CV

CURRENT APPOINTMENT:

Research Assistant Professor
Department of Molecular, Cellular, and Biomedical Sciences
University of New Hampshire, Durham NH
August 2023-Current

EDUCATION:

University of California, Davis, Ph.D., Pharmacology and Toxicology, December 2018
Saint Cloud State University, MS, Cell and Molecular Biology, May 2012
Minnesota State University Moorhead, BA, Ecology and Evolutionary Biology, May 2009

PREVIOUS APPOINTMENTS:

Project Scientist (2021-2023) - University of New Hampshire, Civil and Environmental Engineering

• Bioinformatics and statistical analysis of eDNA samples with Alison Watts, Civil and Environmental Engineering

Bioinformatics Analyst (2020-2021) - University of Minnesota, Minnesota Supercomputer Institute

• Cancer genomics. Bulk/single-cell gene expression profiling. Whole genome structural analysis of leukemia and prostate cancer, including human controlled-access data. Clinical and research pipeline development with SLURM, PBS, AWS, Docker, and git.

Postdoctoral Scholar (2019-2020) - University of Minnesota, Department of Ecology, Evolution, and Behavior

• Identification of the premature termination codons and molecular mechanisms that contribute to cave and surface phenotypes of Astyanax mexicanus. Analyzed multiple population whole-genome sequences and gene expression profiles to associate genetic variation with cavefish phenotypes.

Graduate Research - University of California Davis, Department of Environmental Toxicology

• Mapping the Genetic Basis of Rapid Evolution to Industrial Pollutants in Atlantic Killifish. Conducted a comparative analysis of genome structure of killifish and other sequenced vertebrates. Used a quantitative genomic approach to determine the architecture of rapidly evolved resistance to the teratogenicity of pollutants in coastal killifish populations.

RESEARCH FUNDING:

Active

NHAES Hatch, PI. Spider-web eDNA for forest biodiversity. $75,000 (2026-2029)
NHAES Graduate Research Assistantship, PI. $52,000 (2026-2028)
NERRS Science Collaborative, Co-PI. Novel technologies to quantify river herring migration before and after dam removal. $595,000 (2026-2029)

Completed

Hawai’i Division of Aquatic Resources, Co-PI. Hawaiian Estuaries Biodiversity. $89,000 (2024-2025)
NHAES Collaborative Research Enhancement and Team Exploration (CREATE) program grant, Co-PI. eDNA Biodiversity of Multi-Trophic Aquaculture (Aquafort). $50,000 (2023-2026)
USGS NH Water Resources Research Center (State Water Resources Research Institute Program), PI. $30,000 (2023-2025)

Pending

NHAES CREATE, Co-PI (with R. Moll). eDNA and LiDAR biodiversity atlas, Bartlett Experimental Forest. $50,000 (Submitted 2026)

FELLOWSHIPS AND HONORS:

National Institute of Environmental Health Sciences Predoc Training Fellowship (2016-2018)
National Science Foundation GK-12 Teaching Fellowship, Bodega Marine Laboratory (2014-2015)
Society of Environmental Toxicology and Chemistry Research Scholarship (2014)
George Freiderich Wildlife Protection Fund Fellowship (2013)

PUBLICATIONS:

Watts, A. W., Gold, Z., Patin, N. V., Adams, N. G., Baker, J. D., El Baidouri, F., Grey, E., Holmes, A. E., Jacobson, K., Jungbluth, S., Kajita, T., Kiledal, A., Lemay, M. A., Montes, E., Muller-Karger, F. E., Miller, J., Ogburn, M. B., Pitz, K. J., Silliman, K., Thompson, A., Thompson, L. R. (2026) Guidance and best practices for species identification using eDNA metabarcoding – When do you call a cod a cod? Metabarcoding and Metagenomics 10: e174450. DOI: 10.3897/mbmg.10.174450

Roback, E.,Ferrufino, E., Moran, R., Mulliniks, C., Shennard, D., Gallop, J., Weagley, J., Miller, J., Rohner, N., Kowalko, J., McGaugh, S. (2025) Population genomics of premature termination codons in cavefish with substantial trait loss. Molecular Biology and Evolution DOI: 10.1093/molbev/msaf012

