Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Unsupervised clustering and epigenetic classification of single cells

(2018) Mahdi Zamanighomi et al.   Nature Communications

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Disruption of spatiotemporal hypoxic signaling causes congenital heart disease in mice

(2017) Xuejun Yuan et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2017) Alicia N Schep et al.   NATURE METHODS

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

(2017) Rhishikesh Bargaje et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

UROPA: a tool for Universal RObust Peak Annotation

(2017) Maria Kondili et al.   Scientific Reports

Single-Cell Resolution of Temporal Gene Expression during Heart Development

(2016) Daniel M. DeLaughter et al.   DEVELOPMENTAL CELL

Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells

(2016) Guang Li et al.   DEVELOPMENTAL CELL

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

(2015) Daniel H. Kim et al.   Cell Stem Cell

Hoxb1 regulates proliferation and differentiation of second heart field progenitors in pharyngeal mesoderm and genetically interacts with Hoxa1 during cardiac outflow tract development

(2015) Marine Roux et al.   DEVELOPMENTAL BIOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Mesodermal Nkx2.5 is necessary and sufficient for early second heart field development

(2014) Lu Zhang et al.   DEVELOPMENTAL BIOLOGY

RBM24 Is a Major Regulator of Muscle-Specific Alternative Splicing

(2014) Jiwen Yang et al.   DEVELOPMENTAL CELL

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Cardiac Cell Lineages that Form the Heart

(2014) S. M. Meilhac et al.   Cold Spring Harbor Perspectives in Medicine

Duplications of hox gene clusters and the emergence of vertebrates

(2013) Natalia Soshnikova et al.   DEVELOPMENTAL BIOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Signaling and Transcriptional Networks in Heart Development and Regeneration

(2013) B. G. Bruneau   Cold Spring Harbor Perspectives in Biology

miR-1/133a Clusters Cooperatively Specify the Cardiomyogenic Lineage by Adjustment of Myocardin Levels during Embryonic Heart Development

(2013) Katharina Wystub et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Early cardiac development: a view from stem cells to embryos

(2012) P. Van Vliet et al.   CARDIOVASCULAR RESEARCH

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology?

(2011) Sui Huang   BIOESSAYS

Cardiovascular defects in a mouse model of HOXA1 syndrome

(2011) N. Makki et al.   HUMAN MOLECULAR GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Chromatin remodeling in heart development

(2010) Benoit G Bruneau   CURRENT OPINION IN GENETICS & DEVELOPMENT

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors

(2009) Jun K. Takeuchi et al.   NATURE

Lives of a Heart Cell: Tracing the Origins of Cardiac Progenitors

(2008) Silvia Martin-Puig et al.   Cell Stem Cell

Reassessment of Isl1 and Nkx2-5 cardiac fate maps using a Gata4-based reporter of Cre activity

(2008) Qing Ma et al.   DEVELOPMENTAL BIOLOGY

Marking Embryonic Stem Cells with a 2A Self-Cleaving Peptide: A NKX2-5 Emerald GFP BAC Reporter

(2008) Edward C. Hsiao et al.   PLoS One