BIOGRAPHICAL SKETCH
NAME
POSITION TITLE
HLAVACEK, William S.
Scientist 3
eRA COMMONS USER NAME
wshlavacek
EDUCATION/TRAINING
INSTITUTION AND LOCATION
University of Arkansas, Fayetteville, AR
University of Michigan, Ann Arbor, MI
University of Michigan, Ann Arbor, MI
Los Alamos National Laboratory, Los Alamos,
NM
DEGREE
(if applicable)
MM/YY
B.S.
M.S.
Ph.D.
05/89
05/91
12/96
Postdoctoral
1996-2000
FIELD OF STUDY
Chem. Eng.
Chem. Eng.
Chem. Eng.
Theor. Immunol.
A. Personal Statement
I received my PhD working with Michael A. Savageau (Member, Institute of Medicine of the US National
Academies) on theoretical studies of the design principles of genetic regulatory circuits. I did postdoctoral work
with Alan S. Perelson (Fellow, American Academy of Arts and Sciences) on HIV dynamics in lymphoid tissue
and on multivalent ligand-receptor binding. I also did postdoctoral work with Byron Goldstein on modeling of
mammalian cell signaling systems. My primary appointment is in the Theoretical Division of Los Alamos
National Laboratory. I am also affiliated with the Biology department at the University of New Mexico and a
translational research group focused on pancreatic cancer (Clinical Translational Research Division,
Translational Genomics Research Institute). Because mechanistic modeling of cellular regulatory systems
containing important drug targets can in principle be used to better leverage available knowledge when
developing and evaluating drugs, especially molecularly targeted drugs, I am pursuing work that advances the
prospect of mechanistic modeling playing a central role in planning of clinical trials and in evaluation of clinical
data. In this work, my group takes advantage of the theoretical framework of rule-based modeling. I have
approximately 10 years of experience in rule-based modeling and more than 15 years of experience in
modeling of cellular regulatory systems. My research group has made influential contributions to the
development of the rule-based modeling approach in biology, and we have been engaged in the development
of various algorithms and software tools, such as BioNetGen, which now enable simulation of the system-level
dynamics of protein-protein interactions with consideration of site-specific details, i.e., the site dynamics of
biomolecular interaction networks. I collaborate with a number of quantitative experimentalists. For example, in
the area of immunoreceptor signaling, I collaborate with the experimental researchers in the Center for the
Spatiotemporal Modeling of Cell Signaling (stmc.health.unm.edu, systemscenters.org), an NIH/NIGMSsupported national center for systems biology headquartered within the University of New Mexico Cancer
Center and involving researchers from University of New Mexico and the Los Alamos and Sandia National
Laboratories.
B. Positions and Honors
Employment
1989-1996
1996-2000
2000-2004
Graduate Research Assistant, Department of Chemical Engineering, University of
Michigan, Ann Arbor, MI (with Michael A. Savageau)
Postdoctoral Research Associate, Theoretical Biology and Biophysics Group, Theoretical
Division, Los Alamos National Laboratory, Los Alamos, NM (with Alan S. Perelson and
Byron Goldstein)
Limited-term Technical Staff Member, Theoretical Biology and Biophysics Group,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM
2004-2008
Technical Staff Member, Theoretical Biology and Biophysics Group, Theoretical Division,
Los Alamos National Laboratory, Los Alamos, NM
2006-2007
Acting Deputy Center Leader, Center for Nonlinear Studies, Los Alamos National
Laboratory, Los Alamos, NM
2007-present Research Associate Professor, Department of Biology, University of New Mexico,
Albuquerque, NM
2008-present Scientist 3, Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos
National Laboratory, Los Alamos, NM
2010-2011
Visiting Randy Pausch Scholar, Clinical Translational Research Division, Translational
Genomics Research Institute, Scottsdale, AZ (sabbatical)
Other Experience
2002-present Temporary member (9x) or mail/phone reviewer (13x) for >15 different NIH panels/study
sections
2003-2011
Adjunct Assistant Professor, Department of Biology, University of New Mexico,
Albuquerque, NM
2003-present Investigator, Center for Evolutionary and Theoretical Immunology, College of Arts and
Sciences, University of New Mexico, Albuquerque, NM
2007-present Member, Executive Committee, Center for Nonlinear Studies, Los Alamos National
Laboratory, Los Alamos, NM
2007-present Organizer, Annual q-bio Summer School and Conference
2008-present Editorial Board, Mathematical Biology Section, Biology Direct
2009-2011
Editorial Board, Self/Nonself
2009-present Member, Science Council, Information Science and Technology Center, Los Alamos
National Laboratory, Los Alamos, NM
2009-present Researcher, Hematological Malignancies Research Program, University of New Mexico
Cancer Center, Albuquerque, NM
2011-present Adjunct Associate Professor, Department of Biology, University of New Mexico,
Albuquerque, NM
2011-present Adjunct Associate Professor, Research Clinical Translational Division, Translational
Genomics Research Institute, Phoenix, AZ
2013-present Editorial Board, Immunomics
Honors
1986-1989
1990-1993
1992-1993
2010-present
Kodak Scholar
Du Pont Research Fellow
Du Pont Teaching Fellow
Arkansas Academy of Chemical Engineers
C. Selected Peer-reviewed Publications (from ~70, h-index = 28 according to Google Scholar)
1. W. S. Hlavacek, A. Redondo, H. Metzger, C. Wofsy and B. Goldstein (2001) Kinetic proofreading models
for cell signaling predict ways to escape kinetic proofreading. Proc. Natl. Acad. Sci. USA 98, 7295-7300.
2. J. R. Faeder, W. S. Hlavacek, I. Reischl, M. L. Blinov, H. Metzger, A. Redondo, C. Wofsy and B. Goldstein
(2003) Investigation of early events in FcRI-mediated signaling using a detailed mathematical model. J.
Immunol. 170, 3769-3781.
3. M. E. Wall, W. S. Hlavacek and M. A. Savageau (2004) Design of gene circuits: lessons from bacteria. Nat.
Rev. Genet. 5, 34-42.
4. B. Goldstein, J. R. Faeder and W. S. Hlavacek (2004) Mathematical and computational models of immunereceptor signalling. Nat. Rev. Immunol. 4, 445-456.
5. W. S. Hlavacek, et al. (2006) Rules for modeling signal-transduction systems. Science’s STKE 2006:re6.
6. J. Yang, M. I. Monine, J. R. Faeder and W. S. Hlavacek (2008) Kinetic Monte Carlo method for rule-based
modeling of biochemical networks. Phys. Rev. E 78:031910. PMCID: PMC2652652
7. J. R. Faeder, J., M. L. Blinov and W. S. Hlavacek (2009) Rule-based modeling of biochemical systems with
BioNetGen. Methods Mol. Biol. 500, 113-167. ISBN: 978-1-934115-64-0
8. J. Colvin, M. I. Monine, J. R. Faeder, W. S. Hlavacek, D. D. Von Hoff and R. G. Posner (2009) Simulation
of large-scale rule-based models. Bioinformatics 25, 910-917. PMCID: PMC2660871
9. J. Colvin, M. I. Monine, R. N. Gutenkunst, W. S. Hlavacek, D. D. Von Hoff and R. G. Posner (2010)
RuleMonkey: software for stochastic simulation of rule-based models. BMC Bioinformatics 11:404. PMCID:
PMC2921409
10. L. A. Chylek, B. Hu, M. L. Blinov, T. Emonet, J. R. Faeder, B. Goldstein, R. N. Gutenkunst, J. M. Haugh, T.
Lipniacki, R. G. Posner, J. Yang and W. S. Hlavacek (2011) Guidelines for visualizing and annotating rulebased models. Mol. BioSyst. 7, 2779-2795. PMCID: PMC3168731
11. D. Barua, W. S. Hlavacek, T. Lipniacki (2012) A computational model for early events in B cell antigen
receptor signaling: analysis of the roles of Lyn and Fyn. J. Immunol. 189, 646-658. PMCID: PMC3392547
12. M. S. Creamer, E. C. Stites, M. Aziz, J. A. Cahill, C. W. Tan, M. E. Berens, H. Han, K. J. Bussey, D. D. Von
Hoff, W. S. Hlavacek and R. G. Posner (2012) Specification, annotation, visualization and simulation of a
large rule-based model for ERBB receptor signaling. BMC Syst. Biol. 6:107. PMCID: PMC3485121
13. M. Maienschein-Cline, A. R. Dinner, W. S. Hlavacek and F. Mu (2012) Improved predictions of transcription
factor binding sites using physicochemical features of DNA. Nucleic Acids Res. 40:e175. PMCID:
PMC3526315
14. K. R. Martin, D. Barua, A. L. Kauffman, L. M. Westrate, R. G. Posner, W. S. Hlavacek and J. P. MacKeigan
(2013) Computational model for autophagic vesicle dynamics in single cells. Autophagy 9, 74-92. PMCID:
PMC3542220
15. K. Nowak-Lovato, L. B. Alexandrov, A. Banisadr, A. L. Bauer, A. R. Bishop, A. Usheva, F. Mu, E. HongGeller, K. O. Rasmussen, W. S. Hlavacek and B. S. Alexandrov (2013) Binding of nucleoid-associated
protein Fis to DNA is regulated by DNA breathing dynamics. PLOS Comput. Biol. 9:e1002881. PMCID:
PMC3547798
D. Research Support
Ongoing Research Support
P50 GM085273-04
Oliver, Janet M (PI)
08/01/09-07/31/14
Center for the spatiotemporal modeling of cell signaling (STMC)
The goal of my project within this national systems biology center is to model cell signaling systems, especially
IgE receptor signaling.
Role: Co-PI, Project Leader
R13 GM082162-04
Hlavacek, William S, et al. (MPI)
06/10/09-07/31/14
Information processing in cellular signaling and gene regulation
The goal of this project is to organize the annual q-bio Conference, the purpose of which is to advance
modeling of cellular regulatory systems.
Role: Contact MPI
Pending Research Support
R25 GM105608-01
Munsky, B., et al. (MPI)
The q-bio Summer School
The goal of this project is to organize the annual q-bio Summer School, the purpose of which is to advance
modeling of cellular regulatory systems by offering training in statistical, mathematical, and computational
methodologies used in synthetic and systems biology.
Role: MPI
Completed Research Support
P20 RR018754/P20 GM103452-09
Loker, Eric S (PI)
09/30/03-05/31/14
Center for evolutionary and theoretical immunology (CETI)
A goal of CETI is to support new investigators. The goal of my project within this COBRE center was to model
cell signaling processes related to immunity and to develop tools for modeling such processes.
Role: Project Leader
R21 GM080216-02
Hlavacek, William S (PI)
05/01/07-04/30/10
System-wide study of transcriptional control of metabolism
A goal of this project was to develop/demonstrate statistical methods for metabolic network reconstruction from
high-throughput metabolomics data.
Role: PI
R01 GM076570-03
Hlavacek, William S (PI)
07/09/07-05/31/10
Computational tools for rule-based modeling of biochemical systems
A goal of this project was to develop computational tools (viz., BioNetGen, version 2) for rule-based modeling
of biochemical systems, especially cell signaling systems.
Role: PI