Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes
and splice variants and quantify expression genome-wide in a single assay. The volume and …

How noncoding DNA determines gene expression in different cell types is a major unsolved
problem, and critical downstream applications in human genetics depend on improved …

Background The genome of the domestic cow, Bos taurus, was sequenced using a mixture
of hierarchical and whole-genome shotgun sequencing methods. Results We have …

The complex language of eukaryotic gene expression remains incompletely understood.
Despite the importance suggested by many noncoding variants statistically associated with …

RNA, including long noncoding RNA (lncRNA), is known to be an abundant and important
structural component of the nuclear matrix. However, the molecular identities, functional roles …

Low-cost short read sequencing technology has revolutionized genomics, though it is only
just becoming practical for the high-quality de novo assembly of a novel large genome. We …

We introduce Quake, a program to detect and correct errors in DNA sequencing reads.
Using a maximum likelihood approach incorporating quality values and nucleotide specific …

The prevalence of obesity has led to a surge of interest in understanding the detailed
mechanisms underlying adipocyte development. Many protein-coding genes, mRNAs, and …

Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to
study the regulatory mechanisms that facilitate cellular transitions in a human context. To that …

Models for predicting phenotypic outcomes from genotypes have important applications to
understanding genomic function and improving human health. Here, we develop a machine-…