Tran C, Rosenfield GR, Cleves PA, Krediet CJ, Paul MR, Clowez S, Grossman AR, Pringle JR. Photosynthesis and other factors affecting the establishment and maintenance of cnidarian–dinoflagellate symbiosis. Phil Trans R Soc B. 2024 Mar 18;379: 20230079. 

Selmoni O, Bay LK, Exposito-Alonso M, Cleves PA. Finding genes and pathways that underlie coral adaptation. Trend Genetics. 2024 Feb 5;40(3):213-227. doi: 10.1016/j.tig.2024.01.003. Epub 2024 Feb 6. PMID: 38320882.

Tinoco AI, Mitchison-Field LMY, Bradford J, Renicke C, Perrin D, Bay LK, Pringle JR, Cleves PA. Role of the bicarbonate transporter SLC4γ in stony-coral skeleton formation and evolution. Proc Natl Acad Sci U S A. 2023 Jun 13;120(24):e2216144120. doi: 10.1073/pnas.2216144120. Epub 2023 Jun 5. PubMed PMID: 37276409; PubMed Central PMCID: PMC10268325.

Cui G, Konciute MK, Ling L, Esau L, Raina JB, Han B, Salazar OR, Presnell JS, Rädecker N, Zhong H, Menzies J, Cleves PA, Liew YJ, Krediet CJ, Sawiccy V, Cziesielski MJ, Guagliardo P, Bougoure J, Pernice M, Hirt H, Voolstra CR, Weis VM, Pringle JR, Aranda M. Molecular insights into the Darwin paradox of coral reefs from the sea anemone Aiptasia. Sci Adv. 2023 Mar 17;9(11):eadf7108. doi: 10.1126/sciadv.adf7108. Epub 2023 Mar 15. PubMed PMID: 36921053; PubMed Central PMCID: PMC10017044.

Waller RF, Alves-de-Souza C, Cleves PA, Janouškovec J, Kayal E, Krueger T, Szymczak J, Yamada N, Guillou L. Comparative biology and ecology of apicomplexans and dinoflagellates: a unique meeting of minds and biology. Trends Parasitol. 2022 Dec;38(12):1012-1019. doi: 10.1016/j.pt.2022.09.010. PubMed PMID: 36344386.

Cleves PA, Krediet CJ, Lehnert EM, Onishi M, Pringle JR. Insights into coral bleaching under heat stress from analysis of gene expression in a sea anemone model system. Proc Natl Acad Sci U S A. 2020 Nov 17;117(46):28906-28917. doi: 10.1073/pnas.2015737117. Epub 2020 Nov 9. PubMed PMID: 33168733; PubMed Central PMCID: PMC7682557.

Cleves PA, Tinoco AI, Bradford J, Perrin D, Bay LK, Pringle JR. Reduced thermal tolerance in a coral carrying CRISPR-induced mutations in the gene for a heat-shock transcription factor. Proc Natl Acad Sci U S A. 2020 Nov 17;117(46):28899-28905. doi: 10.1073/pnas.1920779117. Epub 2020 Nov 9. PubMed PMID: 33168726; PubMed Central PMCID: PMC7682433.

Cleves PA, Shumaker A, Lee J, Putnam HM, Bhattacharya D. Unknown to Known: Advancing Knowledge of Coral Gene Function. Trends Genet. 2020 Feb;36(2):93-104. doi: 10.1016/j.tig.2019.11.001. Epub 2019 Dec 24. Review. PubMed PMID: 31882190.

Cleves PA, Hart JC, Agoglia RM, Jimenez MT, Erickson PA, Gai L, Miller CT. An intronic enhancer of Bmp6 underlies evolved tooth gain in sticklebacks. PLoS Genet. 2018 Jun;14(6):e1007449. doi: 10.1371/journal.pgen.1007449. eCollection 2018 Jun. PubMed PMID: 29902209; PubMed Central PMCID: PMC6019817.

Erickson PA, Baek J, Hart JC, Cleves PA, Miller CT. Genetic Dissection of a Supergene Implicates Tfap2a in Craniofacial Evolution of Threespine Sticklebacks. Genetics. 2018 Jun;209(2):591-605. doi: 10.1534/genetics.118.300760. Epub 2018 Mar 28. PubMed PMID: 29593029; PubMed Central PMCID: PMC5972429.

Cleves PA, Strader ME, Bay LK, Pringle JR, Matz MV. CRISPR/Cas9-mediated genome editing in a reef-building coral. Proc Natl Acad Sci U S A. 2018 May 15;115(20):5235-5240. doi: 10.1073/pnas.1722151115. Epub 2018 Apr 25. PubMed PMID: 29695630; PubMed Central PMCID: PMC5960312.

Xiang T, Jinkerson RE, Clowez S, Tran C, Krediet CJ, Onishi M, Cleves PA, Pringle JR, Grossman AR. Glucose-Induced Trophic Shift in an Endosymbiont Dinoflagellate with Physiological and Molecular Consequences. Plant Physiol. 2018 Feb;176(2):1793-1807. doi: 10.1104/pp.17.01572. Epub 2017 Dec 7. PubMed PMID: 29217594; PubMed Central PMCID: PMC5813547.

Mansfield KM, Carter NM, Nguyen L, Cleves PA, Alshanbayeva A, Williams LM, Crowder C, Penvose AR, Finnerty JR, Weis VM, Siggers TW, Gilmore TD. Transcription factor NF-κB is modulated by symbiotic status in a sea anemone model of cnidarian bleaching. Sci Rep. 2017 Nov 22;7(1):16025. doi: 10.1038/s41598-017-16168-w. PubMed PMID: 29167511; PubMed Central PMCID: PMC5700166.

Erickson PA, Glazer AM, Killingbeck EE, Agoglia RM, Baek J, Carsanaro SM, Lee AM, Cleves PA, Schluter D, Miller CT. Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks. Evolution. 2016 Apr;70(4):887-902. doi: 10.1111/evo.12897. Epub 2016 Mar 29. PubMed PMID: 26947264; PubMed Central PMCID: PMC4833593.

Ellis NA, Glazer AM, Donde NN, Cleves PA, Agoglia RM, Miller CT. Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks. Development. 2015 Jul 15;142(14):2442-51. doi: 10.1242/dev.124248. Epub 2015 Jun 10. PubMed PMID: 26062935; PubMed Central PMCID: PMC4510868.

Erickson PA, Cleves PA, Ellis NA, Schwalbach KT, Hart JC, Miller CT. A 190 base pair, TGF-β responsive tooth and fin enhancer is required for stickleback Bmp6 expression. Dev Biol. 2015 May 15;401(2):310-23. doi: 10.1016/j.ydbio.2015.02.006. Epub 2015 Feb 27. PubMed PMID: 25732776; PubMed Central PMCID: PMC4424077.

Cleves PA, Ellis NA, Jimenez MT, Nunez SM, Schluter D, Kingsley DM, Miller CT. Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6. Proc Natl Acad Sci U S A. 2014 Sep 23;111(38):13912-7. doi: 10.1073/pnas.1407567111. Epub 2014 Sep 9. PubMed PMID: 25205810; PubMed Central PMCID: PMC4183278.

Erickson PA, Glazer AM, Cleves PA, Smith AS, Miller CT. Two developmentally temporal quantitative trait loci underlie convergent evolution of increased branchial bone length in sticklebacks. Proc Biol Sci. 2014 Aug 7;281(1788):20140822. doi: 10.1098/rspb.2014.0822. PubMed PMID: 24966315; PubMed Central PMCID: PMC4083797.

Glazer AM, Cleves PA, Erickson PA, Lam AY, Miller CT. Parallel developmental genetic features underlie stickleback gill raker evolution. Evodevo. 2014;5:19. doi: 10.1186/2041-9139-5-19. eCollection 2014. PubMed PMID: 24851181; PubMed Central PMCID: PMC4029907.

Cleves MA, Hobbs CA, Cleves PA, Tilford JM, Bird TM, Robbins JM. Congenital defects among liveborn infants with Down syndrome. Birth Defects Res A Clin Mol Teratol. 2007 Sep;79(9):657-63. doi: 10.1002/bdra.20393. PubMed PMID: 17696161.