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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Tim Sands PhD
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| | BMC Bioinformatics, Volume 10 |
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Volume 10 Suppl 13
Meeting abstracts
Stockholm, Sweden. 27 June 2009
Volume 10 Suppl 12
Research
Varenna, Italy. 19 21 May 2008
Volume 10 Suppl 11
Proceedings
Starkville, MS, USA. 2021 February 2009
more supplements 
Methodology article
 
An empirical Bayesian approach for model-based inference of cellular signaling networks
David J Klinke II
BMC Bioinformatics 2009, 10:371 (9November2009)
[Abstract] [Provisional PDF]
Research article
Elucidation of functional consequences of signalling pathway interactions
Adaoha E C Ihekwaba, Phuong T Nguyen, Corrado Priami
BMC Bioinformatics 2009, 10:370 (6November2009)
[Abstract] [Provisional PDF]
Research article
RNA folding on the 3D triangular lattice
Joel Gillespie, Martin Mayne, Minghui Jiang
BMC Bioinformatics 2009, 10:369 (5November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Database
A biosegmentation benchmark for evaluation of bioimage analysis methods
Elisa Drelie Gelasca, Boguslaw Obara, Dmitry Fedorov, Kristian Kvilekval, B. S. Manjunath
BMC Bioinformatics 2009, 10:368 (1November2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Database
GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs
Robert Lawrence, Aaron G Day-Williams, Richard Mott, John Broxholme, Lon R Cardon, Eleftheria Zeggini
BMC Bioinformatics 2009, 10:367 (31October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
(PS)2-v2: template-based protein structure prediction server
Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang
BMC Bioinformatics 2009, 10:366 (31October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods
Stefano Lise, Cedric Archambeau, Massimiliano Pontil, David T Jones
BMC Bioinformatics 2009, 10:365 (30October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
multiplierz: an extensible API based desktop environment for proteomics data analysis
Jignesh R Parikh, Manor Askenazi, Scott B Ficarro, Tanya Cashorali, James T Webber, Nathaniel C Blank, Yi Zhang, Jarrod A Marto
BMC Bioinformatics 2009, 10:364 (29October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
A novel R-package graphic user interface for the analysis of metabonomic profiles
Jose L Izquierdo-Garc a, Ignacio Rodrguez, Angelos Kyriazis, Palmira Villa, Pilar Barreiro, Manuel Desco, Jes s Ruiz-Cabello
BMC Bioinformatics 2009, 10:363 (29October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing
Daniel N Frank
BMC Bioinformatics 2009, 10:362 (29October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy
Zheng Rong Yang
BMC Bioinformatics 2009, 10:361 (29October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Inferring within-patient HIV-1 evolutionary dynamics under anti-HIV therapy using serial virus samples with vSPA
Naoki Hasegawa, Wataru Sugiura, Junko Shibata, Masakazu Matsuda, Fengrong Ren, Hiroshi Tanaka
BMC Bioinformatics 2009, 10:360 (29October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Analysis and comparison of very large metagenomes with fast clustering and functional annotation
Weizhong Li
BMC Bioinformatics 2009, 10:359 (28October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization
Enrico Glaab, Jonathan M Garibaldi, Natalio Krasnogor
BMC Bioinformatics 2009, 10:358 (28October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses
Surendra Kumar, Asmund Skjaeveland, Russell J. S. Orr, Pal Enger, Torgeir Ruden, Bjorn-Helge Mevik, Fabien Burki, Andreas Botnen, Kamran Shalchian-Tabrizi
BMC Bioinformatics 2009, 10:357 (28October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
phyloXML: XML for evolutionary biology and comparative genomics
Mira V Han, Christian M Zmasek
BMC Bioinformatics 2009, 10:356 (27October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Stratification of co-evolving genomic groups using ranked phylogenetic profiles
Shiri Freilich, Leon Goldovsky, Assaf Gottlieb, Eric Blanc, Sophia Tsoka, Christos A Ouzounis
BMC Bioinformatics 2009, 10:355 (27October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB
Aristotelis Chatziioannou, Panagiotis Moulos, Fragiskos N Kolisis
BMC Bioinformatics 2009, 10:354 (27October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Time warping of evolutionary distant temporal gene expression data based on noise suppression
Yury Goltsev, Dmitri Papatsenko
BMC Bioinformatics 2009, 10:353 (26October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Bayesian modeling of ChIP-chip data using latent variables
Mingqi Wu, Faming Liang, Yanan Tian
BMC Bioinformatics 2009, 10:352 (26October2009)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
A structure filter for the Eukaryotic Linear Motif Resource
Allegra Via, Cathryn M Gould, Christine Gem nd, Toby J Gibson, Manuela Helmer-Citterich
BMC Bioinformatics 2009, 10:351 (24October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Local cell metrics: a novel method for analysis of cell-cell interactions
Jing Su, Pedro J Zapata, Chien-Chiang Chen, J Carson Meredith
BMC Bioinformatics 2009, 10:350 (23October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Construction of an annotated corpus to support biomedical information extraction
Paul Thompson, Syed A Iqbal, John McNaught, Sophia Ananiadou
BMC Bioinformatics 2009, 10:349 (23October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
GIFtS: annotation landscape analysis with GeneCards
Arye Harel, Aron Inger, Gil Stelzer, Liora Strichman-Almashanu, Irina Dalah, Marilyn Safran, Doron Lancet
BMC Bioinformatics 2009, 10:348 (23October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Direct calibration of PICKY-designed microarrays
Hui-Hsien Chou, Arunee Trisiriroj, Sunyoung Park, Yue-Ie C Hsing, Pamela C Ronald, Patrick S Schnable
BMC Bioinformatics 2009, 10:347 (23October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Arabidopsis gene co-expression network and its functional modules
Linyong Mao, John L Van Hemert, Sudhansu Dash, Julie A Dickerson
BMC Bioinformatics 2009, 10:346 (21October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
Junbai Wang, Morigen
BMC Bioinformatics 2009, 10:345 (20October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
TIde: a software for the systematic scanning of drug targets in kinetic network models
Marvin Schulz, Barbara M Bakker, Edda Klipp
BMC Bioinformatics 2009, 10:344 (19October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Bayesian inference of biochemical kinetic parameters using the linear noise approximation
Micha Komorowski, B rbel Finkenstdt, Claire V Harper, David A Rand
BMC Bioinformatics 2009, 10:343 (19October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
iQuantitator: A tool for protein expression inference using iTRAQ
John H Schwacke, Elizabeth G Hill, Edward L Krug, Susana Comte-Walters, Kevin L Schey
BMC Bioinformatics 2009, 10:342 (18October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Exploiting structural and topological information to improve prediction of RNA-protein binding sites
Stefan R Maetschke, Zheng Yuan
BMC Bioinformatics 2009, 10:341 (18October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Integrating functional genomics data using maximum likelihood based simultaneous component analysis
Robert A van den Berg, Iven Van Mechelen, Tom F Wilderjans, Katrijn Van Deun, Henk AL Kiers, Age K Smilde
BMC Bioinformatics 2009, 10:340 (16October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Transcription factor site dependencies in human, mouse and rat genomes
Andrija Tomovic, Michael Stadler, Edward J Oakeley
BMC Bioinformatics 2009, 10:339 (16October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networks
Glennie Helles, Rasmus Fonseca
BMC Bioinformatics 2009, 10:338 (16October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Classification and biomarker identification using gene network modules and support vector machines
Malik Yousef, Mohamed Ketany, Larry Manevitz, Louise C Showe, Michael K Showe
BMC Bioinformatics 2009, 10:337 (15October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A permutation-based multiple testing method for time-course microarray experiments
Insuk Sohn, Kouros Owzar, Stephen L George, Sujong Kim, Sin-Ho Jung
BMC Bioinformatics 2009, 10:336 (15October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Clustering of protein domains for functional and evolutionary studies
Pavle Goldstein, Jurica Zucko, Du ica Vujaklija, Anita Kriko, Daslav Hranueli, Paul F Long, Catherine Etchebest, Bojan Basrak, John Cullum
BMC Bioinformatics 2009, 10:335 (15October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Magallanes: a web services discovery and automatic workflow composition tool
