Cooper Laboratory



Name: Vaughn Scott Cooper

Business Address: 425 Bridgeside Pt II, 450 Technology Dr., Pittsburgh, PA 15219. E-Mail Address:

Business Phone: (412) 624-1265 Business Fax: (412) 624-8997




1990-1994 Amherst College A.B. magna cum laude, 1994 Biology


1995-2000 Michigan State University Ph.D., 2000 Zoology & Ecology and Evolutionary Biology & Behavior


2000-2003 University of Michigan Postdoctoral Fellow, Michigan Society of Fellows Dept of Ecology and Evolutionary Biology

2003-2004 University of Michigan Research Scientist Dept. of Pediatrics



2004-2010 University of New Hampshire Assistant Professor, Dept of Microbiology

2010-2015 University of New Hampshire Associate Professor, Dept of Molecular, Cellular, and Biomedical Sciences

2015- University of Pittsburgh Visiting Associate Professor, University of Pittsburgh School of Medicine



Society for the Study of Evolution 1998-

American Society of Microbiology 2000-

International Burkholderia cepacia Working Group 2003-

Society for Molecular Biology and Evolution 2011-



National Merit Scholar 1990

Thomas J. Watson Scholar 1990

Oscar E. Schotte Prize, best honors research in biology, Amherst College. 1994

Lucille Markey Predoctoral Fellow, UCSD 1994

Biotechnology Graduate Fellowship, Michigan State University 1995

Tracy A. Hammer Graduate Student Award (Most promising student)\ College of Natural Sciences, Michigan State University 1998

NSF CAREER award 2009

Outstanding Assistant Professor, University of New Hampshire 2010


Refereed articles

1. Elena SF, Cooper VS, Lenski RE. Punctuated evolution caused by selection of rare beneficial mutations. Science. 1996;272(5269):1802-4. PubMed PMID: ISI:A1996UT11000047.

2. Turner PE, Cooper VS, Lenski RE. Tradeoff between horizontal and vertical modes of transmission in bacterial plasmids. Evolution. 1998;52(2):315-29. PubMed PMID: ISI:000073521700003.

3. Cooper VS, Lenski RE. The population genetics of ecological specialization in evolving Escherichia coli populations. Nature. 2000;407(6805):736-9. PubMed PMID: ISI:000089773900040.

4. Cooper VS, Bennett AF, Lenski RE. Evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment. Evolution. 2001;55(5):889-96. PubMed PMID: ISI:000169403100005.

5. Cooper VS, Schneider D, Blot M, Lenski RE. Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. J Bacteriol. 2001;183(9):2834-41. PubMed PMID: ISI:000168082000015.

6. Riley MS, Cooper VS, Lenski RE, Forney LJ, Marsh TL. Rapid phenotypic change and diversification of a soil bacterium during 1000 generations of experimental evolution. Microbiology-(UK). 2001;147:995-1006. PubMed PMID: ISI:000168105000023.

7. Cooper VS. Long-term experimental evolution in Escherichia coli. X. Quantifying the fundamental and realized niche. BMC Evol Biol. 2002;2(1):12.

8. Cooper VS, Reiskind MH, Miller JA, Shelton KA, Walther BA, Elkinton JS, Ewald PW. Timing of transmission and the evolution of virulence of an insect virus. Proc R Soc Lond B Biol Sci. 2002;269(1496):1161-5.

9. Cooper VS, Carlson WA, LiPuma JJ. Susceptibility of Caenorhabditis elegans to Burkholderia infection depends on prior diet and secreted bacterial attractants. PLoS ONE. 2009;4(11):e7961. Epub November 23, 2009. doi: doi:10.1371/journal.pone.0007961; PMCID:19956737.

10. Cooper VS, Vohr SH, Wrocklage SC, Hatcher PJ. Why Genes Evolve Faster on Secondary Chromosomes in Bacteria. PLoS Comput Biol. 2010;6(4):e1000732; PMCID:20369015.

11. Ellis CN, Cooper VS. Experimental adaptation of Burkholderia cenocepacia to onion medium reduces host range. Appl Environ Microbiol. 2010;76(8):2387-96. Epub 2010/02/16. 10.1128/AEM.01930-09 [doi]. PubMed PMID: 20154121; PMCID:20154121.

