Reinhard Laubenbacher

Reinhard Laubenbacher,

Director

Department: MD-PULMONARY SYSTEMS MEDICINE
Business Phone: (352) 294-2350

About Reinhard Laubenbacher

Dr. Laubenbacher joined the University of Florida in May 2020 as a professor in the Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine. He is the director of the Laboratory for Systems Medicine. Prior to joining UF, he served as director of the Center for Quantitative Medicine and Professor in the Department of Cell Biology in the University of Connecticut School of Medicine. Concurrently, he held an appointment as Professor of Computational Biology at the Jackson Laboratory for Genomic Medicine. He is a fellow of AAAS, the Society for Mathematical Biology, and the American Mathematical Society. Since 2016, he serves as editor-in-chief of the Bulletin of Mathematical Biology, the flagship journal of the Society for Mathematical Biology. Dr. Laubenbacher is a mathematician by training, and his broad research interests lie in computational and mathematical systems biology, with applications to human health. Most of his research is in collaboration with a broad spectrum of scientists and clinicians.

Accomplishments

Fellow
2017 · Society for Mathematical Biology
Fellow
2015 · American Association for the Advancement of Science
Fellow
2012 · American Mathematical Society

Research Profile

The Laubenbacher Lab is part of the Laboratory for Systems Medicine. The overarching focus is the development and application of mathematical and computational technology for the improvement of human health. Interests include multi-scale modeling and control of disease processes, systems biology, and computational immunology. We are highly collaborative, maintaining and seeking partnerships with clinical, basic science, computational, and private sector labs and entities. Our expertise includes the development of mechanistic and data-driven multi-scale models of disease-relevant processes, model-driven control and optimization problems, and cutting-edge data science methods applied to high-dimensional data from the molecular to the patient scale. Currently funded projects include the following.

1. Multiscale modeling of the battle over iron in invasive lung infection (NIH 1 R011AI1351128-01). Invasive aspergillosis is among the most common fungal infection in immunocompromised hosts and carries a poor outcome. Current therapeutic approaches have been focused primarily on the pathogen, but a better understanding of the components of host defense in this infection may lead to the development of new treatments against this infection, possibly in combination with antifungal drugs. Iron is essential to all living organisms, and restricting iron availability is a critical mechanism of antimicrobial host defense against many microorganisms. This mechanism has the potential to be harnessed therapeutically, for example with drugs that enhance the host’s iron sequestration mechanisms. The overarching goal of this project is to develop a multi-scale mathematical model that can serve as a simulation tool of the role of iron in invasive aspergillosis.

2. Modular design of multiscale models, with an application to the innate immune response to fungal respiratory pathogens. (1U01EB024501-01, NSF CBET-1750183) Increased availability of biomedical data sets across spatial and temporal scales makes it possible to calibrate complex models that capture integrated processes from the molecular to the whole organism level. This complexity poses multiple challenges related to mathematical modeling, software design, validation, reproducibility, and extensibility. Visualization of model features and dynamics is a key factor in the usability of models by domain experts, such as experimental biologists and clinicians. This project addresses these challenges in the context of the immune response to an important respiratory fungal infection. Its goal is to develop a novel modular approach to model architecture. The overarching computational goal is to develop a novel approach to the modular design of multiscale models.

3. Control of heterogeneous microbial communities using model-based multi-objective optimization (NIH 1R01GM127909-01, NIH 3 R01 GM127909-01S1) The project addresses an important biomedical problem: how to control biofilms formed by Candida albicans, a dimorphic fungus that is an important cause of both topical and systemic fungal infection in humans, in particular immunocompromised patients. C. albicans biofilms also form on the surface of implantable medical devices, and are a major cause of nosocomial infections. In recent years, it has been recognized that interactions with bacterial species integrated into biofilms can affect C. albicans virulence and other properties, It is therefore important to understand the interactions of C. albicans with bacterial species, in particular metabolic interactions. The next step then is to understand and, ultimately, control how varying compositions of the different microbial species affect their metabolic state and their ability to form biofilms. This project approaches the problem through model-based design of optimal compositions of the bacterial species for control of fungal growth, accomplished through a combination of the construction of a novel computational model of a heterogeneous biofilm consisting of bacterial as well as fungal species, and novel mathematical tools for dimension reduction and optimization. The applicability of the results of this project extends far beyond biofilms, such as studies of the human microbiome.

Open Researcher and Contributor ID (ORCID)

0000-0002-9143-9451

Areas of Interest
  • Disease Modeling
  • Mechanism-based mathematical modeling
  • Systems biology
  • data science

Publications

2021
“E-Cigarette Use in Young Adult Never Cigarette Smokers with Disabilities: Results from the Behavioral Risk Factor Surveillance System Survey”
Int. J. Environ. Res. Public Health. 18(10) [DOI] https://doi.org/10.3390/ijerph18105476.
2021
A modular computational framework for medical digital twins
Proceedings of the National Academy of Sciences. 118(20) [DOI] 10.1073/pnas.2024287118. [PMID] 33972437.
2021
Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review.
Microorganisms. 9(2) [DOI] 10.3390/microorganisms9020417. [PMID] 33671308.
2021
E-Cigarette Use in Young Adult Never Cigarette Smokers with Disabilities: Results from the Behavioral Risk Factor Surveillance System Survey.
International journal of environmental research and public health. 18(10) [DOI] 10.3390/ijerph18105476. [PMID] 34065407.
2021
Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies
PLOS Computational Biology. 17(3) [DOI] 10.1371/journal.pcbi.1008690. [PMID] 33780439.
2021
Using digital twins in viral infection.
Science (New York, N.Y.). 371(6534):1105-1106 [DOI] 10.1126/science.abf3370. [PMID] 33707255.
2020
A Near-Optimal Control Method for Stochastic Boolean Networks.
Letters in biomathematics. 7(1):67-80 [PMID] 34141873.
View on: PubMed
2020
Collectively canalizing Boolean functions
airXiv. [DOI] http://arxiv.org/abs/2008.13741.
2020
Control of Intracellular Molecular Networks Using Algebraic Methods
Bulletin of Mathematical Biology. 82(1) [DOI] 10.1007/s11538-019-00679-w. [PMID] 31919596.
2020
Factors associated with e-cigarette use in U.S. young adult never smokers of conventional cigarettes
International Journal of Environmental Research and Public Health. 17(19) [DOI] https://doi.org/10.3390/ijerph17197271.
2020
Factors Associated with E-Cigarette Use in U.S. Young Adult Never Smokers of Conventional Cigarettes: A Machine Learning Approach.
International journal of environmental research and public health. 17(19) [DOI] 10.3390/ijerph17197271. [PMID] 33027932.
2020
Sensitivity of comorbidity network analysis.
JAMIA open. 3(1):94-103 [DOI] 10.1093/jamiaopen/ooz067. [PMID] 32607491.
2020
Systems biology of ferroptosis: A modeling approach.
Journal of theoretical biology. 493 [DOI] 10.1016/j.jtbi.2020.110222. [PMID] 32114023.
2020
The contribution of microRNA-mediated regulation to short- and long-term gene expression predictability.
Journal of theoretical biology. 486 [DOI] 10.1016/j.jtbi.2019.110055. [PMID] 31647935.
2020
The Dynamics of Canalizing Boolean Networks
Complexity. 2020:1-14 [DOI] 10.1155/2020/3687961.
2019
A mathematical model of combined CD8 T cell costimulation by 4-1BB (CD137) and OX40 (CD134) receptors.
Scientific reports. 9(1) [DOI] 10.1038/s41598-019-47333-y. [PMID] 31350431.
2019
Boolean models in immunology
Systems Immunology: An Introduction to Modeling Methods for Scientists.
2019
Connecting the molecular function of microRNAs to cell differentiation dynamics.
Journal of the Royal Society, Interface. 16(158) [DOI] 10.1098/rsif.2019.0437. [PMID] 31551049.
2019
Dynamics of semilattice networks with strongly connected dependency graph
Automatica. 99:167-174
2019
Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors.
PLoS computational biology. 15(6) [DOI] 10.1371/journal.pcbi.1007026. [PMID] 31194735.
