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		Research article Differential C3NET reveals disease networks of direct physical interactions Gökmen Altay, Mohammad Asim, Florian Markowetz, David E Neal BMC Bioinformatics 2011, 12:296 (21 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra Franziska Hinkelmann, Madison Brandon, Bonny Guang, Rustin McNeill, Grigoriy Blekherman, Alan Veliz-Cuba, Reinhard Laubenbacher BMC Bioinformatics 2011, 12:295 (20 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Multi-target QSAR modelling in the analysis and design of HIV-HCV co-inhibitors: an in-silico study Qi Liu, Han Zhou, Lin Liu, Xi Chen, Ruixin Zhu, Zhiwei Cao BMC Bioinformatics 2011, 12:294 (20 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article FAAST: Flow-space Assisted Alignment Search Tool Fredrik Lysholm, Björn Andersson, Bengt Persson BMC Bioinformatics 2011, 12:293 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study Sabrina Hempel, Aneta Koseska, Zoran Nikoloski, Jürgen Kurths BMC Bioinformatics 2011, 12:292 (19 July 2011) Abstract \| Full text \| PDF \| PubMed
		Software Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn' Christian Bender, Silvia Heyde, Frauke Henjes, Stefan Wiemann, Ulrike Korf, Tim Beißbarth BMC Bioinformatics 2011, 12:291 (19 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Bias detection and correction in RNA-Sequencing data Wei Zheng, Lisa M Chung, Hongyu Zhao BMC Bioinformatics 2011, 12:290 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping Giuseppe Gallone, T Ian Simpson, J Douglas Armstrong, Andrew P Jarman BMC Bioinformatics 2011, 12:289 (18 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes Klaus Jung, Tim Friede, Tim Beißbarth BMC Bioinformatics 2011, 12:288 (15 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Statistical Mutation Calling from Sequenced Overlapping DNA Pools in TILLING Experiments Victor Missirian, Luca Comai, Vladimir Filkov BMC Bioinformatics 2011, 12:287 (14 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview Jeff Skinner, Yuri Kotliarov, Sudhir Varma, Karina L Mine, Anatoly Yambartsev, Richard Simon, Yentram Huyen, Andrey Morgun BMC Bioinformatics 2011, 12:286 (14 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article S3QL: A distributed domain specific language for controlled semantic integration of life sciences data Helena F Deus, Miriã C Correa, Romesh Stanislaus, Maria Miragaia, Wolfgang Maass, Hermínia de Lencastre, Ronan Fox, Jonas S Almeida BMC Bioinformatics 2011, 12:285 (14 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Modeling measurement error in tumor characterization studies Cyril Rakovski, Daniel J Weisenberger, Paul Marjoram, Peter W Laird, Kimberly D Siegmund BMC Bioinformatics 2011, 12:284 (13 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Improving the performance of β-turn prediction using predicted shape strings and a two-layer support vector machine model Zehui Tang, Tonghua Li, Rida Liu, Wenwei Xiong, Jiangming Sun, Yaojuan Zhu, Guanyan Chen BMC Bioinformatics 2011, 12:283 (13 July 2011) Abstract \| Full text \| PDF \| PubMed
		Database Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data David Lopez, David Casero, Shawn J Cokus, Sabeeha S Merchant, Matteo Pellegrini BMC Bioinformatics 2011, 12:282 (12 July 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle Jeh-Ting Hsu, Chien-Hua Peng, Wen-Ping Hsieh, Chung-Yu Lan, Chuan Tang BMC Bioinformatics 2011, 12:281 (12 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking Shiyong Liu, Ilya A Vakser BMC Bioinformatics 2011, 12:280 (11 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Detection of Fused Genes in Eukaryotic Genomes using Gene deFuser: Analysis of the Tetrahymena thermophila genome Hannah MW Salim, Amanda M Koire, Nicholas A Stover, Andre RO Cavalcanti BMC Bioinformatics 2011, 12:279 (11 July 2011) Abstract \| Full text \| PDF \| PubMed
		Software ReadDB Provides Efficient Storage for Mapped Short Reads P Alexander Rolfe, David K Gifford BMC Bioinformatics 2011, 12:278 (7 July 2011) Abstract \| Full text \| PDF \| PubMed
		Software An integrated ChIP-seq analysis platform with customizable workflows Eugenia G Giannopoulou, Olivier Elemento BMC Bioinformatics 2011, 12:277 (7 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Quantitative characterization and analysis of the dynamic NF-κB response in microglia Patrick W Sheppard, Xiaoyun Sun, John F Emery, Rona G Giffard, Mustafa Khammash BMC Bioinformatics 2011, 12:276 (5 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article AlignHUSH: Alignment of HMMs using structure and hydrophobicity information Oruganty Krishnadev, Narayanaswamy Srinivasan BMC Bioinformatics 2011, 12:275 (5 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Detection of lineage-specific evolutionary changes among primate species Mihaela Pertea, Geo M Pertea, Steven L Salzberg BMC Bioinformatics 2011, 12:274 (4 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DivE (Divergence by Evolution), a new methodology for predicting both positive and negative selection in noncoding DNA, is particularly well-suited to detecting lineage-specific selection in large genomes as demonstrated using primate species
		Methodology article Gene set analysis for longitudinal gene expression data Ke Zhang, Haiyan Wang, Arne C Bathke, Solomon W Harrar, Hans-Peter Piepho, Youping Deng BMC Bioinformatics 2011, 12:273 (3 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Improving pan-genome annotation using whole genome multiple alignment Samuel V Angiuoli, Julie C Dunning Hotopp, Steven L Salzberg, Hervé Tettelin BMC Bioinformatics 2011, 12:272 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article DNACLUST: accurate and efficient clustering of phylogenetic marker genes Mohammadreza Ghodsi, Bo Liu, Mihai Pop BMC Bioinformatics 2011, 12:271 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology Holger Pillmann, Klas Hatje, Florian Odronitz, Björn Hammesfahr, Martin Kollmar BMC Bioinformatics 2011, 12:270 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article Network-based group variable selection for detecting expression quantitative trait loci (eQTL) Weichen Wang, Xuegong Zhang BMC Bioinformatics 2011, 12:269 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article New words in human mutagenesis Alexander Y Panchin, Sergey I Mitrofanov, Andrei V Alexeevski, Sergey A Spirin, Yuri V Panchin BMC Bioinformatics 2011, 12:268 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Software SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data Xutao Deng BMC Bioinformatics 2011, 12:267 (29 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software DOSim: An R package for similarity between diseases based on Disease Ontology Jiang Li, Binsheng Gong, Xi Chen, Tao Liu, Chao Wu, Fan Zhang, Chunquan Li, Xiang Li, Shaoqi Rao, Xia Li BMC Bioinformatics 2011, 12:266 (29 June 2011) Abstract \| Full text \| PDF \| PubMed
		Software phenosim - A software to simulate phenotypes for testing in genome-wide association studies Torsten Günther, Inka Gawenda, Karl J Schmid BMC Bioinformatics 2011, 12:265 (29 June 2011) Abstract \| Full text \| PDF \| PubMed
		Software MAVENs: Motion analysis and visualization of elastic networks and structural ensembles Michael T Zimmermann, Andrzej Kloczkowski, Robert L Jernigan BMC Bioinformatics 2011, 12:264 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MAVEN is a new software suite for generating elastic network models from raw program database files or density maps, and is able to integrate model generation, evaluation, analysis and visualization into a user-friendly environment.
		Research article Characterization of a Bayesian genetic clustering algorithm based on a Dirichlet process prior and comparison among Bayesian clustering methods Akio Onogi, Masanobu Nurimoto, Mitsuo Morita BMC Bioinformatics 2011, 12:263 (28 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article A mutation degree model for the identification of transcriptional regulatory elements Changqing Zhang, Jin Wang, Xu Hua, Jinggui Fang, Huaiqiu Zhu, Xiang Gao BMC Bioinformatics 2011, 12:262 (27 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity Tzong-Yi Lee, Neil Bretaña, Cheng-Tsung Lu BMC Bioinformatics 2011, 12:261 (26 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Computable visually observed phenotype ontological framework for plants Jaturon Harnsomburana, Jason M Green, Adrian S Barb, Mary Schaeffer, Leszek Vincent, Chi-Ren Shyu BMC Bioinformatics 2011, 12:260 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
		Software AMDORAP: Non-targeted metabolic profiling based on high-resolution LC-MS Hiroki Takahashi, Takuya Morimoto, Naotake Ogasawara, Shigehiko Kanaya BMC Bioinformatics 2011, 12:259 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article Cell subset prediction for blood genomic studies Christopher R Bolen, Mohamed Uduman, Steven H Kleinstein BMC Bioinformatics 2011, 12:258 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results Ubbo Visser, Saminda Abeyruwan, Uma Vempati, Robin P Smith, Vance Lemmon, Stephan C Schürer BMC Bioinformatics 2011, 12:257 (24 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Semantic inference using chemogenomics data for drug discovery Qian Zhu, Yuyin Sun, Sashikiran Challa, Ying Ding, Michael S Lajiness, David J Wild BMC Bioinformatics 2011, 12:256 (23 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and structure Tulaya Limpiti, Apichart Intarapanich, Anunchai Assawamakin, Philip J Shaw, Pongsakorn Wangkumhang, Jittima Piriyapongsa, Chumpol Ngamphiw, Sissades Tongsima BMC Bioinformatics 2011, 12:255 (23 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis Lionel Blanchet, Agnieszka Smolinska, Amos Attali, Marcel P Stoop, Kirsten AM Ampt, Hans van Aken, Ernst Suidgeest, Tinka Tuinstra, Sybren S Wijmenga, Theo Luider, Lutgarde MC Buydens BMC Bioinformatics 2011, 12:254 (22 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems Kim-Anh Lê Cao, Simon Boitard, Philippe Besse BMC Bioinformatics 2011, 12:253 (22 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Computational study of noise in a large signal transduction network Jukka Intosalmi, Tiina Manninen, Keijo Ruohonen, Marja-Leena Linne BMC Bioinformatics 2011, 12:252 (21 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Determinants of antigenicity and specificity in immune response for protein sequences Yulong Wang, Wenjun Wu, Nicolas N Negre, Kevin P White, Cheng Li, Parantu K Shah BMC Bioinformatics 2011, 12:251 (21 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article NORMA-Gene: A simple and robust method for qPCR normalization based on target gene data Lars-Henrik Heckmann, Peter B Sørensen, Paul Krogh, Jesper G Sørensen BMC Bioinformatics 2011, 12:250 (21 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemysław Biecek, Jerzy Tiuryn, Martin Vingron BMC Bioinformatics 2011, 12:249 (21 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome Jiajie Zhang, Amir Mamlouk, Thomas Martinetz, Suhua Chang, Jing Wang, Rolf Hilgenfeld BMC Bioinformatics 2011, 12:248 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs Leslie Regad, Juliette Martin, Anne-Claude Camproux BMC Bioinformatics 2011, 12:247 (20 June 2011) Abstract \| Full text \| PDF \| PubMed

	All
		Research article Differential C3NET reveals disease networks of direct physical interactions Gökmen Altay, Mohammad Asim, Florian Markowetz, David E Neal BMC Bioinformatics 2011, 12:296 (21 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra Franziska Hinkelmann, Madison Brandon, Bonny Guang, Rustin McNeill, Grigoriy Blekherman, Alan Veliz-Cuba, Reinhard Laubenbacher BMC Bioinformatics 2011, 12:295 (20 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Multi-target QSAR modelling in the analysis and design of HIV-HCV co-inhibitors: an in-silico study Qi Liu, Han Zhou, Lin Liu, Xi Chen, Ruixin Zhu, Zhiwei Cao BMC Bioinformatics 2011, 12:294 (20 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article FAAST: Flow-space Assisted Alignment Search Tool Fredrik Lysholm, Björn Andersson, Bengt Persson BMC Bioinformatics 2011, 12:293 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study Sabrina Hempel, Aneta Koseska, Zoran Nikoloski, Jürgen Kurths BMC Bioinformatics 2011, 12:292 (19 July 2011) Abstract \| Full text \| PDF \| PubMed
		Software Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn' Christian Bender, Silvia Heyde, Frauke Henjes, Stefan Wiemann, Ulrike Korf, Tim Beißbarth BMC Bioinformatics 2011, 12:291 (19 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Bias detection and correction in RNA-Sequencing data Wei Zheng, Lisa M Chung, Hongyu Zhao BMC Bioinformatics 2011, 12:290 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping Giuseppe Gallone, T Ian Simpson, J Douglas Armstrong, Andrew P Jarman BMC Bioinformatics 2011, 12:289 (18 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes Klaus Jung, Tim Friede, Tim Beißbarth BMC Bioinformatics 2011, 12:288 (15 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Statistical Mutation Calling from Sequenced Overlapping DNA Pools in TILLING Experiments Victor Missirian, Luca Comai, Vladimir Filkov BMC Bioinformatics 2011, 12:287 (14 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview Jeff Skinner, Yuri Kotliarov, Sudhir Varma, Karina L Mine, Anatoly Yambartsev, Richard Simon, Yentram Huyen, Andrey Morgun BMC Bioinformatics 2011, 12:286 (14 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article S3QL: A distributed domain specific language for controlled semantic integration of life sciences data Helena F Deus, Miriã C Correa, Romesh Stanislaus, Maria Miragaia, Wolfgang Maass, Hermínia de Lencastre, Ronan Fox, Jonas S Almeida BMC Bioinformatics 2011, 12:285 (14 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Modeling measurement error in tumor characterization studies Cyril Rakovski, Daniel J Weisenberger, Paul Marjoram, Peter W Laird, Kimberly D Siegmund BMC Bioinformatics 2011, 12:284 (13 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Improving the performance of β-turn prediction using predicted shape strings and a two-layer support vector machine model Zehui Tang, Tonghua Li, Rida Liu, Wenwei Xiong, Jiangming Sun, Yaojuan Zhu, Guanyan Chen BMC Bioinformatics 2011, 12:283 (13 July 2011) Abstract \| Full text \| PDF \| PubMed
		Database Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data David Lopez, David Casero, Shawn J Cokus, Sabeeha S Merchant, Matteo Pellegrini BMC Bioinformatics 2011, 12:282 (12 July 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle Jeh-Ting Hsu, Chien-Hua Peng, Wen-Ping Hsieh, Chung-Yu Lan, Chuan Tang BMC Bioinformatics 2011, 12:281 (12 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking Shiyong Liu, Ilya A Vakser BMC Bioinformatics 2011, 12:280 (11 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Detection of Fused Genes in Eukaryotic Genomes using Gene deFuser: Analysis of the Tetrahymena thermophila genome Hannah MW Salim, Amanda M Koire, Nicholas A Stover, Andre RO Cavalcanti BMC Bioinformatics 2011, 12:279 (11 July 2011) Abstract \| Full text \| PDF \| PubMed
		Software ReadDB Provides Efficient Storage for Mapped Short Reads P Alexander Rolfe, David K Gifford BMC Bioinformatics 2011, 12:278 (7 July 2011) Abstract \| Full text \| PDF \| PubMed
		Software An integrated ChIP-seq analysis platform with customizable workflows Eugenia G Giannopoulou, Olivier Elemento BMC Bioinformatics 2011, 12:277 (7 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Quantitative characterization and analysis of the dynamic NF-κB response in microglia Patrick W Sheppard, Xiaoyun Sun, John F Emery, Rona G Giffard, Mustafa Khammash BMC Bioinformatics 2011, 12:276 (5 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article AlignHUSH: Alignment of HMMs using structure and hydrophobicity information Oruganty Krishnadev, Narayanaswamy Srinivasan BMC Bioinformatics 2011, 12:275 (5 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Detection of lineage-specific evolutionary changes among primate species Mihaela Pertea, Geo M Pertea, Steven L Salzberg BMC Bioinformatics 2011, 12:274 (4 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DivE (Divergence by Evolution), a new methodology for predicting both positive and negative selection in noncoding DNA, is particularly well-suited to detecting lineage-specific selection in large genomes as demonstrated using primate species
		Methodology article Gene set analysis for longitudinal gene expression data Ke Zhang, Haiyan Wang, Arne C Bathke, Solomon W Harrar, Hans-Peter Piepho, Youping Deng BMC Bioinformatics 2011, 12:273 (3 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Improving pan-genome annotation using whole genome multiple alignment Samuel V Angiuoli, Julie C Dunning Hotopp, Steven L Salzberg, Hervé Tettelin BMC Bioinformatics 2011, 12:272 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article DNACLUST: accurate and efficient clustering of phylogenetic marker genes Mohammadreza Ghodsi, Bo Liu, Mihai Pop BMC Bioinformatics 2011, 12:271 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology Holger Pillmann, Klas Hatje, Florian Odronitz, Björn Hammesfahr, Martin Kollmar BMC Bioinformatics 2011, 12:270 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article Network-based group variable selection for detecting expression quantitative trait loci (eQTL) Weichen Wang, Xuegong Zhang BMC Bioinformatics 2011, 12:269 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article New words in human mutagenesis Alexander Y Panchin, Sergey I Mitrofanov, Andrei V Alexeevski, Sergey A Spirin, Yuri V Panchin BMC Bioinformatics 2011, 12:268 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
		Software SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data Xutao Deng BMC Bioinformatics 2011, 12:267 (29 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software DOSim: An R package for similarity between diseases based on Disease Ontology Jiang Li, Binsheng Gong, Xi Chen, Tao Liu, Chao Wu, Fan Zhang, Chunquan Li, Xiang Li, Shaoqi Rao, Xia Li BMC Bioinformatics 2011, 12:266 (29 June 2011) Abstract \| Full text \| PDF \| PubMed
		Software phenosim - A software to simulate phenotypes for testing in genome-wide association studies Torsten Günther, Inka Gawenda, Karl J Schmid BMC Bioinformatics 2011, 12:265 (29 June 2011) Abstract \| Full text \| PDF \| PubMed
		Software MAVENs: Motion analysis and visualization of elastic networks and structural ensembles Michael T Zimmermann, Andrzej Kloczkowski, Robert L Jernigan BMC Bioinformatics 2011, 12:264 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MAVEN is a new software suite for generating elastic network models from raw program database files or density maps, and is able to integrate model generation, evaluation, analysis and visualization into a user-friendly environment.
