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), SIAM Journal on Applied Mathematics,
2012, to appear, PDF
- 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
- Multiple Equilibria in Complex
Chemical Reaction Networks: Semiopen Mass Action Systems (with Martin Feinberg), SIAM Journal on Applied Mathematics 70(6): 1859-1877, 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.