2019
PlantSimLab – a modeling and simulation web tool for plant biologists
BMC Bioinformatics. 20(1) [DOI] 10.1186/s12859-019-3094-9. [PMID] 31638901.
2019
Topological Data Analysis.
Bulletin of mathematical biology. 81(7) [DOI] 10.1007/s11538-019-00610-3. [PMID] 31066000.
2018
A Systems Biology Approach to Understanding the Pathophysiology of High-Grade Serous Ovarian Cancer: Focus on Iron and Fatty Acid Metabolism.
Omics : a journal of integrative biology. 22(7):502-513 [DOI] 10.1089/omi.2018.0060. [PMID] 30004845.
2018
An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study.
Molecular microbiology. 110(3):357-369 [DOI] 10.1111/mmi.14086. [PMID] 30047562.
2018
Applications of network analysis to routinely collected health care data: a systematic review.
Journal of the American Medical Informatics Association : JAMIA. 25(2):210-221 [DOI] 10.1093/jamia/ocx052. [PMID] 29025116.
2018
Editorial.
Bulletin of mathematical biology. 80(12):3069-3070 [DOI] 10.1007/s11538-018-0501-8. [PMID] 30171473.
2018
The innate immune response to ischemic injury: a multiscale modeling perspective.
BMC systems biology. 12(1) [DOI] 10.1186/s12918-018-0580-z. [PMID] 29631571.
2017
Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective.
PLoS computational biology. 13(2) [DOI] 10.1371/journal.pcbi.1005352. [PMID] 28166223.
2017
Addressing current challenges in cancer immunotherapy with mathematical and computational modelling.
Journal of the Royal Society, Interface. 14(131) [DOI] 10.1098/rsif.2017.0150. [PMID] 28659410.
2017
Effects of research complexity and competition on the incidence and growth of coauthorship in biomedicine.
PloS one. 12(3) [DOI] 10.1371/journal.pone.0173444. [PMID] 28329003.
2017
Multistate nested canalizing functions and their networks
J. Theor. Comp. Sci.. 675
2017
Optimization and Control of Agent-Based Models in Biology: A Perspective.
Bulletin of mathematical biology. 79(1):63-87 [DOI] 10.1007/s11538-016-0225-6. [PMID] 27826879.
2017
The influence of canalization on the robustness of Boolean networks
Physica D. 353-354:39-47
2016
A computational model of invasive aspergillosis in the lung and the role of iron.
BMC systems biology. 10 [DOI] 10.1186/s12918-016-0275-2. [PMID] 27098278.
2016
Algebraic and discrete mathematical methods for modern biology [book review, Elsevier, Amsterdam, 2015]
SIAM Rev.. 58(2):367-369
2016
AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.
Bioinformatics (Oxford, England). 32(15):2396-8 [DOI] 10.1093/bioinformatics/btw120. [PMID] 27153722.
2016
Costimulation Endows Immunotherapeutic CD8 T Cells with IL-36 Responsiveness during Aerobic Glycolysis.
Journal of immunology (Baltimore, Md. : 1950). 196(1):124-34 [DOI] 10.4049/jimmunol.1501217. [PMID] 26573834.
2016
Editorial.
Bulletin of mathematical biology. 78(1):1-3 [DOI] 10.1007/s11538-015-0134-0. [PMID] 26754090.
2016
Editorial.
Bulletin of mathematical biology. 78(12) [DOI] 10.1007/s11538-016-0223-8. [PMID] 27796721.
2016
Identification of control targets in Boolean molecular network models via computational algebra.
BMC systems biology. 10(1) [PMID] 27662842.
View on: PubMed
2016
The phagosome: Meeting point of the Myddosome, NLRs, and degraded Borrelia burgdorferi
J. Immunology. 196 (1 Supplement)(131.2)
2015
A network biology approach to denitrification in Pseudomonas aeruginosa.
PloS one. 10(2) [DOI] 10.1371/journal.pone.0118235. [PMID] 25706405.
