Bioinformatics 2013年2月最新文章

GENOME ANALYSIS
PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays
Shengping Yang, Stanley Pounds, Kun Zhang, and Zhide Fang
Bioinformatics 2013 29: 299-307

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data
Yongchao Liu, Jan Schröder, and Bertil Schmidt
Bioinformatics 2013 29: 308-315

SRmapper: a fast and sensitive genome-hashing alignment tool
Paul M. Gontarz, Jennifer Berger, and Chung F. Wong
Bioinformatics 2013 29: 316-321

STRUCTURAL BIOINFORMATICS
A knowledge-based orientation potential for transcription factor-DNA docking
Takako Takeda, Rosario I. Corona, and Jun-tao Guo
Bioinformatics 2013 29: 322-330

Non-local residue–residue contacts in proteins are more conserved than local ones
Orly Noivirt-Brik, Gershon Hazan, Ron Unger, and Yanay Ofran
Bioinformatics 2013 29: 331-337

SYSTEMS BIOLOGY
Inference of gene regulatory networks from genome-wide knockout fitness data
Liming Wang, Xiaodong Wang, Adam P. Arkin, and Michael S. Samoilov
Bioinformatics 2013 29: 338-346

Computational modelling of LY303511 and TRAIL-induced apoptosis suggests dynamic regulation of cFLIP
Yuan Shi, Gregory Mellier, Sinong Huang, Jacob White, Shazib Pervaiz, and Lisa Tucker-Kellogg
Bioinformatics 2013 29: 347-354

DATA AND TEXT MINING
A novel link prediction algorithm for reconstructing protein–protein interaction networks by topological similarity
Chengwei Lei and Jianhua Ruan
Bioinformatics 2013 29: 355-364

ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine
Yoshihiko Matsuta, Masahiro Ito, and Yukako Tohsato
Bioinformatics 2013 29: 365-372

BIOIMAGE INFORMATICS
Fast and robust optical flow for time-lapse microscopy using super-voxels
Fernando Amat, Eugene W. Myers, and Philipp J. Keller
Bioinformatics 2013 29: 373-380

APPLICATIONS NOTES
GENOME ANALYSIS
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
Chase A. Miller, Jon Anthony, Michelle M. Meyer, and Gabor Marth
Bioinformatics 2013 29: 381-383

ChromoZoom: a flexible, fluid, web-based genome browser
Theodore R. Pak and Frederick P. Roth
Bioinformatics 2013 29: 384-386

nestly—a framework for running software with nested parameter choices and aggregating results
Connor O. McCoy, Aaron Gallagher, Noah G. Hoffman, and Frederick A. Matsen
Bioinformatics 2013 29: 387-388

RetroSeq: transposable element discovery from next-generation sequencing data
Thomas M. Keane, Kim Wong, and David J. Adams
Bioinformatics 2013 29: 389-390

SEQUENCE ANALYSIS
READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
Raeece Naeem, Mamoon Rashid, and Arnab Pain
Bioinformatics 2013 29: 391-392

STRUCTURAL BIOINFORMATICS
Multistructural hot spot characterization with FTProd
Lane Votapka and Rommie E. Amaro
Bioinformatics 2013 29: 393-394

PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures
Anna Maria Gallina, Paola Bisignano, Maurizio Bergamino, and Domenico Bordo
Bioinformatics 2013 29: 395-397

Characterization of disordered proteins with ENSEMBLE
Mickaël Krzeminski, Joseph A. Marsh, Chris Neale, Wing-Yiu Choy, and Julie D. Forman-Kay
Bioinformatics 2013 29: 398-399

SYSTEMS BIOLOGY
DoseSim: a tool for pharmacokinetic/pharmacodynamic analysis and dose reconstruction
Brad Reisfeld, Jaime H. Ivy, Michael A. Lyons, Jesse M. Wright, Justin L. Rogers, and Arthur N. Mayeno
Bioinformatics 2013 29: 400-401

ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence
David M. Reif, Myroslav Sypa, Eric F. Lock, Fred A. Wright, Ander Wilson, Tommy Cathey, Richard R. Judson, and Ivan Rusyn
Bioinformatics 2013 29: 402-403

Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology
Gang Liu, Apurv Puri, and Sriram Neelamegham
Bioinformatics 2013 29: 404-406

DATA AND TEXT MINING
minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers
Davide Albanese, Michele Filosi, Roberto Visintainer, Samantha Riccadonna, Giuseppe Jurman, and Cesare Furlanello
Bioinformatics 2013 29: 407-408

DATABASES AND ONTOLOGIES
SM2miR: a database of the experimentally validated small molecules’ effects on microRNA expression
Xinyi Liu, Shuyuan Wang, Fanlin Meng, Jizhe Wang, Yan Zhang, Enyu Dai, Xuexin Yu, Xia Li, and Wei Jiang
Bioinformatics 2013 29: 409-411

LETTER TO THE EDITOR
SYSTEMS BIOLOGY
Concerning the accuracy of Fido and parameter choice
Oliver Serang
Bioinformatics 2013 29: 412

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