Recognition and reconstruction of cell differentiation patterns with deep learning

Adjusting the range of cell–cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing

(2023) Simon Schardt et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Cell-cell communication through FGF4 generates and maintains robust proportions of differentiated cell types in embryonic stem cells

(2021) Dhruv Raina et al.   DEVELOPMENT

The transition from local to global patterns governs the differentiation of mouse blastocysts

(2020) Sabine C. Fischer et al.   PLoS One

Automated Design of Pluripotent Stem Cell Self-Organization

(2019) Ashley R.G. Libby et al.   Cell Systems

Blastocyst-like structures generated solely from stem cells

(2018) Nicolas C. Rivron et al.   NATURE

Mouse ICM Organoids Reveal Three-Dimensional Cell Fate Clustering

(2018) Biena Mathew et al.   BIOPHYSICAL JOURNAL

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids

(2017) Alexander Schmitz et al.   Scientific Reports

Cell Fate Specification Based on Tristability in the Inner Cell Mass of Mouse Blastocysts

(2016) Laurane De Mot et al.   BIOPHYSICAL JOURNAL

Asynchronous fate decisions by single cells collectively ensure consistent lineage composition in the mouse blastocyst

(2016) Néstor Saiz et al.   Nature Communications

Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories

(2015) Douglas E. White et al.   Integrative Biology

Gata6, Nanog and Erk signaling control cell fate in the inner cell mass through a tristable regulatory network

(2014) S. Bessonnard et al.   DEVELOPMENT

Pattern recognition in bioinformatics

(2013) D. de Ridder et al.   BRIEFINGS IN BIOINFORMATICS

Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling

(2013) Douglas E. White et al.   PLoS Computational Biology

FGF4 is required for lineage restriction and salt-and-pepper distribution of primitive endoderm factors but not their initial expression in the mouse

(2012) M. Kang et al.   DEVELOPMENT

Two-dimensional spatial patterning in developmental systems

(2012) Keiko U. Torii   TRENDS IN CELL BIOLOGY

Pattern Recognition Software and Techniques for Biological Image Analysis

(2010) Lior Shamir et al.   PLoS Computational Biology

The Graph Neural Network Model

(2008) F. Scarselli et al.   IEEE TRANSACTIONS ON NEURAL NETWORKS