoungmi Kim
- Grier P Page
- Content type: Research article
- Open Access
- Published: 29 August 2005
- Article: 214
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Improved prediction of critical residues for protein function based on network and phylogenetic analyses
Authors
- Boris Thibert
- Dale E Bredesen
- Gabriel del Rio
- Content type: Methodology article
- Open Access
- Published: 26 August 2005
- Article: 213
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A new dynamical layout algorithm for complex biochemical reaction networks
Authors
- Katja Wegner
- Ursula Kummer
- Content type: Methodology article
- Open Access
- Published: 26 August 2005
- Article: 212
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stam – a Bioconductor compliant R package for structured analysis of microarray data
Authors
- Claudio Lottaz
- Rainer Spang
- Content type: Software
- Open Access
- Published: 25 August 2005
- Article: 211