Joshua L. Payne

Research Interests

We use computational models and data-driven approaches to understand the design constraints, robustness, and evolution of gene regulation, primarily at the level of transcription.

CV

Education and Professional Positions

2015  Junior Group Leader, University of Zurich, Switzerland
2012 - 2015 Postdoctoral Research Fellow, University of Zurich, Switzerland
2012 - 2013 Faculty of the Citizen Science Program, Bard College, NY, USA
2009 - 2011 Postdoctoral Research Fellow, Dartmouth, NH, USA
2009 - 2010 Visiting Scientist, IIASA, Austria
2009 Ph.D., Interaction Topologies and Information Flow, Computer Science, The University of Vermont, VT USA, Advisor: Professor Margaret J. Eppstein
2004 - 2009 Graduate Research Fellow, The University of Vermont, VT, USA
2007 - 2008 Graduate Teaching Assistant, The University of Vermont, VT, USA
2004 M.Eng, Operations Research, Rensselaer Polytechnic Institute, NY USA
2003 B.Sc., Mathematics and Computer Science, Regis University, CO USA
2002 - 2003 Intern, The National Center for Atmospheric Research, CO, USA
2000 - 2003 Mathematics Tutor, Regis University, CO, USA

Selected Publications

  • Payne JL., Wagner A. (2015). Mechanisms of mutational robustness in transcriptional regulation. Frontiers in Genetics, 6(322):online. DOI: 10.3389/fgene.2015.00322
  • Payne JL., Wagner A. (2015). Function does not follow form in gene regulatory circuits. Scientific Reports, 5(13015):online. DOI: 10.1038/srep13015
  • Pechenick DA., Payne JL., Moore JH. (2014). Phenotypic Robust- ness and the Assortativity Signature of Human Transcription Factor Networks. PLoS Computational Biology, 10(8):e1003780. DOI: 10.1371/journal.pcbi.1003780
  • Payne JL., Wagner A. (2014). Latent phenotypes pervade gene regulatory circuits. BMC Systems Biology, 8(64):8:64. DOI: 10.1186/1752-0509-8-64
  • Payne JL., Wagner A. (2014). The robustness and evolvability of transcription factor binding sites. Science, 343(6173):875-877. DOI: 10.1126/science.1249046
  • Payne JL., Moore JH., Wagner A. (2014). Robustness, evolvability, and the logic of genetic regulation. Artificial Life, 20(1):111-126. DOI: 10.1162/ARTL_a_00099
  • Payne JL., Wagner A. (2013). Constraint and contingency in multifunctional gene regulatory circuits. PLoS Computational Biology, 9(6):e1003071. DOI: 10.1371/journal.pcbi.1003071
  • Pechenick DA., Moore JH., Payne JL. (2013). The Influence of Assortativity on the Robustness and Evolvability of Gene Regulatory Networks upon Gene Birth. Journal of Theoretical Biology, 330:26-36. DOI: 10.1016/j.jtbi.2013.03.019
  • Payne JL., Giacobini M. Moore JH. (2013). Complex and Dynamic Population Structures: Synthesis, Open Questions, and Future Directions. Soft Computing, 17, pp. 1109-1120. DOI: 10.1007/s00500-013-0994-x
  • Hu T., Payne, Payne JL., Banzhaf W., Moore JH. (2012). Evolutionary Dynamics on Multiple Scales: A Quantitative Analysis of the Interplay Between Genotype, Phenotype, and Fitness in Linear Genetic Programming. Genetic Program- ming and Evolvable Machines, 13, pp. 305-337. DOI: 10.1007/s10710-012-9159-4
  • Pechenick DA., Payne JL., Moore JH. (2012). The Influence of Assortativity on the Robustness of Signal-Integration Logic in Gene Regulatory Networks. Journal of Theoretical Biology, 296, pp. 21-32. DOI: 10.1016/j.jtbi.2011.11.029