El Baidouri, F., Watts, A. W., Miller, J. T., Kelly, M., Sevigny, J. L., Gilbert, H., Thomas, W. K. (2025) An Optimized eDNA Protocol for Fish Tracking in Estuarine Environments. Scientific Reports 15, DOI: 10.1038/s41598-025-85176-y

Miller, J. T., Clark, B. W., Reid, N. M., Karchner, S. I., Roach, J. L., Hahn, M. E., Nacci, D., Whitehead, A. (2024) Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect. Evolutionary Applications 17(1): e13648, DOI: 10.1111/eva.13648

Garduno-Sanchez, M., Hernandez-Lozano, J., Moran, R.L., Gamboa, R.M., Gross, J.B., Rohner, N., Elliott, W., Miller, J., Lozano-Vilano, L., McGaugh, S., Orneles-Garcia, P. (2023) Phylogeographic relationships and morphological evolution between cave and surface Astyanax mexicanus populations (De Fillipi 1853) (Actinopterygii, Characidae). Molecular Ecology, DOI: 10.22541/au.166979535.59484815/v1

Duvernell, D., Remex, N., Miller, J., Schaefer, J. (2023) Variable rates of hybridization among contact zones between a pair of topminnow species, Fundulus notatus and F. olivaceus, Ecology and Evolution, DOI: 10.1002/ece3.10399

Leland, N., Crocker Pearson, K., Burke, M., Miller, J., Watts,. A., Haney, J. (2023) Isolation of Picocyanobacteria (Order Synechococcales) and Occurrence of the Cyanotoxin Anatoxin-A in a Shallow Mesotrophic Pond. Journal of Water Resource and Protection, DOI: 10.4236/jwarp.2023.156017

Zivanovic, A., Miller, J., Munro, S., Li, Y., Passow, C., Simonaitis, P., Lynch, M. Oseth, L., Zhao, S., Feng, F., Wikström, P., Corey, E., Morrissey, C., Henzler, C., Raphael, B., Dehm, S. (2023) Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer. NAR Cancer, DOI: 10.1093/narcan/zcad045

Lee, R., Knutson, T., Munro, S., Miller, J., Heltemes-Harris, L., Jepsen, K., and Farrar, M. (2022) Nuclear corepressors NCOR1/NCOR2 regulate B cell development, maintain genomic integrity, and prevent transformation. Nature Immunology, 1-14, DOI: 10.1038/s41590-022-01343-7

Jellison, B., Elsmore, K., Miller J., NG, G., Ninokowa, A., Hill, T., and Gaylord, B. (2022) Low-pH Seawater Alters Indirect Interactions in Rocky-Shore Tidepools. Ecology and Evolution, DOI: 10.1002/ece3.8607

Warren, W., Aspiras, A., Boggs, T.E., Borowsky, R., Carlson, B., Damen, F., Ferrufino, E., Gross, J., Keene, A., Kenzior, A., Kowalko, J., Lemieux, M. E., McGaugh, S., Miller, J. T., Mommersteeg, M., Moran, R., Peuß, R., Riddle, M., Sifuentes-Romero, I., Stahl, B., Sung, J. Y., Tabin, C., Thakur, S., Rohner, R. (2021) A Chromosome-level Genome of _Astyanax mexicanus. Surface Fish for Comparing Population-specific Genetic Differences Contributing to Trait Evolution. Nature Communications, DOI: 10.1038/s41467-021-21733-z

Miller, J., Reid, N., Nacci, D., Whitehead, A. (2019) Developing a High-Quality Linkage Map for the Atlantic Killifish, Fundulus heteroclitus. G3: Genes, Genomes, Genetics, DOI: 10.1534/g3.119.400262

Rochman, C., Tahir, A., Williams, S., Baxa, D., Lam, R., Miller, J., Teh, F.C., Werorilangi, S., Teh, S. J. (2015) Plastic in seafood: Plastic Debris in Fish and Bivalves Sold for Human Consumption. Scientific Reports, DOI: 10.1038/srep14340

Dubansky, B., Whitehead, A., Miller, J., Rice, C. D., & Galvez, F. (2013) Multitissue Molecular, Genomic, and Developmental Effects of the Deepwater Dorizon Oil Spill on Resident Gulf killifish (Fundulus grandis). Environmental Science and Technology, DOI: 10.1021/es400458p

Kolok, A., Miller, J., Schoenfuss, H. (2012) The Mini Mobile Environmental Monitoring Unit: a Novel Bio-Assessment Tool. Journal of Environmental Monitoring, DOI: 10.1039/C1EM10703H

Wisenden, B., Karst, J, Miller, J., Miller, S.D. Fuselier, L. (2008) Anti-Predator Behavior in Response to Chemical Cues in Umbra limi. Environmental Biology of Fishes, DOI: 10.1007/s10641-007-9255-0

INVITED PRESENTATIONS:

Miller, J. (2026) ‘Use of eDNA in Understanding Lake Biodiversity, Cyanotoxins, and Invasive Species.’ CT Lakes Symposia at WCSU, Virtual.

Miller, J. (2026) ‘eDNA and the New England Seafood Industry.’ NERACOOS Annual Meeting, Portsmouth, NH.

Miller, J. (2026) ‘Spider Webs and Climate Resilient Forests: A New Tool for Monitoring Biodiversity and Species of Concern.’ Yale Forest Forum Seminar Series, Eastford, CT.

Miller, J. (2019) ‘Ocean Change Evolution.’ Invited lecture, Bowdoin College.

PLATFORM PRESENTATIONS:

Miller, J, Clark, B., Champlin, D., Nacci, D., Whitehead, A.W. (2018). ‘Genetic Architecture of Pollution Resistance in Multiple Populations of Killifish.‘ Society for Environmental Toxicology and Chemistry.

Miller, J., Cherr, G., Whitehead, A. (2015). ‘Aquatic Copper-Oxide Nanoparticle Exposure May Target Osmoregulatory Plasticity of Fish from Salinity Variable Environments.‘ Northern California Society of Environmental Toxicology and Chemistry.

Miller, J., Martinovic, D., Bartel, SE., Schoenfuss, HL. (2011). ‘Abiotic Influences on Estrogenic Biomarker Expression in Riverine Conditions of Exposure to Treated Wastewater.‘ International Conference on Pollutant Responses in Marine Organisms.

Miller, J., Martinovic, D., Bartel, SE., Schoenfuss, HL. (2011). ‘Bioassessment of Wastewater’s Estrogenic Impacts: Various Methods of Exposure. Can Biomarkers Be Altered Differentially?‘ Mid-West Society of Environmental Toxicology and Chemistry.

POSTER PRESENTATIONS:

Miller, J., Clark, B., Champlin, D., Nacci, D., Whitehead, A.W. (2018). ‘Genetic Architecture of Pollution Resistance in Multiple Populations of Killifish.‘ Genetics Society of America: Population, Evolutionary, and Quantitative Genetics.

Miller, J., Clark, B., Champlin, D., Nacci, D., Whitehead, A.W. (2017) ‘The Genetic Architecture of Pollution Resistance Among Convergent Populations of Killifish (Fundulus heteroclitus).‘ National Meeting for Society for Environmental Toxicology and Chemistry.

Miller, J., Cherr, G., Whitehead, A. (2014). ‘Impairment of Killifish Osmoregulatory Function by Aquatic Nano-Copper Oxide Exposure.‘ Western Society of Naturalists Annual Meeting.

Miller, J., Pilcher, W., Champlin, D., Proestou, D., Nacci, D., Whitehead, A.W. (2012). ‘Genomic responses to PAHs in 2 pollution tolerant populations of Fundulus heteroclitus.‘ National Meeting for Society for Environmental Toxicology and Chemistry.

Miller, J., Martinovic, D., Bartel, S. E., Schoenfuss, H. L. (2010). ‘Quantifying Exposure & Effects of Endocrine Active Chemicals in the Environment through Parallel Field and Laboratory Studies of Bioindicators in Pimephales promelas.‘ National Meeting for Society of Environmental Toxicology and Chemistry.

TEACHING EXPERIENCE:

• Instructor - University of New Hampshire, Genomics and Bioinformatics (2022-present)
• Instructor - University of New Hampshire, Population Genomics (2022-present)
• Instructor - University of New Hampshire, Genetics Lab (2027)
• Guest Lecture - University of Minnesota, Zoology (November 25th 2019)
• Instructor - Data and Software Carpentry Workshops
  • Genomics (R/Bash), California State University, Monterey Bay (March 22-23 2018)
  • Python (Python/Git/Bash), Minnesota State University (October 27-28 2017)
• Teaching Assistant - Data Intensive Biology Summer Institute, UC Davis
  • Analyzing Next-Generation Sequencing Data Workshop (Summer 2017 and 2018)
• GK-12 Teaching Fellow - National Science Foundation:
  • UC Davis Bodega Marine Laboratory (Fall 2014-Spring 2015)
• Graduate Teaching Assistant - University of California, Davis
  • Introduction to Biology: Essentials of Life on Earth (Fall 2017-2018)
  • Introduction to Biology: Principles of Ecology and Evolution (Fall 2016-2017)
  • Environmental Toxicology: Biological Effect of Toxicants (Fall 2014)
• Graduate Teaching Assistant - Louisiana State University
  • Introduction to Biology for Science Majors (Fall 2011-Spring 2012)

PREVIOUS POSITIONS:

Biological Science Technician – United States Park Service (Summer 2010)
Wilderness Technician – United States Forest Service (Summer 2008 and 2009)
Outdoor Education Coordinator - Student Conservation Assoc. (Winter 2007-Summer 2008)

MENTORING:

Graduate Advisees

Adeline Casali, Ph.D., Integrative Biology (2026-present)

Graduate Committees

Zerubabel Demeke, Ph.D., Natural Resource Management, Hyena Diet via Scat Metabarcoding (2026-current)
Javier Arambula Rascon, M.S., Molecular & Cellular Biology, Transcriptomic Profiling of the Actinorhizal Symbiosis: A Dual-Species Approach (2026)
Madison Hurley, Ph.D., Marine Biology, Linking Environmental Change, Microbial Community Assembly, and Function During a Novel Marine Phytoplankton Bloom Using Multi-Omics (2026)
Mia Smith, M.S., Agriculture, Nutrition, and Food Systems, Melon (Cucumis melo) Diversity and Grafting Performance for New England Growers (2026-present)

AFFILIATE MEMBERSHIPS:

Genetics Graduate Faculty, University of New Hampshire (2026-present)
Integrative Biology Graduate Faculty, University of New Hampshire (2026-present)
Bioinformatics Graduate Faculty, University of New Hampshire (2024-present)
Molecular Pathology & Genomics, UMN (Winter 2020-Current)
Center for Population Biology, UC Davis (Winter 2017-2019)
Data Science Initiative, UC Davis (Winter 2017-2019)
Coastal and Marine Sciences Institute, UC Davis (Winter 2016-2019)

CONSULTING:

Tetra Tech Inc. and MassDEP, Diatoms, DNA Metabarcoding QA/QC, Methods, Index Development of Stream Health (2026-2027)

COMMITTEES SERVICE AND TRAINING:

Graduate Program Coordinator, Bioinformatics M.S. and Molecular and Cellular Biotechnology M.S., University of New Hampshire (2026-present)
Special Issue Guest Editor, Genes, Environmental DNA in Ecology (2027)
Amazon Web Service Developer Training with NIH STRIDES (Summer 2020)
Evolutionary Applications Reviewer (2018-Current)
UC Davis Bodega Marine Laboratory Marine Ecology Outreach (2013-2018)
UC Davis Pharmacology and Toxicology Graduate Admissions Committee (Winter 2013)
NorCal Society for Environmental Toxicology and Chemistry Board of Directors (2014-2015)
Archbold Biological Station Volunteer Herpetology and Stream Ecology (Summer 2011)