© 2000 - 2012 Virginia Bioinformatics Institute
Wednesday, 16 May 2012
Laubenbacher, Reinhard , Ph.D.
Faculty - Publications - Laubenbacher, Reinhard

Professor, Virginia Bioinformatics Institute
Director, Education and Outreach
Professor, Department of Mathematics, Virginia Tech

Phone: (540) 231-7506
Email:reinhard@vbi.vt.edu
Fax: 540-231-2606

Administrative Specialist: Betsy Williams
Phone: (540) 231-1649
Email: betsyw@vbi.vt.edu
Fax:540-231-2606

Personal_Page | Education and Outreach Group | Laubenbacher Research Group | | Education and Outreach website



Publications:

2011


D.Cortes WS V. Hower G. Blekherman R. Laubenbacher S. Akman S. Torti V. Shulaev. Differential gene expression in normal and transformed human mammary epithelial cells in response to oxidative stress. Free Radical Biology and Medicine. 2011.  

E. Dimitrova LDG F. Hinkelmann A. Jarrah R. Laubenbacher B. Stigler M. Stillman P. Vera-Licona. Parameter estimation for Boolean models of biological systems. J. Theor. Comp. Sci.. 2011;412:2816–2826.  

F. Hinkelmann DM A. Jarrah and R. Laubenbacher. A mathematical framework for agent-based models of complex biological networks. Bull. Math. Biol.. 2011;73:1583–1603.  

F. Hinkelmann MB B. Guang R. McNeill G. Blekherman A. Veliz-Cuba and R. Laubenbacher. ADAM: Analysis of the Dynamics of Algebraic Models of Biological Systems using Computer Algebra. BMC Bioinformatics. 2011;288:66–72.  

G. Blekherman RL D. Cortes P. Mendes F. Torti S. Akman S. Torti and V. Shulaev. Bioinformatics tools for cancer metabolomics. Metabolomics. 2011.  

J. Chifman AK P. Neupane I. Williams B. Leung P. Mendes V. Hower F.M. Torti S.A. Akman S.V. Torti and R. Laubenbacher. The core control system of intracellular iron homeostasis: a mathematical model. J. Theor. Biol.. 2011.  

Laubenbacher AV-C and R. On the computation of fixed points in Boolean networks. J. Appl. Math. Comp.. 2011.  

Laubenbacher R. Invited Lecture – Algebraic geometry in systems biology. Oslo: University of Oslo Norway; 2011.  

Laubenbacher R. Invited Lecture – Patterns are everywhere: how and why? Blacksburg VA: Kids' Tech University Virginia Tech; 2011.  

Laubenbacher R. Invited Lecture – A systems biology view of cancer. New Orleans LA: School of Pharmacy Xavier University; 2011.  

Laubenbacher R. Structure and dynamics of polynomial dynamical systems. Atlanta; 2011. NSF Engineering Research and Innovation.  

Laubenbacher R. A systems biology approach to cancer drug discovery. In: Dubitzky W Wolkenhauer O Cho K.H. Yokota H., ed. Encyclopedia of Systems Biology. New York: Springer Verlag; 2011.  

Murrugarra D, Laubenbacher R. Regulatory patterns in molecular interaction networks. J Theor Biol. 2011;288:66–72.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21872607

2010


Dimitrova ES, Licona MP, McGee J, Laubenbacher R. Discretization of time series data. J Comput Biol. 2010;17:853–868.  http://www.ncbi.nlm.nih.gov/pubmed/20583929

Hinkelmann F, Murrugarra D, Jarrah AS, Laubenbacher R. A Mathematical Framework for Agent Based Models of Complex Biological Networks. Bull Math Biol. 2010.  http://www.ncbi.nlm.nih.gov/pubmed/20878493

Jarrah AS, Laubenbacher R, Veliz-Cuba A. The Dynamics of Conjunctive and Disjunctive Boolean Network Models. Bulletin of Mathematical Biology. 2010;72:1425–1447.  

Laubenbacher ED L.D. Garcia F. Hinkelmann A. Jarrah B. Stigler M. Stillman P. Vera-Licona. Parameter estimation for Boolean models. J. Theor. Comp. Sci.. 2010.  

Laubenbacher FH and R. Boolean models of bistable biological systems. Discrete and Cont. Dynamical Systems. 2010.  

Laubenbacher R. Mathematics-aided medicine.. 2010.  

