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

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

(2016) M Ryan Corces et al.   NATURE GENETICS

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

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

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

HOXA9 promotes hematopoietic commitment of human embryonic stem cells

(2014) V. Ramos-Mejia et al.   BLOOD

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

(2014) Yonit Lavin et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

The Transcription Factors T-bet and Eomes Control Key Checkpoints of Natural Killer Cell Maturation

(2012) Scott M. Gordon et al.   IMMUNITY

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Coexistence of LMPP-like and GMP-like Leukemia Stem Cells in Acute Myeloid Leukemia

(2011) Nicolas Goardon et al.   CANCER CELL

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

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

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY