There is growing recognition that mammalian cells produce many thousands of large intergenic
transcripts 1 , 2 , 3 , 4 . However, the functional significance of these transcripts has been …

Motivation: As high-throughput transcriptome sequencing provides evidence for novel
transcripts in many species, there is a renewed need for accurate methods to classify small …

Sequencing of multiple related species followed by comparative genomics analysis constitutes
a powerful approach for the systematic understanding of any genome. Here, we use the …

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves
the precision and sensitivity of evolutionary inference, producing more robust results than …

Transcription of long noncoding RNAs (lncRNAs) within gene regulatory elements can modulate
gene activity in response to external stimuli, but the scope and functions of such activity …

Candida species are the most common cause of opportunistic fungal infection worldwide.
Here we report the genome sequences of six Candida species and compare these and related …

To gain insight into how genomic information is translated into cellular and developmental
programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) …

The comparison of related genomes has emerged as a powerful lens for genome interpretation.
Here we report the sequencing and comparative analysis of 29 eutherian genomes. We …

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the
scientific and medical communities to interpret the human genome sequence and apply it to …

Long noncoding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally
resemble mRNAs but do not encode proteins. Recent genome-wide studies in humans and the …