C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

SCPortalen: human and mouse single-cell centric database

(2017) Imad Abugessaisa et al.   NUCLEIC ACIDS RESEARCH

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

(2017) Jeanne Chèneby et al.   NUCLEIC ACIDS RESEARCH

Batch effects and the effective design of single-cell gene expression studies

(2017) Po-Yuan Tung et al.   Scientific Reports

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

(2016) David J. Arenillas et al.   BIOINFORMATICS

Targeted reduction of highly abundant transcripts using pseudo-random primers

(2016) Ophélie Arnaud et al.   BIOTECHNIQUES

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Single-cell profiling reveals that eRNA accumulation at enhancer–promoter loops is not required to sustain transcription

(2016) Samir Rahman et al.   NUCLEIC ACIDS RESEARCH

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Single-cell RNA-sequencing: The future of genome biology is now

(2016) Simone Picelli   RNA Biology

TagDust2: a generic method to extract reads from sequencing data

(2015) Timo Lassmann   BMC BIOINFORMATICS

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Bursty Gene Expression in the Intact Mammalian Liver

(2015) Keren Bahar Halpern et al.   MOLECULAR CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

(2015) Ning Leng et al.   NATURE METHODS

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU

(2014) Jessica Severin et al.   NATURE BIOTECHNOLOGY

TFAP2C governs the luminal epithelial phenotype in mammary development and carcinogenesis

(2014) A R Cyr et al.   ONCOGENE

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

(2014) Sarah A. Munro et al.   Nature Communications

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Transcriptional control of cancer metastasis

(2013) Brian Ell et al.   TRENDS IN CELL BIOLOGY

Regulation of EMT by TGFβ in cancer

(2012) Carl-Henrik Heldin et al.   FEBS LETTERS

Histone Demethylase KDM5B Collaborates with TFAP2C and Myc To Repress the Cell Cycle Inhibitor p21cip (CDKN1A)

(2012) P.-P. Wong et al.   MOLECULAR AND CELLULAR BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching

(2012) Dave T. P. Tang et al.   NUCLEIC ACIDS RESEARCH

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

Dynamics of TGF-β induced epithelial-to-mesenchymal transition monitored by Electric Cell-Substrate Impedance Sensing

(2011) David Schneider et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

AP-2γ promotes proliferation in breast tumour cells by direct repression of the CDKN1A gene

(2009) Christopher M J Williams et al.   EMBO JOURNAL

Gfi-1 represses CDKN2B encoding p15INK4B through interaction with Miz-1

(2009) S. Basu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TGF-β regulates the expression of transcription factor KLF6 and its splice variants and promotes co-operative transactivation of common target genes through a Smad3–Sp1–KLF6 interaction

(2008) Luisa M. Botella et al.   BIOCHEMICAL JOURNAL

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

ALDH isozymes downregulation affects cell growth, cell motility and gene expression in lung cancer cells

(2008) Jan S Moreb et al.   Molecular Cancer

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS