Volume 10, issue 1, December 2009
455 articles in this issue
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Comparison of sequence-dependent tiling array normalization approaches
Authors
- Ho-Ryun Chung
- Martin Vingron
- Content type: Methodology article
- Open Access
- Published: 30 June 2009
- Article: 204
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Integrated analysis of DNA copy number and gene expression microarray data using gene sets
Authors (first, second and last of 5)
- Renée X Menezes
- Marten Boetzer
- Judith M Boer
- Content type: Research article
- Open Access
- Published: 29 June 2009
- Article: 203
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NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction
Authors (first, second and last of 4)
- Alex N Nguyen Ba
- Anastassia Pogoutse
- Alan M Moses
- Content type: Research article
- Open Access
- Published: 29 June 2009
- Article: 202
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A-MADMAN: Annotation-based microarray data meta-analysis tool
Authors (first, second and last of 7)
- Andrea Bisognin
- Alessandro Coppe
- Stefania Bortoluzzi
- Content type: Software
- Open Access
- Published: 29 June 2009
- Article: 201
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Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis
Authors (first, second and last of 4)
- Ming Yi
- Uma Mudunuri
- Robert M Stephens
- Content type: Software
- Open Access
- Published: 29 June 2009
- Article: 200
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DOTcvpSB, a software toolbox for dynamic optimization in systems biology
Authors
- Tomáš Hirmajer
- Eva Balsa-Canto
- Julio R Banga
- Content type: Software
- Open Access
- Published: 29 June 2009
- Article: 199
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A Bayesian approach to efficient differential allocation for resampling-based significance testing
Authors
- Shane T Jensen
- Sameer Soi
- Li-San Wang
- Content type: Research article
- Open Access
- Published: 28 June 2009
- Article: 198
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ResBoost: characterizing and predicting catalytic residues in enzymes
Authors (first, second and last of 6)
- Ron Alterovitz
- Aaron Arvey
- Kimmen Sjölander
- Content type: Methodology article
- Open Access
- Published: 27 June 2009
- Article: 197
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Triangle network motifs predict complexes by complementing high-error interactomes with structural information
Authors (first, second and last of 4)
- Bill Andreopoulos
- Christof Winter
- Michael Schroeder
- Content type: Research article
- Open Access
- Published: 27 June 2009
- Article: 196
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Ab initio and homology based prediction of protein domains by recursive neural networks
Authors (first, second and last of 6)
- Ian Walsh
- Alberto JM Martin
- Gianluca Pollastri
- Content type: Research article
- Open Access
- Published: 26 June 2009
- Article: 195
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Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis
Authors (first, second and last of 4)
- Otávio JB Brustolini
- Luciano G Fietto
- Flávia ML Passos
- Content type: Research article
- Open Access
- Published: 25 June 2009
- Article: 194
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Filtering Genes for Cluster and Network Analysis
Authors
- David Tritchler
- Elena Parkhomenko
- Joseph Beyene
- Content type: Methodology article
- Open Access
- Published: 23 June 2009
- Article: 193
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OrthoClusterDB: an online platform for synteny blocks
Authors (first, second and last of 7)
- Man-Ping Ng
- Ismael A Vergara
- Nansheng Chen
- Content type: Database
- Open Access
- Published: 23 June 2009
- Article: 192
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Unsupervised assessment of microarray data quality using a Gaussian mixture model
Authors
- Brian E Howard
- Beate Sick
- Steffen Heber
- Content type: Research article
- Open Access
- Published: 22 June 2009
- Article: 191
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Modeling the role of p53 pulses in DNA damage- induced cell death decision
Authors (first, second and last of 6)
- Tingzhe Sun
- Chun Chen
- Pingping Shen
- Content type: Research article
- Open Access
- Published: 22 June 2009
- Article: 190
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Platform dependence of inference on gene-wise and gene-set involvement in human lung development
Authors (first, second and last of 12)
- Rose Du
- Kelan Tantisira
- Scott T Weiss
- Content type: Research article
