Barrick Lab :: Publications

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Preprints
136. Kurnia, K., Gifford, I., Santala, V., Barrick, J.E., ^Santala, S. (2026) Dual-chassis strategy for bridging adaptive evolution and rational design for synthetic biology. bioRxiv DOI: 10.64898/2026.06.02.729570
135. ^Navarro-Escalante, L., VanDieren, A.J., ^Barrick, J.E. (2025) Genetic biosensor for optimizing double-stranded RNA production by bacterial symbionts. bioRxiv DOI: 10.64898/2026.01.18.700149
134. Ashraf, A H M Z., Weaver, K.K., Lariviere, P.J., ^Barrick, J.E. (2025) Natural competence promotes high rates of DNA transfer between strains of the core bee gut bacterium Snodgrassella alvi. bioRxiv DOI: 10.64898/2025.12.12.693966
133. Gomez, J.B., Barrick, J.E., ^Waters, C.M. (2025) Phages use contingency loci as a bet-hedging strategy. bioRxiv DOI: 10.1101/2025.10.21.683753
132. ^Lariviere, P.J., Ashraf, A H M Z., Gifford, I., Tanguma, S.L., Barrick, J.E., ^Moran, N.A. (2024) Virulence-linked adhesin drives mutualist colonization of the bee gut via biofilm formation. bioRxiv DOI: 10.1101/2024.10.14.618124
In Press
131. Kambar, N., Song, Y., Herrera, C.M., Baliga, M., Leonard, S.P., Barrick, J.E., Trent, M.S., Moran, N.A., ^Leal, C.* (2026) Symbiotic bacteria produce non-lytic vesicles with nucleic acid cargo. Nat. Commun. DOI: 10.10.1038/s41467-026-73834-2
2026
130. *Morton, A.K., *Chaudhari, K., Matibag, B.D., Iyengar, V.B., Dullen, K.E., VanDieren, A.J., Parker, J.K., Mishler, D.M., ^Barrick, J.E. (2026) Refactored genetic parts for modular assembly of the E. coli MccV type I secretion system used to screen class II microcin candidates from plant-associated bacteria. BMC Biotechnol. 26:66. DOI: 10.1186/s12896-026-01148-8 PMID: 41933322
129. Rhyan, N., Koshy, I.S., Dinh, R., VanDieren, A.J., Mishler, D.M., ^Barrick, J.E. (2026) Expression of a phage RecET recombinase system improves detection of shorter DNA fragments by an Acinetobacter baylyi ADP-ISx antibiotic gene biosensor strain. microPubl. Biol. DOI: 10.17912/micropub.biology.002084 PMID: 42099571
2025
128. VanDieren, A.J., ^Barrick, J.E. (2025) Evolution in response to prophage activation attenuates the virulence of culturable Serratia symbiotica relatives of aphid endosymbionts. mBio 16:e0204125. DOI: 10.1128/mbio.02041-25 PMID: 40919815
127. Fernandes, S.E., Ortega, H., Vaillancourt, M., Galdino, A.C.M., Stotland, A., Mun, K.S., Aguilar, D., Doi, Y., Lee, J.S., Burgener, E.B., Barrick, J.E., Schertzer J.W., ^Jorth, P. (2025). Evolutionary loss of an antibiotic efflux pump increases Pseudomonas aeruginosa quorum sensing mediated virulence in vivo. Nat. Commun. 16:8397. DOI: 10.1038/s41467-025-63284-7 PMID: 40998772
126. ^Gifford, I., Vergis, M.R., ^Barrick, J.E. (2025) Genome evolution of Acinetobacter baylyi ADP1 during laboratory domestication: acquired mutations impact competence and metabolism. Appl. Env. Microbiol. 91:e0093625. DOI: 10.1128/aem.00936 PMID: 40827875
125. Navarro-Escalante, L., Ashraf, A H M Z., Leonard, S.P., ^Barrick, J.E. (2025) Protecting honey bees through microbiome engineering. Curr. Opin. Insect Sci. 72:101416. DOI: 10.1016/j.cois.2025.101416 PMID: 40769317
124. VanDieren, A.J., ^Barrick, J.E. (2025) UltraCAST: A Flexible All-In-One Suicide Vector for Modifying Bacterial Genomes Using a CRISPR-Associated Transposon. MicroPubl. Biol. DOI: 10.17912/micropub.biology.001721 PMID: 40827214
123. Zibbu, I., Wilke, C.O., ^Barrick, J.E. (2025). seabreeze: a pipeline for analyzing structural variation between bacterial genome assemblies. J. Open Source Softw. 10:8065. DOI: 10.21105/joss.08065
122. Elias, E., Gifford, I., Didi, L., Fargeon, O., Arad, D., Cohen-Pavon, R., Sorek, G., Levin, L., Melamed, D., Aspit, L., Barrick, J.E., ^Bar-Yaacov, D. 2025. A-to-I mRNA editing recodes hundreds of genes in dozens of species and produces endogenous protein isoforms in bacteria. Nucleic Acids Res. 53:gkaf656. DOI: 10.1093/nar/gkaf656 PMID: 40650968
121. Flatau, R., Krawczyk, A.I., Segoli, M., Barrick, J.E., ^Hawlena, H. (2025) Continuously high Wolbachia incidence in flea populations may result from dual-strain infections with divergent effects. Sci. Rep. 15:21720. DOI: 10.1038/s41598-025-09403-2 PMID: 40593332
120. Chuong, J., Brown, K.W., Gifford, I., Mishler, D.M., ^Barrick, J.E. (2025) Engineered Acinetobacter baylyi ADP1-ISx cells are sensitive DNA biosensors for antibiotic resistance genes and a fungal pathogen of bats. ACS Synth. Biol. 14: 2488-2493. DOI: 10.1021/acssynbio.5c00360 PMID: 40579381 bioRxiv preprint
119. Lozzi, B., Adepoju, L., Espinoza, J.L., Padgen, M., Parra, M., Ricco, A., Castro-Wallace, S., Barrick, J.E., ^O’Rourke A. (2025) Simulated microgravity triggers a membrane adaptation to stress in E. coli REL606. BMC Microbiol. 25:362. DOI: 10.1186/s12866-025-04064-7 PMID: 40484963
118. *Roots, C.T., *Hill, A.M., Wilke, C.O., ^Barrick, J.E. (2025) Modeling and measuring how codon usage modulates the relationship between burden and yield during protein overexpression in bacteria. J. Biol. Eng. 19:50. DOI: 10.1186/s13036-025-00521-z PMID: 40405198
117. Lay, C.G., Burks, G.R., Li, Z., Barrick, J.E., Schroeder, C.M., Karim, A.S., ^Jewett, M.C. (2025) Cell-free expression of soluble leafhopper proteins from brochosomes. ACS Synth. Biol. 21: 987-994. DOI: 10.1021/acssynbio.4c00773 PMID: 40052868
2024
116. Roots, C.T., ^Barrick, J.E. (2024) CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria. Synth. Biol. 9:ysae018. DOI: 10.1093/synbio/ysae018 PMID: 39722801
115. Rodríguez‑Pastor, R. Knossow N., Shahar, N, Hasik, A.Z., Deatherage, D.E., Gutiérrez, R., Harrus, S.,Zaman, L., Lenski, R.E., ^Barrick, J.E., ^Hawlena, H. (2024) Pathogen contingency loci and the evolution of host specificity: Simple sequence repeats mediate Bartonella adaptation to a wild rodent host. PLoS Pathogens 20:e1012591. DOI: 10.1371/journal.ppat.1012591 PMID: 39348417
114. *Gifford, I., *Suárez G.A., ^Barrick, J.E. (2024) Evolution recovers the fitness of Acinetobacter baylyi strains with large deletions through mutations in deletion-specific targets and global post-transcriptional regulators. PLoS Genetics 20:e1011306. DOI: 10.1371/journal.pgen.1011306 PMID: 39283914
113. ^Lariviere, P.J., Ashraf, A H M Z., Navarro-Escalante, L., Leonard, S.P., Miller, L.G., Moran, N.A. ^Barrick, J.E. (2024) One-step genome engineering in bee gut bacterial symbionts. mBio 15:e0139224. DOI: 10.1128/mbio.01392-24 PMID: 39105596
112. *Radde, N., *Mortensen, G.A., Bhat, D., Shah, S., Clements, J.J., Leonard, S.P., McGuffie, M.J., Mishler, D.M., ^Barrick, J.E. (2024) Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology. Nat. Commun. 15: 6242. DOI: 10.1038/s41467-024-50639-9 PMID: 39048554
111. McGuffie, M.J., ^Barrick, J.E. (2024) Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences. PLoS ONE 19:e0304164. DOI: 10.1371/journal.pone.0304164 PMID: 38805426
110. uz-Zaman, Md. H., D'Alton, S., Barrick, J.E., ^Ochman H. (2024) Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli. PLoS Biol. 22:e3002418. DOI: 10.1371/journal.pbio.3002418 PMID: 38713714
109. Diaz Lluberes, I.A., Ahmido, T., Fernando, P.U.A.I., Kosgei, G.K., Bayliff, K.W., Dwenger IV, J.H., Dolocan, A., Barrick, J.E., Smith, C.B. (2024) Exploring the extended spectral signature and remote sensing capabilities of lanthanide enriched arrays of brochosomes. In: W.M. Shensky III, I. Rau, O. Sugihara (eds.). Organic Photonic Materials and Devices XXVI 12883:1288304. DOI: 10.1117/12.3001089
2023
108. Thuronyi, B W., DeBenedictis, E.A., ^Barrick, J.E. (2023) No assembly required: Time for stronger, simpler publishing standards for DNA sequences. PLoS Bio. 21:e3002376. DOI: 10.1371/journal.pbio.3002376 PMID: 37971964
107. Rodríguez-Pastor, R., Hasik, A.Z., Knossow, N., Bar-Shira, E., Shahar, N., Gutiérrez, R., Zaman, L., Harrus, S., Lenski, R.E., Barrick, J.E., ^Hawlena, H. (2023) Bartonella infections are prevalent in rodents despite efficient immune responses. Parasites Vectors 16:315. DOI: 10.1186/s13071-023-05918-7 PMID: 37667323
106. ^Barrick, J.E., ^Blount, Z.D., Lake, D.M., Dwenger IV, J.H., Chavarria-Palma, J.E., Izutsu, M., Wiser, M.J. (2023) Daily transfers, archiving populations, and measuring fitness in the long-term evolution experiment with Escherichia coli. J. Vis. Exp. 198:e65342. DOI: 10.3791/65342 PMID: 37607082
105. *Elston, K.M., *Phillips, L.E., Leonard, S.P., Young, E., Holley, J.C., Ahsanullah, T., McReynolds, B., Moran, N.A., ^Barrick, J.E. (2023) The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae. ISME Commun. 3:9. DOI: 10.1038/s43705-023-00255-3 PMID: 37225918
104. ^Banerjee, P., Burks, G.R., Bialik, S.B., Bello, E., Alleyne, M., Freeman, B.D., Barrick, J.E., Schroeder C.M., Milliron, D.J. (2023) Nanostructure-derived anti-reflectivity in leafhopper brochosomes. Adv. Photonics Res. 202200343. DOI: 10.1002/adpr.202200343 ChemRxiv
103. Elston, K.M., Maeda, G.P., Perreau, J., ^Barrick, J.E. (2023) Addressing the challenges of symbiont-mediated RNAi in aphids. PeerJ 11:e14961. DOI: 10.7717/peerj.14961 PMID: 36874963
102. Burks, G.R., Yao, L., Kalutantirige, F.C., Gray, K.J., Bello, E., Rajagopalan, S., Bialik, S.B., Barrick, J.E., Alleyne, M., Chen, Q., ^Schroeder C.M. (2023) Electron tomography and machine learning for understanding the highly ordered structure of leafhopper brochosomes. Biomacromolecules 24:190-200. DOI: 10.1021/acs.biomac.2c01035 PMID: 36516996
