Alternative polyadenylation by sequential activation of distal and proximal PolyA sites

Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination

(2019) Kinga Kamieniarz-Gdula et al.   MOLECULAR CELL

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

(2019) Tobias Neumann et al.   BMC BIOINFORMATICS

A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes

(2019) Joshua D. Eaton et al.   GENES & DEVELOPMENT

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling

(2018) Justin Brumbaugh et al.   CELL

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation

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Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia

(2018) Shih-Han Lee et al.   NATURE

What Are 3′ UTRs Doing?

(2018) Christine Mayr   Cold Spring Harbor Perspectives in Biology

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters

(2017) Liang Chen et al.   MOLECULAR CELL

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

(2016) Andreas J. Gruber et al.   GENOME RESEARCH

Intronic polyadenylation of PDGFRα in resident stem cells attenuates muscle fibrosis

(2016) Alisa A. Mueller et al.   NATURE

Alternative polyadenylation of mRNA precursors

(2016) Bin Tian et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

(2015) Yongsheng Shi et al.   GENES & DEVELOPMENT

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition

(2015) Nova Fong et al.   MOLECULAR CELL

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

(2014) B. Lackford et al.   EMBO JOURNAL

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

(2014) Chioniso P. Masamha et al.   NATURE

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells

(2014) Andreas R. Gruber et al.   Nature Communications

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

System-wide identification of RNA-binding proteins by interactome capture

(2013) Alfredo Castello et al.   Nature Protocols

Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression

(2013) A. Pandya-Jones et al.   RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Dynamic Protein-Protein Interaction Wiring of the Human Spliceosome

(2012) Anna Hegele et al.   MOLECULAR CELL

Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation

(2012) C. Yao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA polymerase II kinetics inpolopolyadenylation signal selection

(2011) Pedro A B Pinto et al.   EMBO JOURNAL

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

The proteomes of transcription factories containing RNA polymerases I, II or III

(2011) Svitlana Melnik et al.   NATURE METHODS

Pre-mRNA splicing: where and when in the nucleus

(2011) Joonhee Han et al.   TRENDS IN CELL BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex

(2009) Yongsheng Shi et al.   MOLECULAR CELL

Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

(2009) Z. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

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