Jeffrey Evan Barrick

2500 Speedway A5000 University of Texas at Austin Austin, TX 78712 phone: (512) 471-3247 email: [email protected] website: http://barricklab.org

Education

California Institute of Technology (1997–2001) B.S. Chemistry with Honors

Yale University (2001–2006) Ph.D. Molecular and Biophysics

Professional Experience

Associate Professor (2018–present) The University of Texas at Austin Department of Molecular Biosciences (previously Chemistry & Biochemistry) Institute for Cellular and Molecular Biology Fellow of the Lorene Morrow Kelley Professorship Center for Systems and Center for and Ecology, Evolution and Behavior Graduate Program NSF BEACON Center for the Study of Evolution in Action

Assistant Professor (2011–2018) The University of Texas at Austin Department of Molecular Biosciences (previously Chemistry & Biochemistry)

Postdoctoral Fellow (2006–2010) Michigan State University (Richard E. Lenski and Charles A. Ofria)

Graduate Student (2001–2006) Yale University (Ronald R. Breaker)

Title of Dissertation

Discovering and defining metabolite-binding riboswitches and other structured regulatory RNA motifs in

1 Dissertation Advisor

Ronald R. Breaker

Postdoctoral Research Topics

• E. coli experimental evolution and genomics • Digital evolution and artificial life

Postdoctoral Advisors

Richard. E. Lenski and Charles A. Ofria (co-advised)

Current Research Interests

Controlling evolution is key to combating the emergence of drug resistance, preventing the progression of chronic infections and cancers, and maintaining the function of engineered cells. Evolution can also be directed and harnessed for biotechnology and medicine, to create novel therapeutics and optimize microbial strains, for example. My lab uses experimental approaches that leverage the tools of synthetic and to study and manipulate evolution. Our current interests are focused on (1) understanding microbial genome dynamics during adaptive laboratory evolution experiments; (2) dissecting the molecular mechanisms of metabolic innovation and optimization during adaptive evolution; (3) examining how microbes evolve on a whole-genome level when they gain access to genetic codes with new amino acid building blocks; (4) developing antimutator strains and other methods for preventing undesirable evolution when it causes failures in biological engineering; and (5) genetically engineering bacterial symbionts of insects for applications in agriculture.

Professional Societies

Sigma Xi (2001–present) Society for the Study of Evolution (2008-present) Society for Molecular Biology and Evolution (2009–present) American Chemical Society (2010–present) American Society for (2011–present) International Society for Artificial Life (2012-present) Society for Biological Engineering (2014–present) Society of America (2017–present)

Grants

Current Funding

PI

NSF ENG/BIO (CBET-1554179) CAREER: Preventing evolutionary failure in synthetic biology; PI: Barrick; $500,000 total costs; 05/15/2016–05/14/2021.

2

DARPA Insect Allies (HR001117S0002-IA-FP-008) AEPHID: Aphid Endosymbionts for Plant Host Immunization and Defense PI: Barrick 35% contribution; co-PI: Nancy Moran (The University of Texas at Austin) 25% contribution; co-PI: Andrew Ellington (The University of Texas at Austin) 25% contribution; co-PI: Thomas McKnight (Texas A&M University) 15% contribution; $5,029,456 total costs; ~$1,800,000 to Barrick; 07/01/2017–06/30/2021.

UT Austin Vice President for Research Office (Associate Professor Experimental) APX: 3D-Printed Observatories for Visualizing and Accelerating Evolution; PI: Barrick 50% contribution; co-PI: Kory Bieg (The University of Texas at Austin) 50% contribution; co-PI: Robert Newman (North Carolina A&T) 25% contribution; $100,000 total costs; $37,400.00 to Barrick; 11/01/2018–12/31/2019.

Welch Foundation (F-1979) Chemical specificity of DNA uptake by naturally competent bacteria; PI: Barrick; $195,000 total costs; 06/01/2018–05/31/2021.

NSF BEACON Center (DBI-0939454 subcontract) Standardizing measurements of evolutionary stability parameters in synthetic biology; PI: Barrick 40% contribution; co-PI: Dennis Mishler (The University of Texas at Austin) 10% contribution; co-PI Daniel Ducat (Michigan State University) 13% contribution; Björn Hamburger (Michigan State University) 14%; contribution; Michaela TerAvest (Michigan State University) 13% contribution; $84,146 total costs; $44,320 to Barrick; 06/01/2019– 05/31/2020.

Co-PI

NSF US-Israel Collab: Are parasites in complex communities more evolvable? Bridging ecology and evolution with computational modeling and rodent-bacteria evolution experiments; PI: Luis Zaman (University of Michigan) 50% contribution; co-PI: Barrick 35% contribution; co-PI: (Michigan State University) 15% contribution. $1,594,591 total costs: $482,016 to Barrick; 09/01/2018- 08/31/2023.

Previous Funding

PI

NIH NIGMS (R00) Identifying mutations that promote microbial evolvability; PI: Barrick; $1,250,000 total costs; 02/01/2011–01/31/2014.

Welch Foundation (F-1780) Discovering functional nucleic acid families by deep sequencing and fold sampling; PI: Barrick; $180,000 total costs; 06/01/2012– 05/31/2015.

3 Cancer Prevention & Research Institute of Texas (RP130124) Deep sequencing oncoviral evolvomes as a personalized cancer diagnostic tool; PI: Barrick; $260,633 total costs; 06/01/2013–11/30/2015.

NSF BEACON Center (DBI-0939454 subcontract); Evolutionary origins and engineering applications of bacterial DNA secretion machinery; PI: Barrick; $42,940 total costs; 06/01/2013–05/31/2014.

UT Austin (Research Grant) Probing the molecular specificity of natural competence in Acinetobacter baylyi ADP1; PI: Barrick; $6,000 total costs; 10/15/2013–08/31/2014.

NSF BEACON Center (DBI-0939454 subcontract); Cross-institutional iGEM synthetic evolutionary biology team; PI: Barrick 40% contribution; co-PIs: Andrew Ellington (The University of Texas at Austin) 5% contribution; Robert Newman (North Carolina A&T State University) 35% contribution; Randall Hayes (North Carolina A&T State University) 5% contribution; Scott Harrison (North Carolina A&T State University) 5% contribution; Gregory Goins (North Carolina A&T State University) 5% contribution; Jian Han (North Carolina A&T State University) 5% contribution; $48,839 total costs; $19,912 to Barrick; 06/01/2013–05/31/2014.

NSF BEACON Center (DBI-0939454 subcontract); Illuminating evolution in action with an expanded genetic code; PI: Barrick 50% contribution; co-PI: Robert Newman (North Carolina A&T State University) 30% contribution; co-PI Scott Harrison (North Carolina A&T State University) 20% contribution; $170,136 total costs; $105,204 to Barrick; 06/01/2013–05/31/2015

NSF BEACON Center (DBI-0939454 subcontract); Mechanistic basis of mutations potentiating the evolution of citrate utilization in the LTEE; PI: Barrick 40% contribution; co-PI: Christopher Marx (University of Idaho) 30% contribution; co-PI: Zachary Blount (Michigan State University) 30% contribution; $134,570 total costs; $54,185 to Barrick. 05/01/2014–04/30/2015.

NSF BEACON Center (DBI-0939454 subcontract); Directed evolution of novel protein functions using expanded genetic codes; PI: Barrick 40% contribution; co- PI: Bryan Davies (The University of Texas at Austin) 20% contribution; Robert Newman (North Carolina A&T State University) 40% contribution; $131,524 total costs; $34,732 to Barrick; 05/01/2015–04/30/2016.

NSF BEACON Center (DBI-0939454 subcontract); Evolution of cultured stem cells; PI: Barrick 25% contribution; co-PI: Austin Cooney (The University of Texas at Austin) 40% contribution; co-PI: Holly Wichman (University of Idaho) 25% contribution; co-PI James Bull (The University of Texas at Austin) 10% contribution; $83,352 total costs, $20,450 to Barrick; 05/01/2016–04/30/2017.

4 NSF I-Corps (IIP-1744677) Diagnosing the mutational failure modes of cells so that biotech companies can shorten R&D time and optimize production PI: Barrick; $50,000 total costs; 06/01/2017–5/31/2018.

NSF BEACON Center (DBI-0939454 subcontract) Decoy mutations: engineering fitness landscapes to delay unwanted evolution; PI: Barrick 50% contribution; co-PI: Luis Zaman (University of Michigan) 30% contribution; co-PI: Christoph Adami (Michigan State University) 20% contribution; $59,368 total costs; $23,125 to Barrick; 06/01/2017–05/31/2018.

NSF BEACON Center (DBI-0939454 subcontract) Detecting unplanned evolution in plasmid repositories; PI: Barrick 50% contribution; co-PI: Eva Top (University of Idaho) 25% contribution; co-PI: Robert Newman (North Carolina A&T) 25% contribution; $87,127 total costs; $39,075 to Barrick; 06/01/2018–05/31/2019.

NSF BEACON Center (DBI-0939454 subcontract) Multiplex measurement of mutation rates and spectra; PI: Barrick 50% contribution; co-PI: Maitreya Dunham (University of Washington, Seattle) 50% contribution; $84,770 total costs; $46,167 to Barrick; 06/01/2015–05/31/2018.

Welch Foundation (F-1780) Comparing the chemical utility of alternative genetic codes; PI: Barrick; $195,000 total costs; 06/01/2015–05/31/2018.

Co-PI

NSF BEACON Center (DBI-0939454 subcontract); Reducing yeast evolvability; PI: Maitreya Dunham (University of Washington, Seattle) 55% contribution; co-PI: Barrick 45% contribution; $61,667 total costs; $28,938 to Barrick; 05/01/2016– 04/30/2017.

NSF BEACON Center (DBI-0939454 subcontract); Using evolution to explore antimicrobial resistance and spur new antimicrobial development; PI: Chris Waters (Michigan State University) 50% contribution; co-PI: Joseph Graves (North Carolina A&T State University) 45% contribution; co-PI: Barrick 5% contribution; $87,739 total costs; $5,200 to Barrick; 05/01/2016–04/30/2017.

NSF BEACON Center (DBI-0939454 subcontract); Applying evolution in action to understand the mechanisms of novel antimicrobial therapies; PI: Chris Waters (Michigan State University) 40% contribution; co-PI Joseph Graves (North Carolina A&T State University) 40% contribution; co-PI: Barrick 20% contribution; $169,302 total costs; $33,182 to Barrick; 05/01/2015–04/30/2016.

NSF BEACON Center (DBI-0939454 subcontract); Evolution in action: evolving resistance to metallic/metallic oxide nanoparticles in bacteria; PI: Joseph Graves (North Carolina A&T State University) 40% contribution; co-PI: Barrick 20%

5 contribution; PI: Chris Waters (Michigan State University) 40% contribution. $111,463 total costs; $15,594 total costs to Barrick; 05/01/2014–04/30/2015.

NSF BEACON Center (DBI-0939454 subcontract); Searching for self-encoded RNAs: Remnants of the RNA World? PI: Chris Waters (Michigan State University) 40% contribution; co-PI: Barrick 30% contribution; co-PI: Shin-Han Shiu (Michigan State University) 30% contribution; $98,949 total costs; $37,780 to Barrick; 06/01/2013–05/31/2014.

Army Research Office MURI (W911NF-12-1-0390) Associating growth conditions with cellular composition in Gram-negative bacteria; PI: Claus Wilke (The University of Texas at Austin) 12% contribution; co-PI: Barrick 11% contribution; co-PI: Edward Marcotte (The University of Texas at Austin) 11% contribution; co-PI: Pradeep Ravikumar (The University of Texas at Austin) 11% contribution; co-PI: Stephen Trent (University of Georgia) 11% contribution; co-PI: Claus Wilke (The University of Texas at Austin) 11% contribution; co-PI: Ioannis Paschalidis (Boston University) 11% contribution; co-PI: Saniel Ségre (Boston University) 11% contribution; co-PI: Christopher Marx (University of Idaho) 11% contribution; $5,000,000 total costs; $859,802 to Barrick; 08/01/2012–02/28/2018.

DARPA BRICS (HR0011-15-C0095) Control of bee behavior by stably engineered gut microbial communities; PI: Nancy Moran (The University of Texas at Austin) 35% contribution; co-PI: Barrick 30% contribution; co-PI: Andrew Ellington (The University of Texas at Austin) 20% contribution; co-PI: Bryan Davies (The University of Texas at Austin) 10% contribution; co-PI: Hal Alper (The University of Texas at Austin) 5% contribution; $2,480,500 total costs; $797,191 to Barrick; 07/01/2015–12/31/2017. No cost extension to 6/30/2018.

Publications

Key: *Equal contributions ^Corresponding author(s) Researchers Advised by Barrick Please note these article types as indicated: 1 Refereed articles 2 Invited articles 3Book chapters

Publications while in rank of Associate Professor

1 77. Geng, Peng, Leonard, Sean P., Mishler, Dennis M., ^Barrick, Jeffrey E. (2019) Synthetic genome defenses against selfish DNA elements stabilize engineered bacteria against evolutionary failure. ACS Synth. Biol. 8 (3), 521-531.

1 76. Deatherage, Daniel E., Leon, Dacia, Rodriguez, Álvaro E., Omar, Salma, ^Barrick, Jeffrey E. (2018) Directed evolution of with lower- than-natural plasmid mutation rates. Nucleic Acids Res. 46 (17), 9236-9250.

1 75. *McGuffey, J.C., *Leon, D., Dhanji, E.Z., Mishler, D.M., ^Barrick, Jeffrey E. (2018) Bacterial production of gellan gum as a do-it-yourself alternative to agar. J. Microbiol. Biol. Educ. 19 (2), 182-184.

6 Publications while in rank of Assistant Professor

1 74. Leonard, Sean P., Perutka, Jiri, Powell, J. Elijah, Geng, Peng, Richhart, Darby, Byrom, Michelle, Kar, Shaunak, Davies, Bryan W., Ellington, Andrew D., ^Moran, Nancy A., ^Barrick, Jeffrey E. Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids. ACS Synth. Biol. 7 (5), 1279-1290.

1 73. Leon, Dacia, D’Alton, Simon, Quandt, Erik M., ^Barrick, Jeffrey E. Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides PLoS Genet. 14 (4), e1007348.

1 72. *Good, Benjamin H., *McDonald, Michael J., Barrick, Jeffrey E., Lenski, Richard E., ^Desai, Michael M. The dynamics of molecular evolution over 60,000 generations. Nature 551, 45-50.

1 71. *Bull, J. James, ^*Barrick, Jeffrey E. (2017) Arresting evolution. Trends Genet. 33, 910-920.

1 70. Suárez, Gabriel A., Renda, Brian A., Dasgupta, Aurko, ^Barrick, Jeffrey E. (2017) Reduced mutation rate and increased transformability of transposon-free Acinetobacter baylyi ADP1-ISx. Appl. Environ. Microbiol. 83, e01025-17

2 69. ^Barrick, Jeffrey E. (2017) In future () generations. “Voices” piece in What is the role of circuit design in the advancement of synthetic biology? Part 2. Cell Syst. 24, 467-477.

1 68. Brown, Colin W., Sridhara, Viswanadham, Boutz, Daniel R., Person, Maria D., Marcotte, Edward M., Barrick, Jeffrey E., ^Wilke, Claus O. (2017) Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. BMC Genomics 18, 301.

1 67. ^Caglar, Mehmet U., Houser, John R., Barnhart, Craig S., Boutz, Daniel R., Carroll, Sean M., Dasgupta, Aurko, Lenoir, Walter F., Smith, Bartram L., Sridhara, Viswanadham, Sydykova, Dariya K., Vander Wood, Drew, Marx, Chrisopher J., ^Marcotte, Edward M., ^Barrick, Jeffrey E., ^Wilke, Claus O. (2017) The E. coli molecular phenotype under different growth conditions. Sci. Rep. 7, 45303.

1 66. Deatherage, Daniel E., Kepner, Jamie L., Bennett, Albert F., ^Lenski, Richard E., ^Barrick, Jeffrey E. (2017) Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures. Proc. Natl. Acad. Sci. U.S.A. 114 (10), E1904-E1912.

1 65. Monk, Jordan W., Leonard, Sean P., Brown, Colin W., Hammerling, Michael J., Mortensen, Catherine, Gutierrez, Alejandro E., Shin, Nathan Y., Watkins, Ella, ^Mishler, Dennis M., ^Barrick, Jeffrey E. (2017) Rapid and inexpensive

7 evaluation of nonstandard amino acid incorporation in Escherichia coli. ACS Synth. Biol. 6 (1), 45-54.

1 64. Renda, Brian A., Chan, Cindy, Parent, Kristin N., ^Barrick, Jeffrey E. (2016) Emergence of a competence reducing filamentous phage from the genome of Acinetobacter baylyi ADP1. J. Bacteriol. 198 (23), 3209-3219.

1 63. *Tenaillon, Olivier, *Barrick, Jeffrey E., Ribeck, Noah, Deatherage, Daniel E., Blanchard, Jeffrey L., Dasgupta, Aurko, Wu, Gabriel C., Wielgoss, Sébastien, Cruveiller, Stéphane, Medigue, Claudine, Schneider, Dominique, *^Lenski, Richard E. (2016) Tempo and mode of genome evolution in a 50,000-generation experiment. Nature 536 (7615), 165-170.

1 62. Hammerling, Michael J., Gollihar, Jimmy, Mortensen, Catherine, Alnahhas, Razan N., Ellington, Andrew D., ^Barrick, Jeffrey E. (2016) Expanded genetic codes create new mutational routes to rifampicin resistance in Escherichia coli. Mol. Biol. Evol. 33 (8), 2054-2063.

1 61. Quandt, Erik M., Gollihar, Jimmy, Blount, Zachary D., Ellington, Andrew D., Georgiou, George, ^Barrick, Jeffrey E. (2015) Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. eLife 4, e09696.

1 60. Houser, John R., Barnhart, Craig, Boutz, Daniel R., Carroll, Sean M., Dasgupta, Aurko, Michener, Joshua K., Needham, Brittany D., Papoulas, Ophelia, Sridhara, Viswanadham, Sydykova, Dariya K., Marx, Christopher J., Trent, M. Stephen, ^Barrick, Jeffrey E., ^Marcotte, Edward M., ^Wilke, Claus O. (2015) Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes in response to glucose starvation. PLoS Comput. Biol. 11 (8):e1004400.

1 59. ^Maddamsetti, Rohan, Hatcher, Philip J., Cruveiller, Stéphane, Médigue, Claudine, Barrick, Jeffrey E., Lenski, Richard E. (2015) Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment. Mol. Biol. Evol. 32 (11), 2897-2904.

1 58. Jack, Benjamin R., Leonard, Sean P., Mishler, Dennis M., Renda, Brian A., Leon, Dacia, Suárez, Gabriel A., ^Barrick, Jeffrey E. (2015) Predicting the genetic stability of engineered DNA sequences with the EFM Calculator. ACS Synth. Biol. 4 (8):939-943.

1 57. ^Perry, Elizabeth B., Barrick, Jeffrey E., Bohannan, Brendan J.M. (2015) The molecular and genetic basis of repeatable coevolution between Escherichia coli and bacteriophage T3 in a laboratory microcosm. PLoS ONE 10 (6), e0130639.

8 1 56. Quandt, Erik M., Summers, Ryan M., Subramanian, Mani V., ^Barrick, Jeffrey E. (2015) Draft genome sequence of the bacterium Pseudomonas putida CBB5, which can utilize caffeine as a sole carbon and nitrogen source. Genome Announc. 3 (3), e00640-15.

1 55. Maddamsetti, Rohan, Lenski, Richard E., ^Barrick, Jeffrey E. (2015) Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli. Genetics 200 (2), 619-631.

1 54. ^Graves, Joseph L., Tajkarimi, Mehrdad, Cunningham, Quincy, Campbell, Adero, Nonga, Herve, Harrison, Scott H., Barrick, Jeffrey E. (2015) Rapid evolution of silver nanoparticle resistance in Escherichia coli. Front. Genet. 6, 42.

1 53. Renda, Brian A., Dasgupta, Aurko, Leon, Dacia, ^Barrick, Jeffrey E. (2015) Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution. J. Bacteriol. 197 (5), 872-881.

1,2 52. Deatherage, Daniel E., Traverse, Charles C., Wolf, Lindsey N., ^Barrick, Jeffrey E. (2015) Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq. Front. Genet. 5, 468.

1 51. Sridhara, Viswanadham, Meyer, Austin G., Rai, Piyush, Barrick, Jeffrey E., Ravikumar, Pradeep, Ségre, Daniel, ^Wilke, Claus O. (2014) Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli. PLoS ONE 9 (12), e114608.

1 50. *Alnahhas, Razan N., *Slater, Ben, Huang, Yunle, Mortensen, Catherine, Monk, Jordan W., Okasheh, Yousef, Howard, Marco D., Gottel, Neil R., ^Hammerling, Michael J., ^Barrick, Jeffrey E. (2014) The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts. J. Biol. Eng. 8 (1), 28.

1 49. ^Barrick, Jeffrey E., Colburn, Geoffrey, Deatherage, Daniel E., Traverse, Charles C., Strand, Matthew D., Borges, Jordan J., Knoester, Daniel B., Reba, Aaron, Meyer, Austin G. (2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics 15 (1), 1039.

1 48. Colin, Raeside, Gaffé, Joël, Deatherage, Daniel E., Tenaillon, Olivier, Briska, Adam M., Ptashkin, Ryan N., Cruveiller, Stéphane, Médigue, Claudine, Lenski, Richard E., Barrick, Jeffrey E., ^Schneider, Dominique (2014) Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. mBio 5 (9), e01377-14.

9 2,3 47. Deatherage, Daniel E., ^Barrick, Jeffrey E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151, 165-188.

1 46. *Renda, Brian A., *Hammerling, Michael J., ^Barrick, Jeffrey E. (2014) Engineering reduced evolutionary potential for synthetic biology. Mol. Biosyst. 10 (7), 1668-1678.

1 45. Hammerling, Michael J., Ellefson, Jared W., Boutz, Daniel R., Marcotte, Edward M., Ellington, Andrew D., ^Barrick, Jeffrey E. (2014) Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nat. Chem. Biol. 10 (3), 178-180.

1 44. Quandt, Erik M., Deatherage, Daniel E., Ellington, Andrew D., ^Georgiou, George, ^Barrick, Jeffrey E. (2014) Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 111 (6), 2217-2222.

1 43. ^Hammerling, Michael J., ^Gottel, Neil R., Alnahhas, Razan N., Slater, Ben, Huang, Yunle, Okasheh, Yousef, Howard, Marco, Mortensen, Catherine, Monk, Jordan, Detelich, Madeline, Lannan, Ryan S., Pitaktong, Areen, Weaver, Evan, Das, Siddharth, ^Barrick, Jeffrey E. (2013) BBF RFC95: Open Sequence Initiative: a part submission standard to complement modern DNA assembly techniques. DSpace@MIT http://hdl.handle.net/1721.1/81334

1,2 42. ^Barrick, Jeffrey E., ^Lenski, Richard E. (2013) Genome dynamics during experimental evolution. Nat. Rev. Genet. 14 (12), 827-834.

1 41. Summers, Ryan M., Seffernick, Jennifer L., Quandt, Erik M., Yu, Chi Li, Barrick, Jeffrey E., ^Subramanian, Mani V. (2013) Caffeine junkie: an unprecedented GST- dependent oxygenase required for caffeine degradation by P. putida CBB5. J. Bacteriol. 195 (17), 3933-3939.

1 40. Quandt, Erik M., Hammerling, Michael J., Summers, Ryan M., Otoupal, Peter B., Slater, Ben, Alnahhas, Razan N., Dasgupta, Aurko, Bachman, James L., Subramanian, Mani V., ^Barrick, Jeffrey E. (2013) Decaffeination and measurement of caffeine content by addicted Escherichia coli with a refactored N- demethylation operon from Pseudomonas putida CBB5. ACS Synth. Biol. 2, 301- 307.

1 39. Han, Pu, Niestemski, Liang Ren, Barrick, Jeffrey E., ^Deem, Michael W. (2013) Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system. Phys. Biol. 10 (2), 025004.

1 38. *Wielgoss, Sébastien, *Barrick, Jeffrey E., *Tenaillon, Olivier, Wiser, Michael J., Dittmar, W. James, Cruveiller, Stéphane, Chane-Woon-Ming, Béatrice, Médigue,

10 Claudine, ^Lenski, Richard E., ^Schneider, Dominique. (2013) Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Proc. Natl. Acad. Sci. U.S.A. 110 (1), 222-227.

1 37. ^Blount, Zachary D., Barrick, Jeffrey E., Davidson, Carla J., ^Lenski, Richard E. (2012) Genomic analysis of a key innovation in an experimental E. coli population. Nature 489 (7417), 513-518.

1 36. Jerome, John P., Klahn, Brian, Bell, Julia A., Barrick, Jeffrey E., Brown, Charles T., ^Mansfield, Linda S. (2012) Draft genome sequences of two Campylobacter jejuni clinical isolates, NW and D2600. J. Bacteriol. 194 (20), 5707-5708.

1,2 35. Reba, Aaron, Meyer, Austin G., ^Barrick, Jeffrey E. (2012) Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection. In: C. Adami et al. (eds.). Artificial Life XIII: Proceedings of the Thirteenth International Conference on the Synthesis and Simulation of Living Systems. pp 473-480. Cambridge, MA: MIT Press.

1 34. Kholmanov, Iskandar N., Stoller, Meryl D., Edgeworth, Jonathan, Lee, Wi Hyoung, Li, Huifeng, Lee, Jongho, Barnhart, Craig, Potts, Jeffrey R., Piner, Richard, Akinwande, Deji, Barrick, Jeffrey E., ^Ruoff, Rodney S. (2012) Nanostructured hybrid transparent conductive films with antibacterial properties. ACS Nano 6 (6), 5157-5163.

2 33. Wolf, Lindsey N., ^Barrick, Jeffrey E. (2012) Tracking winners and losers in E. coli evolution experiments. Microbe 2 (3), 124-128.

1 32. ^Meyer, Justin R., Dobias, Devin T., Weitz, Joshua S., Barrick, Jeffrey E., Quick, Ryan T., Lenski, Richard E. (2012) Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335 (6067), 428-432.

1 31. Nahku, Ranno, Peebo, Karl, Valgepea, Kaspar, Barrick, Jeffrey E., Adamberg, Kaarel, ^Vilu, Raivo (2011) Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture. Microbiology 157, 2604-2610.

1 30. Wielgoss, Sébastien, Barrick, Jeffrey E., Tenaillon, Olivier, Cruveiller, Stéphane, Chane-Woon-Ming, Béatrice, Médigue, Claudine, Lenski, Richard E., ^Schneider, Dominique (2011) Mutation rate inferred from synonymous substitutions in a long- term evolution experiment with Escherichia coli. G3: Genes, Genomes, Genetics 1 (3), 183-186.

1 29. *Woods, Robert J., *^Barrick, Jeffrey E., Cooper, Tim F., Shrestha, Utpala, Kauth, Mark R., ^Lenski, Richard E. (2011) Second-order selection for evolvability

11 in a large Escherichia coli population. Science 331 (6023), 1433-1436.

1 28. Jerome, John P., Bell, Julia A., Plovanich-Jones, Anne E., Barrick, Jeffrey E., Brown, Charles T., ^Mansfield, Linda S. (2011) Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host. PLoS ONE 6 (1), e16399.

Publications as postdoctoral fellow

1 27. ^Barrick, Jeffrey E., Kauth, Mark R., Strelioff, Christopher C., Lenski, Richard E. (2010) Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol. Biol. Evol. 27 (6), 1338-1347.

1 26. *Barrick, Jeffrey E., *Yu, Dong Su, Yoon, Sung Ho, Jeong, Haeyoung, Oh, Tae Kwang, Schneider, Dominique, ^Lenski, Richard E., ^Kim, Jihyun F. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461 (7268), 1243-1247.

2,3 25. Barrick, Jeffrey E., ^Lenski, Richard E. (2009) Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harbor Symp. Quant. Biol. 74, 119-129.

1,2 24. ^Lenski, Richard E., Barrick, Jeffrey E., Ofria, Charles (2006) Balancing robustness and evolvability. PLoS Biol. 4 (12), e428.

Publications as graduate student

2,3 23. Barrick, Jeffrey E. (2009). Predicting riboswitch regulation on a genomic scale. Methods Mol. Biol. 540, 1-13.

1 22. Regulski, Elizabeth E., Moy, Ryan H., Weinberg, Zasha, Barrick, Jeffrey E., Yao, Zizhen, Ruzzo, Walter L., ^Breaker, Ronald R. (2008) A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol. Microbiol. 68 (4), 918-932.

1 21. Weinberg, Zasha, Regulski, Elizabeth E., Hammond, Ming C., Barrick, Jeffrey E., Yao, Zizhen, Ruzzo, Walter L., ^Breaker, Ronald R. (2008) The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA 14 (5), 822-828.

1,2 20. Barrick, Jeffrey E., ^Breaker, Ronald R. (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol. 8 (11), R239.

1 19. ^Weinberg, Zasha, Barrick, Jeffrey E., Yao, Zizhen, Roth, Adam, Kim, Jane N., Gore, Jeremy, Wang, Joy X., Lee, Elaine R., Block, Kirsten F., Sudarsan,

12 Narasimhan, Neph, Shane, Tompa, Martin, Ruzzo, Walter L., ^Breaker, Ronald R. (2007) Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res. 35 (14), 4809-4819

1 18. ^Yao, Zizhen, Barrick, Jeffrey E., Weinberg, Zasha, Neph, Shane, Breaker, Ronald R., Tompa, Martin, Ruzzo, Walter L. (2007) A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLOS Comput. Biol. 3 (7), e126.

1 17. Roth, Adam, Winkler, Wade C., Regulski, Elizabeth E., Lee, Bobby W.K., Lim, Jinsoo, Jona, Inbal, Barrick, Jeffrey E., Ritwik, Ankita, Kim, Jane N., Welz, Rüdiger, Iwata-Reuyl, Dirk, ^Breaker, Ronald R. (2007) A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nat. Struct. Mol. Biol. 14 (4), 308-317.

2 16. ^Barrick, Jeffrey E., Breaker, Ronald R. (2007) The Power of Riboswitches. Scientific American 296 (1), 50-57.

1 15. Puerta-Fernandez, Elena, Barrick, Jeffrey E., Roth, Adam, ^Breaker, Ronald R. (2006) Identification of a new, non-coding RNA in extremophilic eubacteria. Proc. Natl. Acad. Sci U.S.A. 103 (51), 19490-19495.

1 14. Sudarsan, Narasimhan, Hammond, Ming C., Block, Kirsten F., Welz Rüdiger, Barrick, Jeffrey E., Roth, Adam, ^Breaker, Ronald R. (2006) Tandem riboswitch architectures exhibit complex gene control functions. Science 314 (5797), 300-304.

1 13. Corbino, Keith A., Barrick, Jeffrey E., Lim, Jinsoo, Welz, Rüdiger, Tucker, Brian J., Puskarz, Izabela, Mandal, Maumita, Rudnick, Noam D., ^Breaker, Ronald R. (2005) Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol. 6 (8), R70.

1 12. Barrick, Jeffrey E., Sudarsan, Narasimhan, Weinberg, Zasha, Ruzzo, Walter L., ^Breaker, Ronald R. (2005) 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA 11 (5), 774-784.

1 11. Mandal, Maumita, Lee, Mark, Barrick, Jeffrey E., Weinberg, Zasha, Emilsson, Gail M., Ruzzo, Walter L., ^Breaker, Ronald R. (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306 (5694), 275-279.

1 10. Barrick, Jeffrey E., Corbino, Keith A., Winkler, Wade C., Nahvi, Ali, Mandal, Maumita, Collins, Jennifer, Lee, Mark, Roth, Adam, Sudarsan, Narasimhan, Jona, Inbal, Wickiser, John K., ^Breaker, Ronald R. (2004) New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. U.S.A. 101 (17), 6421-6426.

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1 9. Nahvi, Ali, Barrick, Jeffrey E., ^Breaker, Ronald R. (2004) Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res. 32 (1), 143-150.

1 8. Mandal, Maumita, Boese, Benjamin, Barrick, Jeffrey E., Winkler, Wade C., ^Breaker, Ronald R. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113 (5), 577-586.

1 7. Sudarsan, Narasimhan, Barrick, Jeffrey E., ^Breaker, Ronald R. (2003) Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9 (6), 644-647.

1 6. Winkler, Wade C., Nahvi, Ali, Sudarsan, Narasimhan, Barrick, Jeffrey E., ^Breaker, Ronald R. (2003) An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol. 10 (9), 701-707.

Publications as undergraduate student

1 5. Barrick, Jeffrey E., ^Roberts, Richard W. (2003). Achieving specificity in selected and wild-type N peptide–RNA complexes: The importance of discrimination against noncognate RNA targets. Biochemistry 42 (44), 12998-13007.

1 4. Barrick, Jeffrey E., ^Roberts, Richard W. (2002). Sequence analysis of an artificial family of RNA-binding peptides. Protein Sci. 11 (11), 2688-2696.

1 3. Barrick, Jeffrey E., Takahashi, Terry T., Ren, Jinsong, Xia, Tianbing, ^Roberts, R.W. (2001) Large libraries reveal diverse solutions to an RNA recognition problem. Proc. Natl. Acad. Sci. U.S.A. 98 (22), 12374-12378.

2 2. Barrick, Jeffrey E., Takahashi, Terry T., Balakin, Andrey, ^ Roberts, Richard W. (2001) Selection of RNA-binding peptides using mRNA-peptide fusions. Methods 23 (3), 287-293.

2,3 1. Liu, Rihe, Barrick, Jeffrey E., Szostak, Jack W., ^Roberts, Richard W. (2000) Optimized synthesis of RNA-protein fusions for in vitro protein selection. Methods Enzymol. 318, 268-293.

Papers Submitted for Publication

1 2. Deatherage, Daniel E., Leon, Dacia, Rodriguez, Alvaro E., Omar, Salma K., ^Barrick, Jeffrey E., Directed evolution of Escherichia coli with lower-than- natural plasmid mutation rates. Submitted April 6, 2018.

2,3 1. ^Barrick, Jeffrey E. Limits to predicting E. coli evolution in a long-term experiment. Proceedings of Santa Fe Institute Workshop on Limits to Prediction. Submitted December 26, 2016.

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Publications Edited

None

Books

None

Surveys, Editorials, and Reviews

2. Camp, Tyler, Mishler, Dennis M., ^Barrick, Jeffrey E. (2016) Negative design to prevent evolutionary failure. Benchling Blog https://benchling.com/pub/efm-calculator

1. Wolf, Lindsey N., Barrick, Jeffrey E. (2012) Tracking winners and losers in E. coli evolution experiments. Microbe 2 (3), 124-128.

Chapters in Books

1. Barrick, Jeffrey E. (2009). Predicting riboswitch regulation on a genomic scale. Methods Mol. Biol. 540, 1-13.

Articles in Conference Proceedings

1. Reba, Aaron, Meyer, Austin G., ^Barrick, Jeffrey E. (2012) Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection. In: C. Adami et al. (eds.). Artificial Life XIII: Proceedings of the Thirteenth International Conference on the Synthesis and Simulation of Living Systems. pp 473-480. Cambridge, MA: MIT Press.

Articles in Workshop Proceedings

None

Technical Reports

1. Hammerling, Michael J., Gottel, Neil R., Alnahhas, Razan N., Slater, Ben, Huang, Yunle, Okasheh, Yousef, Howard, Marco, Mortensen, Catherine, Monk, Jordan, Detelich, Madeline, Lannan, Ryan S., Pitaktong, Areen, Weaver, Evan, Das, Siddharth, Barrick, Jeffrey E. (2013) BBF RFC95: Open Sequence Initiative: a part submission standard to complement modern DNA assembly techniques. DSpace@MIT http://hdl.handle.net/1721.1/81334

Software

3. ^Barrick, J.E., Deatherage, D.E. (2017) breseq: software for comprehensively identifying mutations in next-generation re-sequencing data for haploid microbial

15 genomes and mixed populations. License: GPLv2. Website: http://barricklab.org/breseq; Repository: https://github.com/barricklab/breseq.

2. ^Barrick, J.E. (2017) bpopsim: software for simulations of mutational dynamics in evolving microbial populations. License: GPLv2. Repository: https://github.com/barricklab/bpopsim.

1. Jack, B.R. ^Barrick, J.E. (2015) Evolutionary Failure Mode (EFM) Calculator: a web tool for predicting the genetic stability of engineered DNA sequences. Website: http://barricklab.org/efm; Repository: https://github.com/barricklab/efm-calculator

Patents Issued

1. Nancy Moran, Jeffrey Barrick, Sean Leonard. Engineered Microbial Population. Patent No. US 2019/0015528 A1. Jan. 17, 2019. 2. Breaker, Ronald R., Nahvi, Ali, Sudarsan, Narasimhan, Ebert, Margaret S., Winkler, Wade, Barrick, Jeffrey E., Wickiser, J. Kenneth. Riboswitches, methods for their use, and compositions for use with riboswitches. Patent No. US 7,794,931 B2. Sept. 14, 2010.

Awards and Honors

2019–2022 Fellow of the Lorene Morrow Kelley Professorship 2018–2019 Defense Science Study Group 2016 NSF CAREER Award 2015 1st Centennial Award for Population and Evolutionary Genetics, Genetics Society of America (for paper published in Genetics) 2015 College of Natural Sciences Teaching Excellence Award 2014 UT Austin Friar Centennial Teaching Fellowship Semi-finalist 2012 Elected to UT Austin Society for Teaching Excellence 2012 Best Paper Award, Synthetic Biology Track, ALife XIII Conference 2010 Society for Molecular Biology and Evolution, Annual Meeting Travel Award 2009 NIH Pathway to Independence Award (K99/R00) 2006–2008 NSF Postdoctoral Research Fellowship in Biological Informatics 2006 RNA Society/Scaringe Young Scientist Award 2003, 2004 Yale Molecular Biophysics & Biochemistry Graduate Student Excellence in Teaching Awards 2001–2006 Howard Hughes Medical Institute Predoctoral Fellowship 2001 Hertz Foundation Fellowship Finalist 2000 Caltech George W. Green Memorial Prize 1999, 2000, Caltech Summer Undergraduate Research Fellowships 2001 1999, 2000 Caltech Upper Class Merit Awards 1997–2001 Dorothy B. and Harrison C. Lingle Scholarship 1997–1999 Caltech Entering Freshman Merit Award

16 Service

Departmental

2012–present Biochemistry Honors Advisor 2018–present Biochemistry Degree Curriculum Reform Committee, Chair 2018–present Molecular Biosciences, Senior Faculty Search Committee 2018–present Q15 CMB Qualifying Exam Committee 2015–2016 Molecular Biosciences, Junior Faculty Search Committee 2014–2015 Molecular Biosciences, Junior Faculty Search Committee 2013–2014 Molecular Biosciences & Computer Science, Joint Hire Junior Faculty Search Committee 2011–2013 Chemistry Department, Undergraduate Summer Orientation Presentation 2012 UT Austin DNA Sequencing Facility Advisory Board 2012 Biochemistry Seminar Committee

College

2012–present Dean’s Scholars Honors Program Steering Committee 2015–present Faculty Advisor, Microbe Hackers Synthetic Biology, Freshman Research Initiative (FRI) Stream 2017-2018 Teaching Evaluation Committee 2016-2017 Teaching Evaluation Task Force 2016, 2017 Docent, Teaching Discovery Day 2015–2016 21st Century Education Working Group 2012–2015 Beckman Scholars Program Steering Committee 2012 Undergraduate Research Forum, Poster Evaluator

