Publications

Listed in reverse chronological order by year, and categorized by publication type.

Refereed Journal Publications

[25] *Aguilar-Rodríguez, José, *Payne, Joshua L., & Wagner, Andreas (2017) "A thousand empirical adaptive landscapes and their navigability." Nature Ecology & Evolution, 1, 0045. [pdf]

José Aguilar-Rodríguez received the SIB Best Swiss Bioinformatics Graduate Paper Award for this manuscript. 


[24] Khalid, Fahad, Aguilar-Rodríguez, José, Wagner, Andreas, & Payne, Joshua L. (2016) "Genonets Server - A web server for the construction, analysis, and visualization of genotype networks." Nucleic Acids Research, 44, W70-W76. [pdf] [webserver]

[23] Payne, Joshua L. (2016) "No tradeoff between versatility and robustness in gene circuit motifs." Physica A, 449, 192-199. [pdf]

[22] SIB Swiss Institute of Bioinformatics Members (including Payne, Joshua L.) (2016) "The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases." Nucleic Acids Research, 44, D27-D37. [pdf]

[21] Payne, Joshua L., & Wagner, Andreas (2015) "Mechanisms of mutational robustness in transcriptional regulation." Frontiers in Genetics, 6, 332. [pdf]

[20] Payne, Joshua L., & Wagner, Andreas (2015) "Function does not follow form in gene regulatory circuits." Scientific Reports, 5, 13015. [pdf]

[19] Pechenick, Dov A., Payne, Joshua L., & Moore, Jason H. (2014) "Phenotypic Robustness and the Assortativity Signature of Human Transcription Factor Networks." PLoS Computational Biology, 10, e1003780. [pdf]

[18] Payne, Joshua L., & Wagner, Andreas (2014) "Latent Phenotypes Pervade Gene Regulatory Circuits." BMC Systems Biology, 8, p. 64. [pdf]

[17] Payne, Joshua L., & Wagner, Andreas (2014) "The Robustness and Evolvability of Transcription Factor Binding Sites." Science, 343, pp. 875-877. [pdf]

      This paper received a rating of "very good" by the Faculty of 1000 Developmental Biology. [link]

        See commentary in Nature Reviews Genetics. [link]
    

[16] Payne, Joshua L., Moore, Jason H., & Wagner, Andreas (2014) "Robustness, Evolvability, and the Logic of Genetic Regulation." Artificial Life, 20, pp. 111-126. [pdf]

[15] Payne, Joshua L., & Wagner, Andreas (2013) "Constraint and Contingency in Multifunctional Gene Regulatory Circuits." PLoS Computational Biology, 9, p.e1003071. [pdf]

[14] Pechenick, Dov A., Moore, Jason H., & Payne, Joshua L. (2013) "The Influence of Assortativity on the Robustness and Evolvability of Gene Regulatory Networks upon Gene Birth." Journal of Theoretical Biology, 330, pp. 26-36. [pdf]

[13] Payne, Joshua L., Giacobini, Mario, & Moore, Jason H. (2013) "Complex and Dynamic Population Structures: Synthesis, Open Questions, and Future Directions." Soft Computing, 17, pp. 1109-1120. [pdf]

[12] *Hu, Ting, *Payne, Joshua L., Banzhaf, Wolfgang, & Moore, Jason H. (2012) "Evolutionary Dynamics on Multiple Scales: A Quantitative Analysis of the Interplay Between Genotype, Phenotype, and Fitness in Linear Genetic Programming." Genetic Programming and Evolvable Machines, 13, pp. 305 - 337. [pdf]

[11] *Pechenick, Dov A., *Payne, Joshua L., Moore, Jason H. (2012) "The Influence of Assortativity on the Robustness of Signal-Integration Logic in Gene Regulatory Networks." Journal of Theoretical Biology, 296, pp. 21-32. [pdf]

[10] Payne, Joshua L., Harris, Kameron D., & Dodds, Peter S. (2011) "Exact Solutions for Social and Biological Contagion Models on Mixed Directed and Undirected, Degree-Correlated Random Networks." Physical Review E, 84, p.016110. [pdf]

