Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions

Understanding axial progenitor biology in vivo and in vitro

(2021) Filip J. Wymeersch et al.   DEVELOPMENT

Quantifying cell transitions in C. elegans with data-fitted landscape models

(2021) Elena Camacho-Aguilar et al.   PLoS Computational Biology

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

Human organoids: model systems for human biology and medicine

(2020) Jihoon Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation

(2018) Vicki Metzis et al.   CELL

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Self-organized Notch dynamics generate stereotyped sensory organ patterns inDrosophila

(2017) Francis Corson et al.   SCIENCE

Gene-free methodology for cell fate dynamics during development

(2017) Francis Corson et al.   eLife

Induced pluripotent stem cell technology: a decade of progress

(2016) Yanhong Shi et al.   NATURE REVIEWS DRUG DISCOVERY

Cdx and T Brachyury Co-activate Growth Signaling in the Embryonic Axial Progenitor Niche

(2016) Shilu Amin et al.   Cell Reports

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

Neuromesodermal progenitors and the making of the spinal cord

(2015) D. Henrique et al.   DEVELOPMENT

Distinct Wnt-driven primitive streak-like populations reflect in vivo lineage precursors

(2014) A. Tsakiridis et al.   DEVELOPMENT

In Vitro Generation of Neuromesodermal Progenitors Reveals Distinct Roles for Wnt Signalling in the Specification of Spinal Cord and Paraxial Mesoderm Identity

(2014) Mina Gouti et al.   PLOS BIOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Geometry, epistasis, and developmental patterning

(2012) F. Corson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Sui Huang   BIOESSAYS

Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells

(2011) Tatsuya Takemoto et al.   NATURE

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

Stem Cell States, Fates, and the Rules of Attraction

(2009) Tariq Enver et al.   Cell Stem Cell

Klf4 reverts developmentally programmed restriction of ground state pluripotency

(2009) G. Guo et al.   DEVELOPMENT

Systems biology of stem cell fate and cellular reprogramming

(2009) Ben D. MacArthur et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Statistical mixture modeling for cell subtype identification in flow cytometry

(2008) Cliburn Chan et al.   CYTOMETRY PART A

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Novel Effectors of Directed and Ngn3-Mediated Differentiation of Mouse Embryonic Stem Cells into Endocrine Pancreas Progenitors

(2007) Ioannis Serafimidis et al.   STEM CELLS