4.6 Review

Generative models of morphogenesis in developmental biology

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Multidisciplinary Sciences

Sculpting tissues by phase transitions

Pierre-Francois Lenne et al.

Summary: Biological systems exhibit phase transitions similar to solid, liquid, and gas states, which play important roles in biological processes and disease development. Interactions and microscopic properties between cells result in macroscopic properties, and emerging technologies can assist in understanding the structure and behavior of biological tissues.

NATURE COMMUNICATIONS (2022)

Article Biochemical Research Methods

A deep generative model of 3D single-cell organization

Rory M. Donovan-Maiye et al.

Summary: We propose a framework for integrative modeling of 3D single-cell multi-channel fluorescent image data, allowing for the representation and localization of diverse subcellular structures. Our model utilizes stacked conditional beta-variational autoencoders to learn latent representations of cell morphology and subcellular structure localization. It is capable of training on different subcellular structures with varying sparsity and reconstruction fidelity. The trained model can predict plausible locations of structures in cells that were not imaged, as well as quantify the variation in the location of subcellular structures. We demonstrate the applicability of our model to new data in a small drug perturbation screen, showing expected differences in the latent representations of drugged and unperturbed cells.

PLOS COMPUTATIONAL BIOLOGY (2022)

Article Biology

Chemotactic smoothing of collective migration

Tapomoy Bhattacharjee et al.

Summary: Collective migration, a fascinating behavior in active matter, has functional implications for biological systems. This study investigates how bacterial populations persist in migration despite perturbations. The researchers discover that the bacteria autonomously smooth out large-scale perturbations by adjusting their ability to sense and respond to the local nutrient gradient, enabling them to continue migrating together.
Review Cell & Tissue Engineering

Synthetic developmental biology: Engineering approaches to guide multicellular organization

Ibrahim Zarkesh et al.

Summary: Synthetic developmental biology is a multidisciplinary concept that utilizes engineering approaches to guide the self-organization of multicellular tissues. Organoids are 3D structures developed in vitro that display important aspects of their in vivo counterparts and are generated through a self-organization process from pluripotent or tissue-specific stem cells. This review introduces a novel classification of engineering approaches based on the extent of microenvironmental manipulation applied to organoids. The authors also discuss how engineering tools can help overcome current limitations in organoid construction.

STEM CELL REPORTS (2022)

Review Biochemistry & Molecular Biology

Human organoids: New strategies and methods for analyzing human development and disease

Nina S. Corsini et al.

Summary: For a long time, animal models have been the primary means of gaining insight into the fundamental principles of human biology and disease. However, due to species differences, some developmental and disease mechanisms have been challenging to study. The advent of organoid technology over a decade ago has provided a new model system to investigate human-specific aspects of biology. The use of human 3D organoids, along with advancements in single-cell technologies, has revealed unprecedented insights into human biology and disease mechanisms.
Review Biophysics

Marangoni effect and cell spreading

Ivana Pajic-Lijakovic et al.

Summary: Cells are sensitive to shear stress, which is generated during physiological processes such as collective cell migration and has an impact on biological processes. The Marangoni effect, induced by the gradient of tissue surface tension, leads to directional cell migration and cell sorting. This phenomenon has been observed in both epithelial cell monolayers and mixed cell monolayers. The Marangoni effect results in the intensive spreading of cancer cells in epithelium.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2022)

Article Multidisciplinary Sciences

Cell clusters adopt a collective amoeboid mode of migration in confined nonadhesive environments

Diane-Laure Pages et al.

Summary: Cell migration is a fundamental process in living organisms and its deregulation is associated with cancer. This study reveals that cancer cell clusters can migrate without focal adhesions when confined into nonadhesive microfabricated channels. These clusters behave like giant super cells, mobilizing their contractility to power their migration. This collective amoeboid mode of migration could facilitate metastatic spread by allowing cells to cross various environments.

SCIENCE ADVANCES (2022)

Article Computer Science, Artificial Intelligence

Learning biophysical determinants of cell fate with deep neural networks

Christopher J. Soelistyo et al.

Summary: Researchers have developed a machine learning approach that can learn the mechanisms behind cell fate and competition from large microscopy datasets. They have created a model that predicts cell fate and discovered that cell density is the most important factor in determining cell fate. Additionally, they have developed a discriminator network that can identify abnormal behavior, paving the way for mechanism-aware drug screening.

