How Computation Is Helping Unravel the Dynamics of Morphogenesis

Collaborative intelligence and gamification for on-line malaria species differentiation

(2019) María Linares et al.   MALARIA JOURNAL

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

(2019) Juan C. Caicedo et al.   CYTOMETRY PART A

MorphoNet: an interactive online morphological browser to explore complex multi-scale data

(2019) Bruno Leggio et al.   Nature Communications

Hemodynamic-mediated endocardial signaling controls in vivo myocardial reprogramming

(2019) Manuel Gálvez-Santisteban et al.   eLife

Visible Machine Learning for Biomedicine

(2018) Michael K. Yu et al.   CELL

Mechanical modeling of collective cell migration: An agent-based and continuum material approach

(2018) Ismael González-Valverde et al.   COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

A comparison of methods to assess cell mechanical properties

(2018) Pei-Hsun Wu et al.   NATURE METHODS

Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms

(2018) Tsung-Li Liu et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

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

(2018) James A. Briggs et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

The devil is in the mesoscale: Mechanical and behavioural heterogeneity in collective cell movement

(2018) Guy B. Blanchard et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos

(2018) Benjamin Schott et al.   PLoS Computational Biology

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems

(2018) Ahmadreza Ghaffarizadeh et al.   PLoS Computational Biology

Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

(2018) Carsten Wolff et al.   eLife

Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities

(2018) Marinka Zitnik et al.   Information Fusion

A fluid-to-solid jamming transition underlies vertebrate body axis elongation

(2018) Alessandro Mongera et al.   NATURE

Deep learning in biomedicine

(2018) Michael Wainberg et al.   NATURE BIOTECHNOLOGY

Active superelasticity in three-dimensional epithelia of controlled shape

(2018) Ernest Latorre et al.   NATURE

Comprehensive functional genomic resource and integrative model for the human brain

(2018) Daifeng Wang et al.   SCIENCE

Dynamic cellular finite-element method for modelling large-scale cell migration and proliferation under the control of mechanical and biochemical cues: a study of re-epithelialization

(2017) Jieling Zhao et al.   Journal of the Royal Society Interface

From morphogen to morphogenesis and back

(2017) Darren Gilmour et al.   NATURE

Quantifying forces in cell biology

(2017) Pere Roca-Cusachs et al.   NATURE CELL BIOLOGY

An objective comparison of cell-tracking algorithms

(2017) Vladimír Ulman et al.   NATURE METHODS

A guide to light-sheet fluorescence microscopy for multiscale imaging

(2017) Rory M Power et al.   NATURE METHODS

Inferring cellular forces from image stacks

(2017) Jim H. Veldhuis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Taking the strain: quantifying the contributions of all cell behaviours to changes in epithelial shape

(2017) Guy B. Blanchard   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mechanocellular models of epithelial morphogenesis

(2017) Alexander G. Fletcher et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Vertex models: from cell mechanics to tissue morphogenesis

(2017) Silvanus Alt et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Three-dimensional forces exerted by leukocytes and vascular endothelial cells dynamically facilitate diapedesis

(2017) Yi-Ting Yeh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation

(2017) Julien Delile et al.   Nature Communications

Cell-like pressure sensors reveal increase of mechanical stress towards the core of multicellular spheroids under compression

(2017) M. E. Dolega et al.   Nature Communications

Three-Dimensional Monolayer Stress Microscopy

(2016) Ricardo Serrano et al.   BIOPHYSICAL JOURNAL

Shape Transformations of Epithelial Shells

(2016) Mahim Misra et al.   BIOPHYSICAL JOURNAL

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

Measuring forces and stressesin situin living tissues

(2016) Kaoru Sugimura et al.   DEVELOPMENT

Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos

(2016) Johannes Stegmaier et al.   DEVELOPMENTAL CELL

EpiTools: An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics

(2016) Davide Heller et al.   DEVELOPMENTAL CELL

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

In vivo quantification of spatially varying mechanical properties in developing tissues

(2016) Friedhelm Serwane et al.   NATURE METHODS

Measuring cell-generated forces: a guide to the available tools

(2016) William J Polacheck et al.   NATURE METHODS

A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage

(2016) Emmanuel Faure et al.   Nature Communications

Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation

(2016) Keisuke Sako et al.   Cell Reports

Unipolar distributions of junctional Myosin II identify cell stripe boundaries that drive cell intercalation throughout Drosophila axis extension

