People in the Hunt Lab

C. Anthony Hunt

Postdoctoral Fellows

Sunwoo Park

Email: parks [at] pharmacy.ucsf.edu

Sunwoo Park is a postdoctoral scholar who is currently developing high performance distributed/parallel modeling and simulation framework for large-scale biological systems. He is an expert in the fields of DEVS M&S, discrete event systems, and distributed/parallel computing. His main research interests include discrete event-oriented M&S, mathematical modeling, multi-agent M&S, system biology, and bioinformatics.

Staff

Glen E. P. Ropella

Email: gepr [at] tempusdictum.com

Glen is a Research Scientist with oversight for software development in the group. He is experienced in multiple aspects of software engineering, modeling and simulation. He is an expert in the design and execution of agent-based models and an expert in the use of the Swarm platform.

Pearl Johnson

Visiting Scientists

Joe LaPointe

Email: lapointeconsulting [at] att.net

Visiting Professor of Systems Biology.

Graduate Students

Jesse Engelberg

Email: jesse [at] amherstcollege.net

Jesse is a graduate student in the UCSF/UCB Joint Graduate Group in Bioengineering. His research focuses on computational modeling of cell biology, especially multicellular tumor spheroids and epithelial cell morphogenesis. His research interests include computational biology, bioinformatics, and modeling and simulation.

Jon Tang

Email: jont [at] socrates.Berkeley.edu

Jon is a graduate student in the UCSF/UCB Joint Graduate Group in Bioengineering. He is interested in computer modeling of biological systems, in particular various aspects of the immune system. He is currently constructing an agent-based model of the leukocyte adhesion cascade and leukocyte transendothelial migration during inflammation.

Mark Grant

Email: mgrant [at] socrates.Berkeley.edu | Homepage

Mark is a graduate student in the UCSF/UCB Joint Graduate Group in Bioengineering, with research emphasis on computational biology and bioinformatics. His most recent project focused on simulation of mammalian tissue morphogenesis. His interests include modeling of biological processes and protein function determination.

Sean H.J. Kim

Email: seanhjk [at] berkeley.edu | Homepage

Sean is a graduate student in the UCSF/UCB Joing Graduate Group in Bioengineering, with interests in multiscale simulation modeling and systems biology. His current research focuses on agent-based modeling of epithelial morphogenesis in vitro. His past research topics include agent-based modeling of the blood-brain barrier and drug transport.

Shahab Sheikh-Bahaei

Email: Shahab.Sheikh-Bahaei [at] ucsf.edu

Shahab Sheikh-Bahaei is a PhD candidate at the UCSF/UCB Joint Graduate Group in Bioengineering. He received his B.S. degree in Electrical Engineering (Electronics) from Isfahan University of Technology, Iran in 1999 and his M.S. degree in Electrical Engineering (Robotics) from University of New Mexico, Albuquerque, NM, USA in 2003. He has worked for Tempus Dictum Inc as a Modeler Engineer contractor for 2 years. Since August 2005 he's been a Graduate Student Researcher at the BioSystems group at UCSF. His areas of interest include modeling and simulation, multi-agent systems, self-organizing systems (complexity theory) and artificial intelligence.

Teddy Lam

Email: tai.ning.lam [at] ucsf.edu

Teddy Lam is a graduate student in the Graduate Program in Pharmaceutical Sciences & Pharmacogenomics at UCSF. His research includes development of computational tools and methods to better understand and predict drug-drug interaction.

Recent Group Alumni

Amy H Lin

Amy H Lin was a postdoc in the Hunt lab with a Ph.D. in mathematics. She worked on a multicellular tumor spheroid model, and she also compared the results of agent-based and equation-based models of different systems.

Anita Grover

Anita Grover is a graduate student in the Graduate Program in Pharmaceutical Sciences & Pharmacogenomics at UCSF. She completed a rotation in the Hunt Lab, with research on in silico drug development devices.

Christine Case

Christine Case is interested in the individualization of therapy with potentially toxic drugs like chemotherapy agents. Her research included modeling the processes of drug elimination and the impact of patient-specific information and health status on those processes, specifically with an emphasis on inflammation. Christine is a graduate from UC Berkeley in Bioengineering.