12. Flynn KM, Vohr SH, Hatcher PJ, Cooper VS. Evolutionary Rates and Gene Dispensability Associate with Replication Timing in the Archaeon Sulfolobus islandicus. Genome Biology and Evolution. 2010;2:859-69. doi: 10.1093/gbe/evq068; PMCID:20978102.

13. Schuster BM, Perry LA, Cooper VS, Whistler CA. Breaking the language barrier: Experimental evolution of non-native Vibrio fischeri in squid tailors luminescence to the host. Symbiosis. 2010;51(1):85-96. doi: 10.1007/s13199-010-0074-2.

14. Abebe E, Akele F-A, Morrison J, Cooper VS, Thomas WK. An insect pathogenic symbiosis between a Caenorhabditis and Serratia. Virulence. 2011;2(2):158-61. doi: 10.4161/viru.2.2.15337. PubMed PMID: PMC3100764.

15. Poltak S, Cooper VS. Ecological succession in long-term experimentally evolved biofilms produces synergistic communities. The ISME journal. 2011;5:369-78. doi: 10.1038/ismej.2010.136. PubMed PMID: 20811470.

16. Schuster BM, Tyzik AL, Donner RA, Striplin MJ, Almagro-Moreno S, Jones SH, Cooper VS, Whistler CA. Ecology and Genetic Structure of a Northern Temperate Vibrio cholerae Population Related to Toxigenic Isolates. Appl Environ Microbiol. 2011;77(21):7568-75. Epub 2011/09/20. doi: 10.1128/aem.00378-11. PubMed PMID: 21926213; PMCID:21926213.

17. Ellis CN, Schuster BM, Striplin MJ, Jones SH, Whistler CA, Cooper VS. Influence of Seasonality on the Genetic Diversity of Vibrio parahaemolyticus in New Hampshire Shellfish Waters as Determined by Multilocus Sequence Analysis. Applied and Environmental Microbiology. 2012;78(10):3778-82. doi: 10.1128/aem.07794-11.

18. Morrow JD, Cooper VS. Evolutionary effects of translocations in bacterial genomes. Genome Biology and Evolution. 2012;4:1256-62. doi: 10.1093/gbe/evs099; PMCID:23160175.

19. Flynn KM, Cooper TF, Moore FBG, Cooper VS. The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape. PLoS Genet. 2013;9(4):e1003426. doi: 10.1371/journal.pgen.1003426; PMCID:23593024.

20. Traverse CC, Mayo-Smith LM, Poltak SR, Cooper VS. Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections. Proceedings of the National Academy of Sciences. 2013;110(3):E250–E9. doi: 10.1073/pnas.1207025110; PMCID:23271804.

21. Cooper VS. The Origins of Specialization: Insights from Bacteria Held 25 Years in Captivity. PLoS Biol. 2014;12(2):e1001790. doi: 10.1371/journal.pbio.1001790; PMCID:24558348.

22. Cooper VS, Staples RK, Traverse CC, Ellis CN. Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms. Genomics.

  1. doi: 10.1016/j.ygeno.2014.09.007. PubMed PMID: 25263109.

23. Ellis CN, Traverse CC, Mayo‐Smith L, Buskirk SW, Cooper VS. Character displacement and the evolution of niche complementarity in a model biofilm community. Evolution. 2014; PMCID:25494960.

24. Turner PE, Williams ES, Okeke C, Cooper VS, Duffy S, Wertz JE. Antibiotic resistance correlates with transmission in plasmid evolution. Evolution. 2014;68(12):3368-80; PMCID:25351426.

25. Abebe-Akele F, Tisa LS, Cooper VS, Hatcher PJ, Abebe E, Thomas WK. Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae. BMC Genomics. 2015;16:531. PubMed PMID: 26187596.

26. Dillon MM, Sung W, Lynch M, Cooper VS. The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia. Genetics. 2015;200(3):935-46. doi: 10.1534/genetics.115.176834; PMCID:25971664.

27. O’Rourke D, Fitzgerald CE, Traverse CC, Cooper VS. There and back again: consequences of biofilm specialization under selection for dispersal. Name: Frontiers in Genetics. 2015;6:18; PMCID:25717335.

28. Whistler CA, Hall JA, Xu F, Ilyas S, Siwakoti P, Cooper VS, Jones SH. Use of Whole-Genome Phylogeny and Comparisons for Development of a Multiplex PCR Assay To Identify Sequence Type 36 Vibrio parahaemolyticus. J Clin Microbiol. 2015;53(6):1864-72. PubMed PMID: 25832299.

29. Xu F, Ilyas S, Hall JA, Jones SH, Cooper VS, Whistler CA. Genetic characterization of clinical and environmental Vibrio parahaemolyticus from the Northeast USA reveals emerging resident and non-indigenous pathogen lineages. Front Microbiol. 2015;6:272. PubMed PMID: 25904905.

30. Dillon, M.M, N. P. Rouillard, B. Van Dam, R. Gallet, V.S. Cooper. Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations. Evolution, published online: 12 FEB 2016 | DOI: 10.1111/evo.12868

Reviews, Proceedings, and Book Chapters

1. Cooper VS. The study of microbial adapation by long-term experimental evolution. In: Seifert HA, Dirita VJ, editors. The evolution of microbial pathogens. Washington, DC: ASM Press; 2006.

2. Cooper VS. Experimental evolution of pathogens. In: Tibayrenc M, editor. Encyclopedia of Infectious Disease. New York: Wiley; 2007.

3. Jones SH, Striplin MJ, Mahoney JC, Cooper VS, Whistler C. Incidence and abundance of pathogenic Vibrio species in the Great Bay Estuary, New Hampshire. In: Lassus P, editor. Proceedings of the Seventh International Conference on Molluscan Shellfish Safety; Nantes, France: Quae Publishing; 2010. p. 127-34.

4. Jones SH, Urquhart E, Hartwick M, Taylor M, Cooper VS, Whistler CA. Long-term trends of pathogenic Vibrio spp. populations in New Hampshire oysters. J Shellfish Res; 8:2015.

5. Xu F, Ilyas S, Hall JA, Jones SH, Cooper VS, Whistler CA. Genetic characterization of clinical and environmental Vibrio parahaemolyticus from the Northeastern US reveals emerging resident and invasive pathogen lineages. J Shellfish Res; 8:2015:

Published Abstracts

1. Cooper JW, Rossi AR, Cooper VS. Steering of High-Performance Computations Using a Pc Workstation. Abstr Pap Am Chem Soc. 1994;208:153-COMP. PubMed PMID: ISI:A1994PA26101460.

2. Cooper VS, Romero EJ, LiPuma JJ, editors. VNTR-based typing of Burkholderia cenocepacia. International Burkholderia cepacia Working Group; 2004; Vancouver, BC.

3 Striplin M, Mahoney, J. C., Cooper, V. S., Whistler, C. A., and Jones, S. H., editor. Identification of Vibrio spp. found in oysters and water from the Great Bay Estuary. 109th Meet Am Soc Microbiol American Society for Microbiology; 2008; Washington, DC.Warren T, Cooper VS. Evolution in Action: Experimental Evolution of Biofilms with Pseudomonas fluorescens. Am. Soc. Microbiol General Meeting, Boston; 2014.

4. Flynn K, Johnson T, Cooper VS. Evolution of diversity and interdependency in Pseudomonas aeruginosa biofilms. PEDIATRIC PULMONOLOGY; 2011:

5. Flynn K, Cooper VS. Evolution in chronic Pseudomonas infections: biotic interactions drive functional convergence in adaptive targets. PEDIATRIC PULMONOLOGY; 2013

6. Warren T, Cooper VS. Evolution in Action: Experimental Evolution of Biofilms with Pseudomonas fluorescens. American Society of Microbiology General Meeting; May, 2014; Boston2014.

7. Jones S, Schuster B, Mahoney J, Yu J, Ellis C, Cooper VS, Whistler C. The occurrence, abundance, phylogeny and virulence potential of pathogenic Vibrio species in New Hampshire shellfish waters. J Shellfish Res; 2011

Other Publications

1. Elena SF, Cooper VS, Lenski RE. Mechanisms of punctuated evolution - Reply. Science. 1996;274(5293):1749-50. PubMed PMID: ISI:A1996VW71200073.




Undergraduate and Graduate Instruction

University of Michigan, 2000-2004

HIST196 Epidemics and History, freshman seminar, 3 credit hours, 16 students 2001-2002 ——— ———————————————————————————————————————————————– UC262 Evolutionary Biology and Human Disease (course co-founder), sophomore-senior non-majors, 4 credit hours, team-taught, 80 students 2001-2003 BIOL111 Emerging and Re-Emerging Infectious Diseases, freshman seminar 16 students, 3 credit hours, 2003

University of New Hampshire, 2004-2015

MICR 503 General Microbiology, 120-140 students, 5 credit hours, 2004-2006 ———————- ————————————————————————————————————————————————————————————– GEN 604 Fundamentals of Genetics, 120-150 students, 4 credit hours, 2011, 2013 MICR 711/811 Genomics and Bioinformatics, 25 students, 4 credit hours, 2005 MICR 795 Problems in Microbiology [topical seminar on microbial evolution], 4-12 students, 2-4 cr, 2004-2011 MICR / GEN 713 / 813 Microbial Ecology and Evolution, 15-25 junior/senior/graduate students, 4 credit hours, 2006-2014. Developed new blog-based method for student participation and discussion GEN715/815 Molecular Evolution, 15-32 junior/senior/graduate students, 4 credit hours, 2008-2010, 2012, 2014 MICR 997 Microbiology Seminar leader, 8-15 PhD students, 1 credit hour, 2005-2006, 2008-9 MICR 905 Current Topics in Microbiology (Microbial Genomics), 5-10 PhD students, 2 credit hours, 2005, 2007, 2012 LSA 950 Scientific Communication (new course for new PhD program in Molecular & Evolutionary Systems Biology that I developed and directed), 8-15 graduate students, 2 credit hours, 2013-4.

**Student research mentorship **

Masters and Ph.D. students

   *Name*                     *Program*                       *Years*     *Present Position*   ---- -------------------------- ------------------------------- ----------- ----------------------------------------------------------------------   1    Morel Henley               Computer Science, M.S           2005-2008   aerospace industry   2    Crystal Ellis              Genetics, M.S., Ph.D.           2005-2011   Harvard / MGH postdoctoral fellow   3    Sarah Comeau (Wrocklage)   Microbiology, M.S.              2006-2009   Cubist Pharmaceuticals   4    Steffen Poltak             Microbiology, Ph.D              2006-2010   Phillips Exeter Academy (NH)   5    Laura Benton               Microbiology, M.S.              2007-2009   St. Michael’s College (VT)   6    Feseha Abebe-Akele         Genetics, Ph.D. (co-advisor)    2007-2013   UNH Bioinformaticist   7    Kenny Flynn                Microbiology, M.S., Ph.D.       2009-2014   RedOwl Analytics   8    Rachel Staples.            Microbiology, M.S               2010-2012   University of Houston   9    Charles Traverse           Microbiology, M.S.              2010-2012   University of Texas, Austin   10   Keith Ferguson             Microbiology, M.S.              2010-2012   Cubist pharmaceuticals   11   Marcus Dillon              Genetics, Ph.D.                 2011-2016   University of Toronto   12   Taylor Warren              Biochemistry, M.S.              2013-14     Biotechnology director and science teacher, Windham High School (NH)   13   Meghan Hartwick            Molecular/Evol Sys Biol Ph.D.   2013-          14   Devon O’Rourke             Molecular/Evol Sys Biol Ph.D.   2014-15     changed advisor with my move   15   Daphne Welter              Microbiology, Ph.D.             2014-15     transferred to Cornell   16   Katrina Harris             Integrative Sys Biol, Ph.D.     2015-       

