Stem cells expand potency and alter tissue fitness by accumulating diverse epigenetic memories

Inflammatory adaptation in barrier tissues

(2021) Rachel E. Niec et al.   CELL

Establishment, maintenance, and recall of inflammatory memory

(2021) Samantha B. Larsen et al.   Cell Stem Cell

C/EBPβ-Dependent Epigenetic Memory Induces Trained Immunity in Hematopoietic Stem Cells

(2020) Bérengère de Laval et al.   Cell Stem Cell

NFI transcription factors provide chromatin access to maintain stem cell identity while preventing unintended lineage fate choices

(2020) Rene C. Adam et al.   NATURE CELL BIOLOGY

Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics

(2020) Daniel Haensel et al.   Cell Reports

Trained immunity, tolerance, priming and differentiation: distinct immunological processes

(2020) Maziar Divangahi et al.   NATURE IMMUNOLOGY

The Role of the Bone Marrow Microenvironment in the Response to Infection

(2020) Courtney B. Johnson et al.   Frontiers in Immunology

Multifunctional Roles of the Actin-Binding Protein Flightless I in Inflammation, Cancer and Wound Healing

(2020) Xanthe L. Strudwick et al.   Frontiers in Cell and Developmental Biology

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Stem cell–driven lymphatic remodeling coordinates tissue regeneration

(2019) Shiri Gur-Cohen et al.   SCIENCE

Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression

(2018) Rene C. Adam et al.   Cell Stem Cell

Stretching the limits: from homeostasis to stem cell plasticity in wound healing and cancer

(2018) Yejing Ge et al.   NATURE REVIEWS GENETICS

Epigenetic control of innate and adaptive immune memory

(2018) Colleen M. Lau et al.   NATURE IMMUNOLOGY

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection

(2017) Thomas Vierbuchen et al.   MOLECULAR CELL

Inflammatory memory sensitizes skin epithelial stem cells to tissue damage

(2017) Shruti Naik et al.   NATURE

Tissue-scale coordination of cellular behaviour promotes epidermal wound repair in live mice

(2017) Sangbum Park et al.   NATURE CELL BIOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Defining stem cell dynamics and migration during wound healing in mouse skin epidermis

(2017) Mariaceleste Aragona et al.   Nature Communications

Impaired Epidermal to Dendritic T Cell Signaling Slows Wound Repair in Aged Skin

(2016) Brice E. Keyes et al.   CELL

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

(2016) Simon Joost et al.   Cell Systems

Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice

(2015) Rene C. Adam et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Distinct Functions for Wnt/β-Catenin in Hair Follicle Stem Cell Proliferation and Survival and Interfollicular Epidermal Homeostasis

(2013) Yeon Sook Choi et al.   Cell Stem Cell

The Epidermis Comprises Autonomous Compartments Maintained by Distinct Stem Cell Populations

(2013) Mahalia E. Page et al.   Cell Stem Cell

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

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

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Identification of Stem Cell Populations in Sweat Glands and Ducts Reveals Roles in Homeostasis and Wound Repair

(2012) Catherine P. Lu et al.   CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Rapid functional dissection of genetic networks via tissue-specific transduction and RNAi in mouse embryos

(2010) Slobodan Beronja et al.   NATURE MEDICINE

A Two-Step Mechanism for Stem Cell Activation during Hair Regeneration

(2009) Valentina Greco et al.   Cell Stem Cell

Stem Cells and Niches: Mechanisms That Promote Stem Cell Maintenance throughout Life

(2008) Sean J. Morrison et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY