PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3′Seq data using vector projections and non-negative matrix factorization

Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation

(2020) Callison E Alcott 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

Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients

(2019) Yuan Chu et al.   ONCOGENE

Alternative polyadenylation dependent function of splicing factor SRSF3 contributes to cellular senescence

(2019) Ting Shen et al.   Aging-US

TAPAS: tool for alternative polyadenylation site analysis

(2018) Ashraful Arefeen et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling

(2018) Justin Brumbaugh et al.   CELL

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

(2018) Georgi Tushev et al.   NEURON

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

(2017) Andrew Routh et al.   NUCLEIC ACIDS RESEARCH

Alternative polyadenylation and RNA-binding proteins

(2016) Ayse Elif Erson-Bensan   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Alternative Polyadenylation: Another Foe in Cancer

(2016) A. E. Erson-Bensan et al.   MOLECULAR CANCER RESEARCH

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

(2015) Bushra Raj et al.   NEURON

NUDT21-spanning CNVs lead to neuropsychiatric disease and altered MeCP2 abundance via alternative polyadenylation

(2015) Vincenzo A Gennarino et al.   eLife

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

(2014) Zheng Xia et al.   Nature Communications

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

(2013) P. Miura et al.   GENOME RESEARCH

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Nonnegative Matrix Factorization: A Comprehensive Review

(2012) Yu-Xiong Wang et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2008) R. Sandberg et al.   SCIENCE

Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology

(2008) Karthik Devarajan   PLoS Computational Biology