Shelly Wanamaker, Ph.D.

Research Scientist I

Shelly comes to GMGI with an innate love for New England and the ocean, having grown up on the North Shore. She joined GMGI in 2021 after spending 10 years on the West Coast, where she developed her interests in marine science. Shelly did postdoctoral research at the University of Washington’s School of Aquatic and Fishery Sciences, studying how environmental factors affect shellfish and salmon health using omics measurements to characterize sensitivity or tolerance traits.

Prior to her postdoctoral work, Shelly completed a year-long National Science Foundation (NSF) Graduate Research Internship at National Oceanic and Atmospheric Administration’s (NOAA)’s Northwest Fisheries Science Center, investigating how ocean acidification affects the physiology of Dungeness crabs and pteropods (sea snails).

Shelly got her Ph.D. in Biological Sciences from the University of California San Diego. In addition to her research at NOAA, her dissertation work included developing a sequencing technology capable of testing millions of protein interactions at one time, which she used to map out different biological pathways in the mustard plant Arabidopsis thaliana (a model for plant research akin to the mouse model for human research).

Shelly has a B.S. in Biochemistry from Simmons College in Boston and also worked as a Research Technician at the Center for Cancer Systems Biology (CCSB), Dana Farber Cancer Institute, in the lab of Dr. Marc Vidal (a GMGI founder and board member), where she contributed to large-scale mapping of protein interactions in human and disease genomes.

Outside of research, Shelly enjoys all outdoor activities, from team sports to trail running, hiking, camping, fly fishing, climbing, surfing, and snowboarding with friends, family, and her dog.

Education

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

Research Interests

I’m passionate about using genomics technologies to improve how we monitor aquatic animal health. With climate change influencing the emergence and spread of both new and old diseases, aquatic animals face increasing challenges in both wild and aquaculture settings.

Restoring and conserving wild populations, as well as maintaining aquaculture populations, in order to meet growing worldwide food demands requires better tools to monitor animal health. We can use genomics technologies to survey millions of molecules simultaneously and identify particular molecular markers that can indicate good health or poor health.

We can then develop diagnostic tests for these markers to help us better monitor aquatic animal health in the lab, in the wild, and in aquaculture settings. My research at GMGI involves using a combination of genomic approaches and developing innovative, portable, and economical molecular tests to help address critical and complex challenges faced by aquatic animals and the human communities that rely on them.

Research Profile Links

https://shellywanamaker.github.io/

https://github.com/shellywanamaker

https://www.linkedin.com/in/shelly-wanamaker-ph-d-670b6121

https://orcid.org/0000-0001-6904-4149

https://www.researchgate.net/profile/Shelly-Wanamaker

https://scholar.google.com/citations?user=j2jUUqMAAAAJ&hl=en

Research Projects

Venkataraman, Y., Huffmyer, A., White, S., Downey-Wall, A., Ashey, J., Becker, D., Bengtsson, Z., Putnam, H., Strand, E., Rodriguez-Casariego, J., Wanamaker, S., Lotterhos, K., Roberts, S. (2024). DNA methylation modulates transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica). bioRxiv, 2024-04. doi: https://doi.org/10.1101/2024.04.04.588108

Major, S.R., Harke, M.J., Cruz-Flores, R., Dhar, A.K., Bodnar, A.G. and SA Wanamaker. (2023) Rapid detection of DNA and RNA shrimp viruses using CRISPR-based diagnostics. Applied and Environmental Microbiology. 0:e02151-02122. https://journals.asm.org/doi/10.1128/aem.02151-22

HM Putnam*, SA Wanamaker*, SJ White, LH Spencer, B Vadopalas, A Natarajan, J Hetzel, E Jaeger, J Soohoo, C Gallardo-Escárate, FW Goetz, and SB Roberts. (2023) Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in an important marine bivalve.  Proceedings of the Royal Society B. In review. Preprint: https://doi.org/10.1101/2022.06.24.497506. * indicates co-first authorship.

SJ Gurr, SA Wanamaker, B Vadopalas, SB Roberts, and HM Putnam. (2022) Acclimatory gene expression of primed clams enhances robustness to elevated pCO2. Molecular Ecologyhttps://doi.org/10.1111/mec.16644.

SA Wanamaker*, YR Venkataraman*, MR Gavery, SB Roberts, D Bhattacharya, A Downey-Wall, JM Eirin-Lopez, KM Johnson, KE Lotterhos, JR Puritz, and HM Putnam. (2021) Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13542. * indicates co-first authorship.

SA Wanamaker, 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 Genomicshttps://doi.org/10.1186/s12864-020-07127-3.

SJ Gurr, SA Wanamaker, B Vadopalas, SB Roberts, and HM Putnam. (2021) Repeat exposure to hypercapnic seawater modifies growth and oxidative status in a tolerant burrowing clam. Journal of Experimental Biology. 224(13): jeb233932. https://doi.org/10.1242/jeb.233932.

BC Willige, M Zander, CY Yoo, A Phan, RM Garza, SA Wanamaker, Y He, JR Nery, H Chen, M Chen, JR Ecker, and J Chory. (2021) Phytochrome-interacting factors trigger environmentally responsive chromatin dynamics in plants. Nature Genetics. 53:955-961. https://doi.org/10.1038/s41588-021-00882-3.

SA Wanamaker*, YR Venkataraman*, MR Gavery, SB Roberts, D Bhattacharya, A Downey-Wall, JM Eirin-Lopez, KM Johnson, KE Lotterhos, JR Puritz, and HM Putnam. (2021) Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13542. * indicates co-first authorship.

SA Wanamaker, 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. https://doi.org/10.1101/574798.

SA Wanamaker. (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. https://escholarship.org/uc/item/0491n31k

SA Wanamaker, 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. https://doi.org/10.1038/nmeth.4343.

SA Wanamaker, 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. Exchhttps://doi.org/10.1038/protex.2017.058.

X Yang, [15 others], SA Wanamaker, [20 others], and M Vidal. (2016) Widespread expansion of protein interaction capabilities by alternative splicing. Cell. 164(4):805-817. https://doi.org/10.1016/j.cell.2016.01.029.

T Rolland, [53 others], SA Wanamaker, [14 others], and M Vidal. (2014) A proteome-scale map of the human interactome network. Cell. 159(5):1212-1226. https://doi.org/10.1016/j.cell.2014.10.050.

R Corominas, [8 others], SA Wanamaker, [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. https://doi.org/10.1038/ncomms4650.

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. https://doi.org/10.1038/nature11288.