- Open Access
- Published: 19 June 2009
- Article: 189
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designGG: an R-package and web tool for the optimal design of genetical genomics experiments
Authors (first, second and last of 6)
- Yang Li
- Morris A Swertz
- Ritsert C Jansen
- Content type: Software
- Open Access
- Published: 18 June 2009
- Article: 188
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geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research
Authors (first, second and last of 5)
- Daniel Glez-Peña
- Fernando DÃaz
- Florentino Fdez-Riverola
- Content type: Software
- Open Access
- Published: 18 June 2009
- Article: 187
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The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays
Authors (first, second and last of 4)
- Daniela Eggle
- Svenja Debey-Pascher
- Joachim L Schultze
- Content type: Research article
- Open Access
- Published: 18 June 2009
- Article: 186
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Automated genome mining for natural products
Authors (first, second and last of 5)
- Michael HT Li
- Peter MU Ung
- David H Sherman
- Content type: Software
- Open Access
- Published: 16 June 2009
- Article: 185
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FuGEFlow: data model and markup language for flow cytometry
Authors (first, second and last of 10)
- Yu Qian
- Olga Tchuvatkina
- Ryan R Brinkman
- Content type: Correspondence
- Open Access
- Published: 16 June 2009
- Article: 184
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The textual characteristics of traditional and Open Access scientific journals are similar
Authors
- Karin Verspoor
- K Bretonnel Cohen
- Lawrence Hunter
- Content type: Research article
- Open Access
- Published: 15 June 2009
- Article: 183
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Structural motifs recurring in different folds recognize the same ligand fragments
Authors (first, second and last of 5)
- Gabriele Ausiello
- Pier Federico Gherardini
- Manuela Helmer-Citterich
- Content type: Methodology article
- Open Access
- Published: 15 June 2009
- Article: 182
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Computing paths and cycles in biological interaction graphs
Authors
- Steffen Klamt
- Axel von Kamp
- Content type: Methodology article
- Open Access
- Published: 15 June 2009
- Article: 181
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Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design
Authors (first, second and last of 8)
- Helen I Field
- Serena A Scollen
- Paul DP Pharoah
- Content type: Software
- Open Access
- Published: 12 June 2009
- Article: 180
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Improved results in proteomics by use of local and peptide-class specific false discovery rates
Authors
- Lau Sennels
- Jimi-Carlo Bukowski-Wills
- Juri Rappsilber
- Content type: Research article
- Open Access
- Published: 12 June 2009
- Article: 179
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TOMOBFLOW: feature-preserving noise filtering for electron tomography
Authors
- Jose-Jesus Fernandez
- Content type: Software
- Open Access
- Published: 12 June 2009
- Article: 178
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Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens
Authors (first, second and last of 12)
- Sam Zaremba
- Mila Ramos-Santacruz
- David Pot
- Content type: Database
- Open Access
- Published: 10 June 2009
- Article: 177
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"PolyMin": software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation
Authors
- Ursula K Frei
- Bernd Wollenweber
- Thomas Lübberstedt
- Content type: Software
- Open Access
- Published: 10 June 2009
- Article: 176
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Local alignment of two-base encoded DNA sequence
Authors
- Nils Homer
- Barry Merriman
- Stanley F Nelson
- Content type: Research article
- Open Access
- Published: 09 June 2009
- Article: 175
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Combining specificity determining and conserved residues improves functional site prediction
Authors
- Olga V Kalinina
- Mikhail S Gelfand
- Robert B Russell
- Content type: Research article
- Open Access
- Published: 09 June 2009
- Article: 174
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Improved ChIP-chip analysis by a mixture model approach
Authors (first, second and last of 4)
- Wei Sun
- Michael J Buck
- Ian J Davis
- Content type: Methodology article
- Open Access
- Published: 07 June 2009
- Article: 173
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Accounting for uncertainty when assessing association between copy number and disease: a latent class model