[9] Dodds, Peter S., Harris, Kameron D., & Payne, Joshua L. (2011) "Direct, Physically Motivated Derivation of the Contagion Condition for Spreading Processes on Generalized Random Networks." Physical Review E, 83, p.056122. [pdf]

[8] Payne, Joshua L., Mazzucco, Rupert, & Dieckmann, Ulf (2011) "The Evolution of Conditional Dispersal and Reproductive Isolation Along Environmental Gradients." Journal of Theoretical Biology, 273, pp. 147-155. [pdf]

[7] *Payne, Joshua L.*+Sinnott-Armstrong, Nicholas, & Moore, Jason H. (2010) "Exploiting Graphics Processing Units for Computational Biology and Bioinformatics." Interdisciplinary Sciences: Computational Life Sciences, Springer-Verlag, 2(3), pp. 213-220. [pdf]

[6] Payne, Joshua L., Dodds, Peter S., & Eppstein, Margaret J. (2009) "Information Cascades on Degree-Correlated Random Networks." Physical Review E, 80, p. 026125. [pdf]

[5] Payne, Joshua L., & Eppstein, Margaret J. (2009) "Evolutionary Dynamics on Scale-Free Interaction Networks." IEEE Transactions on Evolutionary Computation, 13(4), pp. 895-912. [pdf] 

[4] Payne, Joshua L., & Eppstein, Margaret J. (2009) "Pair Approximations of Takeover Dynamics in Regular Population Structures." Evolutionary Computation, 17(2), pp. 203-229. [pdf]

[3] Eppstein, Margaret J., Payne, Joshua L., & Goodnight, Charles C. (2009) "Underdominance, Multiscale Interactions, and Self-Organizing Barriers to Gene Flow." Artificial Evolution and Applications, Special Issue on Artificial Evolution Methods in the Biological and Biomedical Sciences, p. 725049. [pdf]

[2] Dodds, Peter S., & Payne, Joshua L. (2009) "Analysis of a Threshold Model of Social Contagion on Degree-Correlated Networks." Physical Review E, 79, p. 066115. [pdf]

[1] Eppstein, Margaret J., Payne, Joshua L., White, Bill C., & Moore Jason H. (2007) "Genomic Mining For Complex Disease Traits with 'Random Chemistry.'" Genetic Programming and Evolvable Machines, Special Issue on Medical Applications, 8(4), pp. 395 - 411. [pdf]

Refereed Conference Publications

[10] Pechenick, Dov A., Payne, Joshua L., Moore, Jason H. (2013) "An alternative route to robustness: The relationship between assortativity, in-components, and characteristic path length in gene regulatory networks." Proceedings of the European Conference on Artificial Life, ECAL-2013, pp. 364 - 371. [pdf]

[9] Payne, Joshua L. & Moore, Jason H. (2011) "Robustness, Evolvability, and Accessibility in the Signal-Integration Space of Gene Regulatory Circuits." Proceedings of the European Conference on Artificial Life, ECAL-2011, pp. 638 - 645. (best paper award.) [pdf]

[8] Pan, Qinxin, Darabos, Christian, Tyler, Anna, Moore, Jason H., & Payne, Joshua L. (2011) "The Influence of Whole Genome Duplication and Subsequent Diversification on Environmental Robustness and Evolutionary Innovation in Gene Regulatory Networks." Proceedings of the European Conference on Artificial Life, ECAL-2011, pp. 614 - 621. [pdf]

[7] *Hu, Ting, *Payne Joshua L., Banzhaf, Wolfgang, & Moore, Jason H. (2011) "Robustness, Evolvability, and Accessibility in Linear Genetic Programming." Proceedings of the EuroGP Conference 2011, Evostar, Springer's Lecture Notes in Computer Science, vol. 6621, Eds. S. Silva et al., pp. 13-24. (nominated for a best paper award.) [pdf] 

[6] Payne, Joshua L. & Moore, Jason H. (2010) "Sexual Recombination in Self-Organizing Interaction Networks." Proceedings of the EvoCOMPLEX Conference 2010, Evostar, Springer's Lecture Notes in Computer Science, vol. 6024, Eds. Di Chio et al., pp. 41-50. [pdf]

