Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus
Evidence for human microRNA-offset RNAs in small RNA sequencing data
k-link EST clustering : evaluating error introduced by chimeric sequences under different degrees of linkage
Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus
Motif discovery and motif finding from genome-mapped DNase footprint data
Prediction of protein β-residue contacts by Markov logic networks with grounding-specific weights
Comparative study on ChIP-seq data : normalization and binding pattern characterization
Transcriptional landscape estimation from tiling array data using a model of signal shift and drift
Unite and conquer : univariate and multivariate approaches for finding differentially expressed gene sets
Robustness considerations in selecting efficient two-color microarray designs
Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources
TileProbe : modeling tiling array probe effects using publicly available data
Identification of distant family relationships
DYNAMIK : a software environment for cell DYNAmics, Motility, and Information tracKing, with an application to Ras pathways
Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model
Supervised prediction of drug–target interactions using bipartite local models
The impact of incomplete knowledge on evaluation : an experimental benchmark for protein function prediction
High-throughput minor histocompatibility antigen prediction
ADAN : a database for prediction of protein–protein interaction of modular domains mediated by linear motifs
WebArrayDB : cross-platform microarray data analysis and public data repository
HAPLOWSER : a whole-genome haplotype browser for personal genome and metagenome
TTA Lynx : a web-based service for analysis of actinomycete genes containing rare TTA codon
SNP-o-matic
HI: haplotype improver using paired-end short reads
PIQA : pipeline for Illumina G1 genome analyzer data quality assessment
TreeTime : an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration
Affy exon tissues : exon levels in normal tissues in human, mouse and rat
Path: a tool to facilitate pathway-based genetic association analysis
ITM Probe : analyzing information flow in protein networks
ViTraM : visualization of transcriptional modules
Antimony : a modular model definition language