Cindy Chen

Cindy Chen was a postgraduate researcher with research on agent based modeling and simulation for cancer, gene database analysis, and network based modeling for cancer pathways. She also has provided with hardware and software support.

Craig Furman

Craig is a Software Engineer and has worked on the ISL project. He has brought many years of commercial software development experience to the project. He will be starting a PhD in Bioinformatics/Computational Biology soon and would like to focus on the computational issues in Population Genetics, Genome Sequencing and Evolution.

Debbie Lin

Debbie has been involved in modeling systems that are at the intersection of biopharmaceutical science and policy. Specifically, such systems include drug in-licensing processes, drug development pipelines, and biological systems. Her aims include application of engineering methods and a number of simulation tools to explore these topics including agent based modeling software, process manufacturing and decision analytic tools.

Donglei Hu

Jason Ku

Jason was a UCSF MSTP student (incoming Fall 2002) and completed a summer rotation in the Hunt Lab. On rotation, he explored the use of the relatively new agent-based modeling approach in studying and simulating biological systems on the subcellular, cellular and tissue levels. In the long term, he seeks to develop an in silico agent-based model of a system infected or affected by HIV.

Keith Erickson

Keith Erickson graduated from the University of Washington with a B.S. in Chemical Engineering in 1999. He is a doctoral student in the UCSF/UCB Joint Graduate Group in Bioengineering under Professor Adam Arkin with a generous fellowship from the Whitaker Foundation. His research is focused on elucidating the biochemical control mechanisms behind neutrophil chemotaxis using a combination of experimental and computational approaches.

Michael Oakley

Michael Oakley's research is focused on genetic changes that occur in the developing mouse liver, more specifically, how these genetic changes control survival of the organ's vasculature.

Sandy Shaw

Recent Graduates

Abraham Anderson

Abraham Anderson is a doctoral graduate who has been developing network-based analyses of diverse biological systems to support therapeutic target and biomarker discovery. He was affiliated with the Bioengineering Graduate Group, jointly administered by UCSF and UC Berkeley.

Amina Qutub

Amina Qutub is a doctoral graduate from the UCSF/UCB Joint Graduate Group in Bioengineering, with a background in chemical engineering and an emphasis on mathematical modeling and neurobiology. Her thesis research focused on simulating the physiology of the blood-brain barrier, with the long-term goal of improving drug development and delivery for neurological diseases.

Lan Xia

Lan Xia is a doctoral graduate from the comparative biochemistry program at UC Berkeley; she has worked on the mammary gland development and patterning formation project, together with Mark Grant. Her goal is to build up a multi-model biodevice for morphodynamic process applied in mammary gland morphogenesis.

Li Yan

Li Yan is a doctoral graduate from the UCSF/UCB Joint Graduate Group in Bioengineering. Her long-term research goal is to develop simulation techniques that can facilitate and guide drug development, as well as facilitate optimization of drug-based therapies. Her thesis research focused on developing Agent-Based Models (ABMS) of Isolated, Perfused Rat Liver (IPRL).

Robert Otillar

Suman Ganguli

Suman Ganguli was a postdoctoral scholar at Hunt Lab. His research interests centered around formal models of complex biological systems, and he has contributed to projects on developing computational models of multicellular tumor spheroids and of immune cell trafficking. He also has been interested in theoretical and foundational issues regarding formal modeling of biological systems. Specific areas of interest related to the latter are formal methods for multi-agent systems, and theoretical formalisms for biology such as metabolism-repair systems and autopoiesis.

Yu Liu

Yu Liu is a doctoral grauduate from the UCSF/UCB Joint Graduate Group in Bioengineering. Her research focued on drug absorption across small intestine epithelia barrier, a complicated process. To investigate the feasibility of an in silico experiment device to study this process, she used a new computational strategy, agent based modeling, with a goal to develop in silico devices to help expedite the drug development process.

Yuanyuan Xiao

Yuanyuan is a doctoral graduate from the biopharmaceutical sciences at UCSF. Her research interests are microarray data analysis, and generally statistical methods in bioinformatics. Yuanyuan says she still has a lot to learn…