NATURE MACHINE INTELLIGENCE (2022)

Article Physics, Multidisciplinary

Curvature strains as a global orchestrator of morphogenesis

Julius B. Kirkegaard

Summary: Successful morphogenesis requires strict coordination between cells and correct cell intercalation to achieve shape formation.

PHYSICAL REVIEW RESEARCH (2022)

Review Cell Biology

Jamming and arrest of cell motion in biological tissues

Elizabeth Lawson-Keister et al.

Summary: Collective cell motility is crucial in biological processes, with the term 'cell jamming' used to describe the collective arrest of cell motion, driven by mechanisms such as crowding, tension-driven rigidity, and reduction of fluctuations. The review emphasizes the need to identify the dominant mechanism in a given situation, as multiple mechanisms may be operating simultaneously, and discusses how specific biological processes at cell and molecular scales control these physical mechanisms.

CURRENT OPINION IN CELL BIOLOGY (2021)

Review Computer Science, Artificial Intelligence

Normalizing Flows: An Introduction and Review of Current Methods

Ivan Kobyzev et al.

Summary: Normalizing Flows are generative models that can produce tractable distributions, enabling efficient and accurate sampling and density evaluation. This survey article aims to provide a coherent and comprehensive review of the literature on the construction and use of Normalizing Flows for distribution learning, offering context and explanation of the models, reviewing current state-of-the-art literature, and identifying open questions and promising future directions.

IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE (2021)

Article Mechanics

Augmenting physical models with deep networks for complex dynamics forecasting

Yuan Yin et al.

Summary: This paper presents a framework, named APHYNITY, which combines incomplete physical dynamics with deep data-driven models to accurately forecast complex dynamical phenomena and correctly identify relevant physical parameters.

JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT (2021)

Article Biology

Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis

Lotta Hof et al.

Summary: The study conducted a multiscale analysis of organoids, quantifying organoid behavior at the single-cell, individual-organoid, and entire-culture levels. The research provided a systematic picture of the diversity of cell organization in organoids, identifying and quantifying the core regulatory principles of organoid morphogenesis.

BMC BIOLOGY (2021)

Article Developmental Biology

Evolution of organoid technology: Lessons learnt in Co-Culture systems from developmental biology

Ensieh Zahmatkesh et al.

Summary: The development of 3D organoids has opened up new avenues for research in development, physiology, and regenerative medicine. Knowledge of developmental biology helps refine organoids into a more sophisticated platform. Co-culture systems in organoid technology provide highly physiologically relevant systems, with supportive cells facilitating organoid assembly and vascularization.

DEVELOPMENTAL BIOLOGY (2021)

Article Biochemical Research Methods

Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms

Mohammed AlQuraishi et al.

Summary: The perspective discusses the concept of 'differentiable biology' which uses machine-learnable models based on differentiable programs to effectively model biological phenomena. By exploiting knowledge about basic natural phenomena, it overcomes the challenges of sparse, incomplete, and noisy data, benefiting fields such as biophysics and functional genomics. The integration of deep learning with traditional knowledge-based modeling in biological sciences is described as a way to address the challenges of modeling experimental data.

NATURE METHODS (2021)

Review Engineering, Biomedical

Engineering Vascularized Organoid-on-a-Chip Models

Venktesh S. Shirure et al.

Summary: The technology of vascularized organoids is rapidly advancing, with the key goal of reproducing specific organ functions and simulating tumor progression. Vascularization is not only a critical component of individual organ function, but also responsible for linking the fate of all organs and their functions.

ANNUAL REVIEW OF BIOMEDICAL ENGINEERING, VOL 23, 2021 (2021)

Article Biophysics

Glass-like characteristics of intracellular motion in human cells

Christoffer Aberg et al.

Summary: Research indicates that in human cells, objects transported by motor proteins exhibit motion characteristics similar to those in glassy systems, such as heterogeneity, non-ergodicity, and the decoupling of exchange and persistence times at short length scales.

BIOPHYSICAL JOURNAL (2021)

Review Biochemistry & Molecular Biology

Bioelectric signaling: Reprogrammable circuits underlying embryogenesis, regeneration, and cancer

Michael Levin

Summary: Recent advancements in analyzing developmental bioelectric circuits and channelopathies have shed light on the cooperation of cellular collectives towards achieving organ-level structural order. These progressions open up possibilities for utilizing bioelectric signaling in interventions related to developmental disorders, regenerative medicine, cancer reprogramming, and synthetic bioengineering.
Article Nanoscience & Nanotechnology

Effect of biochemical and biomechanical factors on vascularization of kidney organoid-on-a-chip

Han Na Lee et al.

Summary: By mimicking shear stress fluid flow and optimizing extracellular matrix conditions, our kidney organoid-on-a-chip system showed more mature podocytes and vascular structures compared to static culture, with increased sensitivity to nephrotoxic drugs. Physiological flow was demonstrated to play a crucial role in maintaining various physiological functions of kidney organoids.

NANO CONVERGENCE (2021)

Review Engineering, Biomedical

Biomechanics of cells and subcellular components: A comprehensive review of computational models and applications

Chengyuan Wang et al.

Summary: Computational biomechanical models for cells have made significant progress but still face challenges. This review summarizes cellular components at different spatial levels and offers insights into future directions.

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING (2021)

Article Biochemistry & Molecular Biology

Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma

Assaf Zaritsky et al.

Summary: The study utilized a generative neural network and supervised machine learning to classify the metastatic efficiency of melanoma cells, revealing characteristic features of metastatic cells and validating these findings with live cell observations. It demonstrates how artificial intelligence can aid in identifying cell properties predictive of complex phenotypes and integrated cell functions that may be subtle and difficult for human experts to identify in raw imagery.

CELL SYSTEMS (2021)

Review Developmental Biology

Are cell jamming and unjamming essential in tissue development?

Lior Atia et al.

Summary: Recent evidence supports the transition of multicellular tissue from a jammed phase to an unjammed phase, impacting tissue homeostasis and developmental dynamics. The gradual departure from a jammed phase may enable controlled malleability required in development.

CELLS & DEVELOPMENT (2021)

Article Multidisciplinary Sciences

Mining gold from implicit models to improve likelihood-free inference

Johann Brehmer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

The frontier of simulation-based inference

Kyle Cranmer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Physics, Multidisciplinary

Unveiling the predictive power of static structure in glassy systems

V Bapst et al.

NATURE PHYSICS (2020)

Article Biotechnology & Applied Microbiology

Toward Engineering Biosystems With Emergent Collective Functions

Thomas E. Gorochowski et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

Article Computer Science, Artificial Intelligence

Towards explainable deep neural networks (xDNN)

Plamen Angelov et al.

NEURAL NETWORKS (2020)

Article Multidisciplinary Sciences

Engineering synthetic morphogen systems that can program multicellular patterning

Satoshi Toda et al.

SCIENCE (2020)

Review Physics, Applied

Computational models for active matter

M. Reza Shaebani et al.

NATURE REVIEWS PHYSICS (2020)

Review Biochemical Research Methods

Deep learning for cellular image analysis

Erick Moen et al.

NATURE METHODS (2019)

Article Physics, Condensed Matter

Physical Models of Collective Cell Migration

Ricard Alert et al.

Annual Review of Condensed Matter Physics (2019)

Review Genetics & Heredity

Mathematical Models of Organoid Cultures

Sandra Montes-Olivas et al.

FRONTIERS IN GENETICS (2019)

Article Chemistry, Physical

Collective motion of active Brownian particles with polar alignment

Aitor Martin-Gomez et al.

SOFT MATTER (2018)

Article Multidisciplinary Sciences

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

Alessandro Mongera et al.

NATURE (2018)

Article Cell Biology

From pattern to process: studies at the interface of gene regulatory networks, morphogenesis, and evolution

Sarah Jacquelyn Smith et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2018)

Review Cell Biology

Machine learning applications in cell image analysis

Andrey Kan

IMMUNOLOGY AND CELL BIOLOGY (2017)

Article Chemistry, Physical

Cell division and death inhibit glassy behaviour of confluent tissues

D. A. Matoz-Fernandez et al.

SOFT MATTER (2017)

Article Multidisciplinary Sciences

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

Julien Delile et al.