University

2012–present Faculty Advisor, UT Austin synthetic biology team participating in the iGEM (International Genetically Engineered Machine) competition. Website with links to projects: http://barricklab.org/igem 2012–2014 Co-Instructor of Introduction to Next-Generation Sequencing Bioinformatics Summer Short Course, UT Austin Summer Statistics Institute / Center for Computational Biology and Bioinformatics 2013 Organized FBI Academic Biosecurity Workshop at UT Austin

National

2019 Organizing Committee, Synthetic Biology: Engineering, Evolution & Design (SEED) Conference

Community

2014–2016 iGEM team outreach with booth at South by Southwest (SXSW) Create

17 2013 Darwin Day Lecture to public, Texas Memorial Museum, Austin, TX 2011 NSF BEACON Center for the Study of Evolution in Action Blog Post

Seminars/Lectures

Invited Seminars

2018 New York University, Biology Seminar Series, New York, NY 2018 University of Georgia, Department of Microbiology, Athens, GA 2018 DuPont, Wilmington, DE 2018 Gingko Bioworks, Boston, MA 2017 LanzaTech, Skokie, IL 2017 Tsinghua University, Chemical Engineering Department, Beijing, China 2017 Portland State University, Biology Seminar, Portland, OR 2017 University of California, San Diego: qBio Seminar Series, San Diego, CA 2017 Baylor College of Medicine, Department of Biochemistry and Molecular Biology, Houston, TX 2017 University of Idaho, IBEST/CMCI Seminar Series, Moscow, ID 2017 University of California, Irvine, Department of Biomedical Engineering, Irvine, CA 2016 University of Washington, Seattle, Department of Genome Sciences, Seattle, WA 2015 Colorado State University, Department of Chemical & Biological Engineering, Fort Collins, CO 2014 North Carolina A&T University, Department of Biology, Greensboro, NC 2013 University of Maryland, Department of Cell Biology & Molecular Genetics, College Park, MD 2012 University of Illinois, Urbana-Champaign, Department of Microbiology, Urbana- Champaign, IL 2010 Harvard Medical School, Department of Molecular Biology, Cambridge, MA 2010 Johns Hopkins University, Department of Biology, Baltimore, MD 2010 California Institute of Technology, Division of Biology, Pasadena, CA 2010 Emory University, Department of Biology, Atlanta, GA 2010 Northwestern University, Department of Biochemistry, Molecular Biology and Cell Biology, Evanston, IL 2010 University of Michigan, Department of Ecology and Evolutionary Biology, Ann Arbor, MI 2010 University of Pennsylvania, Department of Biology, Philadelphia, PA 2010 University of Southern California, Department of Biological Sciences, Los Angeles, CA 2010 Georgia Institute of Technology, Department of Biology, Atlanta, GA 2010 The University of Texas at Austin, Department of Chemistry and Biochemistry, Austin, TX 2009 The Ohio State University, Department of Microbiology, Columbus, OH 2009 J. Craig Venter Institute, San Diego, CA 2009 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD

18 2009 University of Rochester Medical Center, Department of Microbiology and Immunology, Rochester, NY 2009 University of Texas at Dallas, Department of Molecular and Cell Biology, Richardson, TX

Invited Presentations at Conferences

2017 Peptalk, Engineering Genomes and Hosts Session, San Diego, CA 2016 American Chemical Society, Southwest Regional Meeting, Synthetic Biology Session, Galveston, TX 2015 Biochemical and Molecular Engineering XIX, Puerto Vallarta, Mexico 2015 Molecular Mechanisms in Evolution, Gordon Research Conference, Easton, MA 2015 Big Data in Biology Symposium, Austin, TX 2014 ASM Biodefense and Emerging Diseases Research Meeting, Washington, D.C. 2014 ASM Texas Branch Fall Meeting, Houston, TX 2013 Design Automation Conference, Austin, TX 2011 Annual Computational & Theoretical Biology Symposium, Rice University, Houston, TX 2011 American Society for Microbiology General Meeting, New Orleans, LA 2011 Quantitative Genetics, Gordon Research Conference, Galveston, TX 2006 Annual Meeting of the RNA Society, Seattle, WA 2004 Post-Initiation Activities of RNA Polymerase Conference, Mountain Lake, VA

Contributed Presentations at Conferences

2015 International Conference on Biomolecular Engineering (ICBE), Lost Pines, TX 2012 ALife XIII Conference, East Lansing, MI 2008 Evolution, Minneapolis, MN

Contributed Posters at Conferences

2016 ASM Microbe Annual Meeting, Boston, MA 2013 Synthetic Biology 6.0, London, United Kingdom 2011 Microbial Population Biology, Gordon Research Conference, Andover, NH. 2009 Microbial Population Biology, Gordon Research Conference, Andover, NH. 2007 Microbial Population Biology, Gordon Research Conference, Andover, NH.

Professional Services

Journal Editing and Editorial Boards

None

Conference Chair Positions

None

19 Major Conference Program Committees

2014 ALife XIV Program Committee

Workshops and Specialized Conference Program Committees

2017 Frontiers in Evolutionary Ecology and Genomics Workshop, Beijing, China 2016 NSF I-Corps Regional Program (Southwest Node) 2016 Bioenabled Materials Synthesis & Assembly, Army Science Planning and Strategy Meeting (ASPSM), Aberdeen Proving Grounds, Aberdeen, MD 2016 NASA/NSF Ideas Lab on the Origins of Life, Cambridge, MD 2016 Limits to Prediction, Sante Fe Institute Workshop, Sante Fe, NM 2015 NSF Design Principles for Engineering Biology Workshop, Washington, D.C. 2015 EMBO Practical Course: Measuring intra-species diversity using high-throughput sequencing, Oneiras, Portugal (Co-Organizer) 2008 Rockefeller Foundation Workshop: Evolution of Microbial Heterogeneity and Complexity, Bellagio, Italy

Journal, Conference, and Book Reviewing

Cell, Science, Nature, Nature Communications, Nature Reviews Genetics, Proceedings of the National Academy of Sciences of the U.S.A., eLife, PLoS Biology, PLoS Genetics, PLoS Computational Biology, PLoS ONE, ACS Synthetic Biology, RNA, Nucleic Acids Research, Environmental Microbiology, Molecular Biology and Evolution, Genome Biology and Evolution, BMC Evolutionary Biology, Genetics, Proceedings of the Royal Society B: Biological Sciences, Bioinformatics, Genome Biology, Bioessays, mBio, Applied and Environmental Microbiology, Current Opinions in Microbiology, Molecular Microbiology, Microbiology and Molecular Biology Reviews, Microbial Cell Factories, Bioinformatics

Grant Proposal Reviewing

Ad hoc referee for US National Science Foundation, US Army Research Office, European Science Foundation, Marsden Fund (New Zealand), Netherlands Organisation for Scientific Research (NWO), MacArthur Foundation, Minerva Foundation (Germany), Israel Science Foundation, Texas Sea Grants

