Boolean modelling in plant biology.

Boolean networks computer modelling plant networks stomatal closure

Journal

Quantitative plant biology

ISSN: 2632-8828

Titre abrégé: Quant Plant Biol

Pays: England

ID NLM: 9918452086906676

Informations de publication

Date de publication:
2022

Historique:

received: 17 06 2022

revised: 24 10 2022

accepted: 16 11 2022

medline: 20 4 2023

pubmed: 20 4 2023

entrez: 20 04 2023

Statut: epublish

Résumé

Signalling and genetic networks underlie most biological processes and are often complex, containing many highly connected components. Modelling these networks can provide insight into mechanisms but is challenging given that rate parameters are often not well defined. Boolean modelling, in which components can only take on a binary value with connections encoded by logic equations, is able to circumvent some of these challenges, and has emerged as a viable tool to probe these complex networks. In this review, we will give an overview of Boolean modelling, with a specific emphasis on its use in plant biology. We review how Boolean modelling can be used to describe biological networks and then discuss examples of its applications in plant genetics and plant signalling.

Identifiants

DOI: 10.1017/qpb.2022.26 PMID: 37077966 PMC: PMC10095905

pubmed: 37077966

doi: 10.1017/qpb.2022.26

pii: S2632882822000261

pmc: PMC10095905

doi:

Types de publication

Journal Article Review

Langues

eng

Pagination

e29

Informations de copyright

Déclaration de conflit d'intérêts

The authors declare no conflict of interest.

Références

Bioinformatics. 2013 Jul 01;29(13):i80-8

pubmed: 23813012

Proc Natl Acad Sci U S A. 2018 Oct 16;115(42):E9971-E9980

pubmed: 30282744

Plant Physiol. 1988 Jul;87(3):583-7

pubmed: 16666189

BMC Syst Biol. 2009 Sep 28;3:98

pubmed: 19785753

Bioinformatics. 2006 Jul 15;22(14):e124-31

pubmed: 16873462

Bioinformatics. 2010 May 15;26(10):1378-80

pubmed: 20378558

Source Code Biol Med. 2008 Nov 14;3:16

pubmed: 19014577

Artif Intell Med. 2019 Apr;95:133-145

pubmed: 30420244

Bioinformatics. 2008 Sep 1;24(17):1917-25

pubmed: 18614585

Biosystems. 2009 Jul;97(1):1-8

pubmed: 19505631

J Exp Bot. 2021 Oct 13;72(19):6727-6738

pubmed: 34173817

Curr Opin Plant Biol. 2016 Oct;33:157-167

pubmed: 27518594

PLoS One. 2015 Oct 23;10(10):e0140954

pubmed: 26496494

Front Physiol. 2018 Apr 24;9:431

pubmed: 29740342

J Theor Biol. 1998 Jul 27;193(2):307-19

pubmed: 9714934

J Theor Biol. 2007 Feb 7;244(3):463-9

pubmed: 17010384

Elife. 2020 May 28;9:

