Pathogen detection using short-RNA deep sequencing subtraction and assembly
Comparative studies of de novo assembly tools for next-generation sequencing technologies
Parent-specific copy number in paired tumor–normal studies using circular binary segmentation
A probabilistic method for the detection and genotyping of small indels from population-scale sequence data
A tree-based approach for motif discovery and sequence classification
Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties
Aligning short reads to reference alignments and trees
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates
Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
Robust biclustering by sparse singular value decomposition incorporating stability selection
A procedure to statistically evaluate agreement of differential expression for cross-species genomics
MixupMapper : correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects
Enriching targeted sequencing experiments for rare disease alleles
Varying coefficient model for gene–environment interaction : a non-linear look
The Biological Connection Markup Language : a SBGN-compliant format for visualization, filtering and analysis of biological pathways
Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays
genBlastG : using BLAST searches to build homologous gene models
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
CHASM and SNVBox : toolkit for detecting biologically important single nucleotide mutations in cancer
nucleR : a package for non-parametric nucleosome positioning
RNASAlign : RNA Structural Alignment System
mapDamage : testing for damage patterns in ancient DNA sequences
The variant call format and VCFtools
SEAL : a distributed short read mapping and duplicate removal tool
The LabelHash Server and Tools for substructure-based functional annotation
Xwalk : computing and visualizing distances in cross-linking experiments
PathVisio-MIM : PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)
JSBML : a flexible Java library for working with SBML
Response to “Comments on ‘Bayesian variable selection for disease classification using gene expression data’”
Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim