Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

Divergent transcription: A new feature of active promoters

(2011) Amy C. Seila et al.   CELL CYCLE

Evolution, biogenesis and function of promoter-associated RNAs

(2011) Ryan J. Taft et al.   CELL CYCLE

RNA secondary structure in mutually exclusive splicing

(2011) Yun Yang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dicer-Independent Primal RNAs Trigger RNAi and Heterochromatin Formation

(2010) Mario Halic et al.   CELL

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

RNA polymerase plays both sides: Vivid and bidirectional transcription around and upstream of active promoters

(2010) Pascal Preker et al.   CELL CYCLE

An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila

(2010) Daniel Olivieri et al.   EMBO JOURNAL

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

(2010) H. R. Chiang et al.   GENES & DEVELOPMENT

Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans

(2010) W.-J. Chung et al.   GENOME RESEARCH

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness

(2010) A. M. Burroughs et al.   GENOME RESEARCH

MicroRNA Biogenesis via Splicing and Exosome-Mediated Trimming in Drosophila

(2010) Alex S. Flynt et al.   MOLECULAR CELL

The Yeast 5′-3′ Exonuclease Rat1p Functions during Transcription Elongation by RNA Polymerase II

(2010) Silvia Jimeno-González et al.   MOLECULAR CELL

New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism

(2010) Philipp Kapranov et al.   NATURE

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

(2010) Ryan J Taft et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Whole genome transcriptome analysis

(2010) Alistair R.R. Forrest et al.   RNA Biology

Structure–function studies of the RNA polymerase II elongation complex

(2009) Florian Brueckner et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary

(2009) Colin D. Malone et al.   CELL

Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies

(2009) Chengjian Li et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

A Broadly Conserved Pathway Generates 3′UTR-Directed Primary piRNAs

(2009) Nicolas Robine et al.   CURRENT BIOLOGY

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila

(2009) Kuniaki Saito et al.   NATURE

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

Evolutionary flux of canonical microRNAs and mirtrons in Drosophila

(2009) Eugene Berezikov et al.   NATURE GENETICS

Limitations and possibilities of small RNA digital gene expression profiling

(2009) Sam E V Linsen et al.   NATURE METHODS

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Repertoire of Bovine miRNA and miRNA-Like Small Regulatory RNAs Expressed upon Viral Infection

(2009) Evgeny A. Glazov et al.   PLoS One

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs

(2008) J. E. Babiarz et al.   GENES & DEVELOPMENT

A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach

(2008) E. A. Glazov et al.   GENOME RESEARCH

NELF and GAGA Factor Are Linked to Promoter-Proximal Pausing at Many Genes in Drosophila

(2008) C. Lee et al.   MOLECULAR AND CELLULAR BIOLOGY

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

Direct detection of small RNAs using splinted ligation

(2008) Patricia A Maroney et al.   Nature Protocols

Human branch point consensus sequence is yUnAy

(2008) Kaiping Gao et al.   NUCLEIC ACIDS RESEARCH

A multifunctional human Argonaute2-specific monoclonal antibody

(2008) S. Rudel et al.   RNA

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Argonaute proteins: key players in RNA silencing

(2007) Gyorgy Hutvagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY