Research Opportunities

At Hopkins Marine Station, we encourage Stanford undergraduates to get a taste of our world-class research—early and often. You can collaborate with grad students, post docs, and faculty on a wide range of research activities during the academic year and over the summer.

*Please note: these internship and research opportunities are open to current Stanford students only.*

Summer

There are two research options for undergraduates: HI-SURF or Major Grants. Students typically spend 10 weeks living and learning at the Hopkins Marine Station in Pacific Grove on the Monterey Peninsula, two hours from main campus.

HI-SURF

Application portal now open. Application due: February 15, 2024.

Hopkins Internships - Summer Undergraduate Research Funds (HI-SURF) allow you to start conducting research at Hopkins in the summer after your freshman year. These are paid summer research internships where students work directly with Hopkins faculty, postdoctoral scholars, graduate students, and research staff on ongoