Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells

Cancer progression as a learning process

(2022) Aseel Shomar et al.   iScience

Pioneer factors as master regulators of the epigenome and cell fate

(2022) Aurelio Balsalobre et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic and thermodynamic models of adaptation

(2021) A.N. Gorban et al.   Physics of Life Reviews

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

CALISTA: Clustering and LINEAGE Inference in Single-Cell Transcriptional Analysis

(2020) Nan Papili Gao et al.   Frontiers in Bioengineering and Biotechnology

Pioneer Transcription Factors Initiating Gene Network Changes

(2020) Kenneth S. Zaret   Annual Review of Genetics

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

(2020) Naoya Takayama et al.   Cell Stem Cell

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

Constraints on Human CD34+ Cell Fate due to Lentiviral Vectors Can Be Relieved by Valproic Acid

(2019) Alice Moussy et al.   HUMAN GENE THERAPY

The interplay of chromatin and transcription factors during cell fate transitions in development and reprogramming

(2019) Georgina Peñalosa-Ruiz et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output

(2018) Aydan Bulut-Karslioglu et al.   Cell Stem Cell

Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α

(2018) Sinan Kilic et al.   Nature Communications

Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation

(2017) Kyong-Rim Kieffer-Kwon et al.   MOLECULAR CELL

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

DNA Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells

(2017) Tsukasa Sanosaka et al.   Cell Reports

Integrated time-lapse and single-cell transcription studies highlight the variable and dynamic nature of human hematopoietic cell fate commitment

(2017) Alice Moussy et al.   PLOS BIOLOGY

FANTOM5 CAGE profiles of human and mouse samples

(2017) Shuhei Noguchi et al.   Scientific Data

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

(2016) M Ryan Corces et al.   NATURE GENETICS

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

Systemic epigenetic response to recombinant lentiviral vectors independent of proviral integration

(2016) Tamas Aranyi et al.   Epigenetics & Chromatin

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process

(2016) Angélique Richard et al.   PLOS BIOLOGY

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

The unforeseen challenge: from genotype-to-phenotype in cell populations

(2015) Erez Braun   REPORTS ON PROGRESS IN PHYSICS

Primed and ready: understanding lineage commitment through single cell analysis

(2015) Rachael A. Nimmo et al.   TRENDS IN CELL BIOLOGY

Transcriptional network control of normal and leukaemic haematopoiesis

(2014) Jonathan I. Sive et al.   EXPERIMENTAL CELL RESEARCH

Epigenetic reprogramming induces the expansion of cord blood stem cells

(2014) Pratima Chaurasia et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2014) D. A. Jaitin et al.   SCIENCE

Correlated Spatio-Temporal Fluctuations in Chromatin Compaction States Characterize Stem Cells

(2013) Shefali Talwar et al.   BIOPHYSICAL JOURNAL

Epigenetics: Core misconcept

(2013) M. Ptashne   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Inferring rules of lineage commitment in haematopoiesis

(2012) Cristina Pina et al.   NATURE CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

What makes the cell differentiate?

(2012) Andras Paldi   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

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

(2011) Sui Huang   BIOESSAYS

Systems biology of stem cells: three useful perspectives to help overcome the paradigm of linear pathways

(2011) S. Huang   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin

(2010) Rolf Ohlsson et al.   CHROMOSOMA

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

Fundamental limits on the suppression of molecular fluctuations

(2010) Ioannis Lestas et al.   NATURE

Cell Lineage Determination in State Space: A Systems View Brings Flexibility to Dogmatic Canonical Rules

(2010) Sui Huang   PLOS BIOLOGY

Non-genetic heterogeneity of cells in development: more than just noise

(2009) S. Huang   DEVELOPMENT

Early-warning signals for critical transitions

(2009) Marten Scheffer et al.   NATURE

A new paradigm for hematopoietic cell lineages: revision of the classical concept of the myeloid–lymphoid dichotomy

(2009) Hiroshi Kawamoto et al.   TRENDS IN IMMUNOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS