I investigate gene architecture and regulation, especially within nervous systems. Using my background in molecular genetics, genomics and neurobiology, I develop experimental and computational methods for comparative and functional genomics. I apply these methods in classical and emerging model systems including octopus and squid, nematodes, fish, and human cell fate reprogramming.

Experience

Fellowships

Publications

1. Herbert AL*, Allard CAH*, McCoy MJ*, Wucherpfennig JI, Krueger SP, Chen HI, Gourlay AN, Jackson KD, Abbo LA, Bennett SH, Sears JD, Rhyne AL, Bellono NW, Kingsley DM. Ancient developmental genes underlie evolutionary novelties in walking fish. Current Biology (2024). DOI: https://doi.org/10.1016/j.cub.2024.08.042. (New York Times)(CNN)(Scientific American)(The Guardian)(Science Friday)(New Scientist). *Co-first author.
2. Herbert A, Lee D, McCoy MJ, Wucherpfennig J, Behrens V, Kingsley D. Genetic mechanisms of axial patterning in Apeltes quadracus. Evolution Letters (2024), qrae041. DOI: https://doi.org/10.1093/evlett/qrae041.
3. McCoy MJ and Fire AZ. Parallel gene size and isoform expansion of ancient neuronal genes. Current Biology (2024), S0960982224001635. DOI: https://doi.org/10.1016/j.cub.2024.02.021. (Moroz Dispatch)(Stanford Wu Tsai Neurosciences Institute News)(PreLights Review).
4. Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Król M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi M K, Nyholm S V, Otjacques E, Pérez-Ferrer P A, Ponte G, Pungor J R, Rogers T F, Rosenthal J J C, Rouressol L, Rubas N, Sanchez G, Pereira C, Schultz D T, Seuntjens E, Songco-Casey J O, Stewart I E, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O, Albertin C. Cephalopod-omics: emerging fields and technologies in cephalopod molecular biology and evolution. Biology. Integr. Comp. Biol. (2023). DOI: https://doi.org/10.1093/icb/icad087
5. Lu YL, Liu Y, McCoy MJ, and Yoo AS. MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity. Proceedings of the National Academy of Sciences 118(22):e2015454118 (2021). DOI: https://doi.org/10.1073/pnas.2015454118
6. Cates K*, McCoy MJ*, Kwon JS*, Liu Y*, Abernathy DG, Zhang B, Liu S, Gontarz P, Kim WK, Chen S, Kong W, Ho JN, Burbach KF, Gabel HW, Morris SA, and Yoo AS. Deconstructing stepwise fate conversion of human fibroblasts to neurons by MicroRNAs. Cell Stem Cell 28, 127-140, e9 (2020). DOI: https://doi.org/10.1016/j.stem.2020.08.015 *Co-first author. (Herdy et al. Dispatch)
7. McCoy MJ and Fire AZ. Intron and gene size expansion during nervous system evolution. BMC Genomics 21, 360 (2020). DOI: https://doi.org/10.1186/s1 2864-020-6760-4. (Stanford Wu Tsai Neuroscience Institute Q&A)
8. Wahba L*, Jain N*, Fire AZ*, Shoura MJ*, Artiles KL*, McCoy MJ* and Jeong DE*. An Extensive Meta-Metagenomic search identifies SARS-CoV-2-homologous sequences in pangolin lung viromes. mSphere 5(3):e00160-20 (2020). DOI: https://doi.org/10.1128/mSphere.00160-20. *All authors contributed equally and author order was chosen randomly.
9. McCoy MJ*, Paul AJ*, Victor MB, Richner M, Gabel HW, Gong H, Yoo AS & Ahn T. LONGO: an R package for interactive gene length dependent analysis for neuronal identity. Bioinformatics 34.13, i422-i428. (2018). DOI: https://doi.org/10.1093/bioinformatics/bty243. *Co-first author.
10. Abernathy DG*, Kim W*, McCoy MJ*, Lake A, Ouwenga R, Xing X, Li D, Lee HJ, Heuckeroth RO, Dougherty JD, Wang T, Yoo AS. MicroRNAs induce a permissive chromatin environment that enables neuronal subtype-specific reprogramming of adult human fibroblasts. Cell Stem Cell 21.3, 332-348 e339 (2017). DOI: https://doi.org/10.1016/j.stem.2017.08.002. *Co-first author.

Preprints

1. McCoy MJ and Fire AZ. genesizeR: an R package to incorporate gene size into categorical and quantitative investigations of gene sets. (Submitted)
2. Herbert AL*, Allard CAH*, McCoy MJ*, Wucherpfennig JI, Krueger SP, Chen HI, Gourlay AN, Jackson KD, Abbo LA, Bennett SH, Sears JD, Rhyne AL, Bellono NW, Kingsley DM. The genetic basis of novel trait gain in walking fish. bioRxiv (2023). DOI: https://doi.org/10.1101/2023.10.14.562356. *Co-first author. (Now published in Current Biology)
3. McCoy MJ and Fire AZ. Ancient origins of complex neuronal genes. bioRxiv (2023). DOI: https://doi.org/10.1101/2023.03.28.534655. (Now published in Current Biology)
4. Wahba L*, Jain N*, Fire AZ*, Shoura M*, Artiles K*, McCoy MJ*, Jeong DE*. Identification of a pangolin niche for a 2019-nCoV-like coronavirus through an extensive meta-metagenomic search. bioRxiv (2020). DOI: https://doi.org/10.1101/2020.02.08.939660. *All authors contributed equally. (Now published in mSphere)