Volume 10, issue 1, December 2009
455 articles in this issue
-
-
EDGAR: A software framework for the comparative analysis of prokaryotic genomes
Authors (first, second and last of 7)
- Jochen Blom
- Stefan P Albaum
- Alexander Goesmann
- Content type: Software
- Open Access
- Published: 20 May 2009
- Article: 154
-
Tableau-based protein substructure search using quadratic programming
Authors
- Alex Stivala
- Anthony Wirth
- Peter J Stuckey
- Content type: Methodology article
- Open Access
- Published: 19 May 2009
- Article: 153
-
Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach
Authors (first, second and last of 4)
- Alexandre P Francisco
- Miguel Bugalho
- João A Carriço
- Content type: Methodology article
- Open Access
- Published: 18 May 2009
- Article: 152
-
MIMAS 3.0 is a Multiomics Information Management and Annotation System
Authors (first, second and last of 7)
- Alexandre Gattiker
- Leandro Hermida
- Michael Primig
- Content type: Database
- Open Access
- Published: 18 May 2009
- Article: 151
-
Protein-protein interaction based on pairwise similarity
Authors (first, second and last of 4)
- Nazar Zaki
- Sanja Lazarova-Molnar
- Piers Campbell
- Content type: Research article
- Open Access
- Published: 17 May 2009
- Article: 150
-
How to find simple and accurate rules for viral protease cleavage specificities
Authors (first, second and last of 6)
- Thorsteinn Rögnvaldsson
- Terence A Etchells
- Paulo JG Lisboa
- Content type: Methodology article
- Open Access
- Published: 16 May 2009
- Article: 149
-
The High Throughput Sequence Annotation Service (HT-SAS) – the shortcut from sequence to true Medline words
Authors
- Szymon Kaczanowski
- Pawel Siedlecki
- Piotr Zielenkiewicz
- Content type: Software
- Open Access
- Published: 16 May 2009
- Article: 148
-
Effects of sample size on robustness and prediction accuracy of a prognostic gene signature
Authors
- Seon-Young Kim
- Content type: Research article
- Open Access
- Published: 16 May 2009
- Article: 147
-
Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments
Authors (first, second and last of 4)
- Tianqing Liu
- Nan Lin
- Baoxue Zhang
- Content type: Methodology article
- Open Access
- Published: 15 May 2009
- Article: 146
-
flowClust: a Bioconductor package for automated gating of flow cytometry data
Authors (first, second and last of 4)
- Kenneth Lo
- Florian Hahne
- Raphael Gottardo
- Content type: Software
- Open Access
- Published: 14 May 2009
- Article: 145
-
Application of multiple statistical tests to enhance mass spectrometry-based biomarker discovery
Authors (first, second and last of 4)
- Niclas C Tan
- Wayne G Fisher
- Harold R Garner
- Content type: Research article
- Open Access
- Published: 14 May 2009
- Article: 144
-
PanGEA: Identification of allele specific gene expression using the 454 technology
Authors (first, second and last of 4)
- Robert Kofler
- Tatiana Teixeira Torres
- Christian Schlötterer
- Content type: Software
- Open Access
- Published: 14 May 2009
- Article: 143
-
Incorporating functional inter-relationships into protein function prediction algorithms
Authors
- Gaurav Pandey
- Chad L Myers
- Vipin Kumar
- Content type: Methodology article
- Open Access
- Published: 12 May 2009
- Article: 142
-
Robust MS quantification method for phospho-peptides using 18O/16O labeling
Authors (first, second and last of 6)
- Claus A Andersen
- Stefano Gotta
- Georg C Terstappen
- Content type: Methodology article
- Open Access
- Published: 11 May 2009
- Article: 141
-
Estimating parameters for generalized mass action models with connectivity information
Authors
- Chih-Lung Ko
- Eberhard O Voit
- Feng-Sheng Wang
- Content type: Research article
- Open Access
- Published: 11 May 2009
- Article: 140
-
eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology
Authors (first, second and last of 6)
- Sebastian Schönherr
