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Authors: Tejaswi Gowda 1 ; Samuel Leshner 1 ; Sarma Vrudhula 1 and Seungchan Kim 2

Affiliations: 1 School of Computing and Informatics, Arizona State University, United States ; 2 Division of Computational Biology, Translational Genomics Research Institute, United States

ISBN: 978-989-8111- 17-3

Keyword(s): Gene Regulation, Threshold Logic, Drosophila embryo patterning, Modeling and Simulation of Gene Systems.

Related Ontology Subjects/Areas/Topics: Biocomputing and Biochips ; Biomedical Engineering ; Biomedical Instruments and Devices ; Emerging Technologies ; Telecommunications ; Wireless and Mobile Technologies ; Wireless Information Networks and Systems

Abstract: Precise characterization of gene regulatory mechanisms is a fundamental problem in developmental biology. In this paper we present a new gene regulatory network (GRN) model which is based on threshold logic (TL). Two different set of genes are responsible for the cell patterning of the Drosophila embryo. By using the proposed threshold logic gene regulatory model (TLGRM), we derive the different gene regulatory rules for the gene products involved. We use these rules to model and explain the interaction between the genes. Very large or complex gene regulatory networks are difficult to simulate using a general purpose CPU. Specialized programmable hardware provides additional concurrency and is an alternative to a large and expensive cluster of machines. The steady state gene expression predicted by the model clearly mimics the actual wild-type gene expression along the dorsal-ventral axis in the Drosophila embryo. We thus demonstrate that for a well characterized gene regulatory sys tem, the nature and topology of interaction is enough to model gene regulation. We also demonstrate through proof of concept that using hardware-based simulation, it is possible to achieve orders of magnitude of performance improvement over conventional CPU-based simulation. (More)

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Paper citation in several formats:
Gowda T.; Leshner S.; Vrudhula S.; Kim S. and (2008). THRESHOLD LOGIC GENE REGULATORY MODEL - Prediction of Dorsal-ventral Patterning and Hardware-based Simulation of Drosophila.In Proceedings of the First International Conference on Biomedical Electronics and Devices - Volume 1: BIODEVICES, (BIOSTEC 2008) ISBN 978-989-8111- 17-3, pages 212-219. DOI: 10.5220/0001054302120219

@conference{biodevices08,
author={Tejaswi Gowda and Samuel Leshner and Sarma Vrudhula and Seungchan Kim},
title={THRESHOLD LOGIC GENE REGULATORY MODEL - Prediction of Dorsal-ventral Patterning and Hardware-based Simulation of Drosophila},
booktitle={Proceedings of the First International Conference on Biomedical Electronics and Devices - Volume 1: BIODEVICES, (BIOSTEC 2008)},
year={2008},
pages={212-219},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0001054302120219},
isbn={978-989-8111- 17-3},
}

TY - CONF

JO - Proceedings of the First International Conference on Biomedical Electronics and Devices - Volume 1: BIODEVICES, (BIOSTEC 2008)
TI - THRESHOLD LOGIC GENE REGULATORY MODEL - Prediction of Dorsal-ventral Patterning and Hardware-based Simulation of Drosophila
SN - 978-989-8111- 17-3
AU - Gowda, T.
AU - Leshner, S.
AU - Vrudhula, S.
AU - Kim, S.
PY - 2008
SP - 212
EP - 219
DO - 10.5220/0001054302120219

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