Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes
of complex organisms. The term ‘lncRNAs’ encompasses RNA polymerase I (Pol I), Pol II …

Experimental genomics involves taking advantage of sequence information to investigate and
understand the workings of genes, cells and organisms. We have developed an approach …

Mapping of large sets of high‐throughput sequencing reads to a reference genome is one
of the foundational steps in RNA‐seq data analysis. The STAR software package performs …

This study describes comprehensive polling of transcription start and termination sites and
analysis of previously unidentified full-length complementary DNAs derived from the mouse …

Eukaryotic cells make many types of primary and processed RNAs that are found either in
specific subcellular compartments or throughout the cells. A complete catalogue of these …

We report the generation and analysis of functional data from multiple, diverse experiments
performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE …

The human genome contains many thousands of long noncoding RNAs (lncRNAs). While
several studies have demonstrated compelling biological and disease roles for individual …

The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements
in the human genome sequence. The pilot phase of the Project is focused on a specified …

Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet
unsolved problem because of the non-contiguous transcript structure, relatively short read …

Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated
and has reduced protein-coding potential. The genomic origins and the associations of …