101. *Lariviere, P.J., *Leonard, S.P., Horak, R.D., Powell, J.E., ^Barrick, J.E. (2023) Honey bee functional genomics using symbiont-mediated RNAi. Nat. Protoc. 18:902-928. DOI: 10.1038/s41596-022-00778-4 PMID: 36460809 Preprint
2022
100. Maritan, E., Gallo, M., Srutkova, D., Jelinkova, A., Benada, O., Kofronova, O., Silva-Soares, N.F., Hudcovic, T., Gifford, I., Barrick, J.E., Schwarzer, M, Martino, M. E. (2022) Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals. BMC Biol. 20:290. DOI: 10.1186/s12915-022-01477-y PMID: 36575413
99. Li, Z., Li, Y, Xue A.Z., Dang V., Holmes, V.R., Johnston, J.S., Barrick, J.E., ^Moran, N.A. (2022) The genomic basis of evolutionary novelties in a leafhopper. Mol. Biol. Evol. 39:msac184. DOI: 10.1093/molbev/msac184 PMID: 36026509
98. Rodríguez-Pastor, R., Shafran, Y., Knossow, N., Gutiérrez, R. Harrus, S., Zaman, L., Lenski, R. E., Barrick, J. E., ^Hawlena, H. (2022) A road map for in vivo evolution experiments with blood-borne parasitic microbes. Mol. Ecol. Resour. 22:2843-2859. DOI: 10.1111/1755-0998.13649 PMID: 35599628
97. Gómez-Garzón, C, Barrick, J.E., ^Payne, S.M. (2022) Disentangling the evolutionary history of Feo, the major ferrous iron transport system in bacteria. mBio 13:e03512-21. DOI: 10.1128/mbio.03512-21 PMID: 35012344
96. Elston, K.M., Leonard, S.P., Geng, P., Bialik, S.B., Robinson, E., ^Barrick, J.E. (2022) Engineering insects from the endosymbiont out. Trends Microbiol. 30:79-96. DOI: 10.1016/j.tim.2021.05.004 PMID: 34103228
2021
95. Deatherage, D.E., ^Barrick, J.E. (2021) High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing. Cell Syst. 12:79-96. DOI: 10.1016/j.cels.2021.08.011 PMID: 34536379 bioRxiv
94. Roots, C.T., Lukasiewicz, A., ^Barrick, J.E. (2021) OSTIR: open source translation initiation rate prediction. J. Open Source Softw. 6:3362. DOI: 10.21105/joss.03362
93. Borin, J.M., Avrani, S., Barrick, J.E., Petrie, K.L., ^Meyer, J.R. (2021) Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. Proc. Natl. Acad. Sci. U.S.A. 118:e2104592118. DOI: 10.1073/pnas.2104592118 PMID: 34083444
92. McGuffie, M.C., ^Barrick, J.E. (2021) pLannotate: engineered plasmid annotation. Nucleic Acids Res. 49:W516-W522. DOI: 10.1093/nar/gkab374 PMID: 34019636
91. ^Perreau, J., Patel, D.J., Anderson, H., Maeda, G.P, Elston, K.M., Barrick, J.E., Moran, N.A. (2021) Vertical transmission at the pathogen-symbiont interface: Serratia symbiotica and aphids. mBio 12:e00359-21. DOI: 10.1128/mBio.00359-21 PMID: 33879583
90. Consuegra, J., Gaffé, J., Lenski, R. E., Hindré, T., Barrick, J. E., Tenaillon, O., Schneider, D. (2021) Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria. Nat. Commun. 12:980. DOI: 10.1038/s41467-021-21210-7 PMID: 33579917
89. *Bazurto, J.V., *Riazi, S., D’Alton, S., Deatherage, D.E., Bruger, E.L., Barrick, J.E., ^Marx, C.J. (2021) Global transcriptional response of Methylorubrum extorquens to formaldehyde stress expands the role of EfgA and is distinct from antibiotic translational inhibition. Microorganisms 9:347. DOI: 10.3390/microorganisms9020347 PMID: 33578755
