Ádám M. Halász

   Research Scientist

 

Contact Information

Address:

GRASP Laboratory, Levine Hall L402
University of Pennsylvania
3330 Walnut Street
Philadelphia, PA 19104-6228
USA

Phone:

215-898-5814

Fax:

215-573-2048

Email:

Username halasz at host grasp.upenn.edu

Web:

http://www.seas.upenn.edu/~halasz

Research interests

molecular systems biology, stringent response and persistence in E.coli and M.tb, mesoscopic phenomena in cells, multiple phenotypes and switching mechanisms, rescaling of model parameters from single cells to cell populations, metabolic networks, producibility, extreme conservation laws, biologically inspired controllers for swarms of robots, hybrid dynamical systems models of biomolecular networks, reachability, piecewise linear and multilinear systems, spatial Monte Carlo models

Course(s)

Spring 2007 - ESE680-003 Systems Biology. (course web site)(flyer)

Education

Sept. 2004 – Aug. 2006

NIH-NLM bioinformatics fellowship, University of Pennsylvania
Project: Computational Model for the Stringent Response in Mycobacterium tuberculosis

Mentors: Vijay Kumar and Harvey Rubin

Aug. 1995 – Aug. 1998

Ph.D. in Nuclear Physics, State University of New York at Stony Brook

Thesis: Applications of Random Matrix Theory to QCD

Advisor: Jacobus Verbaarschot

Group leader: Gerald Brown

Aug. 1993 – Dec. 1995

M. A. in Physics, State University of New York at Stony Brook

June 1984 – June 1989

State Diploma in Physics, University of Bucharest, Romania

Atomic physics

Advisor: Viorica Florescu

Research positions

July 2003 – present

Research Scientist, University of Pennsylvania
Molecular systems biology

(funding: DARPA, Penn Genomics Institute)

Supervisor: Vijay Kumar

July 2001 – July 2003

Postdoctoral fellow, University of Pennsylvania

National Digital Medical Archive project (funding: NIH-NLM)

Advisor: Robert Hollebeek

Oct. 1998 – June 2001

Postdoctoral fellow, University of Pennsylvania

Nuclear theory (funding: NSF)

Advisor: Ralph Amado

July 1990 - Aug. 1993

Research scientist, Institute of Environmental Research and Engineering, Bucharest

Environmental radioactivity (funding: Romanian Ministry of Environment)

Supervisors: Iolanda Osvath, Constantin Dovlete

Publications

Computational biology, swarm robotics

Journal publications and book chapters

Á. Halász, V. Kumar, M. Imielinski, C. Belta, O. Sokolsky, S. Pathak, Analysis of Lactose Metabolism in E.coli using Reachability Analysis of Hybrid Systems, IET Systems Biology,  1, 130 (2007)

A.A. Julius, Á. Halász. S. Sakar, V. Kumar, G. J. Pappas, Controlling biological systems: the lactose regulation system of E.coli, IEEE Transactions on Automatic Control Special Issue on Systems Biology, 51-64 (2007).

Berman, S., Á. Halász, V. Kumar, MARCO: A Reachability Algorithm for Multi-Affine Systems with Application to Biological Systems, accepted to the 10th Int’l Workshop on Hybrid Systems: Computation and Control, Pisa, Italy; LNCS 4416, 76-89 (2007).

Berman, S., Á. Halász, V. Kumar, Algorithms for Analysis and Synthesis of a Bio-Inspired Swarm Robotic System, Swarm Robotics Workshop, 9th  Int’l Conference on the Simulation of Adaptive Behavior (SAB’06), Rome, Italy; LNCS 4433, 56-70 (2007).

Imielinski M, C. Belta, H. Rubin, Á Halász, Systematic analysis of conservation relations in E.coli genome-scale metabolic network reveals novel growth media, Biophys J. 2006, Apr 15; 90(8):2659-72.

Imielinski M, C. Belta, Á Halász, H. Rubin, Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities, Bioinformatics. 2005 May 1; 21(9):2008-16.

Belta, C., P. Finin, L. C. Habets, Á. Halász, M. Imielinski, V. Kumar, and H. Rubin, Understanding the bacterial stringent response using reachability analysis of hybrid systems, 7th Int’l workshop on Hybrid Systems: Computation and Control, LNCS 2993, R. Alur and G. J. Pappas (Eds.) 111-125, 2004.

1.       Submitted and in preparation

Á. Halász, M. Imielinski, M. Buckstein, M Marjanovich, J. S. Teh, V. Kumar, H. Rubin, E.coli Persistence as Random Toxin Activation Followed by Slow Deterministic Recovery, (submitted)

M. A. Hsieh, Á. Halász, S. Berman, V. Kumar, Biologically Inspired Redistribution of a Swarm of Robots Among Multiple Sites (submitted).

Á. Halász, V. Kumar, H. Rubin, Kinetic model of ppGpp and growth rate control in Escherichia coli (in preparation)

Á. Halász, A. A. Julius, S. Sakar, V. Kumar, H. Rubin, G. Pappas, Reconciling individual and population-level behavior: towards a single quantitative model of microscopic and macroscopic dynamics in the E. coli  lactose utilization network (in preparation)

Á. Halász, V. Kumar, J. Kim, J. Eberwine, Numerical signatures of phenotypic switching, (in preparation)

Conference proceedings

Á Halász, M. A. Hsieh, S. Berman, V. Kumar, "Dynamic Redistribution of a Swarm of Robots among Multiple Sites", Proc. of the 2007 IEEE/RSJ Conference on Intelligent Robots and Systems, 2320-2325 (2007).

Julius, A. Halasz, V. Kumar, G.J. Pappas, "Controlling biological systems: the lactose regulation system of Escherichia coli", Proc. of the 26th American Control Conference, New York, NY (2007).

Berman, S., Á Halász, V. Kumar, S. Pratt, Bio-Inspired Group Behaviors for the Deployment of a Swarm of Robots to Multiple Destinations, Proc. of the 2007 IEEE International Conference on Robotics and Automation, (ICRA 2007) Rome, Italy.

A.A. Julius, Á. Halász, V. Kumar, G.J. Pappas, Finite state abstraction of a stochastic model of the lactose regulation system of Escherichia coli, Proc. Of the 45th IEEE Conf. Decision and Control 2006, San Diego, USA.

Ahmadzadeh, Á. Halász, S. Prajna, A. Jadbabaie, and V. Kumar., Analysis of the Lactose metabolism in E. coli using sum-of-squares decomposition. ECC-CDC 2005, Seville, Spain, Proc. of the 44th IEEE Conf. Decision and Control 2005.

Conference presentations and posters

A. Julius, Á. Halász, V. Kumar, G. Pappas, A finite model for the random behavior in the lactos regulation system of Escherichia coli, 7th  International Conference on Systems Biology, Yokohama, Japan, October 2006 (poster)

Á. Halász, Kinetic Model of ppGpp in Growth Regulation Offers Possible Mechanism for Persistence in the Presence of Antibiotics, NLM Informatics Training Conference, Vanderbilt University, Nashville, TN, June 2006 (talk)

Á. Halász, M. Imielinski, M. Buckstein, V. Kumar, H. Rubin, A Model for Comprehensive Growth Control Mediated by ppGpp., 6th International Conference on Systems Biology, Boston, MA, October 2005 (poster)

M. Imielinski, C. Belta, H. Rubin, Á. Halász, Systematic analysis of conservation relations in the E. coli genome scale metabolic network reveals novel minimal growth media, 6th International Conference on Systems Biology, Boston, MA, October 2005 (poster)

Á. Halász, V. Kumar, H. Rubin, Classifying Models of the Stringent Response in M.tuberculosis and E.coli, 13th Annual International Conference on Microbial Genomes, Madison, WI, September 2005 (poster)

Á. Halász, M. Imielinski, P. Finin, O. Sokolsky, H. Rubin, and V. Kumar, The lactose utilization network of E.coli as a hybrid system: exploring bistability with reachability analysis, Foundations of Systems Biology in Engineering (FOSBE), Santa Barbara, CA, August 2005 (contributed paper / poster).

Á. Halász, V. Kumar, H. Rubin, Classifying Models of the Stringent Response in M.tuberculosis and E.coli, NLM Informatics Training Conference, National Institutes of Health, Bethesda, MD, June 2005 (poster)

Á. Halász, V. Kumar, M. Imielinski, P. Finin, C. Belta, O. Sokolsky, H. Rubin, Applications of Hybrid Systems Methods to Medium-Sized Biochemical Networks, 2nd Annual Retreat of the Greater Philadelphia Bioinformatics Alliance, Penn State Great Valley, Malvern, PA, October 2004 (talk)

M. Imielinski, C. Belta, Á. Halász, and H. Rubin, Probing metabolite essentiality through in silico genome scale analysis of E. coli production capabilities, 5th International Conference on Systems Biology, Heidelberg, Germany, October 2004 (poster -Best Poster Award)

Á. Halász, M. Buckstein, M. Imielinski, V. Kumar, H. Rubin, Computational Model for the Bacterial Stringent Response, 5th International Conference on Systems Biology, Heidelberg, Germany, October 2004 (poster)

Seminars, lectures, invited talks

Mesoscopic and Stochastic Phenomena Illustrated in the lac Operon, Workshop: Toward Systems Biology, Université Joseph-Fourier, Grenoble, France, October, 2007 (invited talk)

E.coli Persistence as Random Toxin Activation Followed by Slow Deterministic Recovery, BioMaPS Institute, Rutgers University, March 21, 2007 (seminar)

Bacterial Persistence in the Presence of Antibiotics, Infectious Diseases Division, Department of Medicine, University of Pennsylvania, April 20, 2006 (seminar)

Incomplete Parameter Information in Biochemical Network Models, Computer Science and Mathematics Division, Oak Ridge National Laboratory, November 8, 2005 (invited talk)

Hybrid Systems Methods for Biochemical Networks, GRASP student/postdoc seminar, GRASP Laboratory, University of Pennsylvania, October 2005 (seminar)

Hybrid systems methods for biochemical networks, DARPA BioSpice (www.biospice.org) presentation, September 2005. (web seminar)

Nuclear and Atomic Physics

Journal articles and conference proceedings

M. Á. Halász, R.D. Amado, Skyrmion-AntiSkyrmion Annihilation with Omega Mesons , Phys. Rev. D 63 (2001), 054020, hep-ph/0009260 .

R.D. Amado, M. Á. Halász, P. Protopapas , Two Skyrmion Dynamics with Omega Mesons , Phys. Rev. D 61 (2000), 074022, hep-ph/9909426 .

M.Á. Halász, J.C. Osborn, M. Stephanov, J. J. M. Verbaarschot , Random Matrices and the Convergence of Partition Function Zeros in Finite Density QCD , Phys. Rev. D 61 (2000), 076005, hep-lat/9908018 .

M.Á. Halász, Random Matrices and the Glasgow Method , Workshop on QCD at Finite Density, Bielefeld, Germany, April 1998, Nucl. Phys. A642 (1998), 324, hep-lat/9806028 .

M.Á. Halász, A. D. Jackson, R. Shrock, M. Stephanov, J. J. M. Verbaarschot , On the Phase Structure of QCD , Phys. Rev. D58 (1998), 096007, hep-ph/9804290 .

M.Á. Halász, J. V. Steele, G. Q. Li, G. E. Brown , Photon Rates for Heavy-Ion Collisions from Hidden Local Symmetry , Phys. Rev. C58 (1998), 365, nucl-th/9712006 .

M.Á. Halász, J.C. Osborn, J.J.M. Verbaarschot , Random Matrix Triality at Nonzero Chemical Potential , Phys. Rev. D56 (1997), 7059, hep-lat/9704007.

M.Á.Halász, A.D. Jackson, J.J.M. Verbaarschot , Fermion Determinants in Matrix Models of QCD at Nonzero Chemical Potential , Phys. Rev. D56 (1997), 5140, hep-lat/9703006 .

M.Á.Halász, A.D. Jackson, J.J.M. Verbaarschot , Yang-Lee Zeros of a Random Matrix Model for QCD at Finite Density , Phys. Lett. B395 (1997), 293, hep-lat/9611008 .

M.Á.Halász, T.Kalkreuter, J.J.M.Verbaarschot, Universal Correlations in Spectra of the Lattice QCD Dirac Operator , Lattice '96, St.Louis, MO, 4-8 June 1996; Nucl. Phys. Proc. Suppl. 53 (1997), 266, hep-lat/9607042 .

M.Á.Halász, and J.J.M.Verbaarschot , Effective Lagrangians and Chiral Random Matrix Theory , Phys. Rev. D52 (1995), 2563, hep-th/9502096 .

M.Á.Halász, and J.J.M.Verbaarschot , Universal Correlations in Spectra of the Lattice Dirac Operator , Phys. Rev. Lett. 74 (1995), 3920, hep-lat/9501025.

V.Florescu, M.Á.Halász, M.Marinescu , Second-order Corrections to the Wave Functions of a Coulomb Field Electron in a Weak Uniform Harmonic Electric Field , Phys. Rev. A47 (1993), 394.

M.Á.Halász, J. Osborn, M. Stephanov and J.Verbaarschot , Random Matrices and Algorithms for Lattice QCD at m¹0 , in Proceedings of the ECT* Workshop on Understanding Deconfinement in QCD, Trento, Italy, March 1-13, 1999.

M.Á.Halász, Random Matrices and the Glasgow Method, Workshop on QCD at Finite Density, Bielefeld, Germany, April 1998, Nucl. Phys. A642 (1998), 324.

V. Cuculeanu, N. Romanof,  M.Á.Halász, Non-Local Model for Radon and Thoron Diffusion, Fifth International Symposium on the Natural Radiation Environment, Salzburg, Austria, 1991; Published in Radiation Protection Dosimetry 45 (1992), 411.