Curriculum Vitae

Zachary L. Fuller, Ph.D. Department of Biological Sciences Columbia University 606 Fairchild Center, New York, NY 10027 Email: [email protected] Website: www.zfullergenomics.com

Education: 2012-2017 Ph.D. (Biology), The Pennsylvania State University 2008-2012 B.S. (Biology), Creighton University

Research & Work Experience: 2017- Postdoctoral Research Fellow, Columbia University Advised by Dr. Molly Przeworski, Department of Biological Sciences, Columbia University, New York, NY 2015-2017 National Geographic Young Explorer Advised by Dr. Christina Grozinger, Department of Entomology, The Pennsylvania State University, University Park, PA 2012-2017 Ph.D. Candidate, The Pennsylvania State University Advised by Dr. Stephen Schaeffer, Department of Biology, The Pennsylvania State University, University Park, PA 2012-2013 Rotation Student, The Pennsylvania State University Advised by Dr. Webb Miller, and Institute, The Pennsylvania State University, University Park, PA 2009-2012 Undergraduate Researcher, Creighton University Advised by Dr. Soochin Cho, Department of Biology, Creighton University, Omaha, NE

Peer-Reviewed Publications: Zachary L. Fuller, Veronique Mocellin, Luke Morris, Neal Cantin, Julie Peng, Yi Liao, Jihanne Shepherd, Joseph Pickrell, Peter Andolfatto, Mikhail Matz, Line Bay, Molly Przeworski. (2020) Towards a genomic predictor of bleaching in the coral Acropora millepora. Science (in press) bioRxiv Preprint: https://doi.org/10.1101/867754 Zachary L. Fuller, Jeremy Berg, Hakhamanesh Mostafavi, Guy Sella, Molly Przeworski. (2019) Measuring Intolerance to Mutation in Human Genetics. Genetics. DOI: 10.1038/s41588-019-0383-1 Zachary L. Fuller, Spencer Koury, Nitin Phadnis, Stephen Schaeffer. (2018) How Chromosomal Rearrangements Shape Adaptation and Speciation: Case Studies in Drosophila pseudoobscura and its sibling species D. persimils. Molecular Ecology. DOI: 10.1111/mec.14923 Zachary L. Fuller, Christopher Leonard, Randee Young, Stephen Schaeffer, Nitin Phadnis. (2018) Ancestral Polymorphisms Explain the Role of Chromosomal Inversions in Speciation. PLoS Genetics. DOI: 10.1371/journal.pgen.1007526 David Galbraith, Zachary L. Fuller, Axel Brockmann, Maryann Frazier, Mary Gikungu, Karen Kapheim, Jeffrey Kerby, Sarah Kocher, Oleksiy Losyev, Elliud Muli, Harland Patch, Joyce Sakamoto, Scott Stanley, Anthony Vaudo, Christina Grozinger. (2018) Investigating the Viral Ecology of Global Bee Communities with High-throughput Metagenomics. Scientific Reports. 10.1038/s41598-018-27164-z Zachary L. Fuller, Gwilym Haynes, Stephen Richards, Stephen Schaeffer. (2017) Genomics of Natural Populations: Evolutionary Forces that Establish New Gene Arrangements in Drosophila pseudoobscura. Molecular Ecology. DOI: 10.1111/mec.14381 Zachary L. Fuller, Gwilym Haynes, Stephen Richards, Stephen Schaeffer. (2016) Genomics of Natural Populations: How Differentially Expressed Genes Shape the of Chromosomal Inversions in Drosophila pseudoobscura. Genetics. DOI: 10.1534/ genetics.116.191429 Zachary L. Fuller, Elina Nino, Harland Patch, Oscar Bedoya-Reina, Tracey Baumgarten, Elluid Muli, Fiona Mumoki, Aakrosh Ratan, John McGraw, Maryann Frazier, Daniel Masiga, Stephen Schuster, Christina Grozinger, Webb Miller. (2015) Genome-wide Analysis of Signatures of Selection in Populations of African Honey-bees (Apis mellifera). BMC Genomics. DOI: 10.1186/s12864-015-1712-0 Zachary L. Fuller, Gwilym Haynes, Dianhui Zhu, Matthew Batterton, Hsu Chao, Shannon Duggan, Stephen Richards, Stephen Schaeffer. (2014) Evidence for Stabilizing Selection on Codon Usage in Chromosomal Rearrangements of Drosophila pseudoobscura. G3: Genes, Genomes & Genetics. DOI: 10.1534/g3.114.014860

Preprints and In-Review Publications: William Milligan, Zachary L. Fuller, Ipsita Agarwal, Michael Eisen, Molly Przeworski, Guy Sella. (2020) Impact of Essential Workers in the Context of Social Distancing for Epidemic Control. medRxiv Preprint: https://doi.org/10.1101/2020.05.05.20092262 Maurizio Mauro, Shan Wei, Andrzej Breborowicz, Xin Li, Claudia Bognanni, Zachary L. Fuller, Tom Philipp, Zev Williams. (2019) Pervasive, but reversible, catastrophic DNA damage caused by LINE-1 retrotransposons in human primary trophoblasts. (In Review at Fertility & Sterility) Zachary L. Fuller, Spencer Koury, Christopher Leonard, Randee Young, Kobe Ikegami, Jonathan Westlake, Stephen Richards, Stephen Schaeffer, Nitin Phadnis. (2018) Extensive recombination suppression and chromosome-wide differentiation of a segregation distorter in Drosophila. (In Revision at Genetics). bioRxiv Preprint: https://doi.org/10.1101/504126

Grants: Agouron Institute (July 2019-July 2021) “Precision Medicine for Corals: Predicting Bleaching Response from Genomes” Co-Principal Investigator, $440,ooo Direct NIH Ruth L. Kirschstein National Research Service Award (May 2018-May 2020) “Characterizing and Mapping Deleterious Mutations in Humans” Grant Number: F32 GM128318 National Geographic Society (July 2015-July 2017) “High throughput viral metagenomics in Kenyan honeybees” Principal Investigator, $10,000 Direct

Oral Presentations: *Invited Speaker Zachary Fuller, Joe Pickrell, Peter Andolfatto, Mikhail Matz, Line Bay, Molly Przeworski. “Genome-wide association study (GWAS) of bleaching tolerance in a Great Barrier Reef coral”. The Allied Genetics Conference. Virtual. April 23, 2020 Zachary Fuller*, Molly Przeworski. “Towards a genomic predictor of bleaching in the coral Acropora millepora” American Museum of Natural History Comparitive Biology Seminar Series. New York, NY. April 13, 2020 Zachary Fuller, Julie Peng, Jihanne Shepherd, Peter Andolfatto, Joseph Pickrell, Mikhail Matz, Line Bay, Molly Przeworski. “Towards the genetic prediction of bleaching response in Acropora millepora”. Evolution Meeting. Providence, RI. June 25, 2019 Mikhail Matz, Groves Dixon, Yi Liao, Zachary Fuller. “Rampant Cryptic Speciation and Environmental Specialization in Two Massive Coral Species from the Florida Keys.” Society for Integrative and Comparative Biology (SICB) 2019 Annual Meeting. Tampa Bay, FL. January 4, 2019. Zachary Fuller, Yi Liao, Line Bay, Mikhail Matz, Molly Przeworski. “Towards the genetic prediction of bleaching response in coral.” Global Invertebrate Genomics Alliance Research Conference and Workshop. Willemstad, Curacao. October 20, 2018. Zachary Fuller, Christopher Leonard, Randee Young, Stephen Schaeffer. “The Role of Chromosomal Inversions in Speciation.” The New York Population Genetics Conference. Cold Spring Harbor, NY. January 10, 2018 Zachary Fuller, Gwilym Haynes, Stephen Richards, Stephen Schaeffer. “Local Adaptation and the Establishment of Inversions in Natural Populations of Drosophila pseudoobscura Through the Indirect Effects of Suppressed Recombination.” The Allied Genetics Conference. Orlando, FL. July 15, 2016 Christopher Leonard, Zachary Fuller, Randee Young, Stephen Schaeffer, Nitin Phadnis. “Evidence for the Interspecies Transfer of a Driving X Chromosome.” The Allied Genetics Conference. Orlando, FL. July 15, 2016 Zachary Fuller, Gwilym Haynes, Stephen Richards, Stephen Schaeffer. “The Evolutionary Mechanisms that Establish Chromosome Rearrangements in Natural Populations of Drosophila pseudoobscura.” Evolution Meeting (Hamilton Award Symposium). Austin, TX. June 11, 2016 Zachary Fuller, Randee Young, Nitin Phadnis, Stephen Schaeffer. “The Genomic Consequences of Segregation Distortion in Drosophila pseudoobscura.” Penn State Annual Bioinformatics & Genomics Retreat. University Park, PA. August 2015 Zachary Fuller, Gwilym Haynes, Stephen Richards, Stephen Schaeffer. “Unusual Haplotype Structure and Reduced Recombination in Chromosomal Rearrangements of Drosophila pseudoobscura.” Genetics Society of America’s 55th Annual Drosophila Conference. San Diego, CA. March 28th 2014 Zachary Fuller, Gwilym Haynes, Stephen Richards, Stephen Schaeffer. “Identifying the Evolutionary Forces Behind the Maintenance and Origin of Chromosomal Rearrangements in Populations of Drosophila pseudoobscura.” 2013 SMBE Conference. Chicago, IL. July 9th 2013

Upcoming Oral Presentations: Zachary Fuller, Molly Przeworski. “Genomic Tools for Understanding Coral Bleaching” Pacific Symposium for Biocomputing. Waimea, HI. January 2021 [Invited Speaker]

Poster Presentations: Zachary Fuller, Joe Pickrell, Peter Andolfatto, Mikhail Matz, Line Bay, Molly Przeworski. “Genome-wide association study (GWAS) of bleaching tolerance in a Great Barrier Reef coral”. The Biology of Genomes. Cold Spring Harbor (Virtual). May 2020 Mikhail Matz, Zachary Fuller. “LD Networks: Unsupervised Detection of Polygenic Selection”. Society for Integrative and Comparative Biology (SICB) 2020 Annual Meeting. Austin, TX. January 2020 Zachary Fuller, Julie Peng, Jihanne Shepherd, Peter Andolfatto, Joseph Pickrell, Mikhail Matz, Line Bay, Molly Przeworski. “Toward the genetic prediction of bleaching response in Acropora millepora”. 2019 SMBE Conference. Manchester, UK. July 2019. Zachary Fuller, Jeremy Berg, Hakhamanesh Mostafavi, Guy Sella, Molly Przeworski. “A Population Genetics Perspective on Measures of Intolerance to Mutation”. 2018 SMBE Conference. Yokohama, Japan. July 2018. Zachary Fuller, Stephen Schaeffer “Selection Across Environmental Gradients Leads to the Establishment of Chromosomal Inversions in Populations”. Genetics Society of America’s 58th Annual Drosophila Conference. San Diego, CA. April 2017 Christopher Leonard, Zachary Fuller, Randee Young, Stephen Richards, Stephen Schaeffer, Nitin Phadnis “Introgresssion-derived segregation distortion promotes unlikely gene flow”. Genetics Society of America’s 58th Annual Drosophila Conference. San Diego, CA. April 2017 Zachary Fuller, Elina Nino, Harland Patch, Oscar Bedoya-Reina, Jeffery Kerby, Elliud Muli, Maryann Frazier, Webb Miller, Christina Grozinger. “Signals of Adaptive Evolution in Populations of Kenyan Honey Bees, Apis mellifera.” International Conference on Pollinator Biology, Health & Policy. University Park, PA. July 2016 Zachary Fuller, Randee Young, Nitin Phadnis, Stephen Schaeffer. “The Genomic Consequences of the X-linked ‘Sex-Ratio’ Meiotic Drive Element in Drosophila pseudoobscura and Drosophila persimilis.” 2015 SMBE Conference. Vienna, Austria. July 2015 Zachary Fuller, Gwilym Haynes, Shannon Duggan, Dianhuiz Zhu, Stephen Richards, Stephen Schaeffer. “Differential Gene Expression Patterns of Chromosomal Inversion Karyotypes Provide Insight Into the Evolutionary Mechanisms Maintaining Third Chromosome Gene Arrangements of Drosophila pseudoobscura”. Genetics Society of America’s 56th Annual Drosophila Conference. Chicago, IL. March, 2015 Randee Young, Zachary Fuller, Stephen Schaeffer, Nitin Phadnis. “The Molecular Basis of Segregation Distortion in Drosophila pseudoobscura.” Genetics Society of America’s 56th Annual Drosophila Conference. Chicago, IL. March, 2015 Gwilym Haynes, Zachary Fuller, Ian Leopold, Atousa Janshahil, Stephen Richards, Stephen Schaeffer. “Tests of Evolutionary Mechanisms for the Maintenance and Origin of Chromosomal Rearrangements in Drosophila pseudoobscura.” Genetics Society of America’s 54th Annual Drosophila Conference. Washington, D.C. April, 2013 Zachary Fuller, Daniel Bellatti, Jianzhi Zhang, Soochin Cho. “Evolutionary origin and genetic basis of the XY sex reversal in the South American field mouse, Akodon.” 2010 SMBE Conference. Lyon, France

Awards: 2018 NSF Global Invertebrate Genomics Alliance (GIGA) Travel Award 2018 NIH F32 Ruth L. Kirschstein National Research Service Award (NRSA) 2016 Society for the Study of Evolution Hamilton Award Finalist 2016 Troxell Award, Penn State 2015 National Geographic Young Explorer 2013 CBIOS Training Grant Fellowship 2012 Braddock Award, Penn State 2012 Research Fellowship, Penn State 2010 SMBE Diversity Mentoring Program Travel Award 2010 Creighton Biology Association Award 2010 Dean’s Summer Research Fellowship, Creighton 2009 NCAA Division-1 Academic All-American Team Member 2009 Missouri Valley Conference All-Academic Athlete 2008 Magis Award, Creighton

Professional Service: Guest editor for upcoming Special Issue in Journal of Animal Ecology (with Maren Wellenreuther and Lesley Lancaster) “Understanding climate change response in the age of genomics” Organized the “Understanding the genomics of climate change response” symposium at SMBE 2019 Undergraduate Mentor at SMBE 2019

Teaching Experience: The Pennsylvania State University (2013-2017): Primary Instructor Course: Biology 497 - Science Outreach and Communication Instructor of Record. Conceived and developed idea for course. Approved by the Dean’s Office in the Eberly College of Science and taught for the first time in Fall 2015. Guest Lecturer Workshop: Bioinformatics Student Association Invited Speaker (Fall, 2017) Course: Science Writing and Communication (Fall, 2016) Workshop: Introduction to Machine Learning and Data Analytics (Summer, 2016) Course: Concepts and Techniques in Molecular Ecology (Spring, 2016) Graduate Teaching Assistant Course: Biology 230W

Outreach Experience: Sackler Lab of Human Origins Open Lab [Instructor]: Open laboratory visits to the general public two times a month at the American Museum of Natural History, New York, NY. (2017 - ) iSTEAM Saturday Science Workshop [Organizer]: Event attended by 25 middle school teachers from multiple states to learn fundamentals of population genetics (Nov. 19, 2016) Undergraduate DataFest [Mentor] The Pennsylvania State University (2015-2017) Expanding Your Horizons: Female Careers in STEM Fields [Organizer] The Pennsylvania State University (2014-2017) USA Science and Engineering Festival [Exhibit Organizer] Washington D.C. (2014, 2016) Science U: Think Outside the Beaker [Organizer] The Pennsylvania State University (2013-2017) Science U: Exploration U [Organizer, Volunteer] The Pennsylvania State University (2012-207)

Trainees/Mentees Jihanne Shepherd, Undergraduate Student , Columbia University (2019 -) Misha Khan, Undergraduate Summer Researcher, Swarthmore College (2018) Mayanka Dutta, Undergraduate Summer Researcher, Columbia University (2017) Hayley Randolph, Undergraduate Student (now a Ph.D. candidate with Luis Barreiro, University of Chicago), The Pennsylvania State University (2013-2017)

Journal Referee: Biological Reviews, Conservation Biology, Coral Reefs, eLife, Ecology & Evolution, Genetica, Genetics, Genome Biology and Evolution (GBE), Molecular Biology and Evolution (MBE), Molecular Ecology, PLoS Genetics, Scientific Reports Approximately 10 manuscripts annually

Grant Referee: Eva Crane Trust, NCN (Poland National Science Centre), National Geographic Society, National Science Foundation

Professional Memberships: Society of Molecular Biology and Evolution Genetics Society of America Society for the Study of Evolution Global Invertebrate Genomics Alliance

Mobile Application Development: The Evolving Project (Penn State Science U) Tree Investigators (Penn State College of Education) APPLES: Arctic Plant Phenology Learning through Engaged Science (Polar Center at Penn State/UC Davis, Center for Learning with Science and Technology)

Academic Activities: GenoMIX: Genomics & Bioinformatics Graduate Student Group (2015-2017): Vice President The (July, 2013): Summer Institute in Statistical Genetics. Modules Attended – Coalescent Theory, MCMC for Genetic Analysis, Molecular Phylogenetics. Biology Department Graduate Student Association (2012-2017): Outreach Coordinator

Skills: Programming Languages: Python, R, Swift, Objective-C, Java, C/C++ Github Profile: https://github.com/zfuller5280