Literature DB >> 20448808

Multiscale modeling for biologists.

Martin Meier-Schellersheim1, Iain D C Fraser1, Frederick Klauschen1.   

Abstract

Biomedical research frequently involves performing experiments and developing hypotheses that link different scales of biological systems such as, for instance, the scales of intracellular molecular interactions to the scale of cellular behavior and beyond to the behavior of cell populations. Computational modeling efforts that aim at exploring such multiscale systems quantitatively with the help of simulations have to incorporate several different simulation techniques because of the different time and space scales involved. Here, we provide a nontechnical overview of how different scales of experimental research can be combined with the appropriate computational modeling techniques. We also show that current modeling software permits building and simulating multiscale models without having to become involved with the underlying technical details of computational modeling.

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Year:  2009        PMID: 20448808      PMCID: PMC2862646          DOI: 10.1002/wsbm.33

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev Syst Biol Med        ISSN: 1939-005X


  52 in total

1.  The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J Doyle; H Kitano
Journal:  Pac Symp Biocomput       Date:  2002

Review 2.  Leading the way: Directional sensing through phosphatidylinositol 3-kinase and other signaling pathways.

Authors:  Sylvain Merlot; Richard A Firtel
Journal:  J Cell Sci       Date:  2003-09-01       Impact factor: 5.285

3.  Two complementary, local excitation, global inhibition mechanisms acting in parallel can explain the chemoattractant-induced regulation of PI(3,4,5)P3 response in dictyostelium cells.

Authors:  Lan Ma; Chris Janetopoulos; Liu Yang; Peter N Devreotes; Pablo A Iglesias
Journal:  Biophys J       Date:  2004-10-01       Impact factor: 4.033

Review 4.  Cellular automata-based modeling program: synthetic immune system.

Authors:  James Mata; Melvin Cohn
Journal:  Immunol Rev       Date:  2007-04       Impact factor: 12.988

5.  Algorithms and software for stochastic simulation of biochemical reacting systems.

Authors:  Hong Li; Yang Cao; Linda R Petzold; Daniel T Gillespie
Journal:  Biotechnol Prog       Date:  2007-09-26

Review 6.  CellML and associated tools and techniques.

Authors:  Alan Garny; David P Nickerson; Jonathan Cooper; Rodrigo Weber dos Santos; Andrew K Miller; Steve McKeever; Poul M F Nielsen; Peter J Hunter
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2008-09-13       Impact factor: 4.226

Review 7.  Computational models of the heart and their use in assessing the actions of drugs.

Authors:  Denis Noble
Journal:  J Pharmacol Sci       Date:  2008-06       Impact factor: 3.337

8.  Evidence for ectopic neurotransmission at a neuronal synapse.

Authors:  Jay S Coggan; Thomas M Bartol; Eduardo Esquenazi; Joel R Stiles; Stephan Lamont; Maryann E Martone; Darwin K Berg; Mark H Ellisman; Terrence J Sejnowski
Journal:  Science       Date:  2005-07-15       Impact factor: 47.728

9.  Locally controlled inhibitory mechanisms are involved in eukaryotic GPCR-mediated chemosensing.

Authors:  Xuehua Xu; Martin Meier-Schellersheim; Jianshe Yan; Tian Jin
Journal:  J Cell Biol       Date:  2007-07-02       Impact factor: 10.539

10.  Host control of malaria infections: constraints on immune and erythropoeitic response kinetics.

Authors:  Philip G McQueen; F Ellis McKenzie
Journal:  PLoS Comput Biol       Date:  2008-08-22       Impact factor: 4.475

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  35 in total

Review 1.  Systems biology in immunology: a computational modeling perspective.

Authors:  Ronald N Germain; Martin Meier-Schellersheim; Aleksandra Nita-Lazar; Iain D C Fraser
Journal:  Annu Rev Immunol       Date:  2011       Impact factor: 28.527

2.  Multiscale methods for computational RNA enzymology.

Authors:  Maria T Panteva; Thakshila Dissanayake; Haoyuan Chen; Brian K Radak; Erich R Kuechler; George M Giambaşu; Tai-Sung Lee; Darrin M York
Journal:  Methods Enzymol       Date:  2015-01-22       Impact factor: 1.600

3.  Modeling oscillations and spiral waves in Dictyostelium populations.

Authors:  Javad Noorbakhsh; David J Schwab; Allyson E Sgro; Thomas Gregor; Pankaj Mehta
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2015-06-15

Review 4.  Modeling for (physical) biologists: an introduction to the rule-based approach.

Authors:  Lily A Chylek; Leonard A Harris; James R Faeder; William S Hlavacek
Journal:  Phys Biol       Date:  2015-07-16       Impact factor: 2.583

5.  Targeted Proteomics-Driven Computational Modeling of Macrophage S1P Chemosensing.

Authors:  Nathan P Manes; Bastian R Angermann; Marijke Koppenol-Raab; Eunkyung An; Virginie H Sjoelund; Jing Sun; Masaru Ishii; Ronald N Germain; Martin Meier-Schellersheim; Aleksandra Nita-Lazar
Journal:  Mol Cell Proteomics       Date:  2015-07-21       Impact factor: 5.911

6.  Modeling heterogeneous tumor growth dynamics and cell-cell interactions at single-cell and cell-population resolution.

Authors:  Leonard A Harris; Samantha Beik; Patricia M M Ozawa; Lizandra Jimenez; Alissa M Weaver
Journal:  Curr Opin Syst Biol       Date:  2019-09-16

7.  A practical guide to mechanistic systems modeling in biology using a logic-based approach.

Authors:  Anna Niarakis; Tomáš Helikar
Journal:  Brief Bioinform       Date:  2021-07-20       Impact factor: 11.622

Review 8.  Multi-scale modeling in biology: how to bridge the gaps between scales?

Authors:  Zhilin Qu; Alan Garfinkel; James N Weiss; Melissa Nivala
Journal:  Prog Biophys Mol Biol       Date:  2011-06-23       Impact factor: 3.667

9.  Dynamic models of immune responses: what is the ideal level of detail?

Authors:  Juilee Thakar; Mary Poss; Réka Albert; Gráinne H Long; Ranran Zhang
Journal:  Theor Biol Med Model       Date:  2010-08-20       Impact factor: 2.432

10.  A systems immunology approach to plasmacytoid dendritic cell function in cytopathic virus infections.

Authors:  Gennady Bocharov; Roland Züst; Luisa Cervantes-Barragan; Tatyana Luzyanina; Egor Chiglintsev; Valery A Chereshnev; Volker Thiel; Burkhard Ludewig
Journal:  PLoS Pathog       Date:  2010-07-22       Impact factor: 6.823

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