Curriculum Vitae

Education

• Ph.D in Molecular Genetics & Genomics (2018)
  • Washington University in St. Louis, St. Louis, MO
  • Advisor: Andrew S. Yoo, PhD
  • Thesis: Defining neuronal identity using microRNA-mediated neuronal reprogramming
• B.A. in Biology, minor in Chemistry (2011)
  • University of Utah, Salt Lake City, UT (2008-2011)
  • University of Hawaii at Manoa, Honolulu, HI (2005-2008)

Research experience

• Postdoctoral Scholar (2018-Present)
  • Department of Pathology, Stanford University School of Medicine, Stanford, CA
  • Advisor: Andrew Z. Fire, PhD
  • Project: Investigating the causes and consequences of gene size expansion during nervous system evolution.
• Graduate Student (2012-2018)
  • Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO
  • Advisor: Andrew S. Yoo, Ph.D.
  • Project: Defining neuronal identity using microRNA-mediated reprogramming of human skin cells to neurons.
• Laboratory Technician (2008-2012)
  • Department of Pediatrics, Division of Neonatology, University of Utah, Salt Lake City, UT
  • PI: Kurt H. Albertine, Ph.D.
  • Project: Characterizing molecular morphologies of acute and chronic lung injury in a sheep (Ovis aries) model.
• Undergraduate Research (2007–2008)
  • Department of Zoology, University of Hawaii at Manoa, Honolulu, HI
  • PI: Steve Robinow, Ph.D.
  • Project: Characterizing neuronal nuclear hormone receptor (DHR51) in Drosophila melanogaster.

Fellowships

• Whitman Early Career Award (Summer 2023)
  • Marine Biological Laboratory, Woods Hole, MA
• Wu Tsai Interdisciplinary Scholar (2021 – 2022)
  • Stanford University, Stanford, CA
• Whitman Early Career Award (Summer 2019)
  • Marine Biological Laboratory, Woods Hole, MA
• Stanford Genome Training Grant Post-Doctoral Fellowship (2018 – 2019)
  • Institutional National Research Service Award (T32HG000044; Snyder, PI)
• Grass Fellowship in Neuroscience (Summer 2018)
  • Marine Biological Laboratory, Woods Hole, MA
• Interface of Psychology, Neuroscience & Genetics Pre-Doctoral Fellowship (2014 – 2015)
  • Institutional National Research Service Award (T32GM081739; Barch, PI)

Publications

MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts

Abernathy DG*, Kim WK*, McCoy MJ*, Lake AM, Ouwenga R, Lee SW, 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. 2017 Sep 7;21(3):332-348.e9. doi: 10.1016/j.stem.2017.08.002. PMID: 28886366; PMCID: PMC5679239. *Authors contributed equally

LONGO: an R package for interactive gene length dependent analysis for neuronal identity

Matthew J McCoy*, Alexander J Paul*, Matheus B Victor, Michelle Richner, Harrison W Gabel, Haijun Gong, Andrew S Yoo, Tae-Hyuk Ahn (2018). " LONGO: an R package for interactive gene length dependent analysis for neuronal identity." Bioinformatics. Volume 34, Issue 13, Pages i422–i428. *Authors contributed equally

An extensive meta-metagenomic search identifies SARS-CoV-2-homologous sequences in pangolin lung viromes

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). *All authors contributed equally and author order was chosen randomly

Intron and gene size expansion during nervous system evolution

McCoy MJ and Fire AZ. (2020). "Intron and gene size expansion during nervous system evolution." BMC Genomics. 21, 360.

Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs

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, Yoo AS. (2020). "Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs." Cell Stem Cell. *Authors contributed equally

MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity

Lu YL, Liu Y, McCoy MJ, and Yoo AS. (2021). "MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity." PNAS 118(22):e2015454118.

Ancient origins of complex neuronal genes

McCoy MJ and Fire AZ. (2023). "Ancient origins of complex neuronal genes." bioRxiv

The genetic basis of novel trait gain in walking fish

Amy L Herbert*, Corey AH Allard*, Matthew J McCoy*, Julia I Wucherpfennig, Stephanie P Krueger, Heidi I Chen, Allex N Gourlay, Kohle D Jackson, Lisa A Abbo, Scott H Bennett, Joshua D Sears, Andrew L Rhyne, Nicholas W Bellono#, David M Kingsley# (2023). "The genetic basis of novel trait gain in walking fish." bioRxiv

Parallel gene size and isoform expansion of ancient neuronal genes

Matthew J McCoy, Andrew Z Fire (2024). "Parallel gene size and isoform expansion of ancient neuronal genes." Current Biology

Honors & Awards

• Best Poster Award, Bay Area RNA Club, UCSF (2023)
• Best Poster Award, Department of Pathology Retreat, Stanford University (2022)
• Outstanding Presentation Award, IPNG Research Day, Washington University in St. Louis (2015)
• Best Poster Award, Genetics & Computational Biology Retreat, Washington University in St. Louis (2014)
• Outstanding Presentation Award, IPNG Research Day, Washington University in St. Louis (2013)
• Undergraduate Research Scholar, University of Utah (2011)

Teaching experience

• Adjunct Faculty in Biology; BIOL 12 Genomics Data Sciences (Summer 2022)
  • Clovis Community College, Fresno, CA
  • Co-taught with Prof. Rosa Alcazar and Dr. Lindsay Hayes
• Teaching Assistant/Mentor; BIOL 12 Genomics Data Sciences (Spring 2022)
  • Clovis Community College, Fresno, CA
  • Professor Rosa Alcazar
• Mentor to Stanford undergraduate student (Summer 2021)
  • Stanford Bio-X
  • Stanford University, Stanford, CA
• Teaching Assistant; Principles of the Nervous System (Fall 2014)
  • Washington University in St. Louis, St. Louis, MO
  • Professors Larry Salkoff and Thomas Woolsey

Service & Outreach

• Video Interview, 90 Seconds w/ Lisa Kim, Stanford University (2023)
  • “What can octopus teach us about human brains?” Lisa Kim.
  • Link: https://www.youtube.com/watch?v=n3gRRo95Fxs
• Podcast Interview, From Our Neurons to Yours, Stanford University (2023)
  • “The Octopus Brain.” Nick Weiler.
  • Link: https://open.spotify.com/episode/3TQGAcEBgskUjgtztSD50x?si=2e70159aa4804450
• Podcast Interview, The Synapse by Simply Neuroscience, a student-run podcast series (In Production)
  • “The College Neuroscience Network: Stanford University from a Postdoctoral Researcher.”
  • Tony Zhang.
• Printed Interview, Wu Tsai Neurosciences Institute, Stanford University (2022)
  • “Q&A: Evolution of octopus and squid brains could shed light on origins of intelligence.”
  • Rachel Grant.
  • Link: https://neuroscience.stanford.edu/news/qa-evolution-octopus-and-squid-brains-could-shed-light-origins-intelligence
• Invited Grass Fellowship Technical Reviewer (2022)
  • Grass Foundation, Woods Hole, MA
• Invited Grass Fellowship Technical Reviewer (2021)
  • Grass Foundation, Woods Hole, MA
• Co-Organizer of Superworm (Stanford C. elegans community seminars) (2020 – Present)
  • Stanford University, Stanford, CA
• Invited Grass Fellowship Technical Reviewer (2020)
  • Grass Foundation, Woods Hole, MA
• Graduate Student Senate (2013 – 2014)
  • Washington University in St. Louis, St. Louis, MO
• Health Professional Student Leadership Council (2013 – 2014)
  • Washington University in St. Louis, St. Louis, MO
• Student Advisory Committee (2013 – 2014)
  • Washington University in St. Louis, St. Louis, MO
• University Undergraduate Research Association (2009 – 2011)
  • Co-Founder and Vice President
  • University of Utah, Salt Lake City, UT

