Lab Publications

• Stuecker TN, Hood SE, Molina Pineda J, Lenaduwe S, Winter J, Sadhu MJ, Lewis JA. 2025. Improved vectors for retron-mediated CRISPR-Cas9 genome editing in Saccharomyces cerevisiae. G3: Genes|Genomes|Genetics. 15(10):jkaf175
• Sauer EL, Stacy C, Perrine W, Love AC, Lewis JA, DuRant SE. 2025. Diet driven differences in host tolerance are linked to shifts in global gene expression in a common avian host-pathogen system. Molecular Ecology. 12(34):e17793
• Stacy CL, Lenaduwe S, Stuecker TN, Lewis JA.. 2025. MIC*: A framework for interpretable analysis of ordinal viability data. bioRxiv (preprint):10.1101/2025.10.13.682067
• Hardman-Kavanaugh RE, Storey AJ, Stuecker TN, Hood SE, Barrett-Wilt GA, Krishnamurthi VR, Wang Y, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA. 2025. Dynamic global acetylation remodeling during the yeast heat shock response. bioRxiv (preprint):10.1101/2025.01.10.632339
• Molina Pineda J, Scholes AN, and JA Lewis. 2024. A Hypothesis-Based Hop Microbiology Laboratory Module Testing the Plausibility of the Mythical Origin of the India Pale Ale (IPA). Journal of Microbiology and Biology Education. 25(1):e0002024
• Scholes AN, Stuecker TN, Hood SE, Locke CJ, Stacy CL, Zhang Q, and JA Lewis. 2024. Natural variation in yeast reveals multiple paths for acquiring higher stress resistance. BMC Biology. 22(1):149
• Judy KJ, Pinseel E, Downey KM, Lewis JA, Alverson AJ. 2024. The divergent responses of salinity generalists to hyposaline stress provide insights into the colonization of freshwaters by diatoms. Molecular Ecology. 33(22):e17556
• Downey KM, Judy KJ, Pinseel E, Alverson AJ, Lewis JA. 2023. The dynamic response to hypoosmotic stress reveals distinct stages of freshwater acclimation by a euryhaline diatom. Molecular Ecology. 32(11):2766-2783
• Scholes AN, Pollock ED, Lewis JA. 2021. A Wild Yeast Laboratory Activity: From Isolation to Brewing. Journal of Microbiology and Biology Education. 22(2):e00186-21
• Onyshchenko A, Roberts WR, Ruck EC, Lewis JA, Alverson AJ. 2021. The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis. New Phytologist. 232(4):1750-1764
• Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA. 2020. Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome using Tandem Mass Tags. Journal of Proteome Research. 19(3):1183-1995
• Scholes AN and Lewis JA. 2020. Comparison of RNA Isolation Methods on RNA-Seq: Implications for Differential Expression and Meta-Analyses. BMC Genomics. 21(1):249
• McDaniel EM, Stuecker TN, Veluvolu M, Gasch AP, Lewis JA. 2018. Independent mechanisms for acquired salt tolerance versus growth resumption induced by mild ethanol pretreatment in Saccharomyces cerevisiae. mSphere. 3(6):e00574-18
• Stuecker TN, Scholes AN, Lewis JA. 2018. Linkage mapping of yeast cross protection connects gene expression variation to a higher-order organismal trait. PLoS Genetics. 14(4):e100733
• Johnson WH, Douglas MR, Lewis JA, Stuecker TN, Carbonero FG, Austin BJ, Evans-White MA, Entrekin SA, Douglas ME. 2017. Do biofilm communities respond to the chemical signatures of fracking? A test involving streams in North-central Arkansas. BMC Microbiology. 17(1):29
• Nguyen K, Murray S, Lewis JA, Kumar P. 2017. Morphology, cell division, and viability of Saccharomyces cerevisiae at high hydrostatic pressure. arXiv. :
• Lewis JA, Broman AT, Will J, Gasch AP. 2014. Genetic architecture of ethanol-responsive transcriptome variation in Saccharomyces cerevisiae strains. Genetics. 198(1):369-382 PMC4174948
• Wohlbach DJ, Rovinskiy N,Lewis JA, Sardi M, Schackwitz WS, Martin JA, Deshpande S, Daum CG, Lipzen A, Sato TK, Gasch AP. 2014. Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production. Genome Biology and Evolution. 6(9):2557-2566 PMC4202335
• Gonçalves A, Ong I,Lewis JA, Costa VS. 2014. Towards using probabilities and logic to model regulatory networks. 2014 IEEE 27th International Symposium on Computer-Based Medical Systems. :239-242
• Gonçalves A, Ong I, Lewis JA, Costa VS. 2014. Discovering differentially expressed genes in yeast stress data. 2014 IEEE 27th International Symposium on Computer-Based Medical Systems. :537-538
• Lewis JA, Gasch AP. 2012. Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor. G3: Genes|Genomes|Genetics. 2(12):1607-1612 PMC3516482
• Gonçalves A, Ong I, Lewis JA, Costa VS. 2012. A ProbLog model for analyzing gene regulatory networks. 22nd International Conference on Inductive Logic Programming. :38-43
• Lewis JA, Elkon IM, McGee MA, Higbee AJ, Gasch AP. 2010. Exploiting natural variation in Saccharomyces cerevisiae to identify genes for increased ethanol resistance. Genetics. 186(4):1197-1205 PMC2998304
• Lewis JA, Stamper LW, Escalante-Semerena JC. 2009. Regulation of expression of the tricarballylate utilization operon (tcuABC) of Salmonella enterica. Research in Microbiology. 160(3):179-186 PMC2692759
• Lewis JA, Boyd JM, Downs DM, Escalante-Semerena JC. 2009. Involvement of the Cra global regulatory protein in the expression of the iscRSUA operon, revealed during studies of tricarballylate catabolism in Salmonella enterica. Journal of Bacteriology. 191(7):2069-2076 PMC2655522
• Boyd JM, Lewis JA, Escalante-Semerena JC, Downs DM. 2008. Salmonella enterica requires ApbC function for growth on tricarballylate: Evidence of functional redundancy between ApbC and IscU Journal of Bacteriology. 190(13):4596-4602 PMC2446783
• Lewis JA, Escalante-Semerena JC. 2007. Tricarballylate catabolism in Salmonella enterica. The TcuB protein uses 4Fe-4S clusters and heme to transfer electrons from FADH2 in the tricarballylate dehydrogenase (TcuA) enzyme to electron acceptors in the cell membrane. Biochemistry. 46(31):9107-9115
• Lewis JA, Escalante-Semerena JC. 2006. The FAD-dependent tricarballylate dehydrogenase (TcuA) enzyme of Salmonella enterica converts tricarballylate into cis-aconitate. Journal of Bacteriology. 188(15):5479-5486 PMC1540016
• Lewis JA, Horswill AR, Schwem BE, Escalante-Semerena JC. 2004. The Tricarballylate utilization (tcuRABC) genes of Salmonella enterica serovar Typhimurium LT2. Journal of Bacteriology. 186(6):1629-1637 PMC355976