My Bibliography

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Schrope JH, Robertson TF, Horn A, Stevens JJ, Tinnen CW, Rindy J, Hou Y, Rochon E, Beebe DJ, Huttenlocher A. Leukocyte-epithelial physical contacts mediate interstitial migration in vivo. Res Sq. 2026 Feb 5;. doi: 10.21203/rs.3.rs-8594440/v1. PubMed PMID: 41674828; PubMed Central PMCID: PMC12889812.

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Harmer ZP, McClean MN. The Yeast Optogenetic Toolkit (yOTK) for Spatiotemporal Control of Gene Expression in Budding Yeast. Methods Mol Biol. 2025;2840:19-36. doi: 10.1007/978-1-0716-4047-0_2. PubMed PMID: 39724341; PubMed Central PMCID: PMC12288673.

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Humayun M, Jiménez-Torres JA, Li C, Ayuso J, Cintron KL, Ulbrich J, Myers B, Kerr SC, Ahmed A, Beebe DJ. Multiplexed luminal tissue constructs with reconfigurable barriers for dynamic modeling of multi-tissue interactions. Adv Mater Technol. 2025 Dec 1;. doi: 10.1002/admt.202500429. [Epub ahead of print] PubMed PMID: 41693925; PubMed Central PMCID: PMC12900169.

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Cytrynbaum EG, McClean MN. Microbial heterogeneity-mediated treatment evasion and the potential for engineered live biotherapeutic products. Adv Drug Deliv Rev. 2026 Feb;229:115740. doi: 10.1016/j.addr.2025.115740. Epub 2025 Nov 28. Review. PubMed PMID: 41318070; PubMed Central PMCID: PMC12815241.

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Sweeney K, Luffey EL, McClean MN. Protocol to probe how promoters decode TF dynamics in Saccharomyces cerevisiae by combining optogenetic control with microscopy. STAR Protoc. 2024 Sep 20;5(3):103002. doi: 10.1016/j.xpro.2024.103002. Epub 2024 Jul 13. PubMed PMID: 39003745; PubMed Central PMCID: PMC11284393.

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Shand EL, Sweeney K, Sundling KE, McClean MN, Brow DA. Live-cell analysis of IMPDH protein levels during yeast colony growth provides insights into the regulation of GTP synthesis. mBio. 2024 Aug 14;15(8):e0102124. doi: 10.1128/mbio.01021-24. Epub 2024 Jun 28. PubMed PMID: 38940616; PubMed Central PMCID: PMC11323793.

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Stindt KR, McClean MN. Tuning interdomain conjugation to enable in situ population modification in yeasts. mSystems. 2024 Jun 18;9(6):e0005024. doi: 10.1128/msystems.00050-24. Epub 2024 May 15. PubMed PMID: 38747597; PubMed Central PMCID: PMC11326116.

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Harmer ZP, Thompson JC, Cole DL, Venturelli OS, Zavala VM, McClean MN. Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro. ACS Synth Biol. 2024 May 17;13(5):1424-1433. doi: 10.1021/acssynbio.3c00761. Epub 2024 Apr 29. PubMed PMID: 38684225; PubMed Central PMCID: PMC11106771.

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Magesh S, Hurley AI, Nepper JF, Chevrette MG, Schrope JH, Li C, Beebe DJ, Handelsman J. Surface colonization by Flavobacterium johnsoniae promotes its survival in a model microbial community. mBio. 2024 Mar 13;15(3):e0342823. doi: 10.1128/mbio.03428-23. Epub 2024 Feb 8. PubMed PMID: 38329367; PubMed Central PMCID: PMC10936215.

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Harmer ZP, Höhener TC, Landolt AE, Mitchell C, McClean M. Enhancing high-throughput optogenetics: Integration of LITOS with Lustro enables simultaneous light stimulation and shaking. MicroPubl Biol. 2024;2024. doi: 10.17912/micropub.biology.001073. eCollection 2024. PubMed PMID: 38371319; PubMed Central PMCID: PMC10873752.

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Harmer ZP, McClean MN. Correction to "Lustro: High-Throughput Optogenetic Experiments Enabled by Automation and a Yeast Optogenetic Toolkit". ACS Synth Biol. 2023 Nov 17;12(11):3505. doi: 10.1021/acssynbio.3c00623. Epub 2023 Oct 31. PubMed PMID: 37906946; PubMed Central PMCID: PMC10662350.

