Literature DB >> 20192756

Computational morphodynamics: a modeling framework to understand plant growth.

Vijay Chickarmane1, Adrienne H K Roeder, Paul T Tarr, Alexandre Cunha, Cory Tobin, Elliot M Meyerowitz.   

Abstract

Computational morphodynamics utilizes computer modeling to understand the development of living organisms over space and time. Results from biological experiments are used to construct accurate and predictive models of growth. These models are then used to make novel predictions that provide further insight into the processes involved, which can be tested experimentally to either confirm or rule out the validity of the computational models. This review highlights two fundamental challenges: (a) to understand the feedback between mechanics of growth and chemical or molecular signaling, and (b) to design models that span and integrate single cell behavior with tissue development. We review different approaches to model plant growth and discuss a variety of model types that can be implemented to demonstrate how the interplay between computational modeling and experimentation can be used to explore the morphodynamics of plant development.

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Year:  2010        PMID: 20192756      PMCID: PMC4120954          DOI: 10.1146/annurev-arplant-042809-112213

Source DB:  PubMed          Journal:  Annu Rev Plant Biol        ISSN: 1543-5008            Impact factor:   26.379


  106 in total

Review 1.  Plant cell identity. The role of position and lineage.

Authors:  B Scheres
Journal:  Plant Physiol       Date:  2001-01       Impact factor: 8.340

2.  Growth dynamics underlying petal shape and asymmetry.

Authors:  Anne-Gaëlle Rolland-Lagan; J Andrew Bangham; Enrico Coen
Journal:  Nature       Date:  2003-03-13       Impact factor: 49.962

Review 3.  Gene regulatory network models for plant development.

Authors:  Elena R Alvarez-Buylla; Mariana Benítez; Enrique Balleza Dávila; Alvaro Chaos; Carlos Espinosa-Soto; Pablo Padilla-Longoria
Journal:  Curr Opin Plant Biol       Date:  2006-12-04       Impact factor: 7.834

4.  A connectionist model of development.

Authors:  E Mjolsness; D H Sharp; J Reinitz
Journal:  J Theor Biol       Date:  1991-10-21       Impact factor: 2.691

5.  Developmental patterning by mechanical signals in Arabidopsis.

Authors:  Olivier Hamant; Marcus G Heisler; Henrik Jönsson; Pawel Krupinski; Magalie Uyttewaal; Plamen Bokov; Francis Corson; Patrik Sahlin; Arezki Boudaoud; Elliot M Meyerowitz; Yves Couder; Jan Traas
Journal:  Science       Date:  2008-12-12       Impact factor: 47.728

6.  Passing the El Greco test.

Authors:  Przemyslaw Prusinkiewicz; Enrico Coen
Journal:  HFSP J       Date:  2007-09-04

Review 7.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

Review 8.  Transcriptional regulatory circuits: predicting numbers from alphabets.

Authors:  Harold D Kim; Tal Shay; Erin K O'Shea; Aviv Regev
Journal:  Science       Date:  2009-07-24       Impact factor: 47.728

9.  Requirement of the Auxin Polar Transport System in Early Stages of Arabidopsis Floral Bud Formation.

Authors:  K. Okada; J. Ueda; M. K. Komaki; C. J. Bell; Y. Shimura
Journal:  Plant Cell       Date:  1991-07       Impact factor: 11.277

10.  Boolean network simulations for life scientists.

Authors:  István Albert; Juilee Thakar; Song Li; Ranran Zhang; Réka Albert
Journal:  Source Code Biol Med       Date:  2008-11-14
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  26 in total

1.  A model for leaf initiation: determination of phyllotaxis by waves in the generative circle.

Authors:  Barbara Abraham-Shrauner; Barbara G Pickard
Journal:  Plant Signal Behav       Date:  2011-11

2.  Auxin carriers localization drives auxin accumulation in plant cells infected by Frankia in Casuarina glauca actinorhizal nodules.

Authors:  Francine Perrine-Walker; Patrick Doumas; Mikael Lucas; Virginie Vaissayre; Nicholas J Beauchemin; Leah R Band; Jérome Chopard; Amandine Crabos; Geneviève Conejero; Benjamin Péret; John R King; Jean-Luc Verdeil; Valérie Hocher; Claudine Franche; Malcolm J Bennett; Louis S Tisa; Laurent Laplaze
Journal:  Plant Physiol       Date:  2010-09-08       Impact factor: 8.340

3.  The inside view on plant growth.

Authors:  Edgar P Spalding
Journal:  Nat Methods       Date:  2010-07       Impact factor: 28.547

Review 4.  Multiscale models in the biomechanics of plant growth.

Authors:  Oliver E Jensen; John A Fozard
Journal:  Physiology (Bethesda)       Date:  2015-03

Review 5.  Multiscale systems analysis of root growth and development: modeling beyond the network and cellular scales.

Authors:  Leah R Band; John A Fozard; Christophe Godin; Oliver E Jensen; Tony Pridmore; Malcolm J Bennett; John R King
Journal:  Plant Cell       Date:  2012-10-30       Impact factor: 11.277

6.  Towards Measurable Types for Dynamical Process Modeling Languages.

Authors:  Eric Mjolsness
Journal:  Electron Notes Theor Comput Sci       Date:  2010-09-06

7.  Growth dynamics of the Arabidopsis fruit is mediated by cell expansion.

Authors:  Juan-José Ripoll; Mingyuan Zhu; Stephanie Brocke; Cindy T Hon; Martin F Yanofsky; Arezki Boudaoud; Adrienne H K Roeder
Journal:  Proc Natl Acad Sci U S A       Date:  2019-11-22       Impact factor: 11.205

8.  Computational morphodynamics of plants: integrating development over space and time.

Authors:  Adrienne H K Roeder; Paul T Tarr; Cory Tobin; Xiaolan Zhang; Vijay Chickarmane; Alexandre Cunha; Elliot M Meyerowitz
Journal:  Nat Rev Mol Cell Biol       Date:  2011-03-02       Impact factor: 94.444

Review 9.  Ten years of genetics and genomics: what have we achieved and where are we heading?

Authors:  Edith Heard; Sarah Tishkoff; John A Todd; Marc Vidal; Günter P Wagner; Jun Wang; Detlef Weigel; Richard Young
Journal:  Nat Rev Genet       Date:  2010-09-07       Impact factor: 53.242

10.  Variability in the control of cell division underlies sepal epidermal patterning in Arabidopsis thaliana.

Authors:  Adrienne H K Roeder; Vijay Chickarmane; Alexandre Cunha; Boguslaw Obara; B S Manjunath; Elliot M Meyerowitz
Journal:  PLoS Biol       Date:  2010-05-11       Impact factor: 8.029

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