SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming

Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses

(2021) Songlei Liu et al.   NUCLEIC ACIDS RESEARCH

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma

(2020) Aparna Bhaduri et al.   Cell Stem Cell

Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma

(2020) Swati Venkat et al.   GENOME RESEARCH

Differential Alternative Polyadenylation Landscapes Mediate Hematopoietic Stem Cell Activation and Regulate Glutamine Metabolism

(2020) Pia Sommerkamp et al.   Cell Stem Cell

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

(2020) Alison D. Tang et al.   Nature Communications

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations

(2020) Ming-Huei Chen et al.   CELL

The Polygenic and Monogenic Basis of Blood Traits and Diseases

(2020) Dragana Vuckovic et al.   CELL

Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq

(2019) Lin Guo et al.   MOLECULAR CELL

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

(2019) Charlotte Soneson et al.   Nature Communications

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control

(2019) Ivano Legnini et al.   NATURE METHODS

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

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

Poly(A) inclusive RNA isoform sequencing (PAIso−seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails

(2019) Yusheng Liu et al.   Nature Communications

CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones

(2018) Sören Müller et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Widespread intronic polyadenylation diversifies immune cell transcriptomes

(2018) Irtisha Singh et al.   Nature Communications

SpliceRCA: in Situ Single-Cell Analysis of mRNA Splicing Variants

(2018) Xiaojun Ren et al.   ACS Central Science

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Toward the human cellular microRNAome

(2017) Matthew N. McCall et al.   GENOME RESEARCH

Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation

(2017) Yan Song et al.   MOLECULAR CELL

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

(2017) Ruijia Wang et al.   NUCLEIC ACIDS RESEARCH

Alternative polyadenylation of ZEB1 promotes its translation during genotoxic stress in pancreatic cancer cells

(2017) Ilaria Passacantilli et al.   Cell Death & Disease

Massively parallel digital transcriptional profiling of single cells

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

Tissue damage and senescence provide critical signals for cellular reprogramming in vivo

(2016) Lluc Mosteiro et al.   SCIENCE

Evolution and Biological Roles of Alternative 3′UTRs

(2016) Christine Mayr   TRENDS IN CELL BIOLOGY

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

(2015) Evan Z. Macosko et al.   CELL

The Cancer Genome Atlas Analysis Predicts MicroRNA for Targeting Cancer Growth and Vascularization in Glioblastoma

(2015) Hon-Kit Andus Wong et al.   MOLECULAR THERAPY

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

(2015) Binyamin D. Berkovits et al.   NATURE

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

PRMT5 enhances generation of induced pluripotent stem cells from dairy goat embryonic fibroblastsviadown-regulation of p53

(2014) Z. Chu et al.   CELL PROLIFERATION

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

(2014) Hyeshik Chang et al.   MOLECULAR CELL

Genome-wide Functional Analysis Reveals Factors Needed at the Transition Steps of Induced Reprogramming

(2014) Chao-Shun Yang et al.   Cell Reports

The many faces of calmodulin in cell proliferation, programmed cell death, autophagy, and cancer

(2013) Martin W. Berchtold et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Alternative Polyadenylation Mediates MicroRNA Regulation of Muscle Stem Cell Function

(2012) Stéphane C. Boutet et al.   Cell Stem Cell

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

(2009) Christine Mayr et al.   CELL

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

(2009) Mo Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types

(2009) Zhe Ji et al.   PLoS One

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

The kinesin KIF1B  acts downstream from EglN3 to induce apoptosis and is a potential 1p36 tumor suppressor

(2008) S. Schlisio et al.   GENES & DEVELOPMENT