		Research article Characterization of a Bayesian genetic clustering algorithm based on a Dirichlet process prior and comparison among Bayesian clustering methods Akio Onogi, Masanobu Nurimoto, Mitsuo Morita BMC Bioinformatics 2011, 12:263 (28 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article A mutation degree model for the identification of transcriptional regulatory elements Changqing Zhang, Jin Wang, Xu Hua, Jinggui Fang, Huaiqiu Zhu, Xiang Gao BMC Bioinformatics 2011, 12:262 (27 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity Tzong-Yi Lee, Neil Bretaña, Cheng-Tsung Lu BMC Bioinformatics 2011, 12:261 (26 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Computable visually observed phenotype ontological framework for plants Jaturon Harnsomburana, Jason M Green, Adrian S Barb, Mary Schaeffer, Leszek Vincent, Chi-Ren Shyu BMC Bioinformatics 2011, 12:260 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
		Software AMDORAP: Non-targeted metabolic profiling based on high-resolution LC-MS Hiroki Takahashi, Takuya Morimoto, Naotake Ogasawara, Shigehiko Kanaya BMC Bioinformatics 2011, 12:259 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology article Cell subset prediction for blood genomic studies Christopher R Bolen, Mohamed Uduman, Steven H Kleinstein BMC Bioinformatics 2011, 12:258 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results Ubbo Visser, Saminda Abeyruwan, Uma Vempati, Robin P Smith, Vance Lemmon, Stephan C Schürer BMC Bioinformatics 2011, 12:257 (24 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Semantic inference using chemogenomics data for drug discovery Qian Zhu, Yuyin Sun, Sashikiran Challa, Ying Ding, Michael S Lajiness, David J Wild BMC Bioinformatics 2011, 12:256 (23 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and structure Tulaya Limpiti, Apichart Intarapanich, Anunchai Assawamakin, Philip J Shaw, Pongsakorn Wangkumhang, Jittima Piriyapongsa, Chumpol Ngamphiw, Sissades Tongsima BMC Bioinformatics 2011, 12:255 (23 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis Lionel Blanchet, Agnieszka Smolinska, Amos Attali, Marcel P Stoop, Kirsten AM Ampt, Hans van Aken, Ernst Suidgeest, Tinka Tuinstra, Sybren S Wijmenga, Theo Luider, Lutgarde MC Buydens BMC Bioinformatics 2011, 12:254 (22 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems Kim-Anh Lê Cao, Simon Boitard, Philippe Besse BMC Bioinformatics 2011, 12:253 (22 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Computational study of noise in a large signal transduction network Jukka Intosalmi, Tiina Manninen, Keijo Ruohonen, Marja-Leena Linne BMC Bioinformatics 2011, 12:252 (21 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Determinants of antigenicity and specificity in immune response for protein sequences Yulong Wang, Wenjun Wu, Nicolas N Negre, Kevin P White, Cheng Li, Parantu K Shah BMC Bioinformatics 2011, 12:251 (21 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article NORMA-Gene: A simple and robust method for qPCR normalization based on target gene data Lars-Henrik Heckmann, Peter B Sørensen, Paul Krogh, Jesper G Sørensen BMC Bioinformatics 2011, 12:250 (21 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemysław Biecek, Jerzy Tiuryn, Martin Vingron BMC Bioinformatics 2011, 12:249 (21 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research article PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome Jiajie Zhang, Amir Mamlouk, Thomas Martinetz, Suhua Chang, Jing Wang, Rolf Hilgenfeld BMC Bioinformatics 2011, 12:248 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs Leslie Regad, Juliette Martin, Anne-Claude Camproux BMC Bioinformatics 2011, 12:247 (20 June 2011) Abstract \| Full text \| PDF \| PubMed