Volume 10, issue 1, December 2009
455 articles in this issue
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Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB
Authors
- Aristotelis Chatziioannou
- Panagiotis Moulos
- Fragiskos N Kolisis
- Content type: Software
- Open Access
- Published: 27 October 2009
- Article: 354
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Time warping of evolutionary distant temporal gene expression data based on noise suppression
Authors
- Yury Goltsev
- Dmitri Papatsenko
- Content type: Research article
- Open Access
- Published: 26 October 2009
- Article: 353
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Bayesian modeling of ChIP-chip data using latent variables
Authors
- Mingqi Wu
- Faming Liang
- Yanan Tian
- Content type: Methodology article
- Open Access
- Published: 26 October 2009
- Article: 352
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A structure filter for the Eukaryotic Linear Motif Resource
Authors (first, second and last of 5)
- Allegra Via
- Cathryn M Gould
- Manuela Helmer-Citterich
- Content type: Methodology article
- Open Access
- Published: 24 October 2009
- Article: 351
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Local cell metrics: a novel method for analysis of cell-cell interactions
Authors (first, second and last of 4)
- Jing Su
- Pedro J Zapata
- J Carson Meredith
- Content type: Methodology article
- Open Access
- Published: 23 October 2009
- Article: 350
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Construction of an annotated corpus to support biomedical information extraction
Authors (first, second and last of 4)
- Paul Thompson
- Syed A Iqbal
- Sophia Ananiadou
- Content type: Research article
- Open Access
- Published: 23 October 2009
- Article: 349
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GIFtS: annotation landscape analysis with GeneCards
Authors (first, second and last of 7)
- Arye Harel
- Aron Inger
- Doron Lancet
- Content type: Research article
- Open Access
- Published: 23 October 2009
- Article: 348
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Direct calibration of PICKY-designed microarrays
Authors (first, second and last of 6)
- Hui-Hsien Chou
- Arunee Trisiriroj
- Patrick S Schnable
- Content type: Methodology article
- Open Access
- Published: 23 October 2009
- Article: 347
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Arabidopsis gene co-expression network and its functional modules
Authors (first, second and last of 4)
- Linyong Mao
- John L Van Hemert
- Julie A Dickerson
- Content type: Research article
- Open Access
- Published: 21 October 2009
- Article: 346
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BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
Authors
- Junbai Wang
- Morigen
- Content type: Methodology article
- Open Access
- Published: 20 October 2009
- Article: 345
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TIde: a software for the systematic scanning of drug targets in kinetic network models
Authors
- Marvin Schulz
- Barbara M Bakker
- Edda Klipp
- Content type: Software
- Open Access
- Published: 19 October 2009
- Article: 344
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Bayesian inference of biochemical kinetic parameters using the linear noise approximation
Authors (first, second and last of 4)
- Michał Komorowski
- Bärbel Finkenstädt
- David A Rand
- Content type: Methodology article
- Open Access
- Published: 19 October 2009
- Article: 343
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iQuantitator: A tool for protein expression inference using iTRAQ
Authors (first, second and last of 5)
- John H Schwacke
- Elizabeth G Hill
- Kevin L Schey
- Content type: Software
- Open Access
- Published: 18 October 2009
- Article: 342
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Exploiting structural and topological information to improve prediction of RNA-protein binding sites
Authors
- Stefan R Maetschke
- Zheng Yuan
- Content type: Research article
- Open Access
- Published: 18 October 2009
- Article: 341
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Integrating functional genomics data using maximum likelihood based simultaneous component analysis
Authors (first, second and last of 6)
- Robert A van den Berg
- Iven Van Mechelen
- Age K Smilde
- Content type: Research article
- Open Access
- Published: 16 October 2009
- Article: 340
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Transcription factor site dependencies in human, mouse and rat genomes
Authors
- Andrija Tomovic
- Michael Stadler
- Edward J Oakeley
- Content type: Research article
- Open Access
- Published: 16 October 2009
- Article: 339
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Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networks
Authors
- Glennie Helles
- Rasmus Fonseca
- Content type: Research article
- Open Access
- Published: 16 October 2009
- Article: 338
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Classification and biomarker identification using gene network modules and support vector machines
Authors (first, second and last of 5)
- Malik Yousef
- Mohamed Ketany
- Michael K Showe
- Content type: Methodology article
- Open Access
- Published: 15 October 2009
- Article: 337
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A permutation-based multiple testing method for time-course microarray experiments
Authors (first, second and last of 5)
- Insuk Sohn
- Kouros Owzar
- Sin-Ho Jung
- Content type: Methodology article
- Open Access
- Published: 15 October 2009
- Article: 336
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Clustering of protein domains for functional and evolutionary studies
Authors (first, second and last of 9)
- Pavle Goldstein
- Jurica Zucko
- John Cullum
- Content type: Research article
- Open Access
- Published: 15 October 2009
- Article: 335
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Magallanes: a web services discovery and automatic workflow composition tool
Authors
- Javier RÃos
- Johan Karlsson
- Oswaldo Trelles
- Content type: Software
- Open Access
- Published: 15 October 2009
- Article: 334
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Phylogenetic analysis of modularity in protein interaction networks
Authors (first, second and last of 5)
- Sinan Erten
- Xin Li
- Mehmet Koyutürk
- Content type: Methodology article
- Open Access
- Published: 14 October 2009
- Article: 333
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STAR NET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data
Authors
- Daniel Jupiter
- Hailin Chen
- Vincent VanBuren
- Content type: Software
- Open Access
- Published: 14 October 2009
- Article: 332
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ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery
Authors (first, second and last of 6)
- Frank M You
- Naxin Huo
- Olin D Anderson
- Content type: Software
- Open Access
- Published: 13 October 2009
- Article: 331
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BASE - 2nd generation software for microarray data management and analysis
Authors (first, second and last of 4)
- Johan Vallon-Christersson
- Nicklas Nordborg
- Jari Häkkinen
- Content type: Software
- Open Access
- Published: 12 October 2009
- Article: 330
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PLAST: parallel local alignment search tool for database comparison
Authors
- Hoa Van Nguyen
- Dominique Lavenier
- Content type: Software
- Open Access
- Published: 12 October 2009
- Article: 329
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miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression
Authors (first, second and last of 6)
- Wei-Chi Wang
- Feng-Mao Lin
- Na-Sheng Lin
- Content type: Software
- Open Access
- Published: 12 October 2009
- Article: 328
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VANLO - Interactive visual exploration of aligned biological networks
Authors
- Steffen Brasch
- Lars Linsen
- Georg Fuellen
- Content type: Software
- Open Access
- Published: 12 October 2009
- Article: 327
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Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)
Authors (first, second and last of 5)
- Thomas C Wiegers
- Allan Peter Davis
- Carolyn J Mattingly
- Content type: Research article
- Open Access
- Published: 08 October 2009
- Article: 326
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Riboswitch Detection Using Profile Hidden Markov Models
Authors (first, second and last of 5)
- Payal Singh
- Pradipta Bandyopadhyay
- Supratim Sengupta
- Content type: Methodology article
- Open Access
- Published: 08 October 2009
- Article: 325
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KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database
Authors (first, second and last of 5)
- Konstantinos Moutselos
- Ioannis Kanaris
- Fragiskos N Kolisis
- Content type: Software
- Open Access
- Published: 08 October 2009
- Article: 324
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A stochastic context free grammar based framework for analysis of protein sequences
Authors
- Witold Dyrka
- Jean-Christophe Nebel
- Content type: Research article
- Open Access
- Published: 08 October 2009
- Article: 323
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Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions
Authors (first, second and last of 5)
- Holger Fröhlich
- Özgür Sahin
- Tim Beißbarth
- Content type: Research article
- Open Access
- Published: 08 October 2009
- Article: 322
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Discovering multiple realistic TFBS motifs based on a generalized model
Authors (first, second and last of 4)
- Tak-Ming Chan
- Gang Li
- Kin-Hong Lee
- Content type: Methodology article
- Open Access
- Published: 07 October 2009
- Article: 321
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BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature
Authors (first, second and last of 5)
- Guillermo de la Calle
- Miguel GarcÃa-Remesal
- Victor Maojo
- Content type: Methodology article
- Open Access
- Published: 07 October 2009
- Article: 320
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Generation of Gene Ontology benchmark datasets with various types of positive signal
Authors
- Petri Törönen
- Petri Pehkonen
- Liisa Holm
- Content type: Methodology article
- Open Access
- Published: 07 October 2009
- Article: 319
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Kavosh: a new algorithm for finding network motifs
Authors (first, second and last of 9)
- Zahra Razaghi Moghadam Kashani
- Hayedeh Ahrabian
- Ali Masoudi-Nejad
- Content type: Methodology article
- Open Access
- Published: 04 October 2009
- Article: 318
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Enhancing navigation in biomedical databases by community voting and database-driven text classification
Authors (first, second and last of 6)
- Timo Duchrow
- Timur Shtatland
- Ralph Weissleder
- Content type: Research article
- Open Access
- Published: 03 October 2009
- Article: 317
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Unsupervised statistical clustering of environmental shotgun sequences
Authors (first, second and last of 4)
- Andrey Kislyuk
- Srijak Bhatnagar
- Joshua S Weitz
- Content type: Methodology article
- Open Access
- Published: 02 October 2009
- Article: 316
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Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks
Authors
- Sandra Waaijenborg
- Aeilko H Zwinderman
- Content type: Methodology article
- Open Access
- Published: 28 September 2009
- Article: 315
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MetaTM - a consensus method for transmembrane protein topology prediction
Authors (first, second and last of 4)
- Martin Klammer
- David N Messina
- Erik LL Sonnhammer
- Content type: Methodology article
- Open Access
- Published: 28 September 2009
- Article: 314
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Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics
Authors
- Benjamin M Good
- Joseph T Tennis
- Mark D Wilkinson
- Content type: Research article
- Open Access
- Published: 25 September 2009
- Article: 313
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Predicting protein-protein binding sites in membrane proteins
Authors
- Andrew J Bordner
- Content type: Research article
- Open Access
- Published: 24 September 2009
- Article: 312
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Challenges for automatically extracting molecular interactions from full-text articles
Authors
- Tara McIntosh
- James R Curran
- Content type: Research article
- Open Access
- Published: 24 September 2009
- Article: 311
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Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays
Authors
- Peter Tiňo
- Content type: Research article
- Open Access
- Published: 23 September 2009
- Article: 310
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SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services
Authors (first, second and last of 7)
- Damian DG Gessler
- Gary S Schiltz
- Rex T Nelson
- Content type: Software
- Open Access
- Published: 23 September 2009
- Article: 309
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Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously
Authors
- Oscar M Rueda
- Ramon Diaz-Uriarte
- Content type: Methodology article
- Open Access
- Published: 23 September 2009
- Article: 308
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Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function
Authors (first, second and last of 4)
- Petri Törönen
- Pauli J Ojala
- Liisa Holm
- Content type: Research article
- Open Access
- Published: 23 September 2009
- Article: 307
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A methodology for the analysis of differential coexpression across the human lifespan
Authors
- Jesse Gillis
- Paul Pavlidis
- Content type: Research article
- Open Access
- Published: 22 September 2009
- Article: 306