Veliz-Cuba A, Jarrah AS, Laubenbacher R. Polynomial algebra of discrete models in systems biology. Bioinformatics. 2010;26:1637–1643.  http://www.ncbi.nlm.nih.gov/pubmed/20448137

2009


Hower V, Mendes P, Torti FM, et al. A general map of iron metabolism and tissue-specific subnetworks. Molecular Biosystems. 2009;5:422–443.  

Laubenbacher R. Computer algebra in systems biology. The American Mathematical Monthly. 2009:In press.  http://www.citebase.org/abstract?id=oai:arXiv.org:0712.4248

Laubenbacher R. Systems Biology: A Field of Unlimited Possibilities. BioSpace Biotech and Pharmaceutical News and Jobs. 2009.  http://www.biospace.com/news_story.aspx?NewsEntityId=163319

Laubenbacher R. Systems biology recommended as clinical approach to cancer. Science Daily. 2009.  http://www.sciencedaily.com/releases/2009/07/090709110838.htm

Laubenbacher R. Podcast Interview: Cancer systems biology. Genetic Engineering and Biotechnology News. 2009.  http://www.genengnews.com/gencasts.aspx?id=274

Laubenbacher R. Thoughts from SIAM. SIAM News. 2009;42:12.  

Laubenbacher R, Hower V, Jarrah A, et al. A systems biology view of cancer. Biochimica et Biophysica Acta (BBA) – Reviews on Cancer. 2009;In Press, Corrected Proof.  http://www.sciencedirect.com/science/article/B6T23-4WGF111-1/2/7794f68547e6c706c929c9d4d96e6dac

Laubenbacher R, Jarrah AS. Algebraic Models of Biochemical Networks. Methods in Enzymology: Computer Methods, Part B. 2009;467:163–+.  

Robeva R, Laubenbacher R. Mathematical Biology Education: Beyond Calculus. Science. 2009;325:542–543.  

2008


Choi V, Huang Y, Lam V, Potter D, Laubenbacher R, Duca K. Using formal concept analysis for microarray data comparison. Journal of Bioinformatics and Computational Biology. 2008;6:65–75.  

Cipra B. A Woman Who Counted. Science. 2008;319.  http://www.sciencemag.org/cgi/content/full/319/5865/899a

Crowley J. Fall Update for SIAM. SIAM News. 2008;41.  http://www.siam.org/news/news.php?id=1458

Laubenbacher R, Jarrah A, Mortveit H, Ravi SS. A mathematical formalism for agent-based modeling. In: Meyers RA, ed. Encyclopedia of Complexity and Systems Science. Vol. In press. Springer Verlag; 2008.  http://www.citebase.org/abstract?id=oai:arXiv.org:0801.0249

Licona PV, Laubenbacher R. Inference of ecological interaction networks. Annales Zoologici Fennici. 2008;45:459–464.  

Martins A, Vera-Licona P, Laubenbacher R. Model your genes the mathematical way: a mathematical biology workshop for secondary school teachers. Teaching Mathematics and its Applications. 2008;27:91–101.  

Rehmeyer JJ. A Mathematical Tragedy. Science News. 2008;173, No. 9.  http://www.sciencenews.org/articles/20080301/mathtrek.asp

Rehmeyer JJ. An Attack on Fermat. Science News. 2008;173, No 8.  http://www.sciencenews.org/articles/20080223/mathtrek.asp

Romanovski VG, Jarrah AS, Laubenbacher R. The cyclicity problem for two-dimensional polynomial systems. Differential Equations and Control Processes. 2008:In press.  

Shapiro M, Duca KA, Lee K, et al. A virtual look at Epstein-Barr virus infection: Simulation mechanism. Journal of Theoretical Biology. 2008;252:633–648.  http://www.sciencedirect.com/science/article/B6WMD-4RVG3TH-1/2/3348d726c9eefdc06919828972082a84

Sontag E, Veliz-Cuba A, Laubenbacher R, Jarrah AS. The Effect of Negative Feedback Loops on the Dynamics of Boolean Networks. Biophys. J.. 2008;95:518–526.  http://www.biophysj.org/cgi/content/abstract/95/2/518

2007


Camacho D, Vera Licona P, Mendes P, Laubenbacher R. Comparison of Reverse-Engineering Methods Using an in Silico Network. Annals of the New York Academy of Sciences. 2007;1115:73–89.  http://dx.doi.org/10.1196%2Fannals.1407.006

Castiglione F, Duca KA, Jarrah A, Laubenbacher R, Hochberg D, Thorley-Lawson DA. Simulating Epstein-Barr Virus Infection with C-ImmSim. Bioinformatics. 2007;23:1371–1377.  http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm044v1

Dimitrova ES, Jarrah AS, Laubenbacher R, Stigler B. A Grobner fan method for biochemical network modeling. Waterloo, Ontario, Canada: Acm; 2007. Proceedings of the 2007 international symposium on Symbolic and algebraic computation.  

Duca KA, Shapiro M, Delgado-Eckert E, et al. A Virtual Look at Epstein-Barr Virus Infection: Biological Interpretations. PLoS Pathogens. 2007;3:e137.  http://dx.doi.org/10.1371%2Fjournal.ppat.0030137

Jarrah A, Laubenbacher R. Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions. In: Algebraic Biology.; 2007:15–22.  http://dx.doi.org/10.1007%2F978-3-540-73433-8_2

Jarrah A, Laubenbacher R, Stigler B, Stillman M. Reverse Engineering of Dynamic Networks. Annals of the New York Academy of Sciences. 2007;1115:168–177.  http://dx.doi.org/10.1196%2Fannals.1407.012

Jarrah AS, Laubenbacher R, Stigler B, Stillman M. Reverse-engineering of polynomial dynamical systems. Advances in Applied Mathematics. 2007;39:477–489.  http://www.sciencedirect.com/science/article/B6W9D-4M644XM-2/2/4983c54dc48b698f3376c716413080fe

Jarrah AS, Raposa B, Laubenbacher R. Nested canalyzing, unate cascade, and polynomial functions. Physica D: Nonlinear Phenomena. 2007;233:167–174.  http://www.sciencedirect.com/science/article/B6TVK-4P37JBJ-3/2/8e09e9028bfa1beb92ef2437fd05335d

2006


Babson E, Barcelo H, de Longueville M, Laubenbacher R. Homotopy theory of graphs. Journal of Algebraic Combinatorics. 2006;24:31–44.  

Colon-Reyes O, Jarrah A, Laubenbacher R, Sturmfels B. Monomial dynamical systems over finite fields. Complex Systems. 2006;16:333–342.  

Garcia LD, Jarrah AS, Laubenbacher R. Sequential dynamical systems over words. Applied Mathematics and Computation. 2006;174:500–510.  

Laubenbacher R, Mendes P. A discrete approach to top-down modeling of biochemical networks. In: R E, L K, eds. Computational Systems Biology. Elsevier, Academic Press; 2006.  

Laubenbacher R, Pareigis B. Update schedules of sequential dynamical systems. Discrete Applied Mathematics. 2006;154:980–994.  

2005


Barcelo H, Laubenbacher R. Perspectives on A-homotopy theory and its applications. Discrete Mathematics. 2005;298:39–61.  

2004


Colon-Reyes O, Laubenbacher R, Pareigis B. Boolean monomial dynamical systems. Annals of Combinatorics. 2004;8:425–439.  

Jarrah A, Laubenbacher R. Generic Cohen-Macaulay Monomial Ideals. Annals of Combinatorics. 2004;8:45–61.  http://www.ingentaconnect.com/content/klu/26/2004/00000008/00000001/art00005 http://dx.doi.org/10.1007/s00026-004-0204-8

Kling J. The Mathematical Biology Job Market. Science. 2004.  http://biology-web.nmsu.edu/math/Next%20Wave%20--%20Kling.htm

Laubenbacher R, Stigler B. A computational algebra approach to the reverse engineering of gene regulatory networks. Journal of Theoretical Biology. 2004;229:523–537.  

2003


Jarrah AS, Laubenbacher R, Romanovski V. The Sibirsky component of the center variety of polynomial differential systems. Journal of Symbolic Computation. 2003;35:577–589.  

Laubenbacher R, Pareigis B. Decomposition and simulation of sequential dynamical systems. Advances in Applied Mathematics. 2003;30:655–678.  

2002


Stimmer H, Arnold W, Schwaiger M, Laubenbacher C. Magnetic resonance imaging and high-resolution computed tomography in the otospongiotic phase of otosclerosis. Orl-Journal for Oto-Rhino-Laryngology and Its Related Specialties. 2002;64:451–453.  