NATURE COMMUNICATIONS (2017)

Article Biochemical Research Methods

Active Vertex Model for cell-resolution description of epithelial tissue mechanics

Daniel L. Barton et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Computer Science, Interdisciplinary Applications

celIGPU: Massively parallel simulations of dynamic vertex models

Daniel M. Sussman

COMPUTER PHYSICS COMMUNICATIONS (2017)

Review Chemistry, Physical

Minimal model of active colloids highlights the role of mechanical interactions in controlling the emergent behavior of active matter

M. Cristina Marchetti et al.

CURRENT OPINION IN COLLOID & INTERFACE SCIENCE (2016)

Article Multidisciplinary Sciences

Emergent structures and dynamics of cell colonies by contact inhibition of locomotion

Bart Smeets et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Multidisciplinary Sciences

The fin-to-limb transition as the re-organization of a Turing pattern

Koh Onimaru et al.

NATURE COMMUNICATIONS (2016)

Article Chemistry, Physical

Unjamming and cell shape in the asthmatic airway epithelium

Jin-Ah Park et al.

NATURE MATERIALS (2015)

Article Physics, Multidisciplinary

A density-independent rigidity transition in biological tissues

Dapeng Bi et al.

NATURE PHYSICS (2015)

Review Physics, Multidisciplinary

The role of local structure in dynamical arrest

C. Patrick Royall et al.

PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS (2015)

Review Biophysics

Three-dimensional vertex model for simulating multicellular morphogenesis

Satoru Okuda et al.

BIOPHYSICS AND PHYSICOBIOLOGY (2015)

Review Engineering, Biomedical

Multiscale Computational Models of Complex Biological Systems

Joseph Walpole et al.

ANNUAL REVIEW OF BIOMEDICAL ENGINEERING, VOL 15 (2013)

Article Multidisciplinary Sciences

Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing

Markus Basan et al.

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

Article Physics, Multidisciplinary

Hydrodynamics of soft active matter

M. C. Marchetti et al.

REVIEWS OF MODERN PHYSICS (2013)

Article Chemistry, Physical

Disentangling glass and jamming physics in the rheology of soft materials

Atsushi Ikeda et al.

SOFT MATTER (2013)

Review Physics, Multidisciplinary

Active Brownian particles From Individual to Collective Stochastic Dynamics

P. Romanczuk et al.

EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS (2012)

Review Cell Biology

The ins and Outs of the Epithelial to Mesenchymal Transition in Health and Disease

M. Angela Nieto

ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 27 (2011)

Review Cell Biology

Multi-scale modelling and simulation in systems biology

Joseph O. Dada et al.

INTEGRATIVE BIOLOGY (2011)

Article Neurosciences

Effective connectivity: Influence, causality and biophysical modeling

Pedro A. Valdes-Sosa et al.

NEUROIMAGE (2011)

Article Physics, Fluids & Plasmas

Active jamming: Self-propelled soft particles at high density

Silke Henkes et al.

PHYSICAL REVIEW E (2011)

Article Multidisciplinary Sciences

Glass-like dynamics of collective cell migration

Thomas E. Angelini et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Review Biochemistry & Molecular Biology

Multi-scale modeling in biology: How to bridge the gaps between scales?

Zhilin Qu et al.

PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY (2011)

Article Biochemical Research Methods

A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation

Susan D. Hester et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Chemistry, Physical

Critical-like behaviour of glass-forming liquids

Hajime Tanaka et al.

NATURE MATERIALS (2010)

Review Biology

Theoretical modeling of fluid flow in cellular biological media: An overview

George E. Kapellos et al.

MATHEMATICAL BIOSCIENCES (2010)

Article Multidisciplinary Sciences

Multi-scale models of cell and tissue dynamics

Magdalena A. Stolarska et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2009)

Article Engineering, Biomedical

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

Vito Conte et al.

JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS (2008)

Review Dermatology

Tight junctions/adherens junctions: Basic structure and function

Carien M. Niessen

JOURNAL OF INVESTIGATIVE DERMATOLOGY (2007)

Article Developmental Biology

A clock and wavefront mechanism for somite formation

RE Baker et al.

DEVELOPMENTAL BIOLOGY (2006)

Review Biophysics

Mechanical models for living cells - A review

CT Lim et al.

JOURNAL OF BIOMECHANICS (2006)

Article Multidisciplinary Sciences

Diffusion and scaling during early embryonic pattern formation

T Gregor et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

On multiscale approaches to three-dimensional modelling of morphogenesis

R Chaturvedi et al.

JOURNAL OF THE ROYAL SOCIETY INTERFACE (2005)

Review Cell Biology

Prespecification and plasticity: shifting mechanisms of cell migration

P Friedl

CURRENT OPINION IN CELL BIOLOGY (2004)