Literature DB >> 34254127

From Flatland to Jupiter: Searching for Rules of Interaction Across Biological Scales.

Claudia A Grillo1, Mandë Holford2, Nils G Walter3.   

Abstract

In this future-spanning perspective, we examine how an agent-based model could be used to define general rules for interactions across biological systems and evolutionary time. To date, there have been a number of attempts to simulate the emergence of ecological communities using agent-based models of individuals that have evolving traits. Here we speculate whether it is possible to use this computational modeling to simulate self-organizing systems and, importantly, to decipher universal principles that govern biological interactions. This perspective is a thought exercise, meant to extrapolate from current knowledge to how we may make Jupiter-shot leaps to further advance the biosciences in the 21st century.
© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology.

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Year:  2022        PMID: 34254127      PMCID: PMC8825870          DOI: 10.1093/icb/icab159

Source DB:  PubMed          Journal:  Integr Comp Biol        ISSN: 1540-7063            Impact factor:   3.392


  17 in total

Review 1.  Ecological responses to recent climate change.

Authors:  Gian-Reto Walther; Eric Post; Peter Convey; Annette Menzel; Camille Parmesan; Trevor J C Beebee; Jean-Marc Fromentin; Ove Hoegh-Guldberg; Franz Bairlein
Journal:  Nature       Date:  2002-03-28       Impact factor: 49.962

Review 2.  Agent-based modeling of multicell morphogenic processes during development.

Authors:  Bryan C Thorne; Alexander M Bailey; Douglas W DeSimone; Shayn M Peirce
Journal:  Birth Defects Res C Embryo Today       Date:  2007-12

Review 3.  Characterizing emergent properties of immunological systems with multi-cellular rule-based computational modeling.

Authors:  Arvind K Chavali; Erwin P Gianchandani; Kenneth S Tung; Michael B Lawrence; Shayn M Peirce; Jason A Papin
Journal:  Trends Immunol       Date:  2008-10-27       Impact factor: 16.687

4.  Proteomics. Tissue-based map of the human proteome.

Authors:  Mathias Uhlén; Linn Fagerberg; Björn M Hallström; Cecilia Lindskog; Per Oksvold; Adil Mardinoglu; Åsa Sivertsson; Caroline Kampf; Evelina Sjöstedt; Anna Asplund; IngMarie Olsson; Karolina Edlund; Emma Lundberg; Sanjay Navani; Cristina Al-Khalili Szigyarto; Jacob Odeberg; Dijana Djureinovic; Jenny Ottosson Takanen; Sophia Hober; Tove Alm; Per-Henrik Edqvist; Holger Berling; Hanna Tegel; Jan Mulder; Johan Rockberg; Peter Nilsson; Jochen M Schwenk; Marica Hamsten; Kalle von Feilitzen; Mattias Forsberg; Lukas Persson; Fredric Johansson; Martin Zwahlen; Gunnar von Heijne; Jens Nielsen; Fredrik Pontén
Journal:  Science       Date:  2015-01-23       Impact factor: 47.728

5.  Biological order, structure and instabilities.

Authors:  I Prigogine; G Nicolis
Journal:  Q Rev Biophys       Date:  1971-08       Impact factor: 5.318

Review 6.  Tracing the peopling of the world through genomics.

Authors:  Rasmus Nielsen; Joshua M Akey; Mattias Jakobsson; Jonathan K Pritchard; Sarah Tishkoff; Eske Willerslev
Journal:  Nature       Date:  2017-01-18       Impact factor: 49.962

Review 7.  Cryogenic Super-Resolution Fluorescence and Electron Microscopy Correlated at the Nanoscale.

Authors:  Peter D Dahlberg; W E Moerner
Journal:  Annu Rev Phys Chem       Date:  2021-01-13       Impact factor: 12.703

8.  Non-model model organisms.

Authors:  James J Russell; Julie A Theriot; Pranidhi Sood; Wallace F Marshall; Laura F Landweber; Lillian Fritz-Laylin; Jessica K Polka; Snezhana Oliferenko; Therese Gerbich; Amy Gladfelter; James Umen; Magdalena Bezanilla; Madeline A Lancaster; Shuonan He; Matthew C Gibson; Bob Goldstein; Elly M Tanaka; Chi-Kuo Hu; Anne Brunet
Journal:  BMC Biol       Date:  2017-06-29       Impact factor: 7.431

Review 9.  Agent-Based Modeling in Public Health: Current Applications and Future Directions.

Authors:  Melissa Tracy; Magdalena Cerdá; Katherine M Keyes
Journal:  Annu Rev Public Health       Date:  2018-01-12       Impact factor: 21.981

10.  Intrinsic and extrinsic noise of gene expression in lineage trees.

Authors:  Philipp Thomas
Journal:  Sci Rep       Date:  2019-01-24       Impact factor: 4.379

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