Other Service

Research Advising

5 Postdocs supervised (3 current) 12 Graduate students supervised (5 current) 31 Graduate student rotation projects supervised (Microbiology, Cellular and Molecular Biology, and Biochemistry programs) 2 High School students supervised

20 22 Undergraduates supervised (not including iGEM-team or FRI only researchers) 2 International visiting Ph.D. students supervised (Korea, Denmark)

2019 iGEM Team Faculty Advisor, 10 UT Austin undergraduate researchers 2018 iGEM Team Faculty Advisor, 19 UT Austin undergraduate researchers 2017 iGEM Team Faculty Advisor, 11 UT Austin undergraduate researchers 2016 iGEM Team Faculty Advisor, 16 UT Austin undergraduate researchers 2015 iGEM Team Faculty Advisor, 14 UT Austin undergraduate researchers 2014 iGEM Team Faculty Advisor, 5 UT Austin undergraduate researchers 2013 iGEM Team Faculty Advisor, 11 UT Austin and 6 North Carolina A&T State University (HBCU) undergraduate researchers (joint iGEM team) 2012 iGEM Team Faculty Advisor, 6 UT Austin undergraduate researchers

Ph.D. Theses Supervised

2018 Dacia Leon (Microbiology) 2016 Michael Hammerling (Cellular and Molecular Biology) 2016 Brian Renda (Cellular and Molecular Biology)

Masters Theses Supervised

2014 Lindsey Wolf (Microbiology) 2014 Alvaro Rodriguez (Microbiology)

Undergraduate Honors Theses Supervised

2019 Jenna McGuffie (Biology, Health Science Scholars) 2019 France Stark (Biochemistry, Dean’s Scholars) 2019 Stratton Georgoulis (Biochemistry, Dean’s Scholars) 2014 Ryan Lannan (Biochemistry, Dean’s Scholars) 2013 Andrew Porter (Computer Science, Dean’s Scholars)

Trainee Awards/Fellowships

2018 Jenna McGuffey (iGEM team, undergraduate researcher), Goldwater Scholarship 2017 Sean Leonard (Ph.D student co-advised with Nancy Moran), UT Austin Bruton Graduate Continuing Fellowship 2017 Jenna McGuffey (iGEM team, undergraduate researcher), UT Austin TIDES Summer Research Fellowship 2017 Stratton Georgoulis (iGEM team, undergraduate researcher), UT Austin TIDES Summer Research Fellowship 2017 Andrew Ly (iGEM team), UT Austin TIDES Summer Research Fellowship 2017 Sanjana Reddy (iGEM team), UT Austin Archer Fellowship 2017 Matthew Hooper (iGEM team), UT Austin Undergraduate Research Fellowship 2017 Baltazar Zuniga (iGEM team), UT Austin McNair Scholar

21 2017 Prachi Shah and Saamiha Kenkare (iGEM team), UT Austin CNS Award for Excellence in Molecular Biology for poster at Undergraduate Research Forum 2016 Dacia Leon (Ph.D student), UT Austin College of Natural Sciences Summer Fellowship 2016 Razan Alnahhas (iGEM team, undergraduate researcher), NSF Graduate Research Fellowship (received while in Ph.D. program at Rice) 2016 Baltazar Zuniga (iGEM team), UT Austin TIDES Summer Research Fellowship 2016 Grace Long (iGEM team), UT Austin TIDES Summer Research Fellowship 2016 Jenna McGuffey (iGEM team, undergraduate researcher), UT Austin Fall Undergraduate Research Symposium, Computational and Synthetic Biology Session Award Winner 2016 Alex Gutierrez, (iGEM team), UT Austin Aspire Award 2016 iGEM Team, Gold Medal at World Jamboree 2015 Dacia Leon (Ph.D student), American Society for Microbiology Watkins Fellowship 2015 Peter Otoupal (iGEM team), NSF Graduate Research Fellowship, received while in Ph.D. program at the University of Colorado, Boulder 2015 iGEM Team, Gold Medal at World Jamboree 2015 Tyler Camp (iGEM team), UT Austin Fall Undergraduate Research Symposium, Session Award Winner 2014 Michael Hammerling (Ph.D student), UT Austin Graduate Named Continuing Fellowship 2014 Ben Slater (iGEM team), NSF Graduate Research Fellowship, received while an undergraduate at UT and then admitted to Ph.D. program at Yale 2014 Yousef Okasheh (iGEM team), UT Austin Beckman Scholar 2014 iGEM Team, Gold Medal at World Jamboree 2013 iGEM Team, Gold Medal at World Jamboree 2012 Alvaro Rodriguez (Ph.D student), CONACYT Graduate Fellowship 2012 iGEM Team, Best Measurement Award, Americas West Region

Presentations Given at the University

2017 Institute for Cellular and Molecular Biology, Annual Retreat 2016 Institute for Cellular and Molecular Biology, Annual Retreat 2015 Institute for Cellular and Molecular Biology, Annual Retreat 2015 Dean's Scholars Friday Seminar 2014 Microbiota and Metagenomics Symposium 2014 Institute for Cellular and Molecular Biology, Annual Retreat 2013 NSF BEACON Center Seminar 2013 Undergraduate Research Focus Group 2013 Institute for Cellular and Molecular Biology, Annual Retreat 2013 Institute for Computational Engineering and Sciences (ICES) Forum 2012 Department of Physics Nonlinear Dynamics Seminar 2012 ACS Undergraduate Student Chapter 2011 Institute for Cellular and Molecular Biology, Annual Retreat 2010 Institute for Cellular and Molecular Biology, Annual Retreat

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Courses Taught

2019 BCH 339F Foundations of Biochemistry 2018 NSC110H Honors Seminar: Biotechnology and Society 2018 BCH 339F Foundations of Biochemistry 2017 BCH 339F Foundations of Biochemistry 2016 BCH 339F Foundations of Biochemistry 2015 BCH 339F Foundations of Biochemistry 2015 NSC110H Honors Seminar: Microbes as Machines 2014 BIO 370 Foundations of Biochemistry 2013 NSC110H Honors Seminar: Biotechnology and Society 2013 CH 391L Synthetic Biology 2012 CH 339K Biochemistry I 2012 CH 391L Synthetic Biology 2011 CH 339K Biochemistry I

Guest Lectures for Courses

2013–2015 One lecture supervising paper discussion in BCH 395G Biochemistry (Instructor: Andreas Matouschek) 2011–present Two lectures in MOL 395J Molecular Biology (Instructor: Rick Russell) 2012 Lecture in BIO101C (Instructor Jason Shear) 2010 Lecture in PHY 392T Special Topics in Biophysics (Instructor: Vernita Gordon) 2010 One lecture leading paper discussion in CH 391L Molecular Evolution (Instructors: Dean Appling and Barrie Kitto)

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