Gheorghe Craciun
Associate Professor
Department of Mathematics and
Department of Biomolecular Chemistry
University of Wisconsin-Madison
Contact Information:
405 Van Vleck Hall
480 Lincoln Dr
Madison, WI 53706-1388
Phone: (608) 265-3391
Fax: (608) 263-8891
E-mail: craciun at math dot wisc dot edu
Teaching
Research Interests: Mathematical and Computational
Methods in Biology and Medicine
Publications
- Periodic Patterns in
Distributions of Peptide Masses,
(with Shane Hubler),
submitted.
- Counting Chemical Compositions using Ehrhart
Quasi-Polynomials, (with Shane Hubler), submitted.
- The QSSA in
chemical kinetics: As taught and as practiced, (with Casian Pantea, Ankur Gupta, and James B.
Rawlings), submitted.
- Persistence and
permanence of mass-action and power-law dynamical systems, (with Fedor Nazarov and Casian Pantea), submitted, available at
arXiv:1010.3050v2.
- Global injectivity
and multiple equilibria in uni- and bi-molecular reaction networks, (with Casian Pantea and Heinz Koeppl), Discrete
and Continuous Dynamical Systems - Series B, 2012, to appear.
- Mass
distributions of linear chain polymers, (with Shane Hubler), Journal
of Mathematical Chemistry, 2012, to appear.
- Statistical Model for
Biochemical Networks Inference, (with
Jajae Kim, Casian Pantea and Grzegorz A. Rempala), to appear in Communications
in Statistics: Simulation and Computation, 2012. PDF
- Graph-theoretic
characterizations of multistability and monotonicity for biochemical
reaction networks, (with Casian Pantea and Eduardo Sontag), in
Koeppl, H.; Densmore, D.; Setti, G.; di Bernardo, M. (Eds.), Design
and Analysis of Biomolecular Circuits, Springer, 2011. PDF
- Computational
methods for analyzing bistability in biochemical reaction networks, (with Casian Pantea) Proceedings of the IEEE
International Symposium on Circuits and Systems, 549-553, 2010. PDF
- Product-form
stationary distributions for deficiency zero chemical reaction networks, (with David F. Anderson and Thomas G. Kurtz),
Bulletin
of Mathematical Biology, 72:8, 1947-1970, 2010. PDF
- Graph theoretic
approaches to injectivity in general chemical reaction systems, (with Murad Banaji), Advances in Applied Mathematics
44 168-184, 2010. PDF
- Some Geometric
Aspects of Control Points for Toric Patches, (with Luis David Garcia-Puente, Frank Sottile),
Proceedings of the 7th international conference on Mathematical Methods
for Curves and Surfaces, (M. Daehlen et al. Eds). Lecture Notes in Computer Science
5862, 111-135, Springer Heidelberg, 2010. PDF
- Algebraic methods for
inferring biochemical networks: a maximum likelihood approach, (with Casian Pantea and Grzegorz A. Rempala), Computational
Biology and Chemistry, 33(5):361-367, 2009. PDF
- Graph-theoretic
approaches to injectivity and multiple equilibria in systems of
interacting elements, (with
Murad Banaji), Communications in Mathematical Sciences 7:4,
867–900, 2009. PDF
- Time course
analysis of microarray data for the pathway of reproductive development
in female rainbow trout, (with
Yushi Liu, Joseph Verducci, Irvin Schultz, Sharon Hook, James Nagler,
Kaitlin Sundling, and William Hayton), Statistical Analysis and Data Mining,
2:3, 192-208, 2009. PDF
- Toric Dynamical
Systems, (with Alicia
Dickenstein, Anne Shiu, Bernd Sturmfels), Journal of Symbolic Computation 44:11,
1551–1565 , 2009. PDF
- Homotopy methods for
counting reaction network equilibria, (with J. William Helton, Ruth J. Williams), Mathematical
Biosciences 216:2, 140-149, 2008. PDF
- A lifespan-extending
form of autophagy employs the vacuole-vacuole fusion machinery, (with Fusheng Tang, Joseph Watkins, Maria
Bermudez, Russell Gray, Adam Gaban, Ken Portie, Stephen Grace, Maurice
Kleve), Autophagy
4:7, 874-886, 2008. PDF
- Multigraph conditions
for multistability, oscillations and pattern formation in biochemical
reaction networks, (with Maya
Mincheva), Proceedings of IEEE 96:8, 1281-1291, 2008. PDF
- A Combinatorial H4
Tail Library for Exploring the Histone Code, (with Adam L. Garske, John M. Denu), Biochemistry
47:31, 8094-8102, 2008. PDF
- Valence Parity
Renders z-type ions Chemically Distinct, (with Shane Hubler, April Jue, Jason Keith,
Graeme McAlister, Joshua Coon), Journal of the American Chemical Society
130:20, 6388-6394, 2008. PDF
- Identifiability of
chemical reaction networks,
(with Casian Pantea), Journal of Mathematical Chemistry 44:1, 244-259, 2008. PDF
- Understanding
Bistability in Complex Enzyme-Driven Reaction Networks, (with Martin Feinberg and Yangzhong Tang), Proceedings
of the National Academy of Sciences 103:23, 8697-8702, 2006. PDF
- Approximate Traveling
Waves in Linear Reaction-Hyperbolic Equations,
(with Avner Friedman), SIAM Journal on Mathematical Analysis 38:3, 741-758, 2006. PDF
- Multiple Equilibria
in Complex Chemical Reaction Networks: Extensions to Entrapped Species
Models, (with Martin Feinberg), IEE Proceedings Systems Biology
153:4, 179-186, 2006. PDF
- Multiple Equilibria
in Complex Chemical Reaction Networks: II. The Species-Reactions Graph,
(with Martin Feinberg), SIAM Journal on Applied Mathematics
66:4, 1321-1338, 2006. PDF
- Multiple Equilibria
in Complex Chemical Reaction Networks: I. The Injectivity Property,
(with Martin Feinberg), SIAM Journal on Applied Mathematics
65:5, 1526-1546, 2005.
PDF
- A Model of Intracellular
Transport of Particles in an Axon, (with Avner Friedman), Journal of Mathematical Biology, 51:2,
217-246, 2005. PDF
- A Distributed
Parameter Identification Problem in Neuronal Cable Theory Models, (with Jonathan Bell), Mathematical Biosciences 194:1,
1-19, 2005. PDF
- Data Sources and
Computational Approaches for Generating Models of Gene Regulatory
Networks, (with Baltazar Aguda
and Rengul Cetin-Atalay), Reviews in Computational Chemistry, Vol. 21, edited by Kenny Lipkowitz, Raima Larter, and
Thomas R. Cundari, 2005. PDF
- Spatial Domain
Wavelet Design for Feature Preservation in Computational Datasets, (with Ming Jiang, David Thompson, and Raghu
Machiraju), accepted by IEEE Transactions on Visualization and
Computer Graphics 11:2, 149-159, 2005. PDF
- Controlling Release
from the Lipidic Cubic Phase by Selective Alkylation, (with Jeffrey Clogston, David Hart, and
Martin Caffrey), Journal of Controlled Release, 102:2, 441-461, 2005. PDF
- Everybody Else Is:
Networks, Power Laws and Peer Contagion in the Aggressive Recess
Behavior, (with Keith Warren
and Dawn Anderson-Butcher), Nonlinear Dynamics, Psychology, and Life
Sciences, 9:2, 155-173, 2005.
- Mathematical Analysis
of a Modular Network Coordinating the Cell Cycle and Apoptosis, (with Baltazar Aguda and Avner Friedman), Mathematical
Biosciences and Engineering, 2:3, 473-485, 2005. PDF
- Mathematical Models
of the Cell Cycle and Apoptosis,
(with David Goulet, Namyong Lee, Taras Odushkin, Galen Cook Wiens), MBI
Technical Report, 2004.
- Orientation
Preserving Homeomorphisms of the Sphere Have a Cantor Set of Fixed
Points, submitted.
- Image Segmentation
using Neuronal Oscillators, (with
Talia Konkle, Ning Jiang, Jie Zhang, Fatma Gurel, Christopher Scheper),
MBI Technical Report, 2003.
- Physics-based feature
mining for large data exploration, (with
D.S. Thompson, R.K. Machiraju, M. Jiang, J.S. Nair, S.S.D.
Venkata), Computing in Science and Engineering 4:4, 22-30, 2002. PDF
- The Output of
Chemical Reactors Is Almost Always Unique. Why ?, Proceedings of the 14th Annual Edward F.
Hayes Research Forum, p. 184-189, 2001.
- A Framework for
Filter Design Emphasizing Multiscale Feature Preservation, (with David Thompson, Raghu Machiraju and
Ming Jiang), Proceedings of the AHPCRC and CASC/LLNL Third Workshop on
Mining Scientific Datasets , p. 105-111, 2001.
- The Dimension Print
of Most Convex Surfaces, (with
Tudor Zamfirescu), Monatshefte fur Mathematik 123:3, 203-207, 1997. PDF
- Most Homeomorphisms
of the Circle are Semiperiodic,
(with Paul Horja, Mihai Prunescu, Tudor Zamfirescu), Archiv
der Mathematik 64:5, 452-458, 1995. PDF
- Generic Properties of
the Homeomorphisms of Spheres,
Archiv
der Mathematik 62:4, 349-353, 1994.
- On a Covering Theorem, Mathematical Reports 44:2, 109-112,
1992.