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Complex systems, networks, dynamics, critical phenomena, and pattern formation; theoretical and computational systems biology; infectious disease dynamics and host-pathogen interactions; scientific computing and software design.
- Applied Mathematics
- Computational Biology
- Computational Science and Engineering
- Laboratory of Atomic and Solid State Physics (LASSP)
- Center for Applied Mathematics (CAM)
- Life Sciences Core Laboratories: Computational Biology Service Unit (CBSU)
My research lies at the intersection of physics, biology, computer science, and computational science, focused on problems such as: biological information processing; the structure and dynamics of intracellular networks involved in gene regulation, signal transduction, metabolism, development, virulence and defense; infectious disease dynamics and host-pathogen interactions; photosynthetic metabolism and immune responses in plants; and the design and development of software systems for modeling complex biological phenomena.
Daniel Citron, Lei Huang, Kara Karpman, Ben Nicholson
E. Markel, P. Stodghill, Z. Bao, C.R. Myers and B. Swingle, “AlgU controls expression of virulence genes in Pseudomonas syringae pv. tomato DC3000”, J. Bacteriology, in press (2016).
E. Bogart and C.R. Myers, “Multiscale metabolic modeling of C4 plants: connecting nonlinear genome-scale models to leaf-scale metabolism in developing maize leaves”, PLoS ONE 11(3): e0151722 (2016).
J.N. Worley, M. Pombo, Y. Zheng, D. Dunham, C.R. Myers, Z. Fei, G. Martin, "A novel method of transcriptome interpretation reveals a quantitative suppressive effect on tomato immune signaling by two domains in a single pathogen effector protein”, BMC Genomics 17:229 (2016).
A.L. Sellerio, E. Ciusani, N.B. Ben-Moshe, S. Coco, A. Piccinini, C.R. Myers, J.P. Sethna, C. Giampietro, S. Zapperi, and C.A.M. La Porta, “Overshoot during phenotypic switching of cancer cell populations”, Scientific Reports 5, 15464 (2015).
Z. Ding, S. Weissmann, M. Wang, L. Wang, L. Huang, C.R. Myers, T.P. Brutnell, Q. Sun, P. Li, “Identification of photosynthesis-associated C₄ candidate genes through comparative leaf gradient transcriptome in multiple lineages of C₃ and C₄ species”, PLoS ONE 10(10): e0140629. doi:10.1371/journal.pone.0140629 (2015).
A.A. Alemi, M. Bierbaum, C.R. Myers, and J.P. Sethna, “You can run, you can hide: The epidemiology and statistical mechanics of zombies”, Phys. Rev. E 92, 052081 (2015).
B. Barker, N. Sadagopan, Y. Wang, K. Smallbone, C.R. Myers, H. Xi, J.W. Locasale, and Z. Gu, “A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data”, Computational Biology and Chemistry, 2015 Sep 1. pii: S1476-9271(15)30107-9.
J. Hindes and C.R. Myers, “Driven synchronization in random networks of oscillators”, Chaos 25, 073119 (2015).
M.K. Transtrum, B. Machta, K. Brown, B.C. Daniels, C.R. Myers, and J. P. Sethna, “Sloppiness and emergent theories in physics, biology, and beyond”, J. Chem. Phys. 143, 010901 (2015).
L. Huang, D. Kim, X. Liu, C.R. Myers, and J. Locasale, “Estimating relative changes of metabolic fluxes using kinetic flux profiling”, PLoS Computational Biology 10(11): e1003958 (2014).
O. Kogan, M. Khasin, B. Meerson, D. Schneider, and C.R. Myers, “Two-strain competition in quasineutral stochastic disease dynamics”, Phys. Rev. E 90, 042149 (2014).
S. Singh and C.R. Myers, “Outbreak size statistics and scaling laws for externally driven epidemics”, Phys. Rev. E 89, 042108 (2014).
S. Singh, D.J. Schneider, and C.R. Myers, “Using multitype branching processes to quantify statistics of disease outbreaks in zoonotic epidemics”, Phys. Rev. E 89, 032702 (2014).
Z. Bao, P. Stodghill, C.R. Myers, H. Lam, A. Collmer, S. Cartinhour, P. Schweitzer, and B. Swingle, “Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000”, PLoS ONE 9(2): e86628 (2014).
