Dr. Julian Damashek
I am a microbial ecologist and biogeochemist who loves thinking about anything related to microbes, nutrients, or water. I teach about ecology, microbiology, computational biology, genomics, oceanography, and limnology. I enjoy developing active learning projects, teaching about data analysis and presentation, and am always learning ways to improve my inclusive teaching methods.
If you are interested in doing research in my lab or collaborating, please contact me! We are always excited to talk about new collaborations or projects.
Email me: judamash [AT] utica [DOT] edu
CURRENT RESEARCH STUDENTS
Tara Smith (’23)
Tara is refining methods for measuring N isotopes in aquatic samples using MALDI-TOF, in collaboration with colleagues in the chemistry department at Colgate University. Tara is shown collecting duckweed-infested water from the Mohawk River, ignoring the plants to look at the more interesting stuff (nitrogen).
Leah Griffin (’25)
Leah will be starting a project this summer investigating antibiotic resistance in local aquatic ecosystems, funded by the LSAMP program!
Tyler LaFramboise (’24)
Tyler initially applied his computer wizardry to bin and refine hundreds of metagenome-assembled genomes from creek water metagenomes, and is now focusing on studying urea-cycling genes in metagenomes.
Ally Marsh (’23)
Studying nitrogen in the Mohawk River and Oneida Lake. Ally also enjoys tromping through bogs and sampling water from pitcher plants.
Bella Raux (’22)
Investigating dog-owner microbiomes by analyzing 16S amplicon data. Bella is now a R pro (DADA2, phyloseq, tidyverse) and definitely loves computers. She is shown here being not cold on Piseco Lake. Bella will be starting veterinary school at Cornell in fall 2023!
Brie Lohmann (’23)
Brie developed field and lab techniques to study local aquatic microbial communities. She is now using molecular techniques to combine fecal source tracking with N biogeochemistry throughout the Mohawk River watershed. She also clearly takes great joy in collecting bivalves from Oneida Lake!
PREVIOUS RESEARCH STUDENTS
Tanya Kuts (’22)
Tanya studied urea and ammonium cycling in Oneida Lake.
Kristina Kuts (’24)
Kristina studied nitrite cycling in Oneida Lake.
Trinity Howell (Hampton University ’22)
Trinity used machine learning software to identify sources of fecal contamination in estuaries using 16S rRNA sequence data. She was funded by the National Summer Undergraduate Research Project (NSURP) 2021 program.
Nikki Pickett (’21)
Nikki fell in love with debugging computer errors while taking a bioinformatics course and completed a research project studying distribution of antibiotic resistance genes in San Francisco Bay using shotgun metagenomic data. She also definitely loved measuring nutrients in the lab…
Carrilynn Garrett (’23)
Carrilynn worked on starting a field project studying nitrogen cycling in the Mohawk River.
Arijana Dautovic (’23)
Arijana worked on a field project studying microbes in the Mohawk River. She also really enjoyed measuring earthworms.
Matt Fedullo (’20)
Matt designed a project studying antibiotic resistance genes in the Mohawk River near his hometown of Amsterdam, NY. He successfully never fell into the river. Matt will be starting a PA program at Marrywood University next year!
RESEARCH STUDENTS BEFORE UTICA
University of Georgia (Hollibaugh Lab)
Hailey Goldberg (UGA ’20)
Hailey dove into bioinformatics to learn about the ecology of freshwater Thaumarchaeota from using shotgun metagenomes. She quickly became an expert at finding typos in scripts. Hailey completed a MS in Biology (Recombinant DNA Technology track) at NYU and just started a Ph.D. in the BCMB Allied program at Weill Cornell Medicine Graduate School of Medical Sciences!
Aimee Okotie-Oyekan (UGA ’17)
Aimee first learned the fun of working with Thaumarchaeota in the laboratory before mastering the art of DNA extraction and qPCR, and is a co-author on a manuscript on marine polyamine-N oxidation published in Limnology & Oceanography, a manuscript on MGII Euryarchaeota ecology in the South Atlantic Bight published in ISME Communications, and a forthcoming manuscript on nitrification in coastal Antarctic waters (currently under review…). She is currently pursuing a MS in the Environmental Studies Program at the University of Oregon and has an excellent website. We occasionally took breaks from sampling at Sapelo Island to go tromp around the insanely beautiful and desolate beaches!
Stanford University (Francis Lab)
Tynan Challenor (Stanford ’17)
Tynan worked on a pilot project measuring nitrification rates from waters in Artesian Slough (in collaboration with the Casciotti lab and the San José-Santa Clara Regional Wastewater Facility), which he presented at the AGU Fall Meeting in 2014. He spent many hours in front of machines measuring nutrients and isotopes and then learned the wonders of qPCR, and completed a thesis project studying ammonia oxidizers the Sacramento River. After completing a MS in Biomedical Informatics at Stanford, Tynan now works for the UC Berkeley Labor Center.
Aubriana Menendez (Stanford ’17)
Aubriana worked on a pilot project sequencing amoA genes from Artesian Slough water (in collaboration with the San José-Santa Clara Regional Wastewater Facility) and currently works as a user experience researcher at Change Healthcare. Check out her website!
Kade Pettie (Amherst College ’15)
Kade analyzed ammonia-oxidizing communities in samples from the Chukchi Sea (in collaboration with the Arrigo lab) and is a co-author on an article published in Aquatic Microbial Ecology. He excelled at troubleshooting endless qPCR issues. Kade is currently a PhD student in Biology at Stanford.
Kofi Christie (Morehouse College ’14)
Kofi was a SURGE scholar and did a pilot project using stable isotope incubations to measure nitrification rates in creeks at the Baylands Nature Preserve (Palo Alto, CA). Kofi completed a PhD in Environmental Engineering at Vanderbilt, a Presidential Postdoctoral fellowship at Princeton, and is now an Assistant Professor of Environmental Engineering at Louisiana State University! His bowties rivaled Julian’s. (Photo: Stanford SURGE program)
Yari Greaney (Stanford ’15)
Yari was a DNA extracting pro and processed many, many sediment samples from San Francisco Bay. She completed a BS and MS in Earth Systems at Stanford and now works as a Program Manager for Local Politics and Environmental Justice at Preston-Werner Ventures. (Photo: Stanford Splash!)