Publications: Christopher R. Myers


By subject area

Chronologically

  1. 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). [journal]

  2. 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). [journal] [arxiv]

  3. J.N. Worley, M.A. Pombo, Y. Zheng, D.M. Dunham, C.R. Myers, Z. Fei and G.B. 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). [journal]

  4. O. Kogan, K. O'Keeffe, D. Schneider, and C.R. Myers, "Theory of advection-driven long range biotic transport", arXiv:1510.08987 (2015). [arxiv]

  5. 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). [journal][arxiv]

  6. 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). [journal][arxiv]

  7. 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). [journal]

  8. 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", Comp. Biol. and Chem. 1 Sept (2015). [journal][arxiv]

  9. J. Hindes and C.R. Myers, "Driven synchronization in random networks of oscillators", Chaos 25, 073119 (2015). [journal][arxiv]

  10. M.K. Transtrum, B.B. Machta, K.S. Brown, B.C. Daniels, C.R. Myers, and J.P. Sethna, "Perspective: Sloppiness and emergent theories in physics, biology, and beyond", J. Chem. Phys. 143, 010901 (2015). [journal][arxiv]

  11. L. Huang, D. Kim, X. Lu, C.R. Myers, and J.W. Locasale, "Estimating relative changes of metabolic fluxes", PLoS Computational Biology 10(11): e1003958 (2014). [journal] [pdf]

  12. O. Kogan, M. Khasin, B. Meerson, D. Schneider, and C.R. Myers, "Two-strain competition in quasi-neutral stochastic disease dynamics", Phys. Rev. E 90, 042149 (2014). [journal] [pdf] [arxiv]

  13. S. Singh and C.R. Myers, "Outbreak statistics and scaling laws for externally driven epidemics", Phys. Rev. E 89, 042108 (2014). [journal] [pdf] [arxiv]

  14. 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). [journal] [pdf] [Prior version entitled: "The structure of infectious disease outbreaks across the animal-human interface" [arxiv]].

  15. 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). [journal] [pdf]

  16. 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). [journal] [pdf] [arxiv]

  17. C.R. Myers, "Review of Biosimulation: Simulation of Living Systems by D.A. Beard", The Quarterly Review of Biology, Vol. 88, No. 2, 153 (2013). [journal]

  18. 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). [journal] [pdf]

  19. 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). [journal]

  20. 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). [journal] [pdf]

  21. 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). [journal]

  22. 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). [journal]

  23. 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). [journal]

  24. 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). [journal]

  25. 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). [journal]

  26. 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): 746-757 (2009). [journal]

  27. 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). [journal]

  28. 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", Phys. Rev. E 78, 046704 (2008). [pdf] [arxiv]

  29. C.R. Myers, "Satisfiability, sequence niches, and molecular codes in cellular signalling", IET Systems Biology 2(5), 304-312 (2008). [journal] [pdf with supporting information] [pdf] [arxiv]

  30. 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). [journal] [pdf] [pdf (preprint)] [arxiv]

  31. 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). [pdf] [supplementary material]

  32. 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 pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads", Molecular Microbiology 68 (4), 871-889, (2008). [journal] [pdf] [Recommended on Faculty of 1000] [MicroCommentary on paper]

  33. 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). [pdf] [journal] [Rated "Exceptional" on Faculty of 1000] [Review in Biomedical Computation Review (News Bytes)]

  34. 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 signalling and down-regulation model", IET Systems Biology 1(3), 190-202 (2007). [pdf] [arxiv]

  35. C.R. Myers, R.N. Gutenkunst and J.P. Sethna, "Python unleashed on systems biology", Computing in Science and Engineering, 9(3), 34-37 (2007). [pdf] [arxiv]

  36. C.R. Myers and J.P. Sethna, "Python for education: computational methods for nonlinear systems", Computing in Science and Engineering, 9(3), 75-79 (2007). [pdf] [arxiv]

  37. R.N. Gutenkunst, F.P. Casey, J.J. Waterfall, C.R. Myers, and J.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". [pdf] [journal]

  38. A.O. Ferreira, C.R. Myers, J.S. Gordon, G.B. Martin, M. Vencato, A. Collmer, M.D. Wehling, J.R. 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, allows de novo reconstruction of the Hrp cis element, and identifies novel coregulated genes", Molecular Plant-Microbe Interactions 19(11), 1167-1179 (2006). [pdf] [journal] [supplementary table S2]