88. ^Card, K.J., Thomas, M.D., Graves, J.L., Barrick, J.E., Lenski, R.E. (2021) Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 118: e2016886118. DOI: 10.1073/pnas.2016886118 PMID: 33441451
87. *Gifford, I., *Dasgupta, A., ^Barrick, J.E. (2021) Rates of gene conversions between Escherichia coli ribosomal operons. G3 11:jkaa002. DOI: 10.1093/g3journal/jkaa002 PMID: 33585862
86. Elston, K.M., Perreau, J., Maeda, G.P., Moran, N.A., ^Barrick, J.E. (2021) Engineering a culturable Serratia symbiotica strain for aphid paratransgenesis. Appl. Env. Microbiol. 87:e02245-20. DOI: 10.1128/AEM.02245-20 PMID: 33277267
2020
85. *Sher, A.A., *Jerome, J.P., Bell, J.A., Yu, J., Kim, H.Y., Barrick, J.E., ^Mansfield, L.S. (2020) Experimental evolution of Campylobacter jejuni leads to loss of motility, rpoN (σ54) deletion and genome reduction. Front. Microbiol. 11:579989 DOI: 10.3389/fmicb.2020.579989 PMID: 33240235
84. ^Barrick, J.E. (2020) Limits to predicting evolution: Insights from a long-term experiment with Escherichia coli. In: W. Banzhaf, B.H.C. Cheng, K. Deb, K.E. Holekamp, R.E. Lenski, C. Ofria, R.T. Pennock, W.F. Punch, D.J. Whittaker (eds.). Evolution in Action: Past, Present and Future: A Festschrift in Honor of Erik D. Goodman. pp 63-76. Springer Series on Genetic and Evolutionary Computation. Cham, Switzerland: Springer. Full Text DOI: 10.1007/978-3-030-39831-6_7
83. ^Barrick, J.E., Deatherage D.E., ^Lenski, R.E. (2020) A test of the repeatability of measurements of relative fitness in the long-term evolution experiment with Escherichia coli. In: W. Banzhaf, B.H.C. Cheng, K. Deb, K.E. Holekamp, R.E. Lenski, C. Ofria, R.T. Pennock, W.F. Punch, D.J. Whittaker (eds.). Evolution in Action: Past, Present and Future: A Festschrift in Honor of Erik D. Goodman. pp 77-89. Springer Series on Genetic and Evolutionary Computation. Cham, Switzerland: Springer. Full Text DOI: 10.1007/978-3-030-39831-6_8
82. ^*Blount, Z.D., ^*Maddamsetti, R., *Grant, N.A., Ahmed, S.T., Jagdish, T., Sommerfeld, B.A., Tillman, A., Moore, J., Slonczewski, J.L., Barrick, J.E., Lenski, R.E. (2020) Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment. eLife 9:e55414. Full Text PMID: 32469311
81. Suárez, G.A., Dugan, K.R., Renda, B.A., Leonard, S.P., Gangavarapu, L.S., ^Barrick, J.E. (2020) Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining. Nucleic Acids Res. 48:4585–4600. Full Text PMID: 32232367
80. Leonard, S.P., Powell, J.E., Perutka, J., Geng, P., Heckmann, L.C., Horak, R.D., Davies, B.W., Ellington, A.D., ^Barrick, J.E., and ^Moran, N.A. (2020) Engineered symbionts activate honey bee immunity and limit pathogens. Science 367:573–576. DOI: 10.1126/science.aax9039 PMID: 32001655
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    2019
    79. Zhang, X., Deatherage, D.E., Zheng, H., Georgoulis, S.J., ^Barrick, J.E. (2019) Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria. Nat. Comm. 10:5809. DOI: 10.1038/s41467-019-13709-x Full Text, PMID: 31863068
  • Nature Ecology & Evolution Behind the Paper Post: Satellite plasmids: evolutionary stability experiments come full orbit

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