- Hansi Weißensteiner
- Anita Brandstätter
- Content type: Database
- Open Access
- Published: 11 May 2009
- Article: 139
-
PCOPGene-Net: Holistic Characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships
Authors (first, second and last of 5)
- Mario Huerta
- Juan Cedano
- Enrique Querol
- Content type: Software
- Open Access
- Published: 09 May 2009
- Article: 138
-
On finding minimal absent words
Authors (first, second and last of 4)
- Armando J Pinho
- Paulo JSG Ferreira
- João MOS Rodrigues
- Content type: Research article
- Open Access
- Published: 08 May 2009
- Article: 137
-
Infrastructure for the life sciences: design and implementation of the UniProt website
Authors (first, second and last of 9)
- Eric Jain
- Amos Bairoch
- Elisabeth Gasteiger
- Content type: Database
- Open Access
- Published: 08 May 2009
- Article: 136
-
CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants
Authors
- Pufeng Du
- Liyan Jia
- Yanda Li
- Content type: Software
- Open Access
- Published: 08 May 2009
- Article: 135
-
Validating subcellular localization prediction tools with mycobacterial proteins
Authors (first, second and last of 6)
- Daniel Restrepo-Montoya
- Carolina VizcaÃno
- Manuel A Patarroyo
- Content type: Research article
- Open Access
- Published: 07 May 2009
- Article: 134
-
SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes
Authors
- Hideya Kawaji
- Yoshihide Hayashizaki
- Carsten O Daub
- Content type: Software
- Open Access
- Published: 07 May 2009
- Article: 133
This is part of 1 collection: -
On validation and invalidation of biological models
Authors
- James Anderson
- Antonis Papachristodoulou
- Content type: Research article
- Open Access
- Published: 07 May 2009
- Article: 132
-
SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip
Authors (first, second and last of 9)
- Hironori Fujisawa
- Youko Horiuchi
- Nori Kurata
- Content type: Methodology article
- Open Access
- Published: 06 May 2009
- Article: 131
-
Willows: a memory efficient tree and forest construction package
Authors
- Heping Zhang
- Minghui Wang
- Xiang Chen
- Content type: Software
- Open Access
- Published: 05 May 2009
- Article: 130
-
Improving classification in protein structure databases using text mining
Authors
- Antonis Koussounadis
- Oliver C Redfern
- David T Jones
- Content type: Methodology article
- Open Access
- Published: 05 May 2009
- Article: 129
-
Identification of differentially expressed subnetworks based on multivariate ANOVA
Authors
- Taeyoung Hwang
- Taesung Park
- Content type: Methodology article
- Open Access
- Published: 30 April 2009
- Article: 128
-
Automated FingerPrint Background removal: FPB
Authors
- Simone Scalabrin
- Michele Morgante
- Alberto Policriti
- Content type: Software
- Open Access
- Published: 30 April 2009
- Article: 127
-
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning
Authors (first, second and last of 4)
- Philippe Lemey
- Martin Lott
- Vincent Moulton
- Content type: Research article
- Open Access
- Published: 27 April 2009
- Article: 126
-
Survey-based naming conventions for use in OBO Foundry ontology development
Authors (first, second and last of 9)
- Daniel Schober
- Barry Smith
- Susanna-Assunta Sansone
- Content type: Correspondence
- Open Access
- Published: 27 April 2009
- Article: 125
-
Marker-free image registration of electron tomography tilt-series
Authors (first, second and last of 8)
- Carlos Oscar Sanchez Sorzano
- Cédric Messaoudi
- JM Carazo
- Content type: Methodology article
- Open Access
- Published: 27 April 2009
- Article: 124
-
FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families
Authors (first, second and last of 10)
- Jinyu Wu
- Xiang Xu
- Xiaokun Li
- Content type: Database
- Open Access
- Published: 25 April 2009
- Article: 123
-
Granger causality vs. dynamic Bayesian network inference: a comparative study
Authors
- Cunlu Zou