2015
Dimension reduction of large sparse AND-NOT network models
Electronic Notes in Theorical Computer Science. 316:83-95
2015
Iron acquisition and oxidative stress response in aspergillus fumigatus.
BMC systems biology. 9 [DOI] 10.1186/s12918-015-0163-1. [PMID] 25908096.
2015
Optimal harvesting for a predator-prey agent-based model using difference equations.
Bulletin of mathematical biology. 77(3):434-59 [DOI] 10.1007/s11538-014-0060-6. [PMID] 25559457.
2015
You can do anything with a math degree
Blog On Teaching and Learning Mathematics, American Mathematical Society. (January) [DOI] http://blogs.ams.org/matheducation/.
2014
A Mathematical Model of Skeletal Muscle Disease and Immune Response in themdxMouse
BioMed Research International. 2014:1-11 [DOI] 10.1155/2014/871810. [PMID] 25013809.
2014
A systems biology approach to iron metabolism.
Advances in experimental medicine and biology. 844:201-25 [DOI] 10.1007/978-1-4939-2095-2_10. [PMID] 25480643.
2014
Algebraic models and their use in systems biology
Discrete and Topological Models in Molecular Biology, Springer Verlag, NY.
2014
An algebra-based method for inferring gene regulatory networks.
BMC systems biology. 8 [DOI] 10.1186/1752-0509-8-37. [PMID] 24669835.
2014
Optimization of agent-based models: scaling methods and heuristic algorithms
J. Artificial Societies and Social Simulation. 17(2)
2014
Steady state analysis of Boolean molecular network models via model reduction and computational algebra.
BMC bioinformatics. 15 [DOI] 10.1186/1471-2105-15-221. [PMID] 24965213.
2014
Using difference equations to find optimal tax structures on the SugarScape
J. Economic Interaction and Coordination. 9(2):233-253
2013
Agent-based models and optimal control in biology: a discrete approach
Mathematical Concepts and Methods in Modern Biology, Elsevier.
2013
AND-NOT logic framework for steady state analysis of Boolean network models
Appl. Math. Inf. Sci.. 7(4)
2013
Boolean nested canalizing functions: a comprehensive analysis
J. Theor. Comp. Sci.. 481:24-36
2013
Computational systems biology: discrete models of gene regulatory networks
Undergraduate Mathematics for the Life Sciences: Processes, Models, and Directions, T. Comar, J. Carpenter, and G. Ledder (eds.), Mathematical Association of America, Washington, D.C..
2013
Evolutionary events in a mathematical sciences research collaboration network
Scientometrics. 99(3):973-998
2013
Finite Fields in Biology
Handbook of Finite Fields, CRC Press, Boca Raton, FL.
2013
Stabilizing gene regulatory networks through feedforward loops.
Chaos (Woodbury, N.Y.). 23(2) [DOI] 10.1063/1.4808248. [PMID] 23822505.
2013
Structure and dynamics of acyclic networks
Discrete Event Dynamic Systems. [DOI] DOI 10.1007/s10626-013-0174-2.
2013
The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide.
PloS one. 8(9) [DOI] 10.1371/journal.pone.0074939. [PMID] 24073228.
2013
The number of canalyzing functions over any finite set
Open J. of Discrete Math. 3(3):130-136
2012
Agent based modeling, mathematical formalism for
Computational complexity, Springer, New York. 1-6:88-104
2012
Modeling stochasticity and variability in gene regulatory networks.
EURASIP journal on bioinformatics & systems biology. 2012(1) [DOI] 10.1186/1687-4153-2012-5. [PMID] 22673395.
2012
Monomial dynamical systems over Fq with bidirectional cycle dependency graph
Far East Journal of Dynamical Systems. 20(2):77-93
