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  1. Card, K. J., T. LaBar, J. B. Gomez, and R. E. Lenski. 2019. Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection. PLOS Biology, in press. (Open access) [doi:10.5061/dryad.g41hg96]

  2. Lamrabet, O., J. Plumbridge, M. Martin, R. E. Lenski, D. Schneider, and T. Hindré. 2019. Plasticity of promoter-core sequences allows bacteria to compensate for the loss of a key global regulatory gene. Molecular Biology and Evolution 36: 1121-1133. (Paper) [10.5061/dryad.d02sc44]

  3. Blount, Z. D., R. E. Lenski, and J. B. Losos. 2018. Contingency and determinism in evolution: replaying life’s tape. Science 362: 655 (review summary) and Science 362: eaam5979 (full review article). (Review Summary)

  4. Peng, F., S. Widmann, A. Wünsche, K. Duan, K. A. Donovan, R. C. J. Dobson, R. E. Lenski, and T. F. Cooper. 2018. Effects of beneficial mutations in pykF gene vary over time and across replicate populations in a long-term experiment with bacteria. Molecular Biology and Evolution 35: 202-210. (Abstract)

  5. Good, B. H., M. J. McDonald, J. E. Barrick, R. E. Lenski, and M. M. Desai. 2017. The dynamics of molecular evolution over 60,000 generations. Nature 551: 45-50. (Abstract)

  6. Meyer, J. R., D. T. Dobias, S. J. Medina, L. Servilio, A. Gupta, and R. E. Lenski. 2016. Ecological speciation of bacteriophage Lambda in allopatry and sympatry. Science 354:1301-1304. (Abstract)[10.5061/dryad.4qb79]

  7. Burmeister, A. R., R. E. Lenski, and J. R. Meyer. 2016. Host coevolution alters the adaptive landscape of a virus. Proceedings of the Royal Society, London B 283: 20161528. (Article)[10.5061/dryad.2tj43]

  8. Lenski, R. E., M. J. Wiser, N. Ribeck, Z. D. Blount, J. R. Nahum, J. J. Morris, L. Zaman, C. B. Turner, B. D. Wade, R. Maddamsetti, A. R. Burmeister, E. J. Baird, J. Bundy, N. A. Grant, K. J. Card, M. Rowles, K. Weatherspoon, S. E. Papoulis, R. Sullivan, C. Clark, J. S. Mulka, and N. Hajela. 2015. Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli. Proceedings of the Royal Society, London B 282:20152292. (Article)[doi:10.5061/dryad.gd3dq]

  9. Maddamsetti, R., R. E. Lenski, and J. E. Barrick. 2015. Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli. Genetics 200:619-631. (Abstract)[10.5061/dryad.3m00k]

  10. Ostrowski, E. A., C. Ofria, and R. E. Lenski. 2015. Genetically integrated traits and rugged adaptive landscapes in digital organisms. BMC Evolutionary Biology 15:83. (Article)[10.5061/dryad.hh650]

  11. Plucain, J., T. Hindré, M. Le Gac, O. Tenaillon, S. Cruveiller, C. Médigue, N. Leiby, W. R. Harcombe, C. J. Marx, R. E. Lenski, D. Schneider. 2014. Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli. Science 343:1366-1369. (Full Text PDF)[doi:10.5061/dryad.12c6b]

  12. Wiser, M. J., N. Ribeck, and R. E. Lenski. 2013. Long-term dynamics of adaptation in asexual populations. Science 342:1364-1367. (Full Text PDF)[doi:10.5061/dryad.0hc2m]

  13. Covert, A. W. III, R. E. Lenski, C. O. Wilke, and C. Ofria. 2013. Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proceedings of the National Academy of Sciences, USA 110: E3171-E3178. (Abstract)[doi:10.5061/dryad.4hp5n]

  14. Blount, Z. D., J. E. Barrick, C. J. Davidson, and R. E. Lenski. 2012. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489:513-518. (Abstract)[doi:10.5061/dryad.8q6n4]

  15. Zaman, L., C. Ofria, and R. E. Lenski. 2012. Finger-painting fitness landscapes: an interactive tool for exploring complex evolutionary dynamics. Pp. 499-505 in Thirteenth International Conference on the Simulation and Synthesis of Living Systems. (Abstract)

  16. Meyer, J. R., D. T. Dobias, J. S. Weitz, J. E. Barrick, R. T. Quick, and R. E. Lenski. 2012. Repeatability and contingency in the evolution of a key innovation in phage Lambda. Science 335:428-432. (Abstract)[doi:10.5061/dryad.sh7rm2pt]

  17. Khan, A. I., D. M. Dinh, D. Schneider, R. E. Lenski, and T. F. Cooper. 2011. Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332:1193-1196. (Abstract)[doi:10.5061/dryad.5rv40]

  18. Woods, R. J., J. E. Barrick, T. F. Cooper, U. Shrestha, M. R. Kauth, and R. E. Lenski. 2011. Second-order selection for evolvability in a large Escherichia coli population. Science 331:1433-1436. (Abstract)