- Jianfeng Feng
- Content type: Research article
- Open Access
- Published: 24 April 2009
- Article: 122
-
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data
Authors (first, second and last of 10)
- Yoko Fukuda
- Yasuo Nakahara
- Shoji Tsuji
- Content type: Software
- Open Access
- Published: 24 April 2009
- Article: 121
-
Multichromosomal median and halving problems under different genomic distances
Authors
- Eric Tannier
- Chunfang Zheng
- David Sankoff
- Content type: Methodology article
- Open Access
- Published: 22 April 2009
- Article: 120
-
A bag-of-words approach for Drosophila gene expression pattern annotation
Authors (first, second and last of 5)
- Shuiwang Ji
- Ying-Xin Li
- Jieping Ye
- Content type: Methodology article
- Open Access
- Published: 21 April 2009
- Article: 119
-
ACID: annotation of cassette and integron data
Authors (first, second and last of 8)
- Michael J Joss
- Jeremy E Koenig
- Yan Boucher
- Content type: Database
- Open Access
- Published: 21 April 2009
- Article: 118
-
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins
Authors (first, second and last of 5)
- Pawel Durek
- Christian Schudoma
- Dirk Walther
- Content type: Research article
- Open Access
- Published: 21 April 2009
- Article: 117
-
Profile analysis and prediction of tissue-specific CpG island methylation classes
Authors (first, second and last of 4)
- Christopher Previti
- Oscar Harari
- Coral del Val
- Content type: Methodology article
- Open Access
- Published: 21 April 2009
- Article: 116
-
Most parsimonious haplotype allele sharing determination
Authors (first, second and last of 8)
- Zhipeng Cai
- Hadi Sabaa
- Guohui Lin
- Content type: Research article
- Open Access
- Published: 21 April 2009
- Article: 115
-
POINeT: protein interactome with sub-network analysis and hub prioritization
Authors (first, second and last of 10)
- Sheng-An Lee
- Chen-Hsiung Chan
- Chi-Ying F Huang
- Content type: Software
- Open Access
- Published: 21 April 2009
- Article: 114
-
Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation
Authors (first, second and last of 5)
- Konstantinos P Exarchos
- Themis P Exarchos
- Dimitrios I Fotiadis
- Content type: Research article
- Open Access
- Published: 20 April 2009
- Article: 113
-
Island method for estimating the statistical significance of profile-profile alignment scores
Authors
- Aleksandar Poleksic
- Content type: Methodology article
- Open Access
- Published: 20 April 2009
- Article: 112
-
The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes
Authors (first, second and last of 4)
- Todd Riley
- Xin Yu
- Arnold Levine
- Content type: Research article
- Open Access
- Published: 20 April 2009
- Article: 111
-
Data-driven normalization strategies for high-throughput quantitative RT-PCR
Authors (first, second and last of 8)
- Jessica C Mar
- Yasumasa Kimura
- John Quackenbush
- Content type: Methodology article
- Open Access
- Published: 19 April 2009
- Article: 110
This is part of 1 collection: -
Identifying set-wise differential co-expression in gene expression microarray data
Authors
- Sung Bum Cho
- Jihun Kim
- Ju Han Kim
- Content type: Research article
- Open Access
- Published: 16 April 2009
- Article: 109
-
dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation
Authors
- Manoj Hariharan
- Vinod Scaria
- Samir K Brahmachari
- Content type: Database
- Open Access
- Published: 16 April 2009
- Article: 108
-
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning
Authors
- Adrian K Arakaki
- Ying Huang
- Jeffrey Skolnick
- Content type: Methodology article
- Open Access
- Published: 13 April 2009
- Article: 107
-
flowCore: a Bioconductor package for high throughput flow cytometry
Authors (first, second and last of 9)
- Florian Hahne
- Nolwenn LeMeur
- Robert Gentleman
- Content type: Software
- Open Access
- Published: 09 April 2009
- Article: 106