pubmed: 32463362

PLoS One. 2013 Jul 26;8(7):e69008

pubmed: 23922675

Plant Physiol. 2021 Dec 4;187(4):2311-2322

pubmed: 34618035

PLoS Comput Biol. 2007 Oct;3(10):1871-78

pubmed: 17922568

Phys Rev Lett. 2007 Apr 13;98(15):158701

pubmed: 17501391

New Phytol. 2021 Mar;229(5):2765-2779

pubmed: 33187027

Pac Symp Biocomput. 1998;:18-29

pubmed: 9697168

J Theor Biol. 1973 Apr;39(1):103-29

pubmed: 4741704

Methods Mol Biol. 2017;1629:297-315

pubmed: 28623593

BMC Syst Biol. 2009 Jun 06;3:58

pubmed: 19500393

Chaos. 2017 Sep;27(9):093914

pubmed: 28964163

PLoS Biol. 2017 Sep 22;15(9):e2003451

pubmed: 28937978

Plant Methods. 2019 Apr 17;15:38

pubmed: 31019545

Mol Plant. 2015 Apr;8(4):657-9

pubmed: 25620768

Annu Rev Phytopathol. 2014;52:347-75

pubmed: 24906124

J Theor Biol. 2008 Dec 7;255(3):269-77

pubmed: 18692073

Nature. 2003 Mar 13;422(6928):193-7

pubmed: 12634792

J R Soc Interface. 2009 Jul 6;6(36):599-612

pubmed: 18952547

Phys Rev Lett. 2014 Aug 29;113(9):098701

pubmed: 25216014

PLoS Comput Biol. 2007 Aug;3(8):e163

pubmed: 17722974

J Cell Biol. 1986 Dec;103(6 Pt 2):2747-54

pubmed: 3793756

Brief Funct Genomics. 2018 Jul 1;17(4):246-254

pubmed: 29342231

Mol Plant Microbe Interact. 2017 Mar;30(3):215-230

pubmed: 28118091

PLoS Comput Biol. 2014 Nov 13;10(11):e1003930

pubmed: 25393147

BMC Syst Biol. 2012 Aug 29;6:116

pubmed: 22932419

Curr Opin Plant Biol. 2015 Dec;28:154-62

pubmed: 26599955

Development. 1993 Sep;119(1):71-84

pubmed: 8275865

BMC Syst Biol. 2010 Oct 05;4:134

pubmed: 20920363

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Aug;68(2 Pt 1):021904

pubmed: 14525003

Nat Rev Mol Cell Biol. 2008 Dec;9(12):981-91

pubmed: 18971947

Front Physiol. 2020 Aug 13;11:927

pubmed: 32903539

Trends Plant Sci. 2016 Jan;21(1):16-30

pubmed: 26482956

PLoS One. 2019 Aug 22;14(8):e0221358

pubmed: 31437216

Phys Rev Lett. 2017 Jul 14;119(2):028301

pubmed: 28753377

Biosystems. 2006 May;84(2):91-100

pubmed: 16434137

Bioinformatics. 2002 Feb;18(2):261-74

pubmed: 11847074

Brief Bioinform. 2021 Sep 2;22(5):

pubmed: 33539514

Comput Biol Med. 2014 May;48:55-65

pubmed: 24637147

Bioinformatics. 2005 Apr 1;21(7):1211-8

pubmed: 15531600

PLoS One. 2010 Aug 05;5(8):e11793

pubmed: 20700525

PLoS Comput Biol. 2019 Oct 28;15(10):e1007429

pubmed: 31658257

Phys Rev E. 2021 Jan;103(1-1):012402

pubmed: 33601617

Bioinformatics. 2022 Feb 7;38(5):1465-1466

pubmed: 34875008

Bioinformatics. 2017 Mar 1;33(5):770-772

pubmed: 27797783

PLoS One. 2012;7(10):e46798

pubmed: 23056457

Sci Adv. 2021 Jul 16;7(29):

pubmed: 34272246

Trends Plant Sci. 2010 Jul;15(7):395-401

pubmed: 20493758

BMC Bioinformatics. 2020 Apr 15;21(1):142

pubmed: 32293239

Plant J. 2021 Jan;105(2):307-321

pubmed: 33145840

Sci Rep. 2018 Dec 5;8(1):17635

pubmed: 30518777

PLoS Biol. 2006 Oct;4(10):e312

pubmed: 16968132

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 May;75(5 Pt 1):051907

pubmed: 17677098

Arch Biochem Biophys. 1952 Jul;39(1):37-50

pubmed: 12997125

Curr Biol. 2018 Dec 3;28(23):R1356-R1363

pubmed: 30513335

Plant Cell. 2009 Aug;21(8):2357-77

pubmed: 19690149

Theor Biol Med Model. 2006 Mar 16;3:13

pubmed: 16542429

Nature. 2001 Feb 15;409(6822):860-921

pubmed: 11237011

J R Soc Interface. 2008 Aug 6;5 Suppl 1:S85-94

pubmed: 18508746

J Theor Biol. 1973 Dec;42(3):563-85

pubmed: 4588055

Comput Struct Biotechnol J. 2020 Mar 10;18:571-582

pubmed: 32257043

Bioinformatics. 2014 Jan 1;30(1):131-2

pubmed: 24078712

BMC Syst Biol. 2012 Oct 18;6:133

pubmed: 23079107

Curr Biol. 2009 Jun 9;19(11):909-14

pubmed: 19398337

BMC Syst Biol. 2007 Jan 08;1:2

pubmed: 17408509

Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):4781-6

pubmed: 15037758

J Theor Biol. 2010 Oct 21;266(4):641-56

pubmed: 20659480

Plant Physiol. 2021 Dec 4;187(4):2032-2042

pubmed: 35142859

Nature. 1969 Oct 11;224(5215):177-8

pubmed: 5343519

J Theor Biol. 1969 Mar;22(3):437-67

pubmed: 5803332

Nat Rev Mol Cell Biol. 2008 Oct;9(10):770-80

pubmed: 18797474

Nature. 2002 Nov 14;420(6912):206-10

pubmed: 12432404

Front Plant Sci. 2013 Apr 30;4:110

pubmed: 23658556

Acta Biotheor. 2008 Jun;56(1-2):27-49

pubmed: 18379883

Cell Commun Signal. 2013 Jul 01;11:46

pubmed: 23815817

Plant Cell. 2004 Nov;16(11):2923-39

pubmed: 15486106

Front Cell Dev Biol. 2014 Aug 19;2:38

pubmed: 25364745