Volume 10, issue 1, December 2009
455 articles in this issue
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MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs
Authors
- Ahmet Sacan
- Nilgun Ferhatosmanoglu
- Hakan Ferhatosmanoglu
- Content type: Database
- Open Access
- Published: 22 September 2009
- Article: 304
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The first step in the development of text mining technology for cancer risk assessment: identifying and organizing scientific evidence in risk assessment literature
Authors (first, second and last of 4)
- Anna Korhonen
- Ilona Silins
- Ulla Stenius
- Content type: Research article
- Open Access
- Published: 22 September 2009
- Article: 303
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Prediction of antigenic epitopes on protein surfaces by consensus scoring
Authors (first, second and last of 4)
- Shide Liang
- Dandan Zheng
- Martin Zacharias
- Content type: Research article
- Open Access
- Published: 22 September 2009
- Article: 302
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Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum
Authors (first, second and last of 7)
- Scott Bringans
- James K Hane
- Richard P Oliver
- Content type: Research article
- Open Access
- Published: 22 September 2009
- Article: 301
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RCMAT: a regularized covariance matrix approach to testing gene sets
Authors
- Phillip D Yates
- Mark A Reimers
- Content type: Methodology article
- Open Access
- Published: 21 September 2009
- Article: 300
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BayesPeak: Bayesian analysis of ChIP-seq data
Authors (first, second and last of 4)
- Christiana Spyrou
- Rory Stark
- Simon Tavaré
- Content type: Research article
- Open Access
- Published: 21 September 2009
- Article: 299
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PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees
Authors
- Philippe Gouret
- Julie D Thompson
- Pierre Pontarotti
- Content type: Software
- Open Access
- Published: 19 September 2009
- Article: 298
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Finding local communities in protein networks
Authors
- Konstantin Voevodski
- Shang-Hua Teng
- Yu Xia
- Content type: Methodology article
- Open Access
- Published: 18 September 2009
- Article: 297
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NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction
Authors
- Morten Nielsen
- Ole Lund
- Content type: Methodology article
- Open Access
- Published: 18 September 2009
- Article: 296
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Accurate microRNA target prediction correlates with protein repression levels
Authors (first, second and last of 16)
- Manolis Maragkakis
- Panagiotis Alexiou
- Artemis G Hatzigeorgiou
- Content type: Research article
- Open Access
- Published: 18 September 2009
- Article: 295
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Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses
Authors (first, second and last of 6)
- Waranyu Wongseree
- Anunchai Assawamakin
- Nachol Chaiyaratana
- Content type: Methodology article
- Open Access
- Published: 17 September 2009
- Article: 294
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Efficient oligonucleotide probe selection for pan-genomic tiling arrays
Authors (first, second and last of 4)
- Adam M Phillippy
- Xiangyu Deng
- Steven L Salzberg
- Content type: Methodology article
- Open Access
- Published: 16 September 2009
- Article: 293
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A first principles approach to differential expression in microarray data analysis
Authors
- Robert A Rubin
- Content type: Methodology article
- Open Access
- Published: 16 September 2009
- Article: 292
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Automated seeding of specialised wiki knowledgebases with BioKb
Authors (first, second and last of 4)
- Jonathan R Manning
- Ann Hedley
- Donald R Dunbar
- Content type: Software
- Open Access
- Published: 16 September 2009
- Article: 291
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Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information
Authors
- Marcio L Acencio
- Ney Lemke
- Content type: Methodology article
- Open Access
- Published: 16 September 2009
- Article: 290
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In Silico screening for functional candidates amongst hypothetical proteins
Authors (first, second and last of 5)
- Claus Desler
- Prashanth Suravajhala
- Lene Juel Rasmussen
- Content type: Methodology article
- Open Access
- Published: 16 September 2009
- Article: 289
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Exploratory and inferential analysis of gene cluster neighborhood graphs
Authors
- Theresa Scharl
- Ingo Voglhuber
- Friedrich Leisch
- Content type: Methodology article
- Open Access
- Published: 14 September 2009
- Article: 288
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Epitopia: a web-server for predicting B-cell epitopes
Authors (first, second and last of 4)
- Nimrod D Rubinstein
- Itay Mayrose
- Tal Pupko
- Content type: Software
- Open Access
- Published: 14 September 2009
- Article: 287
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ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites
Authors (first, second and last of 5)
- Chao Li
- Yuhua Li
- Valentin Dinu
- Content type: Software
- Open Access
- Published: 11 September 2009
- Article: 286
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Erratum to: Feature selection environment for genomic applications
Authors
- FabrÃcio Martins Lopes
- David Corrêa Martins Jr
- Roberto M Cesar Jr
- Content type: Erratum
- Open Access
- Published: 10 September 2009
- Article: 285
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CASSIOPE: An expert system for conserved regions searches
Authors (first, second and last of 7)
- Virginie Lopez Rascol
- Anthony Levasseur
- Pierre Pontarotti
- Content type: Research article
- Open Access
- Published: 10 September 2009
- Article: 284
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RRW: repeated random walks on genome-scale protein networks for local cluster discovery
Authors
- Kathy Macropol
- Tolga Can
- Ambuj K Singh
- Content type: Research article
- Open Access
- Published: 09 September 2009
- Article: 283
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Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics
Authors
- Matteo Rè
- Graziano Pesole
- David S Horner
- Content type: Methodology article
- Open Access
- Published: 08 September 2009
- Article: 282
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Context-driven discovery of gene cassettes in mobile integrons using a computational grammar
Authors (first, second and last of 5)
- Guy Tsafnat
- Enrico Coiera
- Jon R Iredell
- Content type: Methodology article
- Open Access
- Published: 08 September 2009
- Article: 281
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EDGE3: A web-based solution for management and analysis of Agilent two color microarray experiments
Authors (first, second and last of 4)
- Aaron L Vollrath
- Adam A Smith
- Christopher A Bradfield
- Content type: Software
- Open Access
- Published: 04 September 2009
- Article: 280
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XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services
Authors (first, second and last of 4)
- Johannes Wagener
- Ola Spjuth
- Jarl ES Wikberg
- Content type: Methodology article
- Open Access
- Published: 04 September 2009
- Article: 279
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Genephony: a knowledge management tool for genome-wide research
Authors
- Angelo Nuzzo
- Alberto Riva
- Content type: Software
- Open Access
- Published: 03 September 2009
- Article: 278
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Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
Authors (first, second and last of 4)
- Wenhui Wang
- Juan Nunez-Iglesias
- Fengzhu Sun
- Content type: Research article
- Open Access
- Published: 03 September 2009
- Article: 277
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Regression applied to protein binding site prediction and comparison with classification
Authors (first, second and last of 4)
- Joachim Giard
- Jérôme Ambroise
- Benoît Macq
- Content type: Research article
- Open Access
- Published: 03 September 2009
- Article: 276
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Comparative study of gene set enrichment methods
Authors (first, second and last of 7)
- Luca Abatangelo
- Rosalia Maglietta
- Nicola Ancona
- Content type: Research article
- Open Access
- Published: 02 September 2009
- Article: 275
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MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
Authors
- Torsten Blum
- Sebastian Briesemeister
- Oliver Kohlbacher
- Content type: Software
- Open Access
- Published: 01 September 2009
- Article: 274
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The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families
Authors
- Riccardo Percudani
- Alessio Peracchi
- Content type: Database
- Open Access
- Published: 01 September 2009
- Article: 273
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Correlating gene and protein expression data using Correlated Factor Analysis
Authors (first, second and last of 6)
- Chuen Seng Tan
- Agus Salim
- Yudi Pawitan
- Content type: Research article
- Open Access
- Published: 01 September 2009
- Article: 272
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An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis σ66 promoters
Authors
- Ronna R Mallios
- David M Ojcius
- David H Ardell
- Content type: Research article
- Open Access
- Published: 28 August 2009
- Article: 271
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A reliable measure of similarity based on dependency for short time series: an application to gene expression networks
Authors (first, second and last of 6)
- Mônica G Campiteli
- Frederico M Soriani
- Gustavo H Goldman
- Content type: Methodology article
- Open Access
- Published: 28 August 2009
- Article: 270
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Global haplotype partitioning for maximal associated SNP pairs
Authors (first, second and last of 4)
- Ali Katanforoush
- Mehdi Sadeghi
- Elahe Elahi
- Content type: Methodology article
- Open Access
- Published: 27 August 2009
- Article: 269
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QPCR: Application for real-time PCR data management and analysis
Authors (first, second and last of 6)
- Stephan Pabinger
- Gerhard G Thallinger
- Zlatko Trajanoski
- Content type: Software
- Open Access
- Published: 27 August 2009
- Article: 268
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Enhanced protein fold recognition through a novel data integration approach
Authors
- Yiming Ying
- Kaizhu Huang
- Colin Campbell
- Content type: Research article
- Open Access
- Published: 26 August 2009
- Article: 267
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Genoviz Software Development Kit: Java tool kit for building genomics visualization applications
Authors (first, second and last of 8)
- Gregg A Helt
- John W Nicol
- Ann E Loraine
- Content type: Software
- Open Access
- Published: 25 August 2009
- Article: 266
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dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
Authors (first, second and last of 6)
- Gregor Rot
- Anup Parikh
- Blaz Zupan
- Content type: Software
- Open Access
- Published: 25 August 2009
- Article: 265
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GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction
Authors (first, second and last of 8)
- Yao Yu
- Kang Tu
- Yixue Li
- Content type: Software
- Open Access
- Published: 25 August 2009
- Article: 264
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Assessing the druggability of protein-protein interactions by a supervised machine-learning method
Authors
- Nobuyoshi Sugaya
- Kazuyoshi Ikeda
- Content type: Research article
- Open Access
- Published: 25 August 2009
- Article: 263
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Integrative modeling of transcriptional regulation in response to antirheumatic therapy
Authors (first, second and last of 5)
- Michael Hecker
- Robert Hermann Goertsches
- Reinhard Guthke
- Content type: Methodology article
- Open Access
- Published: 24 August 2009
- Article: 262
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Computing power of quantitative trait locus association mapping for haploid loci
Authors
- Derek Gordon
- Andrew R Zinn
- Content type: Software
- Open Access
- Published: 23 August 2009
- Article: 261
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MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering
Authors (first, second and last of 4)
- Eun-Youn Kim
- Seon-Young Kim
- Dougu Nam
- Content type: Methodology article
- Open Access
- Published: 22 August 2009
- Article: 260
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Ovarian cancer detection from metabolomic liquid chromatography/mass spectrometry data by support vector machines
Authors (first, second and last of 8)
- Wei Guan
- Manshui Zhou
- Facundo M Fernández
- Content type: Research article
- Open Access
- Published: 22 August 2009
- Article: 259
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p3d – Python module for structural bioinformatics
Authors
- Christian Fufezan
- Michael Specht
- Content type: Software
- Open Access
- Published: 21 August 2009
- Article: 258
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Structure-based substrate screening for an enzyme
Authors (first, second and last of 5)
- Tao Xu
- Lujia Zhang
- Tianbi Li
- Content type: Methodology article
- Open Access
- Published: 21 August 2009
- Article: 257
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The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations
Authors (first, second and last of 7)
- Xue Lin
- Bahman Afsari
- Donald Geman
- Content type: Research article
- Open Access
- Published: 20 August 2009
- Article: 256