2012
On the computation of fixed points in Boolean networks
J. Appl. Math. Comp.. 39(1-2):145-153
2012
The core control system of intracellular iron homeostasis: a mathematical model.
Journal of theoretical biology. 300:91-9 [DOI] 10.1016/j.jtbi.2012.01.024. [PMID] 22286016.
2012
The Number of Multistate Nested Canalyzing Functions
Physica D. 241:929-938
2011
A mathematical framework for agent based models of complex biological networks.
Bulletin of mathematical biology. 73(7):1583-602 [DOI] 10.1007/s11538-010-9582-8. [PMID] 20878493.
2011
A systems biology approach to cancer drug discovery
Encyclopedia of Systems Biology, Springer Verlag, New York.
2011
ADAM: analysis of discrete models of biological systems using computer algebra.
BMC bioinformatics. 12 [DOI] 10.1186/1471-2105-12-295. [PMID] 21774817.
2011
Algebraic methods in mathematical biology.
Bulletin of mathematical biology. 73(4):701-5 [DOI] 10.1007/s11538-011-9643-7. [PMID] 21400021.
2011
Bioinformatics tools for cancer metabolomics.
Metabolomics : Official journal of the Metabolomic Society. 7(3):329-343 [PMID] 21949492.
View on: PubMed
2011
Boolean models of bistable biological systems
Discrete and Cont. Dynamical Systems. 4(6):1414-1456
2011
Differential gene expression in normal and transformed human mammary epithelial cells in response to oxidative stress.
Free radical biology & medicine. 50(11):1565-74 [DOI] 10.1016/j.freeradbiomed.2011.03.002. [PMID] 21397008.
2011
Mathematics in the Public Mind: the U.S.A.
Public Awareness of Mathematics, E. Behrends, N. Crato, F. Rodrigues (Eds.), Springer Verlag, Heidelberg.
2011
Parameter estimation for Boolean models of biological systems
J. Theor. Comp. Sci.. 412:2816-2826
2011
Preface [Issue on biomathematics: newly developed applied mathematics and new mathematics arising from biosciences]
Discrete Contin. Dyn. Syst. Ser.. S 4
2011
Regulatory patterns in molecular interaction networks.
Journal of theoretical biology. 288:66-72 [DOI] 10.1016/j.jtbi.2011.08.015. [PMID] 21872607.
2010
Congressional Testimony on 21st Century Biology
Hearing of the Subcommittee on Research and Education of the House Committee on Science and Technology. June 29 [DOI] http://science.house.gov/publications/Testimony.aspx?TID=15466.
2010
Discretization of time series data.
Journal of computational biology : a journal of computational molecular cell biology. 17(6):853-68 [DOI] 10.1089/cmb.2008.0023. [PMID] 20583929.
2010
Polynomial algebra of discrete models in systems biology.
Bioinformatics (Oxford, England). 26(13):1637-43 [DOI] 10.1093/bioinformatics/btq240. [PMID] 20448137.
2010
Science advocacy, letter to the editor
Notices of the Amer. Math. Soc. . 57(7)
2010
The dynamics of conjunctive and disjunctive Boolean network models.
Bulletin of mathematical biology. 72(6):1425-47 [DOI] 10.1007/s11538-010-9501-z. [PMID] 20087672.
2010
“Voici ce que j’ai trouvé:” Sophie Germain’s grand plan to prove Fermat’s Last Theorem
Historia Mathematica. 37(4):641-692
2009
A general map of iron metabolism and tissue-specific subnetworks.
Molecular bioSystems. 5(5):422-43 [DOI] 10.1039/b816714c. [PMID] 19381358.
2009
A systems biology view of cancer.
Biochimica et biophysica acta. 1796(2):129-39 [DOI] 10.1016/j.bbcan.2009.06.001. [PMID] 19505535.
2009
Algebraic models in systems biology
Methods in Enzymology. 467:163-196
2009
Algebraic models of biochemical networks.