J. Hindes, S. Singh, C.R. Myers, and D.J. Schneider, “Epidemic fronts in complex networks with metapopulation structure", Phys. Rev. E 88, 012809 (2013).
M.J. Filiatrault, P.V. Stodghill, J. Wilson, B.G. Butcher, H. Chen, C.R. Myers and S.W. Cartinhour, “CrcZ and CrcX regulate carbon source utilization in Pseudomonas syringae pathovar tomato strain DC3000”, RNA Biol. 10(2): 245-55 (2013).
E. Markel, B.G. Butcher, C.R. Myers, P.V. Stodghill, S.W. Cartinhour, and B. Swingle, “Regulons of three Pseudomonas syringae pv. tomato DC3000 Iron Starvation Sigma Factors” Appl. Environ. Microbiol. 79(2): 725-727 (2013).
M.J. Filiatrault, P.V. Stodghill, C.R. Myers, P.A. Bronstein, B.G. Butcher, H. Lam, G. Grills, P. Schweitzer, W. Wang, D.J. Schneider, S.W. Cartinhour, “Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000”, PLoS One 6(12): e29335 (2011).
E. Markel, C. Maciak, B. Butcher, C.R. Myers, P. Stodghill, Z. Bao, S. Cartinhour, and B. Swingle, “An ECF sigma factor mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores”, J. Bacteriology 193(20): 5775-83 (2011).
S.A Goff, M. Vaughn, S. McKay, E. Lyons, A.E. Stapleton, D. Gessler, N. Matasci, L. Wang, M. Hanlon, A. Lenards, A. Muir, N. Merchant, S. Lowry, S. Mock, M. Helmke, A. Kubach, M. Narro, N. Hopkins, D. Micklos, U. Hilgert, M. Gonzales, C. Jordan, E. Skidmore, R. Dooley, J. Cazes, R. McLay, Z. Lu, S. Pasternak, L. Koesterke, W.H. Piel, R. Grene, C. Noutsos, K. Gendler, X. Feng, C. Tang, M. Lent, S-j. Kim, K. Kvilekval, B.S. Manjunath, V. Tannen, A. Stamatakis, M. Sanderson, S.M. Welch, K. Cranston, P. Soltis, D. Soltis, B. O'Meara, C. Ane, T. Brutnell, D.J. Kleibenstein, J.W. White, J. Leebens-Mack, M.J. Donoghue, E.P. Spalding, T.J. Vision, C.R. Myers, D. Lowenthal, B.J. Enquist, B. Boyle, A. Akoglu, G. Andrews, S. Ram, D. Ware, L. Stein, D, Stanzione, “The iPlant Collaborative: Cyberinfrastructure for Plant Biology”, Frontiers in Plant Genetics and Genomics 2 (2011).
B.G. Butcher, P.A. Bronstein, C.R. Myers, P.V. Stodghill, J.J. Bolton, E.J. Markel, M.J. Filiatrault, B. Swingle, A. Gaballa, J.D. Helmann, S.W. Cartinhour, “Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000”, J. Bacteriology 193(18): 4598-611 (2011).
P. Li, L. Ponnala, N. Gandotra, L. Wang, Y. Si, S.L. Tausta, T. Kebrom, N. Provart, R. Patel, C.R. Myers, E. Reidel, R. Turgeon, P. Liu, Q. Sun, T. Nelson and T.P. Brutnell, "The developmental dynamics of the maize leaf transcriptome as revealed through ultra high-throughput sequencing", Nature Genetics 42(12): 1060-7 (2010).
S. Moll, D.J. Schneider, P. Stodghill, C.R. Myers, S.W. Cartinhour, and M.J. Filiatrault, “Construction of an rsmX co-variance model and identification of five rsmX non-coding RNAs in Pseudomonas syringae pv. tomato DC3000”, RNA Biology 7(5): 1-9 (2010).
E. Sakk, D.J. Schneider, C.R. Myers, and S.W. Cartinhour, “The effect of target vector selection on the invariance of classifier performance measures”, IEEE Transactions on Neural Networks 20(5): 745-757 (2009).
P.A. Bronstein, M.J. Filiatrault, C.R. Myers, M. Rutske, D.J. Schneider, and S.W. Cartinhour, “Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro”, BMC Microbiology 8:209 (2008).
F.P. Casey, J.J. Waterfall, R.N. Gutenkunst, C.R. Myers and J.P. Sethna, “Variational method for estimating the rate of convergence of Markov Chain Monte Carlo algorithms”, Physical Review E 78, 046704 (2008).
C.R. Myers, “Satisfiability, sequence niches, and molecular codes in cellular signaling”, IET Systems Biology 2(5), 304-312 (2008).
B.C. Daniels, Y-J. Chen, J.P. Sethna, R.N. Gutenkunst, and C.R. Myers, “Sloppiness, robustness, and evolvability in systems biology”, Current Opinion in Biotechnology 19(4), 389-395 (2008).
M. Lindeberg, C.R. Myers, A. Collmer, and D.J. Schneider, “Roadmap to new virulence determinants: Locations of virulence and host-association genes relative to the core and variable genome highlight regions of genome innovation in Pseudomonas syringae”, Molecular Plant-Microbe Interactions 21(6), 685-700 (2008).
B. Swingle, D. Thete, M. Moll, C.R. Myers, D.J. Schneider, and S.W. Cartinhour, “Characterization of the PvdS-regulated promoter motif of Pseudomonas syringae DC3000 reveals PvdS regulon members and insights regarding PvdS function in other pseudomonads”, Molecular Microbiology 68(4), 871-889 (2008).
R.N. Gutenkunst, J.J. Waterfall, F.P. Casey, K.S. Brown, C.R. Myers, and J.P. Sethna, “Universally sloppy parameter sensitivities in systems biology”, PLoS Computational Biology 3(10), e189 (2007).
F.P. Casey, D. Baird, Q. Feng, R.N. Gutenkunst, J.J. Waterfall, C.R. Myers, K.S. Brown, R.A. Cerione and J.P. Sethna, “Optimal experimental design in an EGFR signaling and down-regulation model”, IET Systems Biology 1(3), 190-202 (2007).
C.R. Myers, R.N. Gutenkunst and J.P. Sethna, “Python unleashed on systems biology”, Computing in Science & Engineering, 9(3), 34-37 (2007).
R.N. Gutenkunst, F.P. Casey, J.J. Waterfall, C.R. Myers, James P. Sethna, “Extracting falsifiable predictions from sloppy models”, Ann. N.Y. Acad. Sci. 1115:203-211 (2007). [In "Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference"]
M. Lindeberg, S.W. Cartinhour, C.R. Myers, L.M. Schecter, D.J. Schneider, and A. Collmer, “Closing the circle on the discovery of genes encoding Hrp regulon members and type III secretion system effectors in the genomes of three model Pseudomonas syringae strains”, Mol. Plant-Microbe Int. 19(11), 1151-1158 (2006).
M. Vencato, F. Tian, J.R. Alfano, C.R. Buell, S.W. Cartinhour, G.A. DeClerck, D.S. Guttman, J. Stavrinides, V. Joardar, M. Lindeberg, P.A. Bronstein, J.W. Mansfield, C.R. Myers, A. Collmer, and D.J. Schneider, “Bioinformatics-enabled inventory of the Hrp regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A”, Mol. Plant-Microbe Int. 19(11), 1193-1206 (2006).
A. Ferreira, C.R. Myers, J.S. Gordon, G.B. Martin, M. Vencato, A. Collmer, M.D. Wehling, J. Alfano, G. Moreno-Hagelsieb, W.F. Lamboy, G. DeClerck, D.J. Schneider, and S.W. Cartinhour, “Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv. tomato DC3000, demonstrates de novo reconstruction of the Hrp cis element, and identifies novel co-regulated genes”, Mol. Plant-Microbe Int. 19(11), 1167-1179 (2006).
J.J. Waterfall, F.P. Casey, R.N. Gutenkunst, K.S. Brown, C.R. Myers, P.W. Brouwer, V. Elser and J.P. Sethna, “The sloppy model universality class and the Vandermonde matrix”, Phys. Rev. Lett. 97, 150601 (2006).
K. S. Brown, C. C. Hill, G. A. Calero, C. R. Myers, K. H. Lee, J. P. Sethna and R. A. Cerione, “The statistical mechanics of complex signaling networks: nerve growth factor signaling”, Physical Biology 1, 184-195 (2004).
C.R. Myers, “Software systems as complex networks: structure, function, and evolvability of software collaboration graphs”, Phys. Rev. E 68, 046116 (2003). [Also republished in the November 1, 2003 issue of The Virtual Journal of Biological Physics Research ]
L.O. Eastgate, J.P. Sethna, M. Rauscher, T. Cretegny, C.-S. Chen, and C.R. Myers, “Fracture in mode I using a conserved phase-field model”, Phys. Rev. E 65, 036117 (2002).
C. R. Myers, T. Cretegny, N.P. Bailey, C.-S. Chen, A.J. Dolgert, L.O. Eastgate, E. Iesulauro, A. R. Ingraffea, M. Rauscher, and J.P. Sethna, “Software methodologies for multiscale descriptions of defects, deformation and fracture”, Proceedings of the 10th International Conference on Fracture (2001).
E. Iesulauro, K. Dodhia, T. Cretegny, C.-S. Chen, C. R. Myers, and A. R. Ingraffea, “Continuum-atomistic modeling for crack initiation and propagation in polycrystals”, Proceedings of the 10th International Conference on Fracture (2001).
J.P. Sethna, K.A. Dahmen, and C.R. Myers, “Crackling noise”, Nature 410, 242 (2001).
T. Vegge, J.P. Sethna, S.-A. Cheong, K.W. Jacobsen, C.R. Myers and D.C. Ralph, “Calculation of quantum tunneling for a spatially extended defect: the dislocation kink in copper has a low effective mass”, Phys. Rev. Lett. 86, 1546 (2001).
N. Bailey, J.P. Sethna, C.R. Myers, “Dislocation mobility in two-dimensional Lennard-Jones material”, Mat. Res. Soc. Symp. Proc., 578, 249 (2000).
B. Carter, C. S. Chen, L. P. Chew, N. Chrisochoides, G. R. Gao, G. Heber, A. R. Ingraffea, R. Krause, C. Myers, D. Nave, K. Pingali, P. Stodghill, S. Vavasis, P. A. Wawrzynek, “Parallel FEM Simulation of Crack Propagation - Challenges, Status, and Perspectives”, Lecture Notes in Computer Science, Vol. 1800, pp. 443-449, Springer Verlag (2000).
C.R. Myers, S.R. Arwade, E. Iesulauro, P.A. Wawrzynek, M. Grigoriu, A.R. Ingraffea, P.R. Dawson, M.P. Miller, and J.P. Sethna, “Digital Material: a framework for multiscale modeling of defects in solids”, Mat. Res. Soc. Symp. Proc., Vol. 538, p. 509 (1999).
C.R. Myers, “The dynamics of localized coherent structures and the role of adaptive software in multiscale modeling”, Structured Adaptive Mesh Refinement (SAMR) Grid Methods, The IMA Volumes in Mathematics and Its Applications (Springer-Verlag), Vol. 117, p. 111 (1999).
C.R. Myers, B.E. Shaw, and J.S. Langer, “Slip complexity in a crustal-plane model of an earthquake fault”, Phys. Rev. Lett. 77, 972 (1996).
J.S. Langer, J.M. Carlson, C.R. Myers, and B.E. Shaw, “Slip complexity in dynamic models of earthquake faults”, Proceedings of the National Academy of Sciences Colloquium on "Earthquake Prediction: The Scientific Challenge", Irvine, CA, Feb. 1995.
C.R. Myers and J.S. Langer, “Rupture propagation, dynamical front selection, and the role of small length scales in a model of an earthquake fault”, Phys. Rev. E 47, 3048 (1993).
C.R. Myers and J.P. Sethna, “Collective dynamics of sliding charge density waves: II. Finite-size effects”, Phys. Rev. B 47, 11194 (1993).
C.R. Myers and J.P. Sethna, “Collective dynamics of sliding charge density waves: I. Critical phenomena”, Phys. Rev. B 47, 11171 (1993).
C.R. Myers, C.J. Umrigar, J.P. Sethna and J.D. Morgan III, “Fock's expansion, Kato's cusp conditions, and the exponential ansatz”, Phys. Rev. A 44, 5537 (1991).
R.V. Jensen and C.R. Myers, “Images of the critical points of nonlinear maps”, Phys. Rev. A 32, 1222 (1985).