[5] Payne, Joshua L. & Eppstein, Margaret J. (2008) "The Influence of Scaling and Assortativity on Takeover Times in Scale-Free Topologies." Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2008, Eds. Keijzer et al., pp. 241-248. (nominated for a best paper award.) [pdf]

[4] Payne, Joshua L. & Eppstein, Margaret J. (2007) "Takeover Times on Scale-Free Topologies." Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2007, Eds. Thierens, D. et al., pp. 308 - 315. [pdf]

[3] Payne, Joshua L., Eppstein, Margaret, J., & Goodnight, Charles J. (2007) "Sensitivity of Self-Organized Speciation to Long-Distance Dispersal." Proceedings of the IEEE Symposium on Artificial Life, 2007, pp. 1 - 7. (best student paper award.) [pdf]  

[2] Payne, Joshua L. & Eppstein, Margaret J. (2006) "Emergent Mating Topologies in Spatially Structured Genetic Algorithms." Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2006, Eds. Keijzer, M. et al., pp. 207 - 214. [pdf]

[1] Payne Joshua L. & Eppstein, Margaret J. (2005) "A Hybrid Genetic Algorithm with Pattern Search for Finding Heavy Atoms in Protein Crystals." Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2005, Eds. Beyer, H.G. et al., pp. 377 - 384. (nominated for a best paper award.) [pdf]

Refereed Workshop Publications

[1] Eppstein, Margaret, J., Payne, Joshua L., & Goodnight, Charles, J. (2006) "Speciation by Self-Organizing Barriers to Gene Flow in Simulated Populations with Localized Mating." Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2006, Workshop on Complexity through Development and Self-Organizing Representations (CODESOAR). [pdf]

Refereed Book Chapters

[2] *Pattin, Kristine A., *Payne, Joshua L., Hill, Douglas P., Caldwell, Thomas, Fisher, Jonathan M., & Moore, Jason H. (2011) "Exploiting Expert Knowledge of Protein-Protein Interactions in a Computational Evolution System for Detecting Epistasis." In Genetic Programming Theory and Practice, Ed. R. Riolo et al., Springer-Verlag, pp. 195-210. [pdf] [Amazon]

[1] Payne, Joshua L., Greene, Casey S., Hill, Douglas P., & Moore, Jason H. (2010) "Sensible Initialization of a Computational Evolution System using Expert Knowledge for Epistasis Analysis in Human Genetics." In Exploitation of Linkage Learning in Evolutionary Algorithms, Ed. Y.P. Chen, Springer-Verlag, pp. 215 - 226.


Minimally Refereed Publications


[3] Payne, Joshua L. & Eppstein, Margaret J. (2008) "Parameterizing Pair Approximations for Takeover Dynamics." Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2008, late-breaking papers, Eds. Keijzer et al., pp. 2199-2204. [pdf]

[2] Payne, Joshua L. & Eppstein, Margaret J. (2007) "Using Pair Approximations to Predict Takeover Dynamics in Spatially Structured Populations." Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2007, late-breaking papers, Eds. Thierens, D. et al., pp. 2557 - 2563. [pdf]


[1] Eppstein, Margaret J., Payne, Joshua L., White, Bill C., & Moore, Jason, H. (2006) "Hill Climbing through 'Random Chemistry' for Detecting Epistasis." Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2006, late-breaking papers, Ed. Grahl, J. [pdf]


Invited Contributions

[2] Wagner, Andreas & Payne, Joshua L. "Robustness and Evolvability in Molecular Evolution." In Encyclopedia of Evolutionary Biology, Elsevier, pp. 484 - 488. [Amazon]

[1] Payne, Joshua L.
 (2012)
 "Pair Approximations." In Encyclopedia of Theoretical Ecology, Eds. A. Hastings & L. Gross, University of California Press, pp. 531-534. [pdf][Amazon]

Dissertation

Payne, Joshua L. "Interaction Topologies and Information Flow." (2009) The University of Vermont. [pdf]

 * denotes equal contribution
 + denotes undergraduate student