Authors (first, second and last of 7)
- Juan R González
- Isaac Subirana
- LluÃs Armengol
- Content type: Methodology article
- Open Access
- Published: 06 June 2009
- Article: 172
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T-REX: software for the processing and analysis of T-RFLP data
Authors (first, second and last of 5)
- Steven W Culman
- Robert Bukowski
- Daniel H Buckley
- Content type: Software
- Open Access
- Published: 06 June 2009
- Article: 171
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A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling
Authors (first, second and last of 5)
- Daniel G Pinheiro
- Pedro AF Galante
- Wilson A Silva Jr
- Content type: Software
- Open Access
- Published: 06 June 2009
- Article: 170
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A core-attachment based method to detect protein complexes in PPI networks
Authors (first, second and last of 4)
- Min Wu
- Xiaoli Li
- See-Kiong Ng
- Content type: Methodology article
- Open Access
- Published: 02 June 2009
- Article: 169
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Fpocket: An open source platform for ligand pocket detection
Authors
- Vincent Le Guilloux
- Peter Schmidtke
- Pierre Tuffery
- Content type: Software
- Open Access
- Published: 02 June 2009
- Article: 168
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Measure of synonymous codon usage diversity among genes in bacteria
Authors
- Haruo Suzuki
- Rintaro Saito
- Masaru Tomita
- Content type: Methodology article
- Open Access
- Published: 01 June 2009
- Article: 167
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mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection
Authors
- Kosuke M Teshima
- Hideki Innan
- Content type: Software
- Open Access
- Published: 30 May 2009
- Article: 166
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A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data
Authors (first, second and last of 4)
- Xiaofeng Dai
- Timo Erkkilä
- Harri Lähdesmäki
- Content type: Methodology article
- Open Access
- Published: 29 May 2009
- Article: 165
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Sample size calculation for microarray experiments with blocked one-way design
Authors (first, second and last of 5)
- Sin-Ho Jung
- Insuk Sohn
- Phyllis C Leppert
- Content type: Methodology article
- Open Access
- Published: 28 May 2009
- Article: 164
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Analyzing miRNA co-expression networks to explore TF-miRNA regulation
Authors
- Sanghamitra Bandyopadhyay
- Malay Bhattacharyya
- Content type: Methodology article
- Open Access
- Published: 28 May 2009
- Article: 163
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Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses
Authors (first, second and last of 7)
- Gordon W Slysz
- Charles AH Baker
- David C Schriemer
- Content type: Software
- Open Access
- Published: 27 May 2009
- Article: 162
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GAGE: generally applicable gene set enrichment for pathway analysis
Authors (first, second and last of 5)
- Weijun Luo
- Michael S Friedman
- Peter J Woolf
- Content type: Research article
- Open Access
- Published: 27 May 2009
- Article: 161
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IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico
Authors (first, second and last of 5)
- Tzong-Yuan Wu
- Chi-Chun Hsieh
- Yuh-Show Tsai
- Content type: Methodology article
- Open Access
- Published: 27 May 2009
- Article: 160
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Transmembrane protein topology prediction using support vector machines
Authors
- Timothy Nugent
- David T Jones
- Content type: Research article
- Open Access
- Published: 26 May 2009
- Article: 159
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Orymold: ontology based gene expression data integration and analysis tool applied to rice
Authors (first, second and last of 6)
- Jaume Mercadé
- Antonio Espinosa
- Tamara Maes
- Content type: Software
- Open Access
- Published: 23 May 2009
- Article: 158
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IDSS: deformation invariant signatures for molecular shape comparison
Authors
- Yu-Shen Liu
- Yi Fang
- Karthik Ramani
- Content type: Methodology article
- Open Access
- Published: 22 May 2009
- Article: 157
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Differential splicing using whole-transcript microarrays
Authors
- Mark D Robinson
- Terence P Speed
- Content type: Methodology article
- Open Access
- Published: 22 May 2009
- Article: 156