We define a “threaded blockset,” which is a novel generalization of the classic notion of a
multiple alignment. A new computer program called TBA (for “threaded blockset aligner”) …

H2A.Z is an evolutionary conserved histone variant involved in transcriptional regulation,
antisilencing, silencing, and genome stability. The mechanism(s) by which H2A.Z regulates …

Background DNA methylation plays an essential role in the regulation of gene expression.
While its presence near the transcription start site of a gene has been associated with …

Orphan nuclear receptor ERRα (NR3B1) is recognized as a key regulator of mitochondrial
biogenesis, but it is not known whether ERRα and other ERR isoforms play a broader role in …

We have performed a survey of soluble human protein complexes containing components of
the transcription and RNA processing machineries using protein affinity purification coupled …

The shift from outcrossing to selfing is common in flowering plants 1 , 2 , but the genomic
consequences and the speed at which they emerge remain poorly understood. An excellent …

Comparative sequence analysis has become an essential component of studies aiming to
elucidate genome function. The increasing availability of genomic sequences from multiple …

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of
orthologous regulatory regions from multiple species. It does so by identifying the best …

Despite the central importance of noncoding DNA to gene regulation and evolution, understanding
of the extent of selection on plant noncoding DNA remains limited compared to that of …

This article analyzes mammalian genome rearrangements at higher resolution than has
been published to date. We identify 3171 intervals, covering ∼92% of the human genome, …