The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal

(2019) Stephanie Z. Xie et al.   Cell Stem Cell

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

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

(2018) Jason D. Buenrostro et al.   CELL

Chromatin conformation analysis of primary patient tissue using a low input Hi-C method

(2018) Noelia Díaz et al.   Nature Communications

Integrated Stress Response Activity Marks Stem Cells in Normal Hematopoiesis and Leukemia

(2018) Peter van Galen et al.   Cell Reports

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

(2018) Aleksandra Pękowska et al.   Cell Systems

Autophagy maintains the metabolism and function of young and old stem cells

(2017) Theodore T. Ho et al.   NATURE

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

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

(2017) Alicia N Schep et al.   NATURE METHODS

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

Systemic Virus Infections Differentially Modulate Cell Cycle State and Functionality of Long-Term Hematopoietic Stem Cells In Vivo

(2017) Christoph Hirche et al.   Cell Reports

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Chronic interleukin-1 exposure drives haematopoietic stem cells towards precocious myeloid differentiation at the expense of self-renewal

(2016) Eric M. Pietras et al.   NATURE CELL BIOLOGY

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

(2016) M Ryan Corces et al.   NATURE GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

CDK6 Levels Regulate Quiescence Exit in Human Hematopoietic Stem Cells

(2015) Elisa Laurenti et al.   Cell Stem Cell

Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation

(2015) Claire Mazumdar et al.   Cell Stem Cell

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

(2015) F. Notta et al.   SCIENCE

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

The unfolded protein response governs integrity of the haematopoietic stem-cell pool during stress

(2014) Peter van Galen et al.   NATURE

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

Chromatin state dynamics during blood formation

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

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment

(2013) Elisa Laurenti et al.   NATURE IMMUNOLOGY

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Isolation of Single Human Hematopoietic Stem Cells Capable of Long-Term Multilineage Engraftment

(2011) F. Notta et al.   SCIENCE

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

A Distinctive DNA Damage Response in Human Hematopoietic Stem Cells Reveals an Apoptosis-Independent Role for p53 in Self-Renewal

(2010) Michael Milyavsky et al.   Cell Stem Cell

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Hematopoietic Stem Cells Reversibly Switch from Dormancy to Self-Renewal during Homeostasis and Repair

(2008) Anne Wilson et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY