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College of Arts & Sciences
Department of Biological Sciences

Graduate Student Directory

Chase W. Nelson

Degree Program: Integrative Biology
Room: CLS 501
Major Professor: Austin L. Hughes, deceased (Oct. 2015)


Personal website:

CURRICULUM VITAE / RESUMÉ: Short (1-page) C.V., full C.V., or musical theatre resumé available at these links.

Check out "Chasing two passions," an interview with Hannah Spicher.



Adaptive evolution, biological sequence analysis, cancer, digital genetics, experimental evolution, lethal mutagenesis, molecular evolution, mutation, mutation accumulation, neutral evolution, neutral theory, population genetics

Current Research Areas:

Bioinformatics of pooled next-generation sequencing analysis of viral populations (including HIV, SIV, SHFV and influenza); molecular evolution studied using geographic information systems; cancer from an evolutionary perspective 


Check out SNPGenie, my software for evolutionary analysis of pooled next-generation sequencing data


BA Honors, Biology (2010) Oberlin College

Awards & Honors:

  1. Gerstner Postdoctoral Fellowship in Bioinformatics and Computational Biology, American Museum of Natural History (2016-2018)
  2. NSF Graduate Research Fellowship (2013-2016) 
  3. F1000 Poster Prize Winner, International Society for Computational Biology, Great Lakes Bioinformatics Conference (2015)
  4. Kathryn Hinnant-Johnson, M.D. Memorial Fellowship: University of South Carolina (2015)
  5. USC STEM Award: University of South Carolina (2015)
  6. NSF EAPSI Fellowship: Dr. Wen-Hsiung Li, Academia Sinica, Taipei, Taiwan (2013) 
  7. NSF Graduate Research Fellowship Program Honorable Mention (2012) 
  8. University of South Carolina Presidential Fellow (2011 – present) 
  9. NSF ESPCoR Middleware Training Program Fellow (2011 – 2012) 
  10. High Honors in Biology, Oberlin College (2010) 
  11. Society of Sigma Xi, The Scientific Research Society Oberlin Chapter (2010) 
  12. Joshua Levitt Memorial Prize in Biology, Oberlin College (2010) 
  13. NSF STEM Scholar in Computation and Modeling (2009 – 2010) 
  14. Norman H. Wright Prize in Biology, Oberlin College (2009) 
  15. John F. Oberlin Scholar (2006 – 2010) 
  16. Ohio Collaborative Conference On Bioinformatics, Third Place Paper Award: Lichtenberg et al. (2009) 
  17. NIH IDeA Networks of Biomedical Research Excellence Fellow (2009) 

Presentations & Workshops:

  1. ENCODE 2015 Research Applications and Users Meeting. Bolger Center, Potomac, MD, June 29 - July 1, 2015. Presentation: SNPGenie: a software platform for detecting natural selection in pooled next-generation sequencing samples.
  2. Great Lakes Bioinformatics Conference 2015. International Society for Computational Biology, Purdue University, West Lafayette, IN, May 18-20. Poster: SNPGenie: a software platform for detecting natural selection in pooled next-generation sequencing samples.
  3. GIS Institute 2013. Center For Digital Humanities, University of South Carolina, Calcott Building, Columbia, SC 29201, May 20-31, 2013. Presentation: The spatial distribution of genetic variation in classical human leukocyte antigen contact residues.
  4. SCARC 2013: Consuming GIS. South Carolina Arc GIS Users Group, DoubleTree by Hilton, Columbia, SC 29210, February 11-12, 2013. Presentation: Using GIS to analyze genetic variation in pathogen populations: a case study with Plasmodium falciparum.
  5. Workshop in Next Generation Sequence Analysis 2012. Department of Bioinformatics and Genomics, University of North Carolina-Charlotte, Bioinformatics Building, Charlotte, NC 28223, May 17-18, 2012. 
  6. Great Lakes Bioinformatics Conference 2011. International Society For Computational Biology, Ohio University, Athens, OH 45701, May 2-4, 2011. Poster: Selection threshold constrains adaptive evolution in computational evolution experiments.
  7. Evolution 2010. SSE, SSB & ASN, Department of Biology, Portland State University, Oregon Convention Center, Portland, OR 97232, June 25-29, 2010. Poster: Differential gene expression in Arabidopsis thaliana mutation accumulation lines.
  8. Ohio Collaborative Conference on Bioinformatics 2007. Ohio Bioinformatics Consortium, Miami University, Oxford, OH 45056, July 9-11, 2007.


  1. Bailey AL, Lauck M, Ghai RR, Nelson CW, Heimbruch K, Hughes AL, Goldberg TL, Kuhn JH, Jasinska AJ, Freimer NB, Apetrei C, O’Connor DH [2016] Arteriviruses, pegiviruses, and lentiviruses are common among wild African monkeys. Journal of Virology 90(15):6724-6737.
  2. Nelson C [2016] Austin L. Hughes: the neutral theory of evolutionInference: International Review of Science 2(2).
  3. Nelson CW [2016] Remembering Austin L. Hughes. Infection, Genetics and Evolution 40:262-5.
  4. Moncla LH, Zhong G, Nelson CW, Dinis JM, Mutschler J, Hughes AL, Watanabe T, Kawaoka Y, Friedrich TC [2016] Selective bottlenecks shape evolutionary pathways taken during mammalian adaptation of a 1918-like avian influenza virus. Cell Host & Microbe 19(2):169-80.
  5. Nelson CW [2016] The humble scientist. The New Atlantis 47:98-102.
  6. Gellerup D, Bagelman A, Nelson CW, Ericsen A, Scarlotta M, Hughes AL, O'Connor S [2015] Conditional immune escape during chronic SIV infection. Journal of Virology 90(1):545-52.
  7. Nelson CW, Moncla LH, Hughes AL [2015] SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data. Bioinformatics 31(22):3709-11.
  8. Nelson C [2015] Haldane's dilemma. Inference: International Review of Science 1(3).
  9. Nelson CW, Hughes AL [2015] Within-host nucleotide diversity of virus populations: Insights from next-generation sequencing. Infection, Genetics and Evolution 30:1-7.
  10. Bailey AL, Lauck A, Weiler A, Sibley SD, Dinis JM, Bergman Z, Nelson CW, Correll M, Gleicher M, Hyeroba D, Tumukunde A, Weny G, Chapman C, Kuhn JH, Hughes AL, Friedrich TC, Goldberg TL, O’Connor DH [2014] High genetic diversity and adaptive potential of two simian hemorrhagic fever viruses in a wild primate population. PLoS ONE 9(3):e90714.
  11. Wilker PR, Dinis JM, Starrett G, Imai M, Hatta M, Nelson CW, O'Connor DH, Hughes AL, Neumann G, Kawaoka Y, Friedrich TC [2013] Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses. Nature Communications 4:2636.
  12. Nelson CW, Sanford JC [2013] Computational evolution experiments reveal a net loss of genetic information despite selection. In: Marks II RJ, Behe MJ, Dembski WA, Gordon BL, Sanford JC (Eds.) Biological Information: New Perspectives, World Scientific, pp. 338-368.
  13. Gryder BE, Nelson CW, Shepard SS [2013] Biosemiotic entropy of the genome: mutations and epigenetic imbalances resulting in cancer. Entropy 15:234-261.
  14. Sanford JC, Nelson CW [2012] The next step in understanding population dynamics: comprehensive numerical simulation. In: Fusté MC (Ed.) Studies in Population Genetics, InTech, pp. 117-136.
  15. Nelson CW, Sanford JC [2011] The effects of low-impact mutations in digital organisms. Theoretical Biology and Medical Modeling 8:9.
  16. Lichtenberg J, Yilmaz A, Kurz K, Liang X, Nelson C, Bitterman T, Stockinger E, Grotewold, Welch LR [2011] Encyclopedias of DNA elements for plant genomes. In: Elnitski L, Piontkivska, Welch LR (Eds.) Advances in Genomic Sequence Analysis and Pattern Discovery, World Scientific, pp. 159-178.
  17. Lichtenberg J, Alam M, Bitterman T, Drews F, Ecker K, Elnitski L, Evans S, Grotewold E, Gu D, Jacox E, Kurz K, Lee SS, Liang X, Majmudar PM, Morris P, Nelson C, Stockinger E, Welch JD, Wyatt S, Yilmaz A, Welch LR [2009] Construction of genomic regulatory encyclopedias: strategies and case studies. IEEE: Proceedings of the Ohio Collaborative Conference on Bioinformatics, pp. 65-70.



I study voice, piano and saxophone, and perform a variety of styles in several venues.

NOW & Upcoming Appearances:

Please consult my website