- M.K. Transtrum, B. Machta, K. Brown, B.C. Daniels, C.R. Myers, and J. Sethna, "Sloppiness and emergent theories in physics, biology, and beyond", J. Chem. Phys. 143, 010901 (2015). [journal][arxiv]
- 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", arXiv:1503.01104 (2015). [arxiv]
- J. Hindes and C.R. Myers, "Driven synchronization in random networks of oscillators", arXiv:1503.00176 (2015). [arxiv]
- 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", arXiv:1502.07969 (2015). [arxiv]
- 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] - 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] - 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", arXiv:1404.4755 (2014).
- S. Singh and C.R. Myers, "Outbreak statistics and scaling laws for
externally driven epidemics",
*Phys. Rev. E*89, 042108 (2014). [journal] [pdf] [arxiv] - 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]. - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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] - 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)] - 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] - 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]
- 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]
- 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]
- 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]
- 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]
- 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] - 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]
- 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",
(submitted).
[arxiv]
- 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] - 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. - 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] - 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]
- 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]
- 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). - 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] - 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] - 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] - 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] - 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] - C.R. Myers,
"A PDESolve Interpreter in Python" (abstract),
*Proceedings of the 6th International Python Conference*, San Jose, CA, Oct. 14-17, 1997. [pdf] - 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]
- 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]
- 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. - 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] - 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] - 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] - C.R. Myers,
"LPARX, a C++ Class Library for Parallel Computing",
*Cornell Theory Center Smart Node Newsletter,*vol. 6, no. 6 (1994). - 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] - 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] - C.R. Myers and J.P. Sethna,
"Collective dynamics of sliding charge density waves: I.
Critical phenomena",
*Phys. Rev. B***47**, 11171 (1993). [pdf] - 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] - R.V. Jensen and C.R. Myers,
"Images of the critical points of nonlinear maps",
*Phys. Rev. A***32**, 1222 (1985). [pdf]