(2016) Robert J Tetley et al.   eLife

Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy

(2016) Yicong Wu et al.   Optica

An integrated modelling framework from cells to organism based on a cohort of digital embryos

(2016) Paul Villoutreix et al.   Scientific Reports

Lagrangian Coherent Structures

(2015) George Haller   Annual Review of Fluid Mechanics

LBIBCell: a cell-based simulation environment for morphogenetic problems

(2015) Simon Tanaka et al.   BIOINFORMATICS

Non-straight cell edges are important to invasion and engulfment as demonstrated by cell mechanics model

(2015) Matthew C. Perrone et al.   Biomechanics and Modeling in Mechanobiology

From Discrete to Continuum Models of Three-Dimensional Deformations in Epithelial Sheets

(2015) Nebojsa Murisic et al.   BIOPHYSICAL JOURNAL

Emergent material properties of developing epithelial tissues

(2015) Pedro F. Machado et al.   BMC BIOLOGY

Colloquium: Mechanical formalisms for tissue dynamics

(2015) Sham Tlili et al.   EUROPEAN PHYSICAL JOURNAL E

Tissue patterning and cellular mechanics

(2015) Evan Heller et al.   JOURNAL OF CELL BIOLOGY

Lighting Up the Force: Investigating Mechanisms of Mechanotransduction Using Fluorescent Tension Probes

(2015) Carol Jurchenko et al.   MOLECULAR AND CELLULAR BIOLOGY

Apico-basal forces exerted by apoptotic cells drive epithelium folding

(2015) Bruno Monier et al.   NATURE

Deep learning

(2015) Yann LeCun et al.   NATURE

Embryo-scale tissue mechanics during Drosophila gastrulation movements

(2015) Matteo Rauzi et al.   Nature Communications

Unified quantitative characterization of epithelial tissue development

(2015) Boris Guirao et al.   eLife

Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results

(2015) P. Van Liedekerke et al.   Computational Particle Mechanics

Vertex Models of Epithelial Morphogenesis

(2014) Alexander G. Fletcher et al.   BIOPHYSICAL JOURNAL

Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation

(2014) Bing He et al.   NATURE

Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data

(2014) Fernando Amat et al.   NATURE METHODS

3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy

(2014) Liang Gao et al.   Nature Protocols

Bubbly vertex dynamics: A dynamical and geometrical model for epithelial tissues with curved cell shapes

(2014) Yukitaka Ishimoto et al.   PHYSICAL REVIEW E

CellFIT: A Cellular Force-Inference Toolkit Using Curvilinear Cell Boundaries

(2014) G. Wayne Brodland et al.   PLoS One

A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis

(2014) Carlos Castro-González et al.   PLoS Computational Biology

Forces in Tissue Morphogenesis and Patterning

(2013) Carl-Philipp Heisenberg et al.   CELL

Comparative study of non-invasive force and stress inference methods in tissue

(2013) S. Ishihara et al.   EUROPEAN PHYSICAL JOURNAL E

Apical contractility in growing epithelium supports robust maintenance of smooth curvatures against cell-division-induced mechanical disturbance

(2013) Satoru Okuda et al.   JOURNAL OF BIOMECHANICS

In vivo cardiac reprogramming contributes to zebrafish heart regeneration

(2013) Ruilin Zhang et al.   NATURE

Quantifying cell-generated mechanical forces within living embryonic tissues

(2013) Otger Campàs et al.   NATURE METHODS

Hydrodynamics of soft active matter

(2013) M. C. Marchetti et al.   REVIEWS OF MODERN PHYSICS

Imaging Morphogenesis: Technological Advances and Biological Insights

(2013) P. J. Keller   SCIENCE

A Model of Epithelial Invagination Driven by Collective Mechanics of Identical Cells

(2012) Ana Hočevar Brezavšček et al.   BIOPHYSICAL JOURNAL

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

(2012) Geoffrey Hinton et al.   IEEE SIGNAL PROCESSING MAGAZINE

$3D+t$ Morphological Processing: Applications to Embryogenesis Image Analysis

(2012) M. A. Luengo-Oroz et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Bayesian inference of force dynamics during morphogenesis

