GENOME ANALYSIS
PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays
Bioinformatics 2013 29: 299-307
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data
Bioinformatics 2013 29: 308-315
SRmapper: a fast and sensitive genome-hashing alignment tool
Bioinformatics 2013 29: 316-321
STRUCTURAL BIOINFORMATICS
A knowledge-based orientation potential for transcription factor-DNA docking
Bioinformatics 2013 29: 322-330
Non-local residue–residue contacts in proteins are more conserved than local ones
Bioinformatics 2013 29: 331-337
SYSTEMS BIOLOGY
Inference of gene regulatory networks from genome-wide knockout fitness data
Bioinformatics 2013 29: 338-346
Computational modelling of LY303511 and TRAIL-induced apoptosis suggests dynamic regulation of cFLIP
Bioinformatics 2013 29: 347-354
DATA AND TEXT MINING
A novel link prediction algorithm for reconstructing protein–protein interaction networks by topological similarity
Bioinformatics 2013 29: 355-364
ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine
Bioinformatics 2013 29: 365-372
BIOIMAGE INFORMATICS
Fast and robust optical flow for time-lapse microscopy using super-voxels
Bioinformatics 2013 29: 373-380
APPLICATIONS NOTES
GENOME ANALYSIS
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
Bioinformatics 2013 29: 381-383
ChromoZoom: a flexible, fluid, web-based genome browser
Bioinformatics 2013 29: 384-386
nestly—a framework for running software with nested parameter choices and aggregating results
Bioinformatics 2013 29: 387-388
RetroSeq: transposable element discovery from next-generation sequencing data
Bioinformatics 2013 29: 389-390
SEQUENCE ANALYSIS
READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
Bioinformatics 2013 29: 391-392
STRUCTURAL BIOINFORMATICS
Multistructural hot spot characterization with FTProd
Bioinformatics 2013 29: 393-394
PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures
Bioinformatics 2013 29: 395-397
Characterization of disordered proteins with ENSEMBLE
Bioinformatics 2013 29: 398-399
SYSTEMS BIOLOGY
DoseSim: a tool for pharmacokinetic/pharmacodynamic analysis and dose reconstruction
Bioinformatics 2013 29: 400-401
ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence
Bioinformatics 2013 29: 402-403
Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology
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
Bioinformatics 2013 29: 407-408
DATABASES AND ONTOLOGIES
SM2miR: a database of the experimentally validated small molecules’ effects on microRNA expression
Bioinformatics 2013 29: 409-411
LETTER TO THE EDITOR
SYSTEMS BIOLOGY
Concerning the accuracy of Fido and parameter choice
Bioinformatics 2013 29: 412