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

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

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation

(2015) Alvaro J González et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Acute Myeloid Leukemia

(2015) Hartmut Döhner et al.   NEW ENGLAND JOURNAL OF MEDICINE

Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature

(2015) Pierre Cauchy et al.   Cell Reports

FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution

(2014) Aaron M. Newman et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Co-inhibition of NF-κB and JNK is synergistic in TNF-expressing human AML

(2014) Andrew Volk et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia

(2014) Liran I. Shlush et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Predicting the human epigenome from DNA motifs

(2014) John W Whitaker et al.   NATURE METHODS

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence

(2014) Giulio Genovese et al.   NEW ENGLAND JOURNAL OF MEDICINE

Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes

(2014) Siddhartha Jaiswal et al.   NEW ENGLAND JOURNAL OF MEDICINE

Preleukemic mutations in human acute myeloid leukemia affect epigenetic regulators and persist in remission

(2014) M. R. Corces-Zimmerman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin state dynamics during blood formation

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

Transcriptional diversity during lineage commitment of human blood progenitors

(2014) L. Chen et al.   SCIENCE

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

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Lymphoid priming in human bone marrow begins before expression of CD10 with upregulation of L-selectin

(2012) Lisa A Kohn et al.   NATURE IMMUNOLOGY

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

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

(2011) Nicolas Goardon et al.   CANCER CELL

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Prospective separation of normal and leukemic stem cells based on differential expression of TIM3, a human acute myeloid leukemia stem cell marker

(2011) M. Jan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

(2010) Hong Ji et al.   NATURE

Hematopoietic stem cell: self-renewal versus differentiation

(2010) Jun Seita et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS