Repitools: an R package for the analysis of enrichment-based epigenomic data - Summary: Epigenetics, the study of heritable somatic phenotypic changes not related to DNA sequence, has emerged as a critical component of the landscape of gene regulation.

Semantic integration of data on transcriptional regulation - Motivation: Experimental and predicted data concerning gene transcriptional regulation are distributed among many heterogeneous sources.

Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data - Deciphering transcription factor networks from microarray data remains difficult.

DensiTree: making sense of sets of phylogenetic trees - Motivation: Bayesian analysis through programs like BEAST (Drummond and Rumbaut, 2007) and MrBayes (Huelsenbeck et al., 2001) provides a powerful m

Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures - Summary: Multiple sequence alignment is an important tool in bioinformatics.

Tuning and controlling gene expression noise in synthetic gene networks - Synthetic gene networks can be used to control gene expression and cellular phenotypes in a variety of applications. In many instances, however, such networks can behave unreliably due to gene expression noise.

varLD: a program for quantifying variation in linkage disequilibrium patterns between populations - Motivation: Linkage disequilibrium (LD) differences between populations can potentially result in failure to replicate primary signals of trait association in independent genome-wide association studie

ArchSchema: a tool for interactive graphing of related Pfam domain architectures - Summary: ArchSchema is a Java Web Start application that generates a dynamic 2D network of related Pfam domain architectures.

HALO--a Java framework for precise transcript half-life determination - Summary: Recent improvements in experimental technologies now allow measurements of de novo transcription and/or RNA decay at whole transcriptome level and determination of precise transcript half-lives.

WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data - Motivation: Fluorescent and luminescent reporter gene systems in combination with automated microplate readers allow real-time monitoring of gene expression on the population level at high precision an