Methods in enzymology. 467:163-196 [DOI] 10.1016/S0076-6879(09)67007-5. [PMID] 19897093.
2009
Computer algebra in systems biology
The American Mathematical Monthly. 116:882-891
2009
Design of experiments and biochemical network inference
Algebraic and Geometric Methods in Statistics, Cambridge University Press.
2009
Mathematical biology education: beyond calculus.
Science (New York, N.Y.). 325(5940):542-3 [DOI] 10.1126/science.1176016. [PMID] 19644095.
2009
System identification for discrete polynomial models of gene regulatory networks
System Identification. 15(1):29-41
2009
The mathematics of agent-based modeling formalisms
Encyclopedia of Complexity and System Science. Springer Verlag, New York.
2008
A virtual look at Epstein-Barr virus infection: simulation mechanism.
Journal of theoretical biology. 252(4):633-48 [DOI] 10.1016/j.jtbi.2008.01.032. [PMID] 18371986.
2008
Finite dynamical systems: a mathematical framework for computer simulation
Mathematical modeling, simulation, visualization and e-learning, Springer, Berlin. 343-358
2008
Inference of ecological interaction networks
Annales Zoologici Fennici. 45(5):459-464
2008
On the Algebraic Geometry of Polynomial Dynamical Systems
Emerging Applications of Algebraic Geometry, Springer. IMA
2008
The Cyclicity Problem for Two-dimensional Polynomial Systems
Differential Equations and Control Processes . ISSN 1817-2172
2008
The effect of negative feedback loops on the dynamics of boolean networks.
Biophysical journal. 95(2):518-26 [DOI] 10.1529/biophysj.107.125021. [PMID] 18375509.
2008
Using formal concept analysis for microarray data comparison.
Journal of bioinformatics and computational biology. 6(1):65-75 [PMID] 18324746.
View on: PubMed
2008
‘Model your genes the mathematical way’ –a mathematical biology workshop for secondary school teachers
Teaching Mathematics and its Applications. 27:91-101
2007
A Groebner Fan based Method for Biochemical Network
Proceedings of ISSAC, ACM Press. 122-126
2007
A Gröbner fan method for biochemical network modeling
ISSAC 2007, ACM, New York. 122-126
2007
A virtual look at Epstein-Barr virus infection: biological interpretations.
PLoS pathogens. 3(10):1388-400 [PMID] 17953479.
View on: PubMed
2007
Comparison of reverse-engineering methods using an in silico network.
Annals of the New York Academy of Sciences. 1115:73-89 [PMID] 17925358.
View on: PubMed
2007
Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions
Proc. of the Second Intl.Conf. on Algebraic Biology. LNCS 4545:15-22
2007
Introduction to Modeling and simulation of biological networks
Proc. Sympos. Appl. Math., 64, AMS Short Course Lecture Notes, Amer. Math. Soc., Providence, RI. 92-106
2007
Mathematical masterpieces. Further chronicles by the explorers
Undergraduate Texts in Mathematics. Readings in Mathematics. Springer, New York.
2007
Mathematical Masterpieces. Undergraduate Texts in Mathematics. Readings in Mathematics
Springer-Verlag, New York.
2007
Nested Canalyzing, Unate Cascade, and Polynomial Functions.
Physica D. Nonlinear phenomena. 233(2):167-174 [PMID] 18437250.
View on: PubMed
2007
Reverse engineering of dynamic networks.
Annals of the New York Academy of Sciences. 1115:168-77 [PMID] 17925347.
View on: PubMed
2007
Reverse-engineering polynomial dynamical systems
Adv. In Appl. Math.. 39:477-489
2007
Simulating Epstein-Barr virus infection with C-ImmSim.
Bioinformatics (Oxford, England). 23(11):1371-7 [PMID] 17341499.
View on: PubMed
2006
Homotopy theory of graphs
J. Alg. Comb.. 24:31-44
2006
Monomial dynamical systems over finite fields
Complex Systems. 16(4):333-342
2006
Sequential dynamical systems over words
Applied Math and Comp.. 174:500-510
2006
Update schedules of sequential dynamical systems
Discrete Applied Mathematics. 154:980-994
2005
A discrete approach to top-down modeling of biochemical networks
Computational Systems Biology, Boston, Elsevier Academic Press. 229-247
2005
Perspectives on A-homotopy theory and its applications
Discrete Mathematics. 298(1-3):39-61
2004
A computational algebra approach to the reverse engineering of gene regulatory networks.
Journal of theoretical biology. 229(4):523-37 [PMID] 15246788.
View on: PubMed
2004
An optimal control problem for in vitro virus competition
Proc. Of the 43rd IEEE Conference on Decision and Control, Bahamas.
2004
Boolean Monomial Dynamical Systems
Annals of Combinatorics. 8:425-439
2004
Generic Cohen-Macaulay monomial ideals
Ann. Comb.. 8(1):45-61
2004
PathSim Visualizer: an information rich virtual environment framework for systems biology
Proc. SIGGRAPH Web3D Session, Los Angeles.
2003
A computer algebra approach to reverse-engineering of biological systems
Proceedings of the Intl. Symposium on Symbolic and Algebraic Computation, Assoc. Comp. Mach., Philadelphia, PA, ACM: New York.
2003
Decomposition and simulation of sequential dynamical systems
Advances in Applied Math. 30:655-678
2003
The Sibirsky component of the center variety of polynomial differential systems
J. Symbolic Comput.. 35(5):577-589
2002
Symbolic Computation: solving equations in algebra, geometry, and engineering
Amer. Math. Soc, Providence, RI,.
2002
The Role of Bioinformatics in Toxicogenomics and Proteomics
Proceedings from NATO Advanced Workshop on Toxicogenomics and Proteomics. Prague, Czech Republic. October 16-20
2001
Equivalence relations on finite dynamical systems
Advances in Applied Math. 237-251
2001
Foundations of a connectivity theory for simplicial complexes
Adv. Appl. Math.. 26:97-128
2001
Generic ideals and the Moreno-Socias conjecture
Proceedings of the 2001 International Symposium on Symbolic and Algebraic Computation, ACM, New York.
2001
Lagrange and the solution of numerical equations
Historia Mathematica. 28(3):220-231
2000
A new algorithm for the Quillen-Suslin theorem for polynomial rings
Contributions to Algebra and Geometry. 41(1):23-32
2000
An algorithm for the Quillen-Suslin Theorem for quotients of polynomial rings by monomial ideals
J. Symbolic Comput.. 30:555-571
2000
Permanental ideals
J. Symbolic Comput.. 30:195-205
2000
Special Issue on Symbolic Computation in Algebra, Analysis, and Geometry – Foreword of the Guest Editors
J. Symb. Comput. . 29(4-5)
1999
Monomial orderings, rewriting systems, and Groebner bases for the commutator ideal of a free algebra
J. Symbolic Comput. . 27:133-141
1998
Combinatorial homotopy of simplicial complexes and complex information systems
Applications of Computational Algebraic Geometry, American Math. Soc., Providence, RI,.
1998
On higher class groups of orders
Math. Z . 228:229-246
1997
An algorithm for the Quillen-Suslin theorem for monoid rings
J Pure Appl Algebra. 117-118:395-429
1996
A normal form algorithm for modules over k[x,y]/(x,y)
J. Algebra. 184(3):1001-1024
1996
Finitely generated modules over pullback rings
J. Algebra. 184(1):304-322
1996
History of mathematics and the internet
