3.8 Article

Mechanistic models of cell-fate transitions from single-cell data

Related references

Note: Only part of the references are listed.
Review Biotechnology & Applied Microbiology

The Importance of Computational Modeling in Stem Cell Research

Antonio del Sol et al.

Summary: The generation of omics data has enabled the development of computational models in stem cell research. Single-cell technologies provide the framework for addressing challenges in the field and guiding the design of new strategies for stem cell therapies.

TRENDS IN BIOTECHNOLOGY (2021)

Article Multidisciplinary Sciences

A rationally engineered decoder of transient intracellular signals

Claude Lormeau et al.

Summary: Cells encode information by modulating signal dynamics. Researchers developed a synthetic short-pulse decoder in yeast using TopoDesign tool, demonstrating the principles for decoding short signals.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

Susanne C. van den Brink et al.

NATURE (2020)

Article Biochemical Research Methods

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

Aditya Pratapa et al.

NATURE METHODS (2020)

Review Cell Biology

A Dynamical Paradigm for Molecular Cell Biology

John J. Tyson et al.

TRENDS IN CELL BIOLOGY (2020)

Article Multidisciplinary Sciences

Multistable and dynamic CRISPRi-based synthetic circuits

Javier Santos-Moreno et al.

NATURE COMMUNICATIONS (2020)

Review Biotechnology & Applied Microbiology

Eleven grand challenges in single-cell data science

David Laehnemann et al.

GENOME BIOLOGY (2020)

Article Multidisciplinary Sciences

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH

Chee-Huat Linus Eng et al.

NATURE (2019)

Article Multidisciplinary Sciences

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

Samuel G. Rodriques et al.

SCIENCE (2019)

Article Multidisciplinary Sciences

The emergent landscape of the mouse gut endoderm at single-cell resolution

Sonja Nowotschin et al.

NATURE (2019)

Review Cell Biology

Self-Organization in Pattern Formation

Francois Schweisguth et al.

DEVELOPMENTAL CELL (2019)

Article Biochemical Research Methods

High-definition spatial transcriptomics for in situ tissue profiling

Sanja Vickovic et al.

NATURE METHODS (2019)

Article Multidisciplinary Sciences

Drugs modulating stochastic gene expression affect the erythroid differentiation process

Anissa Guillemin et al.

PLOS ONE (2019)

Article Multidisciplinary Sciences

Massive computational acceleration by using neural networks to emulate mechanism-based biological models

Shangying Wang et al.

NATURE COMMUNICATIONS (2019)

Article Physics, Multidisciplinary

Guiding self-organized pattern formation in cell polarity establishment

Peter Gross et al.

NATURE PHYSICS (2019)

Article Multidisciplinary Sciences

Maximizing the information learned from finite data selects a simple model

Henry H. Mattingly et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

James A. Briggs et al.

SCIENCE (2018)

Article Multidisciplinary Sciences

Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

Leonardo Beccari et al.

NATURE (2018)

Article History & Philosophy Of Science

THE TENSION BETWEEN BIG DATA AND THEORY IN THE OMICS ERA OF BIOMEDICAL RESEARCH

Sui Huang

PERSPECTIVES IN BIOLOGY AND MEDICINE (2018)

Article Multidisciplinary Sciences

A living mesoscopic cellular automaton made of skin scales

Liana Manukyan et al.

NATURE (2017)

Article Multidisciplinary Sciences

Self-organized Notch dynamics generate stereotyped sensory organ patterns in Drosophila

Francis Corson et al.

SCIENCE (2017)

Article Biochemistry & Molecular Biology

Stem Cell Differentiation as a Non-Markov Stochastic Process

Patrick S. Stumpf et al.

CELL SYSTEMS (2017)

Article Biophysics

Untangling the Hairball: Fitness-Based Asymptotic Reduction of Biological Networks

Felix Proulx-Giraldeau et al.

BIOPHYSICAL JOURNAL (2017)

Review Genetics & Heredity

Transition states and cell fate decisions in epigenetic landscapes

Naomi Moris et al.

NATURE REVIEWS GENETICS (2016)

Article Biochemistry & Molecular Biology

Cell Fate Decision as High-Dimensional Critical State Transition

Mitra Mojtahedi et al.

PLOS BIOLOGY (2016)

Article Developmental Biology

Positional information and reaction-diffusion: two big ideas in developmental biology combine

Jeremy B. A. Green et al.

DEVELOPMENT (2015)

Article Developmental Biology

Mathematically guided approaches to distinguish models of periodic patterning

Tom W. Hiscock et al.

DEVELOPMENT (2015)

Article Multidisciplinary Sciences

Stem cell differentiation as a many-body problem

Bin Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Topological sensitivity analysis for systems biology

Ann C. Babtie et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemistry & Molecular Biology

Statistical Mechanics of Pluripotency

Ben D. MacArthur et al.

Article Multidisciplinary Sciences

Circuit-level input integration in bacterial gene regulation

Lorena Espinar et al.

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

Review Biochemistry & Molecular Biology

Bistability, Bifurcations, and Waddington's Epigenetic Landscape

James E. Ferrell

CURRENT BIOLOGY (2012)

Article Cell Biology

Towards a statistical mechanics of cell fate decisions

Jordi Garcia-Ojalvo et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2012)

Review Multidisciplinary Sciences

Functional roles for noise in genetic circuits

Avigdor Eldar et al.

NATURE (2010)

Article Biophysics

Parameter inference for biochemical systems that undergo a Hopf bifurcation

Paul D. W. Kirk et al.

BIOPHYSICAL JOURNAL (2008)

Review Biology

Models of stochastic gene expression

Johan Paulsson

PHYSICS OF LIFE REVIEWS (2005)

Article Physics, Multidisciplinary

Cell fates as high-dimensional attractor states of a complex gene regulatory network

S Huang et al.

PHYSICAL REVIEW LETTERS (2005)

Article Multidisciplinary Sciences

Stochastic gene expression in a single cell

MB Elowitz et al.

SCIENCE (2002)