Differential effects of chromatin regulators and transcription factors on gene regulation : a nucleosomal perspective
Scoring-and-unfolding trimmed tree assembler : concepts, constructs and comparisons
Efficient change point detection for genomic sequences of continuous measurements
PE-Assembler
Identifying cancer driver genes in tumor genome sequencing studies
GPU-BLAST : using graphics processors to accelerate protein sequence alignment
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing
MTR : taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks
Improving structure alignment-based prediction of SCOP families using Vorolign Kernels
PETcofold : predicting conserved interactions and structures of two multiple alignments of RNA sequences
Predicting in vitro drug sensitivity using Random Forests
SLIM : a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures
Inference of gene networks—application to Bifidobacterium
Fast and efficient dynamic nested effects models
Evolutionary design principles and functional characteristics based on kingdom-specific network motifs
Prognostic transcriptional association networks : a new supervised approach based on regression trees
A hybrid approach to extract protein–protein interactions
PriSM : a primer selection and matching tool for amplification and sequencing of viral genomes
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
GimmeMotifs : a de novo motif prediction pipeline for ChIP-sequencing experiments
The uniqueome : a mappability resource for short-tag sequencing
Analyzing marginal cases in differential shotgun proteomics
SESAME (SEquence Sorter & AMplicon Explorer) : genotyping based on high-throughput multiplex amplicon sequencing
PLEXY : efficient target prediction for box C/D snoRNAs
RSEQtools : a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
Real-world comparison of CPU and GPU implementations of SNPrank : a network analysis tool for GWAS
TE Displayer for post-genomic analysis of transposable elements
Accelerating reaction–diffusion simulations with general-purpose graphics processing units