Newsletter of the British Society for the History of Mathematics. 28:56-57
1996
Mathematical masterpieces: teaching with original sources
R. Calinger (ed.), History of Mathematics: Sources, Studies and Pedagogic Integration, MAA, Washington.
1995
Almost split sequences for dedekind-like rings (part II)
Comm. Algebra. 23:111-130
1994
Eisenstein’s misunderstood geometric proof of the quadratic reciprocity theorem
College Math J. 25:29-34
1994
Gauss, Eisenstein, and the “third” proof of the quadratic reciprocity theorem: ein kleines Schauspiel,
Mathematical Intelligencer . 16:67-72
1994
Great problems of mathematics: a workshop for high school students
College Math. J. . 25:112-114
1994
Recovering motivation in mathematics: teaching with original sources
UME Trends.
1993
Algebraic K-theory of poset representations
K-Theory. 7:17-21
1993
Great theorems: the art of mathematics – a course based on original sources
Newsletter of the International Study Group on the History and Pedagogy of Mathematics . 28:9-10
1993
Theory of Algebraic Invariants by D. Hilbert, translated from the German by R. Laubenbacher.
Cambridge University Press, New York.
1992
G_0 of integral group rings for groups with cyclic sylow subgroups
Algebraic K-Theory, Commutative Algebra and Algebraic Geometry, Contemporary Math. 126
1992
Great problems of mathematics: a course based on original sources
Amer. Math. Monthly. 99(4):313-317
1992
SK_2 and K_3 of dihedral groups
Canadian Journal of Math. 44(3):591-623
1991
Almost split sequences for Dedekind-like rings (part I)
J. London Math. Soc.. s2-43(2):225-235
1991
The structure of the integral group ring of a finite group with cyclic sylow subgroups,
Comm. Algebra. 19(8):2281-2290
1990
On SG_n of orders
J. Algebra . 133:125-131
1989
Honors mathematics in the liberal arts curriculum
National Honors Report . 10:21-22
1988
Generalized Mayer-Vietoris sequences in algebraic K-theory
J Pure Appl Algebra. 51(1-2):175-192
1987
On the K-theory of ZG, G a group of square-free order
Algebraic K-theory: Connections With Geometry and Topology, NATO Adv. Sci. Inst. Ser. C Math. Phys. Sci.. 279:189-208
Addressing current challenges in cancer immunotherapy with mathematical and computational modeling
. [DOI] 10.1101/146902.
Comparative Analysis of Linear and Nonlinear Dimension Reduction Techniques on Mass Cytometry Data
. [DOI] 10.1101/273862.
Control of Intracellular Molecular Networks Using Algebraic Methods
. [DOI] 10.1101/682989.
Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies
. [DOI] 10.1101/2021.01.20.427417.
Multiscale mechanistic modelling of the host defense in invasive aspergillosis reveals leukocyte activation and iron acquisition as drivers of infection outcome
. [DOI] 10.1101/2021.06.08.447590.

Grants

May 2020 ACTIVE
Multiscale modeling of the battle over iron in invasive lung infection
Role: Principal Investigator
Funding: NATL INST OF HLTH NIAID
May 2020 ACTIVE
Modular design of multiscale models, with an application to the innate immune response to fungal respiratory pathogens
Role: Principal Investigator
Funding: NATL INST OF HLTH NIBIB
May 2020 ACTIVE
Control of heterogeneous microbial communities using model-based multi-objective optimization
Role: Principal Investigator
Funding: UNIV OF CONNECTICUT via NATL INST OF HLTH NIGMS

Education

Ph.D. mathematics
1985 · Northwestern University

Contact Details

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