  19. Crozat, E., T. Hindré, L. Kühn, J. Garin, R. E. Lenski, and D. Schneider. 2011. Altered regulation of the OmpF porin by Fis in Escherichia coli during an evolution experiment and between B and K12 strains. Journal of Bacteriology 193:429-440. (Abstract)

  20. Strelioff, C. C., R. E. Lenski, and C. Ofria. 2010. Evolutionary dynamics, epistatic interactions, and biological information. Journal of Theoretical Biology 266:584-594. (Abstract)

  21. Barrick, J. E., M. R. Kauth, C. C. Strelioff, and R. E. Lenski. 2010. Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Molecular Biology and Evolution 27:1338-1347. (Abstract)

  22. Blount, Z. D., C. Z. Borland, and R. E. Lenski. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences, USA 105:7899-7906. (Abstract)(Acrobat file)

  23. Cooper, T. F., S. K. Remold, R. E. Lenski, and D. Schneider. 2008. Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli. PLoS Genetics 4:e35 [10 pp]. (Article)

  24. Beerenwinkel, N., L. Pachter, B. Sturmfels, S. F. Elena, and R. E. Lenski. 2007. Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evolutionary Biology 7:60 [12 pp]. (Article)

  25. Elena, S. F., C. O. Wilke, C. Ofria, and R. E. Lenski. 2007. Effects of population size and mutation rate on the evolution of mutational robustness. Evolution 61:666-674. (Abstract)

  26. Misevic, D., C. Ofria, R. E. Lenski. 2006. Sexual reproduction reshapes the genetic architecture of digital organisms. Proceedings of the Royal Society, London B 273:457-464. (Link to PDF)

  27. Cooper, T. F., R. E. Lenski, and S. F. Elena. 2005. Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex. Proceedings of the Royal Society, London B 272:311-317. (Article)

  28. Misevic, D., R. E. Lenski, and C. Ofria. 2004. Sexual reproduction and Muller's ratchet in digital organisms. Pp. 340-345 in J. Pollack, M. Bedau, P. Husbands, T. Ikegami, and R. A. Watson, eds. Artificial Life IX: Proceedings of the Ninth International Conference on the Simulation and Synthesis of Living Systems. MIT Press, Cambridge, Massachusetts. (Acrobat file)

  29. Remold, S. K., and R. E. Lenski. 2004. Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coli. Nature Genetics 36:423-426. (Nature Genetics)(Acrobat file)

  30. Wilke, C. O., R. E. Lenski, and C. Adami. 2003. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. BMC Evolutionary Biology 3:3. (Link)

  31. Cooper, T. F., D. E. Rozen, and R. E. Lenski. 2003. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proceedings of the National Academy of Sciences, USA 100:1072-1077. (Abstract)(Acrobat file)

  32. Lenski, R. E. 2001. Come fly, and leave the baggage behind (Perspective). Science 294:533-534. (Reprint)(Acrobat file)

  33. Elena, S. F., and R. E. Lenski. 2001. Epistasis between new mutations and genetic background and a test of genetic canalization. Evolution 55:1746-1752. (Abstract)(Acrobat file)

  34. Remold, S. K., and R. E. Lenski. 2001. Contribution of individual random mutations to genotype-by-environment interactions in Escherichia coli. Proceedings of the National Academy of Sciences, USA 98:11388-11393. (Abstract)(Acrobat file)

  35. Wilke, C. O, J. Wang, C. Ofria, R. E. Lenski, and C. Adami. 2001. Evolution of digital organisms at high mutation rate leads to survival of the flattest. Nature 412:331-333. (Abstract)(Acrobat file)

  36. Moore, F. B-G., D. E. Rozen, and R. E. Lenski. 2000. Pervasive compensatory adaptation in Escherichia coli. Proceedings of the Royal Society, London B, 267:515-522. (Abstract)(Acrobat file)

  37. Lenski, R. E., C. Ofria, T. C. Collier, and C. Adami. 1999. Genome complexity, robustness, and genetic interactions in digital organisms. Nature 400:661-664. (Link)(Acrobat file)

  38. Bohannan, B. J. M., M. Travisano, and R. E. Lenski. 1999. Epistatic interactions can lower the cost of resistance to multiple consumers. Evolution 53:292-295. (Abstract)(Acrobat file)

  39. Elena, S. F., L. Ekunwe, N. Hajela, S. A. Oden, and R. E. Lenski. 1998. Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103:349-358. (Abstract)(Acrobat file)

  40. Elena, S. F., and R. E. Lenski. 1997. Test of synergistic interactions among deleterious mutations in bacteria. Nature 390:395-398. (Abstract)(Acrobat file) [doi:10.5061/dryad.rg8mb]

  41. Lenski, R. E., V. Souza, L. P. Duong, Q. G. Phan, T. N. M. Nguyen, and K. P. Bertrand. 1994. Epistatic effects of promoter and repressor functions of the Tn10 tetracycline-resistance operon on the fitness of Escherichia coli. Molecular Ecology 3:127-135. (Acrobat file)

  42. Lenski, R. E. 1988. Experimental studies of pleiotropy and epistasis in Escherichia coli. II. Compensation for maladaptive pleiotropic effects associated with resistance to virus T4. Evolution 42:433-440. (Acrobat file)

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