Shelly Wanamaker, Ph.D.

Research Scientist I

Originally from Massachusetts, Shelly joins us from the West Coast where she spent the past 10 years. After completing her B.S. at Simmons College in Boston, she continued as a Research Technician in Marc Vidal’s lab at the Center for Cancer Systems Biology (CCSB), Dana Farber Cancer Institute in Boston where she became fascinated with big data and how network biology brings resolution to genotype-to-phenotype relationships. In 2011, Shelly joined Joe Ecker’s Genomic Analysis Lab at the Salk Institute in San Diego as a Research Assistant and was inspired to pursue a Ph.D. while developing a new high throughput assay for mapping protein interactions (CrY2H-seq). Shelly began the Biological Sciences Ph.D. program in 2013 where she continued in Joe Ecker’s lab now focused on applying CrY2H-seq to understanding protein interactions that directly contribute to gene regulation in the model plant Arabidopsis thaliana. Towards the end of the program, she became interested in how systems biology could be used in applied research and completed a year-long NSF Graduate Research Internship at NOAA’s Northwest Fishery Science Center using omics to investigate how physiology and genetics in marine invertebrates are affected by ocean acidification. She returned to San Diego in the summer of 2018, completing her dissertation “High resolution molecular networks from novel ‘omics’ approaches elucidate survival strategies in organisms from land to sea”, and received my Ph.D. In the Fall of 2018, Shelly began as a Postdoctoral Researcher in Steven Roberts’ lab in the School of Aquatic and Fishery Sciences at University of Washington where she studied how the environment impacts marine animals at the physiological and molecular systems level. She conducted experiments that simulated various ocean conditions and used omics technologies (like epigenomics, proteomics, and metabolomics) in combination with physiological assays to measure animal response. In March of 2021, Shelly started her current position as a Research Scientist at Gloucester Marine Genomics Institute. Outside of research, Shelly enjoys all outdoor activities from co-ed team sports to trail running, hiking, backpacking, camping, fly-fishing, climbing, and snowboarding with friends, family, and her dog.


978-879-4575 x 111


Research Interests

I am broadly interested in leveraging genomics technologies to improve how aquatic animal health is monitored. With climate change progression and the emergence of new diseases, aquatic animals are facing increasing health challenges in the wild and in aquaculture settings. Efforts to restore and conserve wild populations as well as maintain aquaculture populations to meet the growing food demands worldwide all require tools to assess animal health. Genomics technologies have the power to survey millions of molecules simultaneously and identify particular molecular markers that can indicate good health or poor health. These markers can then be used to develop diagnostic tests to improve how aquatic animal health is monitored in the field. Towards this my research at GMGI involves a combination of genomic approaches and innovative molecular diagnostic assay development.


2018 - Ph.D. Biology (Cell, Molecular, Genetics track), University of California San Diego
2010 - B.S. Biochemistry, Simmons University (formerly Simmons College)

Prior Positions

2018-2021: Postdoctoral Researcher, School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA USA
2013-2018: Graduate Student Researcher, Salk Institute for Biological Studies, La Jolla, CA USA
2011-2013: Research Assistant II, Salk Institute for Biological Studies, La Jolla, CA USA
2010-2011: Lab Technician, Center for Cancer Systems Biology, Dana Farber Cancer Institute, Boston, MA USA

Research Profile Links

Research Projects


SA Trigg, KM Mitchell, R Elliott Thompson, B Eudeline, B Vadopalas, EB Timmins-Schiffman, SB Roberts. (2020) Temporal proteomic profiling reveals critical developmental processes and temperature-influenced differences in a bivalve mollusc. BMC Genomics

SJ Gurr, SA Trigg, B Vadopalas, SB Roberts, and HM Putnam. (2020) Repeat Exposure to Hypercapnic Seawater Modifies Performance and Oxidative Status in a Tolerant Burrowing Clam. Journal of Experimental Biology. (in review). bioRxiv

BC Willige, M Zander, A Phan, RM Garza, SA Trigg, Y He, JR Nery, H Chen, JR Ecker, and J Chory. (2020) PHYTOCHROME INTERACTING FACTORs trigger environmentally responsive chromatin dynamics. Nature Genetics. (In review). bioRxiv

ET Montaño, [32 others], SA Trigg, K Pogliano, and J Pogliano. (2020) Isolation and Characterization of Streptomyces Bacteriophages and the Biosynthetic Arsenals of their Associated Hosts. PLoS One. (In review). bioRxiv

SA Trigg, P McElhany, M Maher, D Perez, DS Busch, and KM Nichols. (2019) Uncovering mechanisms of global ocean change effects on Dungeness crab (Cancer magister) through metabolomics analysis. Scientific Reports.

SA Trigg. (2018) High-resolution molecular networks from novel’omics’ approaches elucidate survival strategies in organsisms from land to sea. UC San Diego. ProQuest ID: Trigg_ucsd_0033D_17575. Merritt ID: ark:/13030/m5t77f99.

SA Trigg, RM Garza, A MacWilliams, JR Nery, A Bartlett, R Castanon, A Goubil, J Feeney, R O’Malley, SC Huang, ZZ Zhang, M Galli, and JR Ecker (2017) CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 14(8):819-825.

SA Trigg, RM Garza, A MacWilliams, JR Nery, A Bartlett, R Castanon, A Goubil, J Feeney, R O’Malley, SC Huang, ZZ Zhang, M Galli, and JR Ecker (2017) CrY2H-seq interactome screening. Protoc. Exch

X Yang, [15 others], SA Trigg, [20 others], and M Vidal. (2016) Widespread expansion of protein interaction capabilities by alternative splicing. Cell. 164(4):805-817.

T Rolland, [53 others], SA Trigg, [14 others], and M Vidal. (2014) A proteome-scale map of the human interactome network. Cell. 159(5):1212-1226.

R Corominas, [8 others], SA Trigg, [18 others], M Vidal, and LM Iakoucheva. (2014) Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nat commun. 5:3650.

O Rozenblatt-Rosen, [36 others], S Wanamaker, [13 others], and M Vidal. (2012) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature. 487(7408):491-495.