2001


Barcelo H, Kramer X, Laubenbacher R, Weaver C. Foundations of a connectivity theory for simplicial complexes. Advances in Applied Mathematics. 2001;26:97–128.  

Laubenbacher R, McGrath G, Pengelley D. Lagrange and the solution of numerical equations. Historia Mathematica. 2001;28:220–231.  

Laubenbacher R, Pareigis B. Equivalence relations on finite dynamical systems. Advances in Applied Mathematics. 2001;26:237–251.  

2000


Cattani E, Laubenbacher RC. Special issue on symbolic computation in algebra, analysis, and geometry – Foreword of the guest editors. Journal of Symbolic Computation. 2000;29:483.  

Laubenbacher R, Schlauch K. An algorithm for the Quillen-Suslin Theorem for quotients of polynomial rings by monomial ideals. Journal of Symbolic Computation. 2000;30:555–571.  

Laubenbacher RC, Swanson I. Permanental ideals. Journal of Symbolic Computation. 2000;30:195–205.  

1999


Hermiller SM, Kramer XH, Laubenbacher RC. Monomial orderings, rewriting systems, and Grobner bases for the commutator ideal of a free algebra. Journal of Symbolic Computation. 1999;27:133–141.  

1998


Kolster M, Laubenbacher RC. On higher class groups of orders. Mathematische Zeitschrift. 1998;228:229–246.  

1997


Laubenbacher RC, Woodburn CJ. An algorithm for the Quillen-Suslin theorem for monoid rings. Journal of Pure and Applied Algebra. 1997;117:395–429.  

1996


Arnold DM, Laubenbacher RC. Finitely generated modules over pullback rings. Journal of Algebra. 1996;184:304–332.  

Laubenbacher RC, Sturmfels B. A normal form algorithm for modules over k[x,y]/(xy). Journal of Algebra. 1996;184:1001–1024.  

1995


Arnold DM, Laubenbacher RC. Almost Split-Sequences for Dedekind-Like Rings .2. Communications in Algebra. 1995;23:111–130.  

1994


Laubenbacher RC, Pengelley DJ. Gauss, Eisenstein, and the 3rd Proof of the Quadratic Reciprocity Theorem – Ein-Kleines-Schauspiel. Mathematical Intelligencer. 1994;16:67–72.  

Pengelley RL and D. Eisenstein. College Mathematics Journal. 1994;25:29–34.  

R. Laubenbacher DP and MS. Recovering motivation in mathematics: teaching with original sources. UME Trends. 1994;6.  

Siddoway RL and M. Great Problems of mathematics: a workshop for high school students. College Mathematics Journal. 1994:112–114.  

1993


Pengelley RL and D. Great theorems: the art of mathematics . Newsletter of the International Study Group on the History and Pedagogy of Mathematics. 1993;28:9–10.  

1992


Laubenbacher RC, Magurn BA. Sk2 and K3 of Dihedral Groups. Canadian Journal of Mathematics-Journal Canadien De Mathematiques. 1992;44:591–623.  

Laubenbacher RC, Pengelley DJ. Great Problems of Mathematics – a Course Based on Original Sources. American Mathematical Monthly. 1992;99:313–317.  

Vandeflierdt E, Bauer R, Laubenbacher C, Didic M, Langhammer HR, Pabst HW. Early Diagnosis of Morphological-Functional Changes of the Airways by a Simple Method of Inhalation Scintigraphy. Nuklearmedizin. 1992;31:7–15.  

1991


Arnold DM, Laubenbacher RC. Almost Split-Sequences for Dedekind-Like Rings. Journal of the London Mathematical Society-Second Series. 1991;43:225–235.  

Laubenbacher RC, Webb DL. The Structure of the Integral Group-Ring of a Finite-Group with Cyclic Sylow Subgroups. Communications in Algebra. 1991;19:2281–2290.  

1990


Laubenbacher RC, Webb DL. On Sgn of Orders. Journal of Algebra. 1990;133:125–131.  

1989


Pengelley RL and D. Honors mathematics in the liberal arts curriculum. National Honors Report. 1989;10:21–22.  

1988


Laubenbacher RC. Generalized Mayer-Vietoris Sequences in Algebraic K-Theory. Journal of Pure and Applied Algebra. 1988;51:175–192.