The landscape of alternative polyadenylation in single cells of the developing mouse embryo

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

(2020) Vikram Agarwal et al.   Cell Reports

Overlapping Activities of ELAV/Hu Family RNA Binding Proteins Specify the Extended Neuronal 3′ UTR Landscape in Drosophila

(2020) Lu Wei et al.   MOLECULAR CELL

A systematic evaluation of the design and context dependencies of massively parallel reporter assays

(2020) Jason C. Klein et al.   NATURE METHODS

The UCSC Genome Browser database: 2021 update

(2020) Jairo Navarro Gonzalez et al.   NUCLEIC ACIDS RESEARCH

APID database: redefining protein–protein interaction experimental evidences and binary interactomes

(2019) Diego Alonso-López et al.   Database-The Journal of Biological Databases and Curation

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data

(2019) Eldad David Shulman et al.   NUCLEIC ACIDS RESEARCH

RNA Binding Protein CELF2 Regulates Signal-Induced Alternative Polyadenylation by Competing with Enhancers of the Polyadenylation Machinery

(2019) Rakesh Chatrikhi et al.   Cell Reports

PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks

(2019) Jianan Lin et al.   PLoS Computational Biology

Alternative 3′ UTRs Modify the Localization, Regulatory Potential, Stability, and Plasticity of mRNAs in Neuronal Compartments

(2018) Georgi Tushev et al.   NEURON

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Alternative 3′ UTRs direct localization of functionally diverse protein isoforms in neuronal compartments

(2018) Camilla Ciolli Mattioli et al.   NUCLEIC ACIDS RESEARCH

PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes

(2017) Ruijia Wang et al.   NUCLEIC ACIDS RESEARCH

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

(2017) Stefan Semrau et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation

(2017) Mariana M. Fontes et al.   Scientific Reports

Distal Alternative Last Exons Localize mRNAs to Neural Projections

(2016) J. Matthew Taliaferro et al.   MOLECULAR CELL

Alternative polyadenylation of mRNA precursors

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

Evolution and Biological Roles of Alternative 3′UTRs

(2016) Christine Mayr   TRENDS IN CELL BIOLOGY

3’UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells

(2016) Yonit Hoffman et al.   PLoS Genetics

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

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

(2015) Yongsheng Shi et al.   GENES & DEVELOPMENT

ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System

(2015) Katarzyna Oktaba et al.   MOLECULAR CELL

Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization

(2015) Binyamin D. Berkovits et al.   NATURE

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Global Analyses of the Effect of Different Cellular Contexts on MicroRNA Targeting

(2014) Jin-Wu Nam et al.   MOLECULAR CELL

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Posttranscriptional regulation of gene networks by GU-rich elements and CELF proteins

(2014) Irina A. Vlasova et al.   RNA Biology

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

(2013) S. Lianoglou et al.   GENES & DEVELOPMENT

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

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

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Alternative cleavage and polyadenylation: the long and short of it

(2013) Bin Tian et al.   TRENDS IN BIOCHEMICAL SCIENCES

ELAV mediates 3' UTR extension in the Drosophila nervous system

(2012) V. Hilgers et al.   GENES & DEVELOPMENT

Extensive alternative polyadenylation during zebrafish development

(2012) I. Ulitsky et al.   GENOME RESEARCH

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing

(2012) Mainul Hoque et al.   NATURE METHODS

E2F mediates enhanced alternative polyadenylation in proliferation

(2012) Ran Elkon et al.   GENOME BIOLOGY

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing

(2011) Y. Fu et al.   GENOME RESEARCH

Mechanisms and Consequences of Alternative Polyadenylation

(2011) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

Neuron-specific ELAV/Hu proteins suppress HuR mRNA during neuronal differentiation by alternative polyadenylation

(2011) Kyle D. Mansfield et al.   NUCLEIC ACIDS RESEARCH

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

(2011) P. J. Shepard et al.   RNA

Signals for pre-mRNA cleavage and polyadenylation

(2011) Bin Tian et al.   Wiley Interdisciplinary Reviews-RNA

The importance of CELF control: molecular and biological roles of the CUG-BP, Elav-like family of RNA-binding proteins

(2011) Twishasri Dasgupta et al.   Wiley Interdisciplinary Reviews-RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples

(2010) Andrew H. Beck et al.   PLoS One

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

(2009) Christine Mayr et al.   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

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

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

(2008) R. Sandberg et al.   SCIENCE