Mathematical approaches to modeling development and reprogramming

Statistical Mechanics of Pluripotency

(2013) Ben D. MacArthur et al.   CELL

Induction of Pluripotency in Mouse Somatic Cells with Lineage Specifiers

(2013) Jian Shu et al.   CELL

Reprogramming somatic cells to pluripotency: A fresh look at Yamanaka’s model

(2013) Yangxin Li et al.   CELL CYCLE

Understanding impediments to cellular conversion to pluripotency by assessing the earliest events in ectopic transcription factor binding to the genome

(2013) Abdenour Soufi et al.   CELL CYCLE

Deterministic direct reprogramming of somatic cells to pluripotency

(2013) Yoach Rais et al.   NATURE

Cancer stem cells: The challenges ahead

(2013) Jan Paul Medema   NATURE CELL BIOLOGY

Mechanisms and models of somatic cell reprogramming

(2013) Yosef Buganim et al.   NATURE REVIEWS GENETICS

Leveling Waddington: the emergence of direct programming and the loss of cell fate hierarchies

(2013) Julia Ladewig et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Origins and implications of pluripotent stem cell variability and heterogeneity

(2013) Patrick Cahan et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths

(2013) Chunhe Li et al.   PLoS Computational Biology

Cancer stem cell dynamics in tumor progression and metastasis: Is the microenvironment to blame?

(2012) Evelyn Fessler et al.   CANCER LETTERS

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Direct Reprogramming of Mouse and Human Fibroblasts into Multipotent Neural Stem Cells with a Single Factor

(2012) Karen L. Ring et al.   Cell Stem Cell

Direct Conversion of Fibroblasts into Stably Expandable Neural Stem Cells

(2012) Marc Thier et al.   Cell Stem Cell

Cancer Stem Cells: Current Status and Evolving Complexities

(2012) Jane E. Visvader et al.   Cell Stem Cell

Quasi-potential landscape in complex multi-stable systems

(2012) J. X. Zhou et al.   Journal of the Royal Society Interface

Lineage conversion methodologies meet the reprogramming toolbox

(2012) Ignacio Sancho-Martinez et al.   NATURE CELL BIOLOGY

Epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier

(2012) A. Watanabe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Predicting rates of cell state change caused by stochastic fluctuations using a data-driven landscape model

(2012) D. R. Sisan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Dynamical-Systems View of Stem Cell Biology

(2012) C. Furusawa et al.   SCIENCE

Highly Coordinated Proteome Dynamics during Reprogramming of Somatic Cells to Pluripotency

(2012) Jenny Hansson et al.   Cell Reports

Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells

(2011) Piyush B. Gupta et al.   CELL

Highly Efficient miRNA-Mediated Reprogramming of Mouse and Human Somatic Cells to Pluripotency

(2011) Frederick Anokye-Danso et al.   Cell Stem Cell

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Cells of origin in cancer

(2011) Jane E. Visvader   NATURE

Direct lineage conversions: unnatural but useful?

(2011) Thomas Vierbuchen et al.   NATURE BIOTECHNOLOGY

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

(2011)   NATURE BIOTECHNOLOGY

Conversion of mouse fibroblasts into cardiomyocytes using a direct reprogramming strategy

(2011) Jem A. Efe et al.   NATURE CELL BIOLOGY

miR-34 miRNAs provide a barrier for somatic cell reprogramming

(2011) Yong Jin Choi et al.   NATURE CELL BIOLOGY

Dedifferentiation, transdifferentiation and reprogramming: three routes to regeneration

(2011) Chris Jopling et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Direct reprogramming of mouse fibroblasts to neural progenitors

(2011) J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying the Waddington landscape and biological paths for development and differentiation

(2011) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stem cells and reprogramming: breaking the epigenetic barrier?

(2011) Yen-Sin Ang et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

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

(2010) Jin Wang et al.   BIOPHYSICAL JOURNAL

Functional Genomics Reveals a BMP-Driven Mesenchymal-to-Epithelial Transition in the Initiation of Somatic Cell Reprogramming

(2010) Payman Samavarchi-Tehrani et al.   Cell Stem Cell

A High Proliferation Rate Is Required for Cell Reprogramming and Maintenance of Human Embryonic Stem Cell Identity

(2010) Sergio Ruiz et al.   CURRENT BIOLOGY

First passage time distribution in stochastic processes with moving and static absorbing boundaries with application to biological rupture experiments

(2010) Zhonghan Hu et al.   JOURNAL OF CHEMICAL PHYSICS

Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network

(2010) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation of Induced Pluripotent Stem Cells from Human Cord Blood Using OCT4 and SOX2

(2009) Alessandra Giorgetti et al.   Cell Stem Cell

Elite and stochastic models for induced pluripotent stem cell generation

(2009) Shinya Yamanaka   NATURE

Direct cell reprogramming is a stochastic process amenable to acceleration

(2009) Jacob Hanna et al.   NATURE

Immortalization eliminates a roadblock during cellular reprogramming into iPS cells

(2009) Jochen Utikal et al.   NATURE

Reprogramming towards pluripotency requires AID-dependent DNA demethylation

(2009) Nidhi Bhutani et al.   NATURE

Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes

(2008) Trond Aasen et al.   NATURE BIOTECHNOLOGY

Generation of Pluripotent Stem Cells from Adult Mouse Liver and Stomach Cells

(2008) T. Aoi et al.   SCIENCE