Publications

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

Preprints

[54] Little evidence the standard genetic code is optimized for resource conservation

Rozhonova, H. & Payne, J. L.
[bioRxiv]

[53] SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution

Stadler, L., Banaei-Esfahani, A., Ciuffa, R., Payne, J. L., & Aebersold, R.
[bioRxiv]

Refereed Journal Publications

[52] From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

Manrubia, S. et al. (including Payne, J. L.)
Physics of Life Reviews (2021), to appear.
[arXiv]

[51] Mutation bias interacts with composition bias to influence adaptive evolution

Cano, A. & Payne, J. L.
PLoS Computational Biology (2020), 16, e1008296.
[pdf][doi]

[50] Enhancers facilitate the birth of de novo genes and gene integration into regulatory networks

Majic, P. & Payne, J. L.
Molecular Biology & Evolution (2020), 37, 1165-1178
[pdf][doi]

[49] Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis

*Payne, J. L., *Menardo, F., Trauner, A., Borrell, S., Gygli, S. M., Loiseau, C., *Gagneux, S., & *Hall, A. R.
PLoS Biology (2019), 17, e3000265
[pdf][doi]

[48] Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks

Zheng, J., Payne, J. L., & Wagner, A.
Science (2019), 365, 347-353
[pdf][doi]

See commentary by Lee & Marx (2019) “Tales from the crypt(ic).” Science, 365, 318-319. [pdf]

[47] The causes of evolvability and their evolution

Payne, J. L., & Wagner, A.
Nature Reviews Genetics (2019), 20, 24-38
[pdf][doi]

[46] The architecture of an empirical genotype-phenotype map

Aguilar-Rodríguez, J., Peel, L., Stella, M., Wagner, A., Payne, J. L.
Evolution (2018), 72, 1242-1260.
[pdf][doi]

[45] RNA-mediated gene regulation is less evolvable than transcriptional regulation

Payne, J. L., Khalid, F., & Wagner, A.
Proceedings of the National Academy of the Sciences (2018), 115, E3481-E3490.
[pdf][doi]

This paper received a rating of “very good” by the Faculty of 1000. [link]

[44] A thousand empirical adaptive landscapes and their navigability

*Aguilar-Rodríguez, J., *Payne, J. L., & Wagner, A.
Nature Ecology & Evolution (2017), 1, 0045.
[pdf][doi]

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

[43] Genonets Server - A web server for the construction, analysis, and visualization of genotype networks

Khalid, F., Aguilar-Rodríguez, J., Wagner, A., & Payne, J. L.
Nucleic Acids Research (2016), 44, W70-W76.
[pdf][doi][webserver]

[42] No tradeoff between versatility and robustness in gene circuit motifs

Payne, J. L.
Physica A (2016), 449, 192-199.
[pdf][doi]

[41] The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

SIB Swiss Institute of Bioinformatics Members (including Payne, J. L.)
Nucleic Acids Research (2016), 44, D27-D37.
[pdf][doi]

[40] Mechanisms of mutational robustness in transcriptional regulation

Payne, J L., & Wagner, A.
Frontiers in Genetics (2015), 6, 332.
[pdf][doi]

[39] Function does not follow form in gene regulatory circuits

Payne, J. L., & Wagner, A.
Scientific Reports (2015), 5, 13015.
[pdf][doi]

[38] Phenotypic robustness and the assortativity signature of human transcription factor networks

Pechenick, D. A., Payne, J. L., & Moore, J. H.
PLoS Computational Biology (2014), 10, e1003780.
[pdf][doi]

[37] Latent phenotypes pervade gene regulatory circuits

Payne, J. L., & Wagner, A.
BMC Systems Biology (2014), 8, p. 64.
[pdf][doi]

[36] The robustness and evolvability of transcription factor binding sites

Payne, J. L., & Wagner, A.
Science (2014), 343, 875-877.
[pdf][doi]

This paper received a rating of “very good” by the Faculty of 1000 Developmental Biology.[link]
See commentary in Nature Reviews Genetics.[link]
I received the SIB Young Bioinformatician Award [link] and the Dan David Prize Scholarship [link] for this manuscript.

[35] Robustness, evolvability, and the logic of genetic regulation

Payne, J. L., Moore, J. H., & Wagner, A.
Artificial Life (2014), 20, 111-126.
[pdf][doi]

[34] Constraint and contingency in multifunctional gene regulatory circuits

Payne, J. L., & Wagner, A.
PLoS Computational Biology (2013), 9, e1003071.
[pdf][doi]

[33] The influence of assortativity on the robustness and evolvability of gene regulatory networks upon gene birth

Pechenick, D. A., Moore, J. H., & Payne, J. L.
Journal of Theoretical Biology (2013), 330, 26-36.
[pdf][doi]

[32] Complex and dynamic population structures: Synthesis, open questions, and future directions

Payne, J. L., Giacobini, M., & Moore, J. H.
Soft Computing (2013), 17, 1109-1120.
[pdf][doi]

[31] Evolutionary dynamics on multiple scales: A quantitative analysis of the interplay between genotype, phenotype, and fitness in linear genetic programming

*Hu, T., *Payne, J. L., Banzhaf, W., & Moore, J. H.
Genetic Programming and Evolvable Machines (2012), 13, 305-337.
[pdf][doi]

[30] The influence of assortativity on the robustness of signal-integration logic in gene regulatory networks

*Pechenick, D. A., *Payne, J. L., Moore, J. H.
Journal of Theoretical Biology (2012), 296, 21-32.
[pdf][doi]

[29] Exact solutions for social and biological contagion models on mixed directed and undirected, degree-correlated random networks

Payne, J. L., Harris, K. D., & Dodds, P. S.
Physical Review E (2011), 84, 016110.
[pdf][doi]

[28] Direct, physically motivated derivation of the contagion condition for spreading processes on generalized random networks

Dodds, P. S., Harris, K. D., & Payne, J. L.
Physical Review E (2011), 83, 056122.
[pdf][doi]

[27] The evolution of conditional dispersal and reproductive isolation along environmental gradients

Payne, J. L., Mazzucco, R., & Dieckmann, U.
Journal of Theoretical Biology (2011), 273, 147-155.
[pdf][doi]

[26] Exploiting graphics processing units for computational biology and bioinformatics

*Payne, J L., *Sinnott-Armstrong, N., & Moore, J. H.
Interdisciplinary Sciences: Computational Life Sciences (2010), 2, 213-220.
[pdf][doi]

[25] Information cascades on degree-correlated random networks

Payne, J. L., Dodds, P. S., & Eppstein, M. J.
Physical Review E (2009), 80, 026125.
[pdf][doi]

[24] Evolutionary dynamics on scale-free interaction networks

Payne, J. L., & Eppstein, M. J.
IEEE Transactions on Evolutionary Computation (2009), 13, 895-912.
[pdf][doi]

[23] Pair approximations of takeover dynamics in regular population structures

Payne, J. L., & Eppstein, M. J.
Evolutionary Computation (2009), 17, 203-229.
[pdf][doi]

[22] Underdominance, multiscale interactions, and self-organizing barriers to gene flow

Eppstein, M. J., Payne, J. L., & Goodnight, C. C.
Artificial Evolution and Applications (2009), 725049.
[pdf]

[21] Analysis of a threshold model of social contagion on degree-correlated networks

Dodds, P. S., & Payne, J. L.
Physical Review E (2009) , 79, 066115.
[pdf][doi]

[20] Genomic mining for complex disease traits with 'Random Chemistry’

Eppstein, M. J., Payne, J L., White, B. C., & Moore J. H.
Genetic Programming and Evolvable Machines (2007) , 8, 395-411.
[pdf][doi]

Refereed Conference Publications

[19] An alternative route to robustness: The relationship between assortativity, in-components, and characteristic path length in gene regulatory networks

Pechenick, D. A., Payne, J. L., Moore, J. H.
ECAL (2013), 364-371.
[pdf][doi]

[18] Robustness, evolvability, and accessibility in the signal-integration space of gene regulatory circuits

Payne, J. L. & Moore, J. H.
ECAL (2011), 638-645.
[pdf][link]

Best paper award

[17] The influence of whole genome duplication and subsequent diversification on environmental robustness and evolutionary innovation in gene regulatory networks

Pan, Q., Darabos, C., Tyler, A., Moore, J. H., & Payne, J. L.
ECAL (2011), 614 – 621.
[pdf][link]

[16] Robustness, evolvability, and accessibility in linear genetic programming

*Hu, T., *Payne J. L., Banzhaf, W., & Moore, J. H.
Lecture Notes in Computer Science (2011), 6621, 13-24.
[pdf][doi]

Nominated for a best paper award

[15] Sexual recombination in self-organizing interaction networks

Payne, J L. & Moore, J. H.
Lecture Notes in Computer Science (2010), 6024, 41-50.
[pdf][doi]

[14] The influence of scaling and assortativity on takeover times in scale-free topologies

Payne, J. L. & Eppstein, M. J.
GECCO (2008), 241-248.
[pdf][doi]

Nominated for a best paper award

[13] Parameterizing pair approximations for takeover dynamics

Payne, J. L. & Eppstein, M. J.
GECCO (2008), 2199-2204.
[pdf][doi]

[12] Takeover times on scale-free topologies

Payne, J. L. & Eppstein, M. J.
GECCO (2007), 308-315.
[pdf][doi]

[11] Sensitivity of self-organized speciation to long-distance dispersal

Payne, J. L., Eppstein, M. J., & Goodnight, C. J.
IEEE Alife (2007), 1-7.
[pdf][doi]

Best student paper award

[10] Using pair approximations to predict takeover dynamics in spatially structured populations

Payne, J. L. & Eppstein, M. J.
GECCO (2007), 2557-2563.
[pdf][doi]

[9] Emergent mating topologies in spatially structured genetic algorithms

Payne, J. L. & Eppstein, M. J.
GECCO (2006), 207-214.
[pdf][doi]

[8] Hill climbing through 'Random Chemistry' for detecting epistasis

Eppstein, M. J., Payne, J. L., White, B. C., & Moore, J., H.
GECCO (2006), late-breaking papers.
[pdf][link]

[7] Speciation by self-organizing barriers to gene flow in simulated populations with localized mating

Eppstein, M. J., Payne, J. L., & Goodnight, C. J.
GECCO (2006), Workshop on Complexity through Development and Self-Organizing Representations.
[pdf][link]

[6] A hybrid genetic algorithm with pattern search for finding heavy atoms in protein crystals

Payne J. L. & Eppstein, M. J.
GECCO (2005), 377 – 384.
[pdf][doi]

Nominated for a best paper award

Refereed Book Chapters

[5] The robustness and evolvability of transcriptional regulation

Aguilar-Rodríguez, J. & Payne, J. L.
In Evolutionary Systems Biology (2020), to appear.

[4] Robustness and evolvability in molecular evolution

Wagner, A. & Payne, J. L.
In Encyclopedia of Evolutionary Biology (2016), Elsevier, 484-488.
[Amazon]

[3] Pair approximations

Payne, J. L.
In Encyclopedia of Theoretical Ecology (2012), University of California Press, 531-534.
[pdf][ Amazon]

[2] Exploiting expert knowledge of protein-protein interactions in a computational evolution system for detecting epistasis

*Patton, K. A., *Payne, J. L., Hill, D. P., Caldwell, T., Fisher, J. M., & Moore, J. H.
In Genetic Programming Theory and Practice (2011), Springer-Verlag, 195-210.
[pdf][Amazon]

[1] Sensible initialization of a computational evolution system using expert knowledge for epistasis analysis in human genetics

Payne, J. L., Greene, C. S., Hill, D. P., & Moore, J. H.
In Exploitation of Linkage Learning in Evolutionary Algorithms (2010), Springer-Verlag, 215-226.
[pdf][Amazon]

Dissertation

Interaction topologies and information flow

Payne, J. L.
The University of Vermont (2009)
[pdf]