(2012) Shuji Ishihara et al.   JOURNAL OF THEORETICAL BIOLOGY

Live-cell delamination counterbalances epithelial growth to limit tissue overcrowding

(2012) Eliana Marinari et al.   NATURE

ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains

(2012) Olaf Ronneberger et al.   NATURE METHODS

Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy

(2012) Raju Tomer et al.   NATURE METHODS

Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model

(2012) Anja Voss-Böhme   PLoS One

Mechanisms of Regulating Cell Topology in Proliferating Epithelia: Impact of Division Plane, Mechanical Forces, and Cell Memory

(2012) Yingzi Li et al.   PLoS One

Physical Biology Returns to Morphogenesis

(2012) R. Keller   SCIENCE

Forces Driving Epithelial Spreading in Zebrafish Gastrulation

(2012) M. Behrndt et al.   SCIENCE

Mechanical Control of Morphogenesis by Fat/Dachsous/Four-Jointed Planar Cell Polarity Pathway

(2012) F. Bosveld et al.   SCIENCE

Mechanical Stress Inference for Two Dimensional Cell Arrays

(2012) Kevin K. Chiou et al.   PLoS Computational Biology

Force Generation, Transmission, and Integration during Cell and Tissue Morphogenesis

(2011) Thomas Lecuit et al.   Annual Review of Cell and Developmental Biology

Wavelet-based image fusion in multi-view three-dimensional microscopy

(2011) Jose L. Rubio-Guivernau et al.   BIOINFORMATICS

Advances in multiphoton microscopy for imaging embryos

(2011) Willy Supatto et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Measuring the multi-scale integration of mechanical forces during morphogenesis

(2011) Guy B Blanchard et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A complex choreography of cell movements shapes the vertebrate eye

(2011) K. M. Kwan et al.   DEVELOPMENT

Biomechanical regulation of contractility: spatial control and dynamics

(2011) Romain Levayer et al.   TRENDS IN CELL BIOLOGY

Cell Flow Reorients the Axis of Planar Polarity in the Wing Epithelium of Drosophila

(2010) Benoît Aigouy et al.   CELL

Exploring the effects of mechanical feedback on epithelial topology

(2010) T. Aegerter-Wilmsen et al.   DEVELOPMENT

Mechanical control of tissue and organ development

(2010) T. Mammoto et al.   DEVELOPMENT

Video force microscopy reveals the mechanics of ventral furrow invagination in Drosophila

(2010) G. W. Brodland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy

(2010) N. Olivier et al.   SCIENCE

Combining Laser Microsurgery and Finite Element Modeling to Assess Cell-Level Epithelial Mechanics

(2009) M. Shane Hutson et al.   BIOPHYSICAL JOURNAL

Live Cells Exert 3-Dimensional Traction Forces on Their Substrata

(2009) Sung Sik Hur et al.   Cellular and Molecular Bioengineering

Increased Cell Bond Tension Governs Cell Sorting at the Drosophila Anteroposterior Compartment Boundary

(2009) Katharina P. Landsberg et al.   CURRENT BIOLOGY

Multi-scale mechanics from molecules to morphogenesis

(2009) Lance Davidson et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation

(2009) Guy B Blanchard et al.   NATURE METHODS

Physical forces during collective cell migration

(2009) Xavier Trepat et al.   Nature Physics

The role of fluctuations and stress on the effective viscosity of cell aggregates

(2009) P. Marmottant et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Individual-based and continuum models of growing cell populations: a comparison

(2008) Helen Byrne et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Tensile forces govern germ-layer organization in zebrafish

(2008) M. Krieg et al.   NATURE CELL BIOLOGY

Nature and anisotropy of cortical forces orienting Drosophila tissue morphogenesis

(2008) Matteo Rauzi et al.   NATURE CELL BIOLOGY

Mechanotransduction in development: a growing role for contractility

(2008) Michele A. Wozniak et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A 3D finite element model of ventral furrow invagination in the Drosophila melanogaster embryo

(2007) V CONTE et al.   Journal of the Mechanical Behavior of Biomedical Materials