*Undergraduate Student Researchers\ *

   *Name*               *Major*                  *Years*     *Position following graduation*   ---- -------------------- ------------------------ ----------- ---------------------------------------------------   1    Sarah Comeau         Microbiology             2004-2006   Cubist Pharmaceuticals   2    Meghan Parks         Microbiology             2005           3    Scott Powers         Microbiology             2004-2006   EMT   4    Angela Kuehn         Microbiology             2005-2007   PhD program, Virginia Commonwealth University   5    Holly Schurk         Microbiology             2005-2006      6    Erica Boudreau       Microbiology             2006-7      FirstLight Pharmaceuticals   7    Keith Morley         Biochemistry             2006-2008   Dartmouth Medical School   8    Stephen Perros       Biochemistry             2006-2007   medical school   9    Charles Traverse     Microbiology             2005-9      M.S., UNH, Ph.D., UT-Austin   10   Kasia Szymanska      Microbiology             2006-7      Mass General Hospital Research   11   Jillian Armstrong    Microbiology             2007           12   Tom Perry\*          Microbiology             2007-8         13   David Dotchin        Microbiology             2007-9         14   Danielle Morse       Microbiology             2007-9      Research technician, Harvard Medical School   15   Julie Morrison       Biochemistry             2007-9      University of Toledo Medical School   16   Rachel Staples       Microbiology             2009-10     Ph.D. Univ of Houston   17   AJ Troiano           Microbiology             2009-10     University of Connecticut Medical School   18   Megan McLaughlin     Microbiology             2009-13     Research specialist, Dana-Farber Cancer Institute   19   Shain Eighmey        Microbiology             2010-       Lonza Biologics   20   Thomas Johnson       Biochemistry             2010-12     University of Texas Ph.D. MCB   21   Melissa Levesque     Microbiology             2010-11     UNH-Manchester, MPH   22   Jordan Stinson       Microbiology             2010-11     Cell Signaling Technologies   23   Taylor Warren        Biology: MCD             2011-13     M.S. Biochemistry, UNH   24   Brian Paul           Chemical Engineering     2011-12     Chemical Engineer   25   Leslie Mayo-Smith    Biology: EEB             2009-12     Research technician, Mass General Hospital   26   Brian van Dam        Biomed Sci               2012-14     EMT   27   Cody Fitzgerald\*    Mathematics / Genetics   2012-15     PhD program, computational biology   28   Gabbie Bergeron      Genetics                 2012-13     Plymouth State College   29   David Morejon\*      Biomed Sci               2012-14     McNair Scholar, UNH Technician   30   Gabrielle Dowell     Genetics                 2013-14        31   Chelsea Jones        Genetics                 2013-14        32   Sarah Kremer         Genetics                 2013-15        33   Caroline Ward\*      Biomed Sci               2013-14     Medical school   34   Nicholas Rouillard   BMS: Micro               2014-15        35   Celeste Souza        BMS: Micro               2014-15        36   Matthew Eskuchen     Biology                  2015-          37   Nathan Phillips      Mathematical Biology     2015-       

Member of Thesis Committee for M.S. or Ph.D.:

   *Name*                *Program*                  *Year*   *Present Position*   ---- --------------------- -------------------------- -------- -------------------------------------------   1    Anne Marie France     MPH, Univ of Michigan      2002        2    Ethan Romero          MPH, Univ of Michigan      2004        3    Darren Bauer          Ph.D. Genetics             2007        4    Alicia Ballok         M.S. Genetics              2007     Postdoctoral fellow, Harvard Microbiology   5    Sana Hussain          M.S. Natural Resources     2008        6    Julia Butzler         Ph.D. Biology, Dartmouth   2009        7    Lauren Perry          M.S. Microbiology          2009     Research coordinator, Recon Strategy   8    Abe Tucker            Ph.D. Genetics             2009     Assistant Professor, Arkansas   9    Brian Schuster        M.S., Microbiology         2011     SeresHealth   10   Way Sung              Ph.D., Genetics            2011     Assistant Professor, UNC-Charlotte   11   Wei Yao               Ph.D., Biochemistry        2013     Postdoctoral fellow, China   12   Lauren Petersen       Ph.D., Microbiology        2014     Postdoctoral fellow, UConn   13   Behailu Aklilu        Ph.D. Biochemistry         2015     Postdoctoral fellow, Texas A&M   14   Mike Taylor           Ph.D. Microbiology         2016        15   Jeffrey Sun           M.S. Microbiology          2014        16   Feng Xu               Ph.D. Microbiology                     17   Kevin Schuster        Ph.D. Biochemistry                     18   Eric Morrison         Ph.D. NRESS                            19   Ashley Marciniewicz   M.S. Microbiology          2016     

*High School student researchers: *

2005: Charles Traverse, 2006: Kaitlyn Schena, 2007: Katie LaRoche, 2008: Robert Keith, 2009: Gabbie Bergeron; 2010: Greta Gadbois, Cody Fitzgerald, Kristen Dowling; 2011: Keely Fitzgerald.



Grant Support

Current Grant Support

Grant number Grant Title Role in Project Years Inclusive Source and Amount ———————- —————————————————————————————————————– —————– —————– —————————————– IOS-1258099 The Molecular Basis of Host Adaptation and Origin of New Mutualisms co-PI (5%) 8/13 – 8/16 NSF IOS


NAI CAN-7 NNA15BB04A RELIVING THE PAST: Experimental Evolution of Major Transitions in the History of Life co-PI (15%) 1/15-1/20 NASA Astrobiology Institutute $920,000

R01GM110444 Molecular mechanisms of adaptive diversity in Burkholderia biofilms PI (15%) 1/15-1/20 NIH-NIGMS $1,432,075

1U01AI124302 Predicting the emergence of antibiotic resistance through multi-omics approaches and Immune System-surveillance PI (22.5%) 3/16-4/21 NIH-NIAID

                                                                                                                                       (MPI)                               \$pending   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Prior Grant Support

DEB-0845851 CAREER: Quantifying pleiotropy by parallel experimental evolution PI 7/09-6/15 NSF DEB $1,000,000 —————– —————————————————————————————————————————————————————————— ——————- ———————————————— ———————————————— IIA-1330641 Collaborative Research: Strengthening the scientific basis for decision-making: Advancing sustainability science and knowledge-action capacities in coupled coastal systems. co-PI\ 8/13-7/15 (terminated early with move to Pitt) NSF EPSCOR-Track II (1 month)
$3,000,000 total, $294,933 to VSC

NHAES- NH00578 Mechanisms of biofilm adaptation and diversification in pathogens and symbionts PI 10/1/11-9/30/15 NH Agricultural Experiment Station $15,000

                                                                                                                                                                                               0.5 month                                                            

R/CE-137 Microbial interactions influencing the emergence of pathogenic vibrios in oysters. PI 3/12-2/14 NOAA /\ Sea Grant (1 month)

DEB-0844157 Collaborative research: Understanding the basis of interactions between adaptive\ PI 7/09-6/12 NSF-DEB $196,775 mutations and their environment
(1 month)

1R15AI082528-01 The roles of adaptive radiation and phenotypic switching in biofilm diversity PI 5/09-4/12 NIH-NIAID $206,500

                                                                                                                                                                                               (1 month)                                                            

1R03AI081102-01 Ecological population structure and emergence of virulent Vibrio parahaemolyticus Co-PI (0.5 month) 6/09-5/11 NIH-NIAID $139,938

NHAES-NH00496 Bacterial-nematode interactions: identifying mechanisms predisposing mutualism or pathogenesis PI (0.5 month) 10/06-9/09 NH Agricultural Experimental Station $241,123

DEB-9801538 DDIG: Causes and consequences of ecological specialization co-PI 6/98-5/00 NSF-DEB $10,000 ———————————————————————————————————————————————————————————————————————————————————————————————————————-

2. Invited Seminars and Lectureships

  1. “Evolutionary ecology of virulence traits in Vibrio cholerae,” Society for the Study of Evolution meetings, Champaign, IL, 6/2002

  2. “VNTR-based typing of Burkholderia cenocepacia.” 9th Annual Meeting, International Burkholderia cepacia Working Group. Vancouver, B.C., Canada. 4/2004

  3. “Liquid C. elegans culture for the study of Burkholderia pathogenesis.” 10th Annual Meeting, International Burkholderia cepacia Working Group. Oklahoma City, OK, 4/2005

  4. “Emerging bacterial pathogens: jacks-of-all-trade, but masters of how much?” Dept of Organismic and Evolutionary Biology, Harvard University. 9/2005

  5. “Adaptive diversification in biofilms produces a synergistic community.” The Forsyth Institute, Harvard University. 1/2009

  6. Evolution of synergistic diversity in experimental biofilms recapitulates evolution in chronic infections.” University of Toledo Medical School, September, 2009.

  7. “Causes and consequences of bacterial adaptation to novel environments,” University of Southern Maine, October, 2009.

  8. “Diversification in experimentally evolved biofilms enhances productivity and recapitulates evolution in chronic infections,” Emerging Pathogens Institute, University of Florida, January 2010.

  9. “Evolution in biofilm communities: ecological engineers and genetic revolutions.” Hughes Summer Lecture Series, Wesleyan University, June 2010.

  10. “Evolution in biofilm communities: ecological engineers and genetic revolutions.” University of Idaho, November, 2010

  11. New England Junior Science and Humanities Symposium (, Plenary Speaker May 2011.

  12. “A tangled bank: laboratory biofilm evolution mimics the ecology of chronic infections.” Department of Microbiology and Molecular Genetics, Michigan State University; September 2011

  13. “Replication timing directs the arrow of genome evolution,” EEBB program, Michigan State University; September 2011

  14. “A tangled bank: laboratory biofilm evolution mimics the ecology of chronic infections.” University of Tennessee-Knoxville, October 2011

  15. “A tangled bank: laboratory biofilm evolution mimics the ecology of chronic infections.” Massachusetts Institute of Technology, November 2011 (student invitation).

