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 |
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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 | |
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) |
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Volume | 9303 |
ISSN (Print) | 0302-9743 |
ISSN (Electronic) | 1611-3349 |
Conference
Conference | 10th International Conference on Information Processing in Cells and Tissues, IPCAT 2015 |
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Country/Territory | United States |
City | San Diego |
Period | 14/09/15 → 16/09/15 |
Bibliographical note
Publisher Copyright:© Springer International Publishing Switzerland 2015.
Funding
Yoli Shavit is supported by the Cambridge International Scholarship Scheme (CISS). The research was carried out during her internship at Microsoft Research Cambridge, UK.
Keywords
- Biological modeling
- Boolean networks
- Gene regulatory networks (GRNs)
- Satisfiability modulo theories (SMT)
- Self-modifying code
- Synthesis