Bioinformatics Advance Access for 15 Feb 2013

Original Papers
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses
Heiner Klingenberg, Kathrin Petra Aßhauer, Thomas Lingner, and Peter Meinicke
Bioinformatics published 15 February 2013, 10.1093/bioinformatics/btt077
[Abstract] [PDF] Creative Commons License OPEN ACCESS

Chemical rule-based filtering of MS/MS spectra
Beáta Reiz, Attila Kertész-Farkas, Sándor Pongor, and Michael P. Myers
Bioinformatics published 15 February 2013, 10.1093/bioinformatics/btt061

Classification of Mislabelled Microarrays using Robust Sparse Logistic Regression
Jakramate Bootkrajang and Ata Kabán
Bioinformatics published 15 February 2013, 10.1093/bioinformatics/btt078

A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies
Min Chen, Miao Zang, Xinlei Wang, and Guanghua Xiao
Bioinformatics published 15 February 2013, 10.1093/bioinformatics/btt068

Prediction of contact matrix for protein-protein interaction
Alvaro J. González, Li Liao, and Cathy H. Wu
Bioinformatics published 15 February 2013, 10.1093/bioinformatics/btt076

Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching
Mark R. Christie, Jacob A. Tennessen, and Michael S. Blouin
Bioinformatics published 30 January 2013, 10.1093/bioinformatics/btt039

Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping
Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang, and Hsueh-Wei Chang
Bioinformatics published 15 February 2013, 10.1093/bioinformatics/btt037

Composition and abstraction of logical regulatory modules: application to multicellular systems
Nuno D. Mendes, Frédéric Lang, Yves-Stan Le Cornec, Radu Mateescu, Gregory Batt, and Claudine Chaouiya
Bioinformatics published 22 January 2013, 10.1093/bioinformatics/btt033

A new way to protect privacy in large-scale genome-wide association studies
Liina Kamm, Dan Bogdanov, Sven Laur, and Jaak Vilo
Bioinformatics published 14 February 2013, 10.1093/bioinformatics/btt066

SPINAL: Scalable Protein Interaction Network Alignment
Ahmet Emre Aladağ and Cesim Erten
Bioinformatics published 14 February 2013, 10.1093/bioinformatics/btt071

Efficient comparison of sets of intervals with NC-lists
Matthias Zytnicki, YuFei Luo, and Hadi Quesneville
Bioinformatics published 14 February 2013, 10.1093/bioinformatics/btt070

An Approximate Bayesian Approach to Mapping Paired-End DNA Reads to a Reference Genome
Anish Man Singh Shrestha and Martin C. Frith
Bioinformatics published 14 February 2013, 10.1093/bioinformatics/btt073

GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, and Erik Lindahl
Bioinformatics published 13 February 2013, 10.1093/bioinformatics/btt055

A Dynamic Bayesian Markov Model for Phasing and Characterizing Haplotypes in Next Generation Sequencing
Yu Zhang
Bioinformatics published 13 February 2013, 10.1093/bioinformatics/btt065

Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics
Andrea Ocone, Andrew J. Millar, and Guido Sanguinetti
Bioinformatics published 13 February 2013, 10.1093/bioinformatics/btt069

Extracting 3D cell parameters from dense tissue environments: application to the development of the mouse heart
Sorin Pop, Alexandre C. Dufour, Jean-François Le Garrec, Chiara V. Ragni, Clémire Cimper, Sigolène M. Meilhac, and Jean-Christophe Olivo-Marin
Bioinformatics published 21 January 2013, 10.1093/bioinformatics/btt027

A new algorithm for context-based biomedical diagram similarity estimation
Songhua Xu, Jianqiang Sheng, and Xiaonan Luo
Bioinformatics published 7 February 2013, 10.1093/bioinformatics/btt030

Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights
Brett Trost and Anthony Kusalik
Bioinformatics published 22 January 2013, 10.1093/bioinformatics/btt031

PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information
Tao Li, Qian-Zhong Li, Shuai Liu, Guo-Liang Fan, Yong-Chun Zuo, and Yong Peng
Bioinformatics published 17 January 2013, 10.1093/bioinformatics/btt029

Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data
Sebastian Thieme and Philip Groth
Bioinformatics published 22 January 2013, 10.1093/bioinformatics/btt028

Application Note
BION web server: predicting non-specifically bound surface ions
Marharyta Petukh, Taylor Kimmet, and Emil Alexov
Bioinformatics published 3 February 2013, 10.1093/bioinformatics/btt032

Applications Note
eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows
Patrick Kiefer, Uwe Schmitt, and Julia A. Vorholt
Bioinformatics published 15 February 2013, 10.1093/bioinformatics/btt080

mRNAStab—a web application for mRNA stability analysis
Andrei Alic, José E. Pérez-Ortín, Joaquín Moreno, and Vicente Arnau
Bioinformatics published 25 January 2013, 10.1093/bioinformatics/btt040

AbCD: arbitrary coverage design for sequencing-based genetic studies
Jian Kang, Kuan-Chieh Huang, Zheng Xu, Yunfei Wang, Gonçalo R. Abecasis, and Yun Li
Bioinformatics published 28 January 2013, 10.1093/bioinformatics/btt041 a website and repository for accessing, analysing and manipulating metabolic networks
Mathias Ganter, Thomas Bernard, Sébastien Moretti, Joerg Stelling, and Marco Pagni
Bioinformatics published 28 January 2013, 10.1093/bioinformatics/btt036

Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes
Dhwani K. Desai, Harald Schunck, Johannes W. Löser, and Julie LaRoche
Bioinformatics published 9 January 2013, 10.1093/bioinformatics/bts721

essaMEM: finding maximal exact matches using enhanced sparse suffix arrays
Michaël Vyverman, Bernard De Baets, Veerle Fack, and Peter Dawyndt
Bioinformatics published 24 January 2013, 10.1093/bioinformatics/btt042

GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity
Hasup Lee, Hahnbeom Park, Junsu Ko, and Chaok Seok
Bioinformatics published 14 February 2013, 10.1093/bioinformatics/btt079

Wessim: A whole exome sequencing simulator based on in silico exome capture
Sangwoo Kim, Kyowon Jeong, and Vineet Bafna
Bioinformatics published 14 February 2013, 10.1093/bioinformatics/btt074

SwarmDock: a server for flexible protein–protein docking
Mieczyslaw Torchala, Iain H. Moal, Raphael A. G. Chaleil, Juan Fernandez-Recio, and Paul A. Bates
Bioinformatics published 23 January 2013, 10.1093/bioinformatics/btt038

TACTICS, an interactive platform for customized high-content bioimaging analysis
Raz Shimoni, Kim Pham, Mohammed Yassin, Min Gu, and Sarah M. Russell
Bioinformatics published 22 January 2013, 10.1093/bioinformatics/btt035

ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
Christopher S. Oehmen and Douglas J. Baxter
Bioinformatics published 29 January 2013, 10.1093/bioinformatics/btt013