  39. M. Vencato, F. Tian, J.R. Alfano, C.R. Buell, S. 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 identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A", Molecular Plant-Microbe Interactions 19(11), 1193-1206 (2006). [pdf] [journal]

  40. M. Lindeberg, S. 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", Molecular Plant-Microbe Interactions 19(11), 1151-1158 (2006). [pdf] [journal]

  41. 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) [pdf] [arxiv]

  42. N. Bailey, T. Cretegny, J.P. Sethna, V.R. Coffman, A.J. Dolgert, C.R. Myers, J. Schiotz, J.J. Mortensen, "Digital Material: a flexible atomistic simulation code", arXiv:cond-mat/0601236 [arxiv]

  43. 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). [pdf]

  44. C. R. Myers, "Software systems as complex networks: structure, function, and evolvability of software collaboration graphs", Phys. Rev. E 68, 046116 (2003). [journal] [pdf] Also republished in the November 1, 2003 issue of The Virtual Journal of Biological Physics Research.

  45. 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). [pdf]

  46. 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). [pdf]

  47. E. Iesulauro, K. Dodhia, T. Cretegny, C.-S. Chen, C. Myers, and A. R. Ingraffea, "Continuum-atomistic modeling for crack initiation and propagation in polycrystals", Proceedings of the 10th International Conference on Fracture (2001). [pdf]

  48. J.P. Sethna, K.A. Dahmen, and C.R. Myers, "Crackling noise", Nature 410, 242 (2001). [pdf] [preprint]. Excerpted as "Crackling noise", Drunken Boat (Online Journal of the Arts) 3 (2001).

  49. 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). [pdf]

  50. N. Bailey, J.P. Sethna, C.R. Myers, "Dislocation mobility in two-dimensional Lennard-Jones material", Mat. Res. Soc. Symp. Proc., 578, 249 (2000); later version Materials Science and Engineering A 309-310 152-155 (2001). [pdf] [preprint]

  51. 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. [pdf]

  52. 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, 509 (1999). [pdf]

  53. 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. [pdf]

  54. C.R. Myers, "A PDESolve Interpreter in Python" (abstract), Proceedings of the 6th International Python Conference, San Jose, CA, Oct. 14-17, 1997. [pdf]

  55. J.P. Sethna and C.R. Myers, "Martensitic Tweed and the Two-Way Shape-Memory Effect", http://www.arxiv.org/abs/cond-mat/9702031 (1997). [arxiv]

  56. A. E. Trefethen, V. S. Menon, C. C. Chang, G. J. Czajkowski, C. Myers, and L. N. Trefethen, "MultiMATLAB: MATLAB on multiple processors", Technical Report 96-239, Cornell Theory Center (1996). [html]

  57. C.-C. Chang, G.J. Czajkowski, X. Liu, V.S. Menon, C.R. Myers, A.E. Trefethen, L.N. Trefethen, "The Cornell MultiMATLAB Project", Proceedings of The 1996 Parallel Object-Oriented Methods and Applications Conference, Santa Fe, NM, Feb. 1996.

  58. C.R. Myers, "Abstractions, applications and accommodations: Thoughts on developing object-oriented software using someone else's class library", Proceedings of The 1996 Parallel Object-Oriented Methods and Applications Conference, Santa Fe, NM, Feb. 1996. [html]

  59. C.R. Myers, B. Shaw and J.S. Langer, "Slip complexity in a crustal-plane model of an earthquake fault", Phys. Rev. Lett. 77, 972 (1996). [pdf]

  60. 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. [pdf]

  61. 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). [pdf]

  62. C.R. Myers and J.P. Sethna, "Collective dynamics of sliding charge density waves: II. Finite-size effects", Phys. Rev. B 47, 11194 (1993). [pdf]

  63. C.R. Myers and J.P. Sethna, "Collective dynamics of sliding charge density waves: I. Critical phenomena", Phys. Rev. B 47, 11171 (1993). [pdf]

  64. 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). [pdf]

  65. R.V. Jensen and C.R. Myers, "Images of the critical points of nonlinear maps", Phys. Rev. A 32, 1222 (1985). [pdf]


By subject area (some papers are listed in multiple areas)

Systems biology: regulation, signaling, metabolism, information processing, and sloppiness

Infectious disease dynamics: networks, landscapes and metapopulations

Plant pathology: regulation of virulence and plant-pathogen interactions

Materials, geophysics, and condensed matter physics: dynamics, patterns and critical phenomena

Computational science: software, systems and algorithms