Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Modeling gene regulation from paired expression and chromatin accessibility data

(2017) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules

(2011) Shihua Zhang et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Endogenous retinoic acid regulates cardiac progenitor differentiation

(2010) S.-C. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY