An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability

DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex

(2020) Vishal Nanavaty et al.   MOLECULAR CELL

A simple new approach to variable selection in regression, with application to genetic fine mapping

(2020) Gao Wang et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Alternative polyadenylation mediates genetic regulation of gene expression

(2020) Briana E Mittleman et al.   eLife

Development of Poly(A)-ClickSeq as a tool enabling simultaneous genome-wide poly(A)-site identification and differential expression analysis

(2019) Nathan D. Elrod et al.   METHODS

Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation

(2019) Tingting Weng et al.   JOURNAL OF CLINICAL INVESTIGATION

DPAC: A Tool for Differential Poly(A) Cluster Usage from Poly(A)-Targeted RNAseq Data

(2019) Andrew Routh   G3-Genes Genomes Genetics

A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation

(2019) Nicholas Bogard et al.   CELL

The Length of the Expressed 3′ UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases

(2019) Elisa Mariella et al.   Frontiers in Genetics

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

(2018) Daniel Dominguez et al.   MOLECULAR CELL

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation

(2018) Eric R. Gamazon et al.   NATURE GENETICS

3′ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk

(2018) Hyun Jung Park et al.   NATURE GENETICS

Genomic atlas of the human plasma proteome

(2018) Benjamin B. Sun et al.   NATURE

What Are 3′ UTRs Doing?

(2018) Christine Mayr   Cold Spring Harbor Perspectives in Biology

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

(2018) Sarah M. Urbut et al.   NATURE GENETICS

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation

(2017) Andrew Routh et al.   NUCLEIC ACIDS RESEARCH

Optimizing the DNA Donor Template for Homology-Directed Repair of Double-Strand Breaks

(2017) Fei Song et al.   Molecular Therapy-Nucleic Acids

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export

(2016) Michaela Müller-McNicoll et al.   GENES & DEVELOPMENT

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

Genetic variants regulating expression levels and isoform diversity during embryogenesis

(2016) Enrico Cannavò et al.   NATURE

Elevated basal serum tryptase identifies a multisystem disorder associated with increased TPSAB1 copy number

(2016) Jonathan J Lyons et al.   NATURE GENETICS

Alternative polyadenylation of mRNA precursors

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

CRISPR-Cas9 mediated genetic engineering for the purification of the endogenous integrator complex from mammalian cells

(2016) David Baillat et al.   PROTEIN EXPRESSION AND PURIFICATION

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

RBFOX1 and RBFOX2 are dispensable in iPSCs and iPSC-derived neurons and do not contribute to neural-specific paternal UBE3A silencing

(2016) Pin-Fang Chen et al.   Scientific Reports

UBE2L3 Polymorphism Amplifies NF-κB Activation and Promotes Plasma Cell Development, Linking Linear Ubiquitination to Multiple Autoimmune Diseases

(2015) Myles J. Lewis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

Identifying Causal Variants at Loci with Multiple Signals of Association

(2014) F. Hormozdiari et al.   GENETICS

A polyadenylation site variant causes transcript-specific BMP1 deficiency and frequent fractures in children

(2014) Somayyeh Fahiminiya et al.   HUMAN MOLECULAR GENETICS

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

(2014) Chioniso P. Masamha et al.   NATURE

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types

(2014) Zheng Xia et al.   Nature Communications

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Alternative polyadenylation and miR-34 family members regulate tau expression

(2013) John R. Dickson et al.   JOURNAL OF NEUROCHEMISTRY

CPEB1 coordinates alternative 3′-UTR formation with translational regulation

(2013) Felice-Alessio Bava et al.   NATURE

Correction: Genetic Diversity and Population Structure of Rice Pathogen Ustilaginoidea virens in China

(2013) Xianyun Sun et al.   PLoS One

DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts

(2013) Daria V. Zhernakova et al.   PLoS Genetics

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A functional haplotype of UBE2L3 confers risk for systemic lupus erythematosus

(2012) S Wang et al.   GENES AND IMMUNITY

Bayesian refinement of association signals for 14 loci in 3 common diseases

(2012) Julian B Maller et al.   NATURE GENETICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells.

(2012) Eva Matoulkova et al.   RNA Biology

Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation

(2012) Laurent F. Thomas et al.   PLoS Computational Biology

Genetics and Regulatory Impact of Alternative Polyadenylation in Human B-Lymphoblastoid Cells

(2012) Oh Kyu Yoon et al.   PLoS Genetics

An alternative polyadenylation signal in TCF7L2 generates isoforms that inhibit T cell factor/lymphoid-enhancer factor (TCF/LEF)-dependent target genes

(2011) J. M. Locke et al.   DIABETOLOGIA

A germline variant in the TP53 polyadenylation signal confers cancer susceptibility

(2011) Simon N Stacey et al.   NATURE GENETICS

Facioscapulohumeral muscular dystrophy and DUX4: breaking the silence

(2011) Silvère M. van der Maarel et al.   TRENDS IN MOLECULAR MEDICINE

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

LocusZoom: regional visualization of genome-wide association scan results

(2010) R. J. Pruim et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

La-Related Protein 4 Binds Poly(A), Interacts with the Poly(A)-Binding Protein MLLE Domain via a Variant PAM2w Motif, and Can Promote mRNA Stability

(2010) R. Yang et al.   MOLECULAR AND CELLULAR BIOLOGY

Recessive mutations in the INS gene result in neonatal diabetes through reduced insulin biosynthesis

(2010) I. Garin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The value of HDL genetics

(2008) Adriaan G Holleboom et al.   CURRENT OPINION IN LIPIDOLOGY

Genome-wide analysis of transcript isoform variation in humans

(2008) Tony Kwan et al.   NATURE GENETICS