Javier Ros, Johan Karlsson, Oswaldo Trelles
BMC Bioinformatics 2009, 10:334 (15October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Phylogenetic analysis of modularity in protein interaction networks
Sinan Erten, Xin Li, Gurkan Bebek, Jing Li, Mehmet Koyutrk
BMC Bioinformatics 2009, 10:333 (14October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data
Daniel Jupiter, Hailin Chen, Vincent VanBuren
BMC Bioinformatics 2009, 10:332 (14October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery
Frank M You, Naxin Huo, Yong Q Gu, Gerard R Lazo, Jan Dvorak, Olin D Anderson
BMC Bioinformatics 2009, 10:331 (13October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
BASE - 2nd generation software for microarray data management and analysis
Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson, Jari Hkkinen
BMC Bioinformatics 2009, 10:330 (12October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
PLAST: parallel local alignment search tool for database comparison
Van Hoa Nguyen, Dominique Lavenier
BMC Bioinformatics 2009, 10:329 (12October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression
Wei-Chi Wang, Feng-Mao Lin, Wen-Chi Chang, Kuan-Yu Lin, Hsien-Da Huang, Na-Sheng Lin
BMC Bioinformatics 2009, 10:328 (12October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
VANLO - Interactive visual exploration of aligned biological networks
Steffen Brasch, Lars Linsen, Georg Fuellen
BMC Bioinformatics 2009, 10:327 (12October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)
Thomas C Wiegers, Allan Peter Davis, K Bretonnel Cohen, Lynette Hirschman, Carolyn J Mattingly
BMC Bioinformatics 2009, 10:326 (8October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Riboswitch Detection Using Profile Hidden Markov Models
Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, A Krishnamachari, Supratim Sengupta
BMC Bioinformatics 2009, 10:325 (8October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database
Konstantinos Moutselos, Ioannis Kanaris, Aristotelis Chatziioannou, Ilias Maglogiannis, Fragiskos N Kolisis
BMC Bioinformatics 2009, 10:324 (8October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A stochastic context free grammar based framework for analysis of protein sequences
Witold Dyrka, Jean-Christophe Nebel
BMC Bioinformatics 2009, 10:323 (8October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions
Holger Fr hlich,  zgr Sahin, Dorit Arlt, Christian Bender, Tim Bei barth
BMC Bioinformatics 2009, 10:322 (8October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Discovering multiple realistic TFBS motifs based on a generalized model
Tak-Ming Chan, Gang Li, Kwong-Sak Leung, Kin-Hong Lee
BMC Bioinformatics 2009, 10:321 (7October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature
Guillermo de la Calle, Miguel Garca-Remesal, Stefano Chiesa, Diana de la Iglesia, Victor Maojo
BMC Bioinformatics 2009, 10:320 (7October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Generation of Gene Ontology benchmark datasets with various types of positive signal
Petri Trnen, Petri Pehkonen, Liisa Holm
BMC Bioinformatics 2009, 10:319 (7October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Kavosh: a new algorithm for finding network motifs
Zahra Razaghi Moghadam Kashani, Hayedeh Ahrabian, Elahe Elahi, Abbas Nowzari-Dalini, Elnaz Saberi Ansari, Sahar Asadi, Shahin Mohammadi, Falk Schreiber, Ali Masoudi-Nejad
BMC Bioinformatics 2009, 10:318 (4October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Enhancing navigation in biomedical databases by community voting and database-driven text classification
Timo Duchrow, Timur Shtatland, Daniel Guettler, Misha Pivovarov, Stefan Kramer, Ralph Weissleder
BMC Bioinformatics 2009, 10:317 (3October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Unsupervised statistical clustering of environmental shotgun sequences
Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff, Joshua S Weitz
BMC Bioinformatics 2009, 10:316 (2October2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks
Sandra Waaijenborg, Aeilko H Zwinderman
BMC Bioinformatics 2009, 10:315 (28September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
MetaTM - a consensus method for transmembrane protein topology prediction
Martin Klammer, David N Messina, Thomas Schmitt, Erik LL Sonnhammer
BMC Bioinformatics 2009, 10:314 (28September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics
Benjamin M Good, Joseph T Tennis, Mark D Wilkinson
BMC Bioinformatics 2009, 10:313 (25September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Predicting protein-protein binding sites in membrane proteins
Andrew J Bordner
BMC Bioinformatics 2009, 10:312 (24September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Challenges for automatically extracting molecular interactions from full-text articles
Tara McIntosh, James R Curran
BMC Bioinformatics 2009, 10:311 (24September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays
Peter Ti o
BMC Bioinformatics 2009, 10:310 (23September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services
Damian DG Gessler, Gary S Schiltz, Greg D May, Shulamit Avraham, Christopher D Town, David Grant, Rex T Nelson
BMC Bioinformatics 2009, 10:309 (23September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously
Oscar M Rueda, Ramon Diaz-Uriarte
BMC Bioinformatics 2009, 10:308 (23September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function
Petri Trnen, Pauli J Ojala, Pekka Marttinen, Liisa Holm
BMC Bioinformatics 2009, 10:307 (23September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A methodology for the analysis of differential coexpression across the human lifespan
Jesse Gillis, Paul Pavlidis
BMC Bioinformatics 2009, 10:306 (22September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Strategies for analyzing highly enriched IP-chip datasets
Simon RV Knott, Christopher J Viggiani, Oscar M Aparicio, Simon Tavar
BMC Bioinformatics 2009, 10:305 (22September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs
Ahmet Sacan, Nilgun Ferhatosmanoglu, Hakan Ferhatosmanoglu
BMC Bioinformatics 2009, 10:304 (22September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The first step in the development of text mining technology for cancer risk assessment: identifying and organizing scientific evidence in risk assessment literature
Anna Korhonen, Ilona Silins, Lin Sun, Ulla Stenius
BMC Bioinformatics 2009, 10:303 (22September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Prediction of antigenic epitopes on protein surfaces by consensus scoring
Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias
BMC Bioinformatics 2009, 10:302 (22September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum
Scott Bringans, James K Hane, Tammy Casey, Kar-Chun Tan, Richard Lipscombe, Peter S Solomon, Richard P Oliver
BMC Bioinformatics 2009, 10:301 (22September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
RCMAT: a regularized covariance matrix approach to testing gene sets
Phillip D Yates, Mark A Reimers
BMC Bioinformatics 2009, 10:300 (21September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
BayesPeak: Bayesian analysis of ChIP-seq data
Christiana Spyrou, Rory Stark, Andy G Lynch, Simon Tavar
BMC Bioinformatics 2009, 10:299 (21September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees
Philippe Gouret, Julie D Thompson, Pierre Pontarotti
BMC Bioinformatics 2009, 10:298 (19September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Finding local communities in protein networks
Konstantin Voevodski, Shang-Hua Teng, Yu Xia
BMC Bioinformatics 2009, 10:297 (18September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction
Morten Nielsen, Ole Lund
BMC Bioinformatics 2009, 10:296 (18September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Accurate microRNA target prediction correlates with protein repression levels
Manolis Maragkakis, Panagiotis Alexiou, Giorgio L Papadopoulos, Martin Reczko, Theodore Dalamagas, George Giannopoulos, George Goumas, Evangelos Koukis, Kornilios Kourtis, Victor A Simossis, Praveen Sethupathy, Thanasis Vergoulis, Nectarios Koziris, Timos Sellis, Panagiotis Tsanakas, Artemis G Hatzigeorgiou
BMC Bioinformatics 2009, 10:295 (18September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses
Waranyu Wongseree, Anunchai Assawamakin, Theera Piroonratana, Saravudh Sinsomros, Chanin Limwongse, Nachol Chaiyaratana
BMC Bioinformatics 2009, 10:294 (17September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Efficient oligonucleotide probe selection for pan-genomic tiling arrays
Adam M Phillippy, Xiangyu Deng, Wei Zhang, Steven L Salzberg
BMC Bioinformatics 2009, 10:293 (16September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A first principles approach to differential expression in microarray data analysis
