- Systems biology: regulation, signaling, metabolism, information processing, and sloppiness
- Infectious disease dynamics: networks, landscapes, and metapopulations
- Host-microbe interactions and plant pathology: host-microbe interactions, and regulation of virulence
- Complex systems, condensed matter physics, materials, and geophysics: dynamics, patterns, and critical phenomena
- Computational science: software, systems, and algorithms
Chronologically
- I.A. Holmes, J.G. Martinez-Fonseca, R. von May, B.A. Sealey, P.A. Cerda, M.R. Grundler, E.P. Westeen, D. Nondorf, J.G Larson, C.R. Myers, T.A. Hendry, "Increased host diversity limits bacterial generalism but may promote microbe-microbe interactions", bioRxiv, https://doi.org/10.1101/2024.04.24.590977, 2024. [bioRxiv]
- J.Z. Kim, N. Perrin-Gilbert, E. Narmanli, P. Klein, C.R. Myers, I. Cohen, JJ. Waterfall, J.P. Sethna, "Γ-VAE: Curvature regularized variational autoencoders for uncovering emergent low dimensional geometric structure in high dimensional data", https://arxiv.org/abs/2403.01078 (2024). [arxiv]
- A.B. Kohlberg, C.R. Myers, L.L. Figueroa, "From buzzes to bytes: A systematic review of automated bioacoustics models used to detect, classify and monitor insects", Journal of Applied Ecology, https://doi.org/10.1111/1365-2664.14630 (2024).[journal]
- I.A. Holmes, A.M. Durso, C.R. Myers, T.A. Hendry. "Changes in capture availability due to infection can lead to detectable biases in population-level infectious disease parameters", PeerJ 12:e16910 https://doi.org/10.7717/peerj.16910 (2024) [journal][bioRxiv]
- W.H. Ng, C.R. Myers, S.H. McArt, S.P. Ellner, "tdsa: An R package for time-dependent sensitivity analysis", Methods in Ecology and Evolution, 10 October 2023, https://doi.org/10.1111/2041-210X.14216. [journal]
- W.H. Ng, C.R. Myers, S. McArt, S.P. Ellner, "A time for every purpose: using time-dependent sensitivity analysis to help understand and manage dynamic ecological systems", American Naturalist. https://doi.org/10.1086/726143 (2023). [journal][bioRxiv]
- T. Salners, K.E. Avila, B. Nicholson, C.R. Myers, J. Beggs, K.A. Dahmen, "Recurrent activity in neuronal avalanches", Scientific Reports 2023 Mar 24;13(1):4871. [journal]
- W.H. Ng, C.R. Myers, S.H. McArt, S.P. Ellner, "Predicting and Controlling Spillover in Multi-Species Disease Transmission Networks: Steady-State Analysis", American Naturalist, Jun;201(6):880-894. doi: 10.1086/724009 (2023). [journal]
- W.H. Ng, C.R. Myers, S.H. McArt, S.P. Ellner, "Pathogen transport amplifies or dilutes disease transmission depending on the host dose-response relationship
", Ecology Letters, https://doi.org/10.1111/ele.13932 (2021) [journal]
- E.D. Lee, B.C. Daniels, C.R. Myers, D.C. Krakauer, J.C. Flack, "Scaling theory of armed conflict avalanches", Physical Review E, 102, 042312 (2020). [journal][arxiv]
- P. Graystock, W.H. Ng, K. Parks, A.D. Tripodi, P.A. Muniz, A.A. Fersch, C.R. Myers, Q.S. McFrederick, S.H. McArt,
"Dominant bee species and floral abundance drive parasite temporal dynamics in plant-pollinator communities", Nature Ecology & Evolution, https://doi.org/10.1038/s41559-020-1247-x (2020). [journal]
- L.L. Figueroa, H. Grab, W.H. Ng, C.R. Myers, P. Graystock, Q.S. McFrederick, S.H. McArt, "Landscape simplification shapes pathogen prevalence in plant-pollinator networks", Ecology Letters, https://doi.org/10.1111/ele.13521 (2020). [journal]
- S.P. Ellner, W.H. Ng, C.R. Myers, "Individual specialization and multi-host epidemics: Disease spread in plant-pollinator networks", The American Naturalist 195, no. 5 (May 2020): E118-E131. [journal][pdf]
- S. Mehringer, C.R. Myers, J. Houchins, L. Rivera, "Mining online training data", Proceedings of PEARC '19: Practice and Experience in Advanced Research Computing, article 84 (2019). [journal]
- E.D. Lee, B.C. Daniels, C.R. Myers, D.C. Krakauer, J.C. Flack, "Emergent regularities and scaling in armed conflict data", arXiv.org/abs/1903.07762 (2019). [arxiv]
- C.R. Myers, "Zen and the art of parameter estimation in systems
biology", invited chapter in Systems Immunology: An Introduction
to Modeling Methods for Scientists, J. Das and C. Jayaprakash
(eds.), CRC Press (2019). [author-produced
pdf]
[access through Cornell Library (restricted)]
[publisher
site]
- O. Kogan, K. O'Keeffe, C.R. Myers, "Fragility of
reaction-diffusion models with respect to competing advective
processes", Phys. Rev. E 96, 022220 (2017). [journal][pdf][arxiv]
- 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 198: 2330-2344 (2016).
[journal]
- 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][pdf][arxiv]
- 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]
- 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]
- 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]
- 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]
- 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]
- J. Hindes and C.R. Myers, "Driven synchronization in random networks of oscillators", Chaos 25, 073119 (2015). [journal][arxiv]
- 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]
- 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]
- 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]
[pdf]
- 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]
- 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]
- 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]
- 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",
arXiv:cond-mat/0601236
[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).
[journal]
[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 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]
By subject area (some papers are listed in multiple areas)
- J.Z. Kim, N. Perrin-Gilbert, E. Narmanli, P. Klein, C.R. Myers, I. Cohen, JJ. Waterfall, J.P. Sethna, "Γ-VAE: Curvature regularized variational autoencoders for uncovering emergent low dimensional geometric structure in high dimensional data", https://arxiv.org/abs/2403.01078 (2024). [arxiv]
- C.R. Myers, "Zen and the art of parameter estimation in systems
biology", invited chapter in Systems Immunology: An Introduction
to Modeling Methods for Scientists, J. Das and C. Jayaprakash
(eds.), CRC Press (2019). [author-produced
pdf]
[access through Cornell Library (restricted)]
[publisher
site]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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.
- I.A. Holmes, A.M. Durso, C.R. Myers, T.A. Hendry. "Changes in capture availability due to infection can lead to detectable biases in population-level infectious disease parameters", PeerJ 12:e16910 https://doi.org/10.7717/peerj.16910 (2024) [journal][bioRxiv]
- W.H. Ng, C.R. Myers, S. McArt, S.P. Ellner, "A time for every purpose: using time-dependent sensitivity analysis to help understand and manage dynamic ecological systems", American Naturalist. https://doi.org/10.1086/726143 (2023). [journal][biorxiv]
- W.H. Ng, C.R. Myers, S.H. McArt, S.P. Ellner, "Predicting and Controlling Spillover in Multi-Species Disease Transmission Networks: Steady-State Analysis", American Naturalist, Jun;201(6):880-894. doi: 10.1086/724009 (2023). [journal]
- W.H. Ng, C.R. Myers, S.H. McArt, S.P. Ellner, "Pathogen transport amplifies or dilutes disease transmission depending on the host dose-response relationship
", Ecology Letters, https://doi.org/10.1111/ele.13932 (2021) [journal]
- P. Graystock, W.H. Ng, K. Parks, A.D. Tripodi, P.A. Muniz, A.A. Fersch, C.R. Myers, Q.S. McFrederick, S.H. McArt,
"Dominant bee species and floral abundance drive parasite temporal dynamics in plant-pollinator communities", Nature Ecology & Evolution, https://doi.org/10.1038/s41559-020-1247-x (2020). [journal]
- L.L. Figueroa, H. Grab, W.H. Ng, C.R. Myers, P. Graystock, Q.S. McFrederick, S.H. McArt, "Landscape simplification shapes pathogen prevalence in plant-pollinator networks", Ecology Letters, https://doi.org/10.1111/ele.13521 (2020). [journal]
