Boolean modeling in systems biology: An overview of methodology and applications

Rui Sheng Wang, Assieh Saadatpour, Réka Albert

Research output: Contribution to journalReview article

174 Citations (Scopus)

Abstract

Mathematical modeling of biological processes provides deep insights into complex cellular systems. While quantitative and continuous models such as differential equations have been widely used, their use is obstructed in systems wherein the knowledge of mechanistic details and kinetic parameters is scarce. On the other hand, a wealth of molecular level qualitative data on individual components and interactions can be obtained from the experimental literature and high-throughput technologies, making qualitative approaches such as Boolean network modeling extremely useful. In this paper, we build on our research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as well as inferring biological regulatory mechanisms from high-throughput data using Boolean models. We finally demonstrate how Boolean models can be applied to perform the structural analysis of cellular networks. This overview aims to acquaint life science researchers with the basic steps of Boolean modeling and its applications in several areas of systems biology.

Original languageEnglish (US)
Article number055001
JournalPhysical Biology
Volume9
Issue number5
DOIs
StatePublished - Oct 1 2012

Fingerprint

Systems Biology
Biological Phenomena
Biological Science Disciplines
Research Personnel
Technology
Research

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Structural Biology
  • Molecular Biology
  • Cell Biology

Cite this

@article{9936fbb8b1534377be193826d24e12b3,
title = "Boolean modeling in systems biology: An overview of methodology and applications",
abstract = "Mathematical modeling of biological processes provides deep insights into complex cellular systems. While quantitative and continuous models such as differential equations have been widely used, their use is obstructed in systems wherein the knowledge of mechanistic details and kinetic parameters is scarce. On the other hand, a wealth of molecular level qualitative data on individual components and interactions can be obtained from the experimental literature and high-throughput technologies, making qualitative approaches such as Boolean network modeling extremely useful. In this paper, we build on our research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as well as inferring biological regulatory mechanisms from high-throughput data using Boolean models. We finally demonstrate how Boolean models can be applied to perform the structural analysis of cellular networks. This overview aims to acquaint life science researchers with the basic steps of Boolean modeling and its applications in several areas of systems biology.",
author = "Wang, {Rui Sheng} and Assieh Saadatpour and R{\'e}ka Albert",
year = "2012",
month = "10",
day = "1",
doi = "10.1088/1478-3975/9/5/055001",
language = "English (US)",
volume = "9",
journal = "Physical Biology",
issn = "1478-3967",
publisher = "IOP Publishing Ltd.",
number = "5",

}

Boolean modeling in systems biology : An overview of methodology and applications. / Wang, Rui Sheng; Saadatpour, Assieh; Albert, Réka.

In: Physical Biology, Vol. 9, No. 5, 055001, 01.10.2012.

Research output: Contribution to journalReview article

TY - JOUR

T1 - Boolean modeling in systems biology

T2 - An overview of methodology and applications

AU - Wang, Rui Sheng

AU - Saadatpour, Assieh

AU - Albert, Réka

PY - 2012/10/1

Y1 - 2012/10/1

N2 - Mathematical modeling of biological processes provides deep insights into complex cellular systems. While quantitative and continuous models such as differential equations have been widely used, their use is obstructed in systems wherein the knowledge of mechanistic details and kinetic parameters is scarce. On the other hand, a wealth of molecular level qualitative data on individual components and interactions can be obtained from the experimental literature and high-throughput technologies, making qualitative approaches such as Boolean network modeling extremely useful. In this paper, we build on our research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as well as inferring biological regulatory mechanisms from high-throughput data using Boolean models. We finally demonstrate how Boolean models can be applied to perform the structural analysis of cellular networks. This overview aims to acquaint life science researchers with the basic steps of Boolean modeling and its applications in several areas of systems biology.

AB - Mathematical modeling of biological processes provides deep insights into complex cellular systems. While quantitative and continuous models such as differential equations have been widely used, their use is obstructed in systems wherein the knowledge of mechanistic details and kinetic parameters is scarce. On the other hand, a wealth of molecular level qualitative data on individual components and interactions can be obtained from the experimental literature and high-throughput technologies, making qualitative approaches such as Boolean network modeling extremely useful. In this paper, we build on our research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as well as inferring biological regulatory mechanisms from high-throughput data using Boolean models. We finally demonstrate how Boolean models can be applied to perform the structural analysis of cellular networks. This overview aims to acquaint life science researchers with the basic steps of Boolean modeling and its applications in several areas of systems biology.

UR - http://www.scopus.com/inward/record.url?scp=84867272347&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84867272347&partnerID=8YFLogxK

U2 - 10.1088/1478-3975/9/5/055001

DO - 10.1088/1478-3975/9/5/055001

M3 - Review article

C2 - 23011283

AN - SCOPUS:84867272347

VL - 9

JO - Physical Biology

JF - Physical Biology

SN - 1478-3967

IS - 5

M1 - 055001

ER -