Presentations

• Oral Presentations
  • Cephalopod International Advisory Committee (CIAC), Sesimbra, Portugal (2022)
    • “Intron and gene size expansion during cephalopod nervous system evolution.”
  • Invited Seminar, Hopkins Marine Station, Stanford University, Stanford, CA (2019)
    • “Intron and gene size expansion during nervous system evolution.”
  • Whitman Fellowship Seminar, Marine Biological Laboratory, Woods Hole, MA (2019)
    • “Intron and gene size expansion during nervous system evolution.”
  • Department Seminar, Department of Genetics, Stanford University, Stanford, CA (2018)
    • “Intron and gene size expansion during nervous system evolution.”
  • Grass Fellowship Symposium, Marine Biological Laboratory, Woods Hole, MA (2018)
    • “Intron and gene size expansion during nervous system evolution.”
  • International Conference on Epigenetics and Bioengineering, Miami, FL (2017)
    • “MicroRNA-mediated reprogramming reveals genomic features underlying neuronal identity.”
  • Developmental, Regenerative and Stem Cell Biology Retreat, WashU, St. Louis, MO (2017)
    • “Long gene expression as a metric for neuronal maturity.”
  • Developmental, Regenerative and Stem Cell Biology Retreat, WashU, St. Louis, MO (2015)
    • “MicroRNA-mediated regulation of DNA and RNA methylation during reprogramming of skin cells to neurons.”
  • IPNG Research Day, WashU, St. Louis, MO (2015)
    • “Epigenetic mechanisms of reprogramming human fibroblasts to neurons.”
  • Genetics and Computational Biology Retreat, WashU, St. Louis, MO (2014)
    • “Direct neuronal reprogramming alters DNA methylation at specific loci.”
  • IPNG Research Day, WashU, St. Louis, MO (2013)
    • “The role of DNA methylation during microRNA-mediated direct reprogramming of human fibroblasts to neurons.”
  • 28th Conference on High-Frequency Ventilation of Infants, Children, and Adults, Salt Lake City, UT (2011)
    • “Epigenetic changes in chromatin structure and DNA methylation in the lung of preterm lambs following three days of mechanical ventilation and 10 weeks of recovery.”
  • Western Society for Pediatric Research, Carmel, CA (2010)
    • “Vitamin A therapy reduces IGF-1 promoter 2 mRNA levels in the lungs of chronically ventilated preterm lambs.”
  • 27th Conference on High-Frequency Ventilation of Infants, Children, and Adults, Salt Lake City, UT (2010)
    • “Vitamin A therapy reduces IGF-1 promoter 2 mRNA levels in the lungs of chronically ventilated preterm lambs.”
  • National Conference on Undergraduate Research, Bozeman, MO (2010)
    • “Retinoids reduce IGF-1 expression in the lung of mechanically ventilated preterm lambs.”
  • Western Society for Pediatric Research, Carmel, CA (2009)
    • “Ventilation mode affects ovine pulmonary IGF-1 epigenetic characteristics.”
  • Utah Conference on Undergraduate Research, Salt Lake City, UT (2009)
    • “Ventilation mode affects ovine pulmonary IGF-1 epigenetic characteristics.”
  • 26th Conference on High-Frequency Ventilation on Infants, Children, and Adults, Salt Lake City, UT (2009)
    • “Ventilation mode affects ovine pulmonary IGF-1 epigenetic characteristics.”
  • National Conference on Undergraduate Research, LaCrosse, WI (2009)
    • “Ventilation mode affects ovine pulmonary IGF-1 epigenetic characteristics.”
• Poster Presentations
  • Bay Area RNA Club, UCSF, San Francisco, CA (2023)
    • “Consequences of gene size variation during evolution.”
  • Department of Pathology Retreat, Stanford University, Stanford, CA (2022)
    • “Consequences of gene size variation during evolution.”
  • Biology of Genomes, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (2022)
    • “Consequences of gene size variation during evolution.”
  • NHGRI Research Training and Career Development Annual Meeting, Saint Louis, MO (2019)
    • “Gene complexity and the evolution of nervous systems.”
  • Department of Pathology Retreat, Stanford University, Stanford, CA (2019)
    • “Gene complexity and the evolution of nervous systems.”
  • Nature Conference on Neurogenetics, New York University, New York, NY (2017)
    • “Long gene expression identifies functional neurons in microRNA-mediated direct reprogramming.”
  • Genetics and Computational Biology Retreat, WashU, St. Louis, MO (2014)
    • “Neuronal reprogramming by microRNAs alters DNA methylation at specific loci.”
  • Midwest Society for Developmental Biology Meeting, WashU, St. Louis, MO (2014)
    • “Neuronal reprogramming by microRNAs alters DNA methylation at specific loci.”
  • Annual Cell & Molecular Biology Mini-Symposium, WashU, St. Louis, MO (2014)
    • “Neuronal reprogramming by microRNAs alters DNA methylation at specific loci.”