Switching gene regulatory networks

Yoli Shavit; Boyan Yordanov; Sara Jane Dunn; Christoph M. Wintersteiger; Youssef Hamadi; Hillel Kugler

doi:10.1007/978-3-319-23108-2_11

Switching gene regulatory networks

Yoli Shavit, Boyan Yordanov, Sara Jane Dunn, Christoph M. Wintersteiger, Youssef Hamadi, Hillel Kugler

Bar-Ilan University - The Alexander Kofkin Faculty of Engineering

Bar-Ilan University

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

A fundamental question in biology is how cells change into specific cell types with unique roles throughout development. This process can be viewed as a program prescribing the system dynamics, governed by a network of genetic interactions. Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. Currently, there are limited tools for the construction and analysis of such self-modifying biological programs.We introduce Switching Gene Regulatory Networks to enable the modeling and analysis of network reconfiguration, and define the synthesis problem of constructing switching networks from observations of cell behavior.We solve the synthesis problem using Satisfiability Modulo Theories (SMT) based methods, and evaluate the feasibility of our method by considering a set of synthetic benchmarks exhibiting typical biological behavior of cell development.

Original language	English
Title of host publication	Information Processing in Cells and Tissues - 10th International Conference, IPCAT 2015, Proceedings
Editors	Stephen Smith, Andy Tyrrell, Michael Lones, Gary Fogel
Publisher	Springer Verlag
Pages	131-144
Number of pages	14
ISBN (Print)	9783319231075
DOIs	https://doi.org/10.1007/978-3-319-23108-2_11
State	Published - 2015
Event	10th International Conference on Information Processing in Cells and Tissues, IPCAT 2015 - San Diego, United States Duration: 14 Sep 2015 → 16 Sep 2015

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9303

Conference

Conference	10th International Conference on Information Processing in Cells and Tissues, IPCAT 2015
Country/Territory	United States
City	San Diego
Period	14/09/15 → 16/09/15

Keywords

Biological modeling
Boolean networks
Gene regulatory networks (GRNs)
Satisfiability modulo theories (SMT)
Self-modifying code
Synthesis

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-319-23108-2_11

Cite this

Shavit, Y., Yordanov, B., Dunn, S. J., Wintersteiger, C. M., Hamadi, Y., & Kugler, H. (2015). Switching gene regulatory networks. In S. Smith, A. Tyrrell, M. Lones, & G. Fogel (Eds.), Information Processing in Cells and Tissues - 10th International Conference, IPCAT 2015, Proceedings (pp. 131-144). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9303). Springer Verlag. https://doi.org/10.1007/978-3-319-23108-2_11

Shavit, Yoli ; Yordanov, Boyan ; Dunn, Sara Jane et al. / Switching gene regulatory networks. Information Processing in Cells and Tissues - 10th International Conference, IPCAT 2015, Proceedings. editor / Stephen Smith ; Andy Tyrrell ; Michael Lones ; Gary Fogel. Springer Verlag, 2015. pp. 131-144 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "A fundamental question in biology is how cells change into specific cell types with unique roles throughout development. This process can be viewed as a program prescribing the system dynamics, governed by a network of genetic interactions. Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. Currently, there are limited tools for the construction and analysis of such self-modifying biological programs.We introduce Switching Gene Regulatory Networks to enable the modeling and analysis of network reconfiguration, and define the synthesis problem of constructing switching networks from observations of cell behavior.We solve the synthesis problem using Satisfiability Modulo Theories (SMT) based methods, and evaluate the feasibility of our method by considering a set of synthetic benchmarks exhibiting typical biological behavior of cell development.",

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author = "Yoli Shavit and Boyan Yordanov and Dunn, {Sara Jane} and Wintersteiger, {Christoph M.} and Youssef Hamadi and Hillel Kugler",

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Shavit, Y, Yordanov, B, Dunn, SJ, Wintersteiger, CM, Hamadi, Y & Kugler, H 2015, Switching gene regulatory networks. in S Smith, A Tyrrell, M Lones & G Fogel (eds), Information Processing in Cells and Tissues - 10th International Conference, IPCAT 2015, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9303, Springer Verlag, pp. 131-144, 10th International Conference on Information Processing in Cells and Tissues, IPCAT 2015, San Diego, United States, 14/09/15. https://doi.org/10.1007/978-3-319-23108-2_11

Switching gene regulatory networks. / Shavit, Yoli; Yordanov, Boyan; Dunn, Sara Jane et al.
Information Processing in Cells and Tissues - 10th International Conference, IPCAT 2015, Proceedings. ed. / Stephen Smith; Andy Tyrrell; Michael Lones; Gary Fogel. Springer Verlag, 2015. p. 131-144 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9303).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Switching gene regulatory networks

AU - Shavit, Yoli

AU - Yordanov, Boyan

AU - Dunn, Sara Jane

AU - Wintersteiger, Christoph M.

AU - Hamadi, Youssef

AU - Kugler, Hillel

N1 - Publisher Copyright: © Springer International Publishing Switzerland 2015.

PY - 2015

Y1 - 2015

N2 - A fundamental question in biology is how cells change into specific cell types with unique roles throughout development. This process can be viewed as a program prescribing the system dynamics, governed by a network of genetic interactions. Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. Currently, there are limited tools for the construction and analysis of such self-modifying biological programs.We introduce Switching Gene Regulatory Networks to enable the modeling and analysis of network reconfiguration, and define the synthesis problem of constructing switching networks from observations of cell behavior.We solve the synthesis problem using Satisfiability Modulo Theories (SMT) based methods, and evaluate the feasibility of our method by considering a set of synthetic benchmarks exhibiting typical biological behavior of cell development.

AB - A fundamental question in biology is how cells change into specific cell types with unique roles throughout development. This process can be viewed as a program prescribing the system dynamics, governed by a network of genetic interactions. Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. Currently, there are limited tools for the construction and analysis of such self-modifying biological programs.We introduce Switching Gene Regulatory Networks to enable the modeling and analysis of network reconfiguration, and define the synthesis problem of constructing switching networks from observations of cell behavior.We solve the synthesis problem using Satisfiability Modulo Theories (SMT) based methods, and evaluate the feasibility of our method by considering a set of synthetic benchmarks exhibiting typical biological behavior of cell development.

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KW - Satisfiability modulo theories (SMT)

KW - Self-modifying code

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DO - 10.1007/978-3-319-23108-2_11

M3 - منشور من مؤتمر

SN - 9783319231075

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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EP - 144

BT - Information Processing in Cells and Tissues - 10th International Conference, IPCAT 2015, Proceedings

A2 - Smith, Stephen

A2 - Tyrrell, Andy

A2 - Lones, Michael

A2 - Fogel, Gary

PB - Springer Verlag

T2 - 10th International Conference on Information Processing in Cells and Tissues, IPCAT 2015

Y2 - 14 September 2015 through 16 September 2015

ER -

Shavit Y, Yordanov B, Dunn SJ, Wintersteiger CM, Hamadi Y, Kugler H. Switching gene regulatory networks. In Smith S, Tyrrell A, Lones M, Fogel G, editors, Information Processing in Cells and Tissues - 10th International Conference, IPCAT 2015, Proceedings. Springer Verlag. 2015. p. 131-144. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-23108-2_11

Switching gene regulatory networks

Abstract

Publication series

Conference

Keywords

All Science Journal Classification (ASJC) codes

Access to Document

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Cite this