- S. P. Ellner, W. H. Ng, C.R. Myers, "Individual specialization and multi-host epidemics: Disease spread in plant-pollinator networks", The American Naturalist 195, no. 5 (May 2020): E118-E131. [journal][pdf]
- O. Kogan, K. O'Keeffe, C.R. Myers, "Fragility of reaction-diffusion models with respect to competing advective processes", Phys. Rev. E 96, 022220 (2017). [journal][pdf][arxiv]
- J. Hindes and C.R. Myers, "Driven synchronization in random networks of oscillators", Chaos 25, 073119 (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", Phys. Rev. E 92, 052081 (2015). [journal][arxiv]
- 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]
- 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]].
- 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]
- I.A. Holmes, J.G. Martinez-Fonseca, R. von May, B.A. Sealey, P.A. Cerda, M.R. Grundler, E.P. Westeen, D. Nondorf, J.G Larson, C.R. Myers, T.A. Hendry, "Increased host diversity limits bacterial generalism but may promote microbe-microbe interactions", bioRxiv, https://doi.org/10.1101/2024.04.24.590977, 2024. [bioRxiv]
- 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 198: 2330-2344 (2016).
[journal]
- 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]
- 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]
- 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]
[pdf]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- T. Salners, K.E. Avila, B. Nicholson, C.R. Myers, J. Beggs, K.A. Dahmen, "Recurrent activity in neuronal avalanches", Scientific Reports 2023 Mar 24;13(1):4871. [journal]
- E.D. Lee, B.C. Daniels, C.R. Myers, D.C. Krakauer, J.C. Flack, "Scaling theory of armed conflict avalanches", Physical Review E, 102, 042312 (2020). [journal][arxiv]
- E.D. Lee, B.C. Daniels, C.R. Myers, D.C. Krakauer, J.C. Flack, "Emergent regularities and scaling in armed conflict data", arXiv.org/abs/1903.07762 (2019). [arxiv]
- J. Hindes and C.R. Myers, "Driven synchronization in random networks of oscillators", Chaos 25, 073119 (2015). [journal][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",
arXiv:cond-mat/0601236 (2006).
[arxiv]
- 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).
[journal]
[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]
- 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]
- 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 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]
J.Z. Kim, N. Perrin-Gilbert, E. Narmanli, P. Klein, C.R. Myers, I. Cohen, JJ. Waterfall, J.P. Sethna, "Γ-VAE: Curvature regularized variational autoencoders for uncovering emergent low dimensional geometric structure in high dimensional data", https://arxiv.org/abs/2403.01078 (2024). [arxiv]
A.B. Kohlberg, C.R. Myers, L.L. Figueroa, "From buzzes to bytes: A systematic review of automated bioacoustics models used to detect, classify and monitor insects", Journal of Applied Ecology, https://doi.org/10.1111/1365-2664.14630 (2024).[journal]
W.H. Ng, C.R. Myers, S.H. McArt, S.P. Ellner, "tdsa: An R package for time-dependent sensitivity analysis", Methods in Ecology and Evolution, 10 October 2023, https://doi.org/10.1111/2041-210X.14216. [journal]
S. Mehringer, C.R. Myers, J. Houchins, L. Rivera, "Mining online training data", Proceedings of PEARC '19: Practice and Experience in Advanced Research Computing, article 84 (2019). [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]
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]
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 (2006)
[arxiv]
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, 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]
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.
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]
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]