  16. “A tangled bank: laboratory biofilm evolution mimics the ecology of chronic infections.” University of Washington; January 2012:

  17. “A tangled bank: laboratory biofilm evolution mimics the ecology of chronic infections.” University of Massachusetts-Amherst; September 2012.

  18. “A tangled bank: laboratory biofilm evolution mimics the ecology of chronic infections.” University of Montana; October 2012

  19. “A tangled bank: laboratory biofilm evolution mimics the ecology of chronic infections.”:International Burkholderia cepacia Working Group, Ann Arbor, MI. April 2013 (keynote).

  20. “Population genomics and community ecology of experimentally evolved Burkholderia biofilms” Department of Organismal and Evolutionary Biology, Harvard University, November 2013.

  21. “Replication timing directs the arrow of genome evolution” FAS Department of Systems Biology, Harvard University, November 2013.

  22. “Population genomics and community ecology of experimentally evolved Burkholderia biofilms” Rutgers-NJ Medical School, November 2013.

  23. “Experimental evolution of Burkholderia and Pseudomonas biofilms: pattern, process, function,” Gordon Research Conference on Acute Respiratory Infections,” Lucca, Italy, February 2014.

  24. “Using evolutionary biology and genomics to understand chronic infections (and why location matters in genomes).” Children’s Hospital Pittsburgh, May, 2014.

  25. “Causes of heterogeneity in evolutionary rate in divided bacterial genomes” International Burkholderia cepacia Working Group Nimes FR, April 2014,

  26. “Experimentally evolved biofilm communities can shed light on chronic infections.” 1^st^ ASM Meeting on Experimental Microbial Evolution, opening plenary, Washington D.C., June 2014.

  27. “Experimental evolution in biofilms to understand adaptation during chronic infections,” Department of Biology, Boston College, October 2014.

  28. “Experimental evolution in biofilms to understand adaptation during chronic infections,” Department of Biology, Emory University, November 2014

  29. “Experimental evolution in biofilms to understand adaptation during chronic infections,” Department of Microbiology, University of Zurich, SUI, 11/ 2014.

  30. “Experimental evolution in biofilms to understand adaptation during chronic infections,” Biology Department, Clark University, 2/2015.

  31. “Evolution in biofilms and the origins of multicellularity.” Department of Molecular and Cellular Biology, University of Montana, April 2015.

  32. “Experimental evolution in biofilms to understand adaptation during chronic infections,” Institute for Genome Science, U. Maryland School of Medicine, Baltimore, MD, May 2015.

  33. Session co-chair, NASA Astrobiology Conference “Survival: Exploring the Effects of Stress on Microbial Evolution Rates and Survival Strategies” Chicago, IL July 2015

  34. “Why genome regions evolve at different rates: lessons from bacteria with multiple chromosomes” University of Pittsburgh-Carnegie Mellon Computational Biology Program, October 2015.

  35. “Experimental evolution to understand adaptation in biofilms” 7^th^ ASM Biofilm Conference, Chicago, IL October 2015.

  36. “Experimental evolution to understand adaptation during infections.” Department of Biology, Carnegie-Mellon University, October 2015.

  37. Simons Foundation Workshop on Dynamics of Microbial Ecology and Evolution, New York, NY Nov 2015.

  38. “Experimental evolution to understand adaptation in biofilms”, MicroBiotec2015 Congress, Portuguese Societies of Microbiology and Biotechnology, Evora, Portgual, Dec 2015. Plenary Speaker.

  39. “How do bacterial populations evolve when growing on surfaces?” Department of Biology, University of Pennsylvania, Feb 2016.

3. Other research related activities

  1. Patent application filed for detection of virulent Vibrio parahaemolyticus strain type ST36 (news release: Whistler CA, Hall J, Jones SH, Cooper, VS.

  2. Founder and Director, EvolvingSTEM, a program for evolution-in-action in high school science classrooms, currently in 5 high schools involving 9 teachers and reaching more than 300 students/year.

  3. Televised lecturer: “Darwin Meets the Hot Zone: Ecology and Emerging Infectious Disease,” Ann Arbor Public Library, Ann Arbor, MI 2003. Also: “The Timing of Biological Evolution,” Saturday Morning Physics, Ann Arbor, MI, 2003

  4. NIH Genetic Variation and Evolution (GVE), ad hoc review (2009-2011,2013,2014)

  5. NIH special emphasis panels (4 different ZRG panels), and two for Microbiome research (2012-13).

  6. NSF Panelist at DEB (2011,2012,2013).

  7. Panelist, NIH Reservoirs of Antibiotic Resistance RFP (2006).

  8. External Advisory Board, Seacoast School of Technology Biotechnology (Exeter, NH) program 2007-

  9. Ad hoc reviewer for NSF, USDA, NASA, Kentucky Science & Engineering Foundation, Austrian Science Foundation, Portuguese Science Foundation, Innovation Canada, Canadian NSERC, NASA Astrobiology Program,

  10. Associate Editor, BMC Microbiology. Invited associate editor, PLoS Genetics.

  11. Ad Hoc reviewer for *Applied & Environmental Microbiology, American Naturalist, Biology Letters, Cell, Ecology, Ecology Letters, Evolution, Genetics, Gen. Biol. Evol., Infection, Genetics, and Evolution, J. Bacteriology, J. Evolutionary Biology, J. Molecular Evolution, J. Phycologica, Molecular Biology and Evolution, Molecular Ecology, Microbiology, Nature, PLoS Biology, PLoS Pathogens, PLoS Genetics, PLoS ONE, Proc. Roy. Soc. Lond. B., PNAS, Q. Rev Biol, Science. *


Research goals

1) To understand how bacteria adapt to new environments and/or cause disease. Biofilm-associated infections are our primary focus. We conduct high-throughput genomic analysis of evolved populations and longitudinal studies of infectious isolates. We also develop genome-based diagnostics for bacterial infections.

2) To advance understanding of evolutionary dynamics in structured communities, relevant to biofilms, solid tumors, and transitions to multicellularity.

3) To explore variation in genome evolutionary rates associated with replication timing and the cell cycle to improve genome legibility, understand speciation, and to guide more rational treatment of disease states

4) Propagate experimental evolution as a both a) a nuanced screen for gain-of-function mutations and b) a method of active learning by students of all ages

5) Details of each of these projects are described in more detail at our lab website:



At University of Pittsburgh, 2015-

  1. Member of Microbiome Search Committee, Department of Medicine

Highlights from University of New Hampshire, 2004-2015

  1. Cross-college Ph.D. program in Molecular and Evolutionary Systems Biology, Chair of organizing committee 2011-14, Program Coordinator, 2014-.

  2. COLSA Undergraduate Research Conference Committee (2005-). Chairman, 2010-13.

  3. Member of the COLSA Dean’s Search Committee (2006-2007) and Genomics Search Committee (2013)

  4. University Tuition Scholarship Selection Committee (2005-2008)

  5. VP Research Research and Engagement program to train faculty seeking external support (2012-present)

  6. Member of graduate admissions committees for Microbiology, Genetics, and/or MESB, 2005-2015

  7. Microbiology Graduate Coordinator (2006-2008). Coordinate application review and assist in assigning assistantships.

  8. Microbiology Seminar Series Coordinator (2005-2007, 2008-9)

  9. Member of the Proteomics Search Committee (2007-2008).

  10. Member of the Vision and Planning Committee for the new Dept. of Cellular, Molecular, and Biomedical Sciences (2008)

  11. Multiple faculty committees associated with the College reorganization and development of new Genetics curriculum (2007-2011)

Community activities

  1. Biannual Panelist for our EvolvingSTEM program and Member, New Hampshire Science Teachers Association

  2. External Advisory Board, Seacoast School of Technology Biotechnology (Exeter, NH) program 2007-2015

  3. Panelist, BioConnectNH ( high school student symposium, March, 2008

  4. Faculty Mentor for Research and Engineering Apprenticeship Program, which encourages economically and socially disadvantaged high school students to pursue careers in math, science, and technology through hands-on experience in research and development (2005-2013)

  5. Faculty Mentor for the McNair Program, a graduate school preparation program for underrepresented undergraduates and for undergraduate students in the UNH UROP and SURF programs (2011-2015)