Robert A Rubin
BMC Bioinformatics 2009, 10:292 (16September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Automated seeding of specialised wiki knowledgebases with BioKb
Jonathan R Manning, Ann Hedley, John J Mullins, Donald R Dunbar
BMC Bioinformatics 2009, 10:291 (16September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information
Marcio L Acencio, Ney Lemke
BMC Bioinformatics 2009, 10:290 (16September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
In Silico screening for functional candidates amongst hypothetical proteins
Claus Desler, Prashanth Suravajhala, May Sanderhoff, Merete Rasmussen, Lene Juel Rasmussen
BMC Bioinformatics 2009, 10:289 (16September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Exploratory and inferential analysis of gene cluster neighborhood graphs
Theresa Scharl, Ingo Voglhuber, Friedrich Leisch
BMC Bioinformatics 2009, 10:288 (14September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Epitopia: a web-server for predicting B-cell epitopes
Nimrod D Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko
BMC Bioinformatics 2009, 10:287 (14September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites
Chao Li, Yuhua Li, Xiangmin Zhang, Phillip Stafford, Valentin Dinu
BMC Bioinformatics 2009, 10:286 (11September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Correction
Feature selection environment for genomic applications
Fabrcio Martins Lopes, David Corr a Martins Jr, Roberto M Cesar Jr
BMC Bioinformatics 2009, 10:285 (10September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
CASSIOPE: An expert system for conserved regions searches
Virginie Lopez Rascol, Anthony Levasseur, Olivier Chabrol, Simona Grusea, Philippe Gouret, Etienne GJ Danchin, Pierre Pontarotti
BMC Bioinformatics 2009, 10:284 (10September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
RRW: repeated random walks on genome-scale protein networks for local cluster discovery
Kathy Macropol, Tolga Can, Ambuj K Singh
BMC Bioinformatics 2009, 10:283 (9September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics
Matteo R , Graziano Pesole, David S Horner
BMC Bioinformatics 2009, 10:282 (8September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Context-driven discovery of gene cassettes in mobile integrons using a computational grammar
Guy Tsafnat, Enrico Coiera, Sally R Partridge, Jaron Schaeffer, Jon R Iredell
BMC Bioinformatics 2009, 10:281 (8September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
EDGE3: A web-based solution for management and analysis of Agilent two color microarray experiments
Aaron L Vollrath, Adam A Smith, Mark Craven, Christopher A Bradfield
BMC Bioinformatics 2009, 10:280 (4September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services
Johannes Wagener, Ola Spjuth, Egon L Willighagen, Jarl ES Wikberg
BMC Bioinformatics 2009, 10:279 (4September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Genephony: a knowledge management tool for genome-wide research
Angelo Nuzzo, Alberto Riva
BMC Bioinformatics 2009, 10:278 (3September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
Wenhui Wang, Juan Nunez-Iglesias, Yihui Luan, Fengzhu Sun
BMC Bioinformatics 2009, 10:277 (3September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Regression applied to protein binding site prediction and comparison with classification
Joachim Giard, Jr me Ambroise, Jean-Luc Gala, Beno t Macq
BMC Bioinformatics 2009, 10:276 (3September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Comparative study of gene set enrichment methods
Luca Abatangelo, Rosalia Maglietta, Angela Distaso, Annarita D'Addabbo, Teresa Maria Creanza, Sayan Mukherjee, Nicola Ancona
BMC Bioinformatics 2009, 10:275 (2September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
Torsten Blum, Sebastian Briesemeister, Oliver Kohlbacher
BMC Bioinformatics 2009, 10:274 (1September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families
Riccardo Percudani, Alessio Peracchi
BMC Bioinformatics 2009, 10:273 (1September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Correlating gene and protein expression data using Correlated Factor Analysis
Chuen Seng Tan, Agus Salim, Alexander Ploner, Janne Lehti, Kee Seng Chia, Yudi Pawitan
BMC Bioinformatics 2009, 10:272 (1September2009)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
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