Cell Fate Decision as High-Dimensional Critical State Transition

Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots

(2016) Carsten Marr et al.   CURRENT OPINION IN BIOTECHNOLOGY

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Critical transitions in chronic disease: transferring concepts from ecology to systems medicine

(2015) Christophe Trefois et al.   CURRENT OPINION IN BIOTECHNOLOGY

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

(2015) Jong Kyoung Kim et al.   Nature Communications

Towards elucidating the connection between epithelial-mesenchymal transitions and stemness

(2014) M. K. Jolly et al.   Journal of the Royal Society Interface

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Bistability, Bifurcations, and Waddington's Epigenetic Landscape

(2012) James E. Ferrell   CURRENT BIOLOGY

Corrigendum: Recovery rates reflect distance to a tipping point in a living system

(2012) Annelies J. Veraart et al.   NATURE

Inferring rules of lineage commitment in haematopoiesis

(2012) Cristina Pina et al.   NATURE CELL BIOLOGY

A Dynamical-Systems View of Stem Cell Biology

(2012) C. Furusawa et al.   SCIENCE

Anticipating Critical Transitions

(2012) M. Scheffer et al.   SCIENCE

Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers

(2012) Luonan Chen et al.   Scientific Reports

Mathematical modelling of stem cell differentiation: the PU.1–GATA-1 interaction

(2011) Campbell Duff et al.   JOURNAL OF MATHEMATICAL BIOLOGY

The ground state of pluripotency

(2010) Jason Wray et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

(2010) Jin Wang et al.   BIOPHYSICAL JOURNAL

Correlations, risk and crisis: From physiology to finance

(2010) Alexander N. Gorban et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Understanding gene circuits at cell-fate branch points for rational cell reprogramming

(2010) Joseph X. Zhou et al.   TRENDS IN GENETICS

Developmental biology: Instructions writ in blood

(2009) Tariq Enver et al.   NATURE

Early-warning signals for critical transitions

(2009) Marten Scheffer et al.   NATURE

A Continuum of Cell States Spans Pluripotency and Lineage Commitment in Human Embryonic Stem Cells

(2009) Shelley R. Hough et al.   PLoS One

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

A Computational Model for Understanding Stem Cell, Trophectoderm and Endoderm Lineage Determination

(2008) Vijay Chickarmane et al.   PLoS One