Volume 10, issue 1, December 2009
455 articles in this issue
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Ultra-Structure database design methodology for managing systems biology data and analyses
Authors (first, second and last of 4)
- Christopher W Maier
- Jeffrey G Long
- Morgan C Giddings
- Content type: Methodology article
- Open Access
- Published: 19 August 2009
- Article: 254
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A fast and efficient gene-network reconstruction method from multiple over-expression experiments
Authors
- Dejan Stokić
- Rudolf Hanel
- Stefan Thurner
- Content type: Research article
- Open Access
- Published: 17 August 2009
- Article: 253
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An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow
Authors
- Trevor Paterson
- Andy Law
- Content type: Methodology article
- Open Access
- Published: 14 August 2009
- Article: 252
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SNAD: sequence name annotation-based designer
Authors
- Igor A Sidorov
- Denis A Reshetov
- Alexander E Gorbalenya
- Content type: Software
- Open Access
- Published: 14 August 2009
- Article: 251
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OnEX: Exploring changes in life science ontologies
Authors (first, second and last of 4)
- Michael Hartung
- Toralf Kirsten
- Erhard Rahm
- Content type: Software
- Open Access
- Published: 13 August 2009
- Article: 250
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EvoRSR: an integrated system for exploring evolution of RNA structural robustness
Authors (first, second and last of 5)
- Wenjie Shu
- Ming Ni
- Shengqi Wang
- Content type: Software
- Open Access
- Published: 13 August 2009
- Article: 249
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Supervised learning for the automated transcription of spacer classification from spoligotype films
Authors
- David J Jeffries
- Neil Abernethy
- Bouke C de Jong
- Content type: Methodology article
- Open Access
- Published: 12 August 2009
- Article: 248
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Accurate and fast methods to estimate the population mutation rate from error prone sequences
Authors
- Bjarne Knudsen
- Michael M Miyamoto
- Content type: Methodology article
- Open Access
- Published: 11 August 2009
- Article: 247
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A structured overview of simultaneous component based data integration
Authors (first, second and last of 5)
- Katrijn Van Deun
- Age K Smilde
- Iven Van Mechelen
- Content type: Research article
- Open Access
- Published: 11 August 2009
- Article: 246
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Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity
Authors (first, second and last of 5)
- Flavien Quintus
- Olivier Sperandio
- Pierre Tuffery
- Content type: Methodology article
- Open Access
- Published: 11 August 2009
- Article: 245
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ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics
Authors
- Jason WH Wong
- Alexander B Schwahn
- Kevin M Downard
- Content type: Methodology article
- Open Access
- Published: 10 August 2009
- Article: 244
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Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures
Authors (first, second and last of 6)
- Chris Thachuk
- José Crossa
- Guy F Davenport
- Content type: Research article
- Open Access
- Published: 06 August 2009
- Article: 243
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R/BHC: fast Bayesian hierarchical clustering for microarray data
Authors (first, second and last of 8)
- Richard S Savage
- Katherine Heller
- David L Wild
- Content type: Software
- Open Access
- Published: 06 August 2009
- Article: 242
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Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels
Authors (first, second and last of 4)
- Kevin Y Yip
- Philip M Kim
- Mark Gerstein
- Content type: Methodology article
- Open Access
- Published: 05 August 2009
- Article: 241
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Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology
Authors (first, second and last of 4)
- Tao Xu
- JianLei Gu
- LinFang Du
- Content type: Methodology article
- Open Access
- Published: 05 August 2009
- Article: 240
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Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis
Authors
- Roberto T Arrial
- Roberto C Togawa
- Marcelo de M Brigido
- Content type: Software
- Open Access
- Published: 04 August 2009
- Article: 239
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Generating rate equations for complex enzyme systems by a computer-assisted systematic method
Authors (first, second and last of 4)
- Feng Qi
- Ranjan K Dash
- Daniel A Beard
- Content type: Methodology article
- Open Access
- Published: 04 August 2009
- Article: 238
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Resolving deconvolution ambiguity in gene alternative splicing
Authors
- Yiyuan She
- Earl Hubbell
- Hui Wang
- Content type: Research article
- Open Access
- Published: 04 August 2009
- Article: 237
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sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures
Authors
- Shu-Dong Zhang
- Timothy W Gant
- Content type: Software
- Open Access
- Published: 31 July 2009
- Article: 236
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TableButler – a Windows based tool for processing large data tables generated with high-throughput methods
Authors (first, second and last of 4)
- Christian Schwager
- Ute Wirkner
- Peter E Huber
- Content type: Software
- Open Access
- Published: 29 July 2009
- Article: 235
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CLEAN: CLustering Enrichment ANalysis
Authors (first, second and last of 4)
- Johannes M Freudenberg
- Vineet K Joshi
- Mario Medvedovic
- Content type: Methodology article
- Open Access
- Published: 29 July 2009
- Article: 234
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A realistic assessment of methods for extracting gene/protein interactions from free text
Authors
- Renata Kabiljo
- Andrew B Clegg
- Adrian J Shepherd
- Content type: Research article
- Open Access
- Published: 28 July 2009
- Article: 233
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BSMAP: whole genome bisulfite sequence MAPping program
Authors
- Yuanxin Xi
- Wei Li
- Content type: Methodology article
- Open Access
- Published: 27 July 2009
- Article: 232
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Enzyme classification with peptide programs: a comparative study
Authors
- Daniel Faria
- António EN Ferreira
- André O Falcão
- Content type: Research article
- Open Access
- Published: 24 July 2009
- Article: 231
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CSA: An efficient algorithm to improve circular DNA multiple alignment
Authors
- Francisco Fernandes
- LuÃsa Pereira
- Ana T Freitas
- Content type: Software
- Open Access
- Published: 23 July 2009
- Article: 230
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mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics
Authors
- Bernhard Thielen
- Stephanie Heinen
- Dietmar Schomburg
- Content type: Software
- Open Access
- Published: 22 July 2009
- Article: 229
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Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation
Authors (first, second and last of 5)
- Kimberly Van Auken
- Joshua Jaffery
- Paul W Sternberg
- Content type: Methodology article
- Open Access
- Published: 21 July 2009
- Article: 228
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Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'
Authors (first, second and last of 7)
- John Draper
- David P Enot
- Hassan Zubair
- Content type: Research article
- Open Access
- Published: 21 July 2009
- Article: 227
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Information management for high content live cell imaging
Authors (first, second and last of 12)
- Daniel Jameson
- David A Turner
- Norman W Paton
- Content type: Software
- Open Access
- Published: 21 July 2009
- Article: 226
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A statistical framework to evaluate virtual screening
Authors (first, second and last of 5)
- Wei Zhao
- Kirk E Hevener
- James M Boyett
- Content type: Methodology article
- Open Access
- Published: 20 July 2009
- Article: 225
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FISim: A new similarity measure between transcription factor binding sites based on the fuzzy integral
Authors (first, second and last of 4)
- Fernando Garcia
- Francisco J Lopez
- Armando Blanco
- Content type: Research article
- Open Access
- Published: 20 July 2009
- Article: 224
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Incorporating rich background knowledge for gene named entity classification and recognition
Authors
- Yanpeng Li
- Hongfei Lin
- Zhihao Yang
- Content type: Research article
- Open Access
- Published: 17 July 2009
- Article: 223
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PCI-SS: MISO dynamic nonlinear protein secondary structure prediction
Authors
- James R Green
- Michael J Korenberg
- Mohammed O Aboul-Magd
- Content type: Research article
- Open Access
- Published: 17 July 2009
- Article: 222
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An introduction to scripting in Ruby for biologists
Authors
- Jan Aerts
- Andy Law
- Content type: Correspondence
- Open Access
- Published: 16 July 2009
- Article: 221
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Erratum to: Algorithm of OMA for large-scale orthology inference
Authors
- Alexander CJ Roth
- Gaston H Gonnet
- Christophe Dessimoz
- Content type: Erratum
- Open Access
- Published: 16 July 2009
- Article: 220
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OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
Authors (first, second and last of 5)
- Fabian Schreiber
- Kerstin Pick
- Burkhard Morgenstern
- Content type: Software
- Open Access
- Published: 16 July 2009
- Article: 219
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Transcriptional programs: Modelling higher order structure in transcriptional control
Authors
- John E Reid
- Sascha Ott
- Lorenz Wernisch
- Content type: Research article
- Open Access
- Published: 16 July 2009
- Article: 218
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A compartmentalized approach to the assembly of physical maps
Authors
- Serdar Bozdag
- Timothy J Close
- Stefano Lonardi
- Content type: Methodology article
- Open Access
- Published: 15 July 2009
- Article: 217
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Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference
Authors
- Lusheng Wang
- Zhanyong Wang
- Wanling Yang
- Content type: Software
- Open Access
- Published: 15 July 2009
- Article: 216
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Regression based predictor for p53 transactivation
Authors
- Sivakumar Gowrisankar
- Anil G Jegga
- Content type: Methodology article
- Open Access
- Published: 14 July 2009
- Article: 215
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Construction and use of gene expression covariation matrix
Authors
- Jérôme Hennetin
- Petri Pehkonen
- Michel Bellis
- Content type: Methodology article
- Open Access
- Published: 13 July 2009
- Article: 214
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A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data
Authors (first, second and last of 7)
- Bjoern H Menze
- B Michael Kelm
- Fred A Hamprecht
- Content type: Research article
- Open Access
- Published: 10 July 2009
- Article: 213
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Error statistics of hidden Markov model and hidden Boltzmann model results
Authors
- Lee A Newberg
- Content type: Methodology article
- Open Access
- Published: 09 July 2009
- Article: 212
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puma: a Bioconductor package for propagating uncertainty in microarray analysis
Authors (first, second and last of 6)
- Richard D Pearson
- Xuejun Liu
- Magnus Rattray
- Content type: Software
- Open Access
- Published: 09 July 2009
- Article: 211
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Iterative refinement of structure-based sequence alignments by Seed Extension
Authors
- Changhoon Kim
- Chin-Hsien Tai
- Byungkook Lee
- Content type: Research article
- Open Access
- Published: 09 July 2009
- Article: 210
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A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests
Authors
- Antonio Carvajal-RodrÃguez
- Jacobo de Uña-Alvarez
- Emilio Rolán-Alvarez
- Content type: Methodology article
- Open Access
- Published: 08 July 2009
- Article: 209
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OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif
Authors (first, second and last of 5)
- Amar Drawid
- Nupur Gupta
- Anirvan M Sengupta
- Content type: Research article
- Open Access
- Published: 07 July 2009
- Article: 208
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Ensemble approach to predict specificity determinants: benchmarking and validation
Authors
- Saikat Chakrabarti
- Anna R Panchenko
- Content type: Research article
- Open Access
- Published: 02 July 2009
- Article: 207
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Representative transcript sets for evaluating a translational initiation sites predictor
Authors
- Jia Zeng
- Reda Alhajj
- Douglas J Demetrick
- Content type: Research article
- Open Access
- Published: 02 July 2009
- Article: 206