BioHybridControl GroupHybrid Systems Theory for Biology – Summer 2005


Meeting Time: 

For the Summer Session 2005, the meetings are scheduled on Mondays at 4:00pm in 337 Cory.


Recently the research community has seen a lot of effort in the field of Systems Biology. Topics like gene-to-gene regulatory networks, gene-to-protein interactions, noise interaction and exploitation, or molecular-level behavior have gained much understanding from the application of mathematical models which Control Engineers or Mathematicians are rather familiar with.

Specifically, Hybrid Systems appear to be a natural framework to model these systems with, because in nature continuous-time evolutions is often torn apart by the happening of discrete events.

Furthermore, stochasticity seems to be a requirement and a leit-motif in natural evolution.

These observations have led us to investigating possible applications of (Stochastic) Hybrid Systems models to the field of biology.

The group will be of course open to more general applications of System Engineering techniques to the field of molecular biology, as well as integrative biology.


Reading Schedule and Additional Material:


Paper or Topic of Discussion


Joshi, K. Neogi, N., and W. Sanders Dynamic Partitioning of Large Discrete Event Biological Systems for Hybrid Simulation and Analysis


H. McAdams, A. Arkin Simulation of Prokaryotic Genetic Circuits


Denise M. Wolf, Adam P. Arkin 15 Minutes of fim: Control of Phase Variation in E. coli


R. Ghosh, A. Tiwari, and C. Tomlin Automated Symbolic Reachability Analysis with Application to Delta-Notch Signaling Automata

June 3, 2005

Phoebus Chen (UCB EECS) will continue with the second part of the MCB primer.

May 27, 2005

Phoebus Chen (UCB EECS) will give an MCB primer on the following topics:

'Overview of Transcription and Translation' and 'Example Mechanisms for Transcription Control'   [slides] [index]

May 20, 2005

Alur, Belta, Ivancic, Kumar, Mintz, Pappas, Rubin, Schug Hybrid Modeling and Simulation of Biomolecular Networks

May 13, 2005

C. Belta, P. Finin, L.C.G.J.M. Habets, A. Halasz, M. Imielinski, V.Kumar, H. Rubin Understanding the bacterial stringent response using reachability analysis of hybrid systems

May 7, 2005

Lincoln, P. and Tiwari, A.  Symbolic systems biology: Hybrid modeling and analysis of biological networks

May 7, 2005

H. de Jong, J.-L. Gouzé, C. Hernandez, M. Page, T. Sari, J. Geiselmann Hybrid modeling and simulation of genetic regulatory networks: A qualitative approach

April 29, 2005

More on Stochastic Resonance

April 22, 2005


L. Gammaitoni, et al. Stochastic resonance

J.E. Levin, J.P. Miller  Broadband neural encoding in the cricket cercal sensory system enhanced by stochastic resonance

J.K. Douglass, et al.  Noise Enhancement of information transfer in crayfish mechanoreceptors by stochastic resonance

D. F. Russell, et al.  Use of behavioural stochastic resonance by paddle fish for feeding


April 21, 2005

Cory 285 – 2.00-3.30 – Ronojoy Ghosh (Stanford) will be lecturing on “Hybrid Models for Biology”.

April 1, 2005

H.H. McAdams, A. Arkin

Stochastic mechanisms in gene expression

C.V. Rao, D. Wolf, A. Arkin

Control, exploitation and tolerance of intracellular noise

March 18, 2005

D.T. Gillespie

Exact Stochastic Simulation of Coupled Chemical Reactions

March 9, 2005

D. Wolf, A. Arkin

Motifs, modules and games in bacteria

March 4, 2005

J. Makin and B. Zhu will be leading a discussion on the research topic “Cortical-basal-thalamic loops”

Reference paper: S. Narajanan

The role of cortico-basal-thalamic loops in cognition: a computational model and preliminary results

February 23, 2005

J. Hu, W.-C. Wu and S. Sastry
Modeling Subtilin Production in Bacillus subtilis Using Stochastic Hybrid Systems

February , 2005

Shai Refzen will be presenting on the topic “Dynamics, Templates and Modules of Cockroaches

Fall 2004



W.J. Blake, M. Kaern, C.R. Cantor, J.J. Collins
Noise in eukaryotic gene expression


F.Isaacs, J. Hasty, C.R. Cantor, J.J. Collins
Prediction and Measurement of an autoregulatory genetic module


J. Hasty, J. Pradines, M. Dolnik, J.J. Collins
Noise-based switches and amplifiers for gene expression


Additional Links:

Biospice Project: www.biospice.org  

Some links to Molecular Biology Glossaries:     Hedgehog Signaling Glossary
Molecular Cell Biology. Table of Contents

Computational Biology at UCB: www.computationalbiology.berkeley.edu

Molecular Cell Biology”, by Lodish et. al. (5th ed.) - book’s on-line resources.



For further information about schedule, material, objectives, or questions regarding the website, please get in touch with:

Alessandro Abate (aabate AT eecs DOT berkeley DOT edu)

Last modified: May 31ts, 2005



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