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Harmer ZP, McClean MN. High-Throughput Optogenetics Experiments in Yeast Using the Automated Platform Lustro. J Vis Exp. 2023 Aug 4;(198). doi: 10.3791/65686. PubMed PMID: 37590537; PubMed Central PMCID: PMC11085938.

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Harmer ZP, McClean MN. Lustro: High-Throughput Optogenetic Experiments Enabled by Automation and a Yeast Optogenetic Toolkit. ACS Synth Biol. 2023 Jul 21;12(7):1943-1951. doi: 10.1021/acssynbio.3c00215. Epub 2023 Jul 11. PubMed PMID: 37434272; PubMed Central PMCID: PMC10368012.

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Sweeney K, McClean MN. Transcription factor localization dynamics and DNA binding drive distinct promoter interpretations. Cell Rep. 2023 May 30;42(5):112426. doi: 10.1016/j.celrep.2023.112426. Epub 2023 Apr 21. PubMed PMID: 37087734; PubMed Central PMCID: PMC10292158.

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Li C, McCrone S, Warrick JW, Andes DR, Hite Z, Volk CF, Rose WE, Beebe DJ. Under-oil open microfluidic systems for rapid phenotypic antimicrobial susceptibility testing. Lab Chip. 2023 Apr 12;23(8):2005-2015. doi: 10.1039/d3lc00066d. PubMed PMID: 36883560; PubMed Central PMCID: PMC10581760.

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Harmer ZP, McClean MN. Lustro: High-throughput optogenetic experiments enabled by automation and a yeast optogenetic toolkit. bioRxiv. 2023 Apr 10;. doi: 10.1101/2023.04.07.536078. PubMed PMID: 37066312; PubMed Central PMCID: PMC10104134.

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Scott TD, Xu P, McClean MN. Strain-dependent differences in coordination of yeast signalling networks. FEBS J. 2023 Apr;290(8):2097-2114. doi: 10.1111/febs.16689. Epub 2022 Dec 4. PubMed PMID: 36416575; PubMed Central PMCID: PMC10121740.

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Bergen AC, Kocik RA, Hose J, McClean MN, Gasch AP. Modeling single-cell phenotypes links yeast stress acclimation to transcriptional repression and pre-stress cellular states. Elife. 2022 Nov 9;11. doi: 10.7554/eLife.82017. PubMed PMID: 36350693; PubMed Central PMCID: PMC9678356.

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Krause HB, Karls AL, McClean MN, Kreeger PK. Cellular context alters EGF-induced ERK dynamics and reveals potential crosstalk with GDF-15. Biomicrofluidics. 2022 Sep;16(5):054104. doi: 10.1063/5.0114334. eCollection 2022 Sep. PubMed PMID: 36217350; PubMed Central PMCID: PMC9547670.

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Harmer ZP, McClean MN. Evaluation of Benzinger et al.: Optogenetic circuits for dynamic signal processing. Cell Syst. 2022 May 18;13(5):347-348. doi: 10.1016/j.cels.2022.04.003. PubMed PMID: 35588696.

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Stindt KR, McClean MN. Give and take in the exometabolome. Nat Microbiol. 2022 Apr;7(4):484-485. doi: 10.1038/s41564-022-01081-4. PubMed PMID: 35314782.

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Li C, Humayun M, Walker GM, Park KY, Connors B, Feng J, Pellitteri Hahn MC, Scarlett CO, Li J, Feng Y, Clark RL, Hefti H, Schrope J, Venturelli OS, Beebe DJ. Under-Oil Autonomously Regulated Oxygen Microenvironments: A Goldilocks Principle-Based Approach for Microscale Cell Culture. Adv Sci (Weinh). 2022 Apr;9(10):e2104510. doi: 10.1002/advs.202104510. Epub 2022 Feb 4. PubMed PMID: 35118834; PubMed Central PMCID: PMC8981459.

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Bergen AC, Hose J, McClean MN, Gasch AP. Integrating multiple single-cell phenotypes links stress acclimation to prior life history in yeast. https://www.biorxiv.org/ 2021.09.08.459442 [Preprint]. 2021. Available from: https://doi.org/10.1101/2021.09.08.459442. doi: 10.1101/2021.09.08.459442.

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Krause HB, Bondarowicz H, Karls AL, McClean MN, Kreeger PK. Design and implementation of a microfluidic device capable of temporal growth factor delivery reveal filtering capabilities of the EGFR/ERK pathway. APL Bioeng. 2021 Dec;5(4):046101. doi: 10.1063/5.0059011. eCollection 2021 Dec. PubMed PMID: 34765858; PubMed Central PMCID: PMC8566012.

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Moreno Morales N, Patel MT, Stewart CJ, Sweeney K, McClean MN. Optogenetic Tools for Control of Public Goods in Saccharomyces cerevisiae. mSphere. 2021 Aug 25;6(4):e0058121. doi: 10.1128/mSphere.00581-21. Epub 2021 Aug 25. PubMed PMID: 34431694; PubMed Central PMCID: PMC8386412.

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Krishnaswamy B, McClean MN. Shining light on molecular communication. ACM Int Conf Nanoscale Comput Commun (2020). 2020 Sep;2020. doi: 10.1145/3411295.3411307. Epub 2020 Oct 7. PubMed PMID: 35425948; PubMed Central PMCID: PMC9006593.

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Grødem EO, Sweeney K, McClean MN. Automated calibration of optoPlate LEDs to reduce light dose variation in optogenetic experiments. Biotechniques. 2020 Oct;69(4):313-316. doi: 10.2144/btn-2020-0077. Epub 2020 Jul 29. PubMed PMID: 32722938; PubMed Central PMCID: PMC7566773.

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Lauterjung KR, Morales NM, McClean MN. Secrete to beat the heat. Nat Microbiol. 2020 Jul;5(7):883-884. doi: 10.1038/s41564-020-0748-3. PubMed PMID: 32587374.

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Letourneau A, Kegel J, Al-Ramahi J, Yachinich E, Krause HB, Stewart CJ, McClean MN. A Microfluidic Device for Imaging Samples from Microbial Suspension Cultures. MethodsX. 2020;7:100891. doi: 10.1016/j.mex.2020.100891. eCollection 2020. PubMed PMID: 32420047; PubMed Central PMCID: PMC7214938.

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Li C, Hite Z, Warrick JW, Li J, Geller SH, Trantow VG, McClean MN, Beebe DJ. Under oil open-channel microfluidics empowered by exclusive liquid repellency. Sci Adv. 2020 Apr;6(16):eaay9919. doi: 10.1126/sciadv.aay9919. eCollection 2020 Apr. PubMed PMID: 32494607; PubMed Central PMCID: PMC7164933.

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An-Adirekkun JM, Stewart CJ, Geller SH, Patel MT, Melendez J, Oakes BL, Noyes MB, McClean MN. A yeast optogenetic toolkit (yOTK) for gene expression control in Saccharomyces cerevisiae. Biotechnol Bioeng. 2020 Mar;117(3):886-893. doi: 10.1002/bit.27234. Epub 2019 Dec 18. PubMed PMID: 31788779; PubMed Central PMCID: PMC7015765.

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Geller SH, Antwi EB, Di Ventura B, McClean MN. Optogenetic Repressors of Gene Expression in Yeasts Using Light-Controlled Nuclear Localization. Cell Mol Bioeng. 2019 Oct;12(5):511-528. doi: 10.1007/s12195-019-00598-9. eCollection 2019 Oct. PubMed PMID: 31719930; PubMed Central PMCID: PMC6816687.

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Sweeney K, Moreno Morales N, Burmeister Z, Nimunkar AJ, McClean MN. Easy calibration of the Light Plate Apparatus for optogenetic experiments. MethodsX. 2019;6:1480-1488. doi: 10.1016/j.mex.2019.06.008. eCollection 2019. PubMed PMID: 31293905; PubMed Central PMCID: PMC6594922.

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Scott TD, Sweeney K, McClean MN. Biological signal generators: integrating synthetic biology tools and in silico control. Curr Opin Syst Biol. 2019 Apr;14:58-65. doi: 10.1016/j.coisb.2019.02.007. Epub 2019 Feb 27. PubMed PMID: 31673669; PubMed Central PMCID: PMC6822565.

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Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol. 2017 Dec;15(12):e2004050. doi: 10.1371/journal.pbio.2004050. eCollection 2017 Dec. PubMed PMID: 29240790; PubMed Central PMCID: PMC5746276.

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Morales NM, McClean MN. Engineered bacteria self-organize to sense pressure. Nat Biotechnol. 2017 Nov;35(11):1045-1047. doi: 10.1038/nbt.3992. Epub 2017 Oct 9. PubMed PMID: 28991269.

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Stewart CJ, McClean MN. Design and Implementation of an Automated Illuminating, Culturing, and Sampling System for Microbial Optogenetic Applications. J Vis Exp. 2017 Feb 19;(120). doi: 10.3791/54894. PubMed PMID: 28287505; PubMed Central PMCID: PMC5407694.

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McClean, Megan Nicole. GSE59864: Saccharomyces cerevisiae ARO80 overexpression. 2015.

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McClean, Megan Nicole. GSM1448308: Control Strain T=0 minutes. 2015.

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McClean, Megan Nicole. GSM1448309: Control Strain T=30 minutes. 2015.

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McClean, Megan Nicole. GSM1448310: Control Strain T=90 minutes. 2015.

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McClean, Megan Nicole. GSM1448311: Control Strain T=180 minutes. 2015.

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McClean, Megan Nicole. GSM1448312: ARO80 GEV Overexpression Strain T=0 minutes. 2015.

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McClean, Megan Nicole. GSM1448313: ARO80 GEV Overexpression Strain T=30 minutes. 2015.

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McClean, Megan Nicole. GSM1448314: ARO80 GEV Overexpression Strain T=90 minutes. 2015.

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McClean, Megan Nicole. GSM1448315: ARO80 GEV Overexpression Strain T=180 minutes. 2015.

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Dexter JP, Xu P, Gunawardena J, McClean MN. Robust network structure of the Sln1-Ypd1-Ssk1 three-component phospho-relay prevents unintended activation of the HOG MAPK pathway in Saccharomyces cerevisiae. BMC Syst Biol. 2015 Mar 25;9:17. doi: 10.1186/s12918-015-0158-y. PubMed PMID: 25888817; PubMed Central PMCID: PMC4377207.

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Bisaria A, Hersen P, McClean MN. Microfluidic platforms for generating dynamic environmental perturbations to study the responses of single yeast cells. Methods Mol Biol. 2014;1205:111-29. doi: 10.1007/978-1-4939-1363-3_8. PubMed PMID: 25213242.

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Melendez J, Patel M, Oakes BL, Xu P, Morton P, McClean MN. Real-time optogenetic control of intracellular protein concentration in microbial cell cultures. Integr Biol (Camb). 2014 Mar;6(3):366-72. doi: 10.1039/c3ib40102b. Epub 2014 Jan 30. PubMed PMID: 24477515.

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Caudy AA, Guan Y, Jia Y, Hansen C, DeSevo C, Hayes AP, Agee J, Alvarez-Dominguez JR, Arellano H, Barrett D, Bauerle C, Bisaria N, Bradley PH, Breunig JS, Bush E, Cappel D, Capra E, Chen W, Clore J, Combs PA, Doucette C, Demuren O, Fellowes P, Freeman S, Frenkel E, Gadala-Maria D, Gawande R, Glass D, Grossberg S, Gupta A, Hammonds-Odie L, Hoisos A, Hsi J, Hsu YH, Inukai S, Karczewski KJ, Ke X, Kojima M, Leachman S, Lieber D, Liebowitz A, Liu J, Liu Y, Martin T, Mena J, Mendoza R, Myhrvold C, Millian C, Pfau S, Raj S, Rich M, Rokicki J, Rounds W, Salazar M, Salesi M, Sharma R, Silverman S, Singer C, Sinha S, Staller M, Stern P, Tang H, Weeks S, Weidmann M, Wolf A, Young C, Yuan J, Crutchfield C, McClean M, Murphy CT, Llinás M, Botstein D, Troyanskaya OG, Dunham MJ. A new system for comparative functional genomics of Saccharomyces yeasts. Genetics. 2013 Sep;195(1):275-87. doi: 10.1534/genetics.113.152918. Epub 2013 Jul 12. PubMed PMID: 23852385; PubMed Central PMCID: PMC3761308.