MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data

(2010) Ravi Gupta et al.   BMC BIOINFORMATICS

Alternative splicing: global insights

(2010) Martina Hallegger et al.   FEBS Journal

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation

(2009) Melissa J. Moore et al.   CELL

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

Jmjd3 contributes to the control of gene expression in LPS-activated macrophages

(2009) Francesca De Santa et al.   EMBO JOURNAL

Chromatin poises miRNA- and protein-coding genes for expression

(2009) A. Barski et al.   GENOME RESEARCH

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

(2009) Jessica Severin et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genome-wide profiling of PPAR :RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis

(2008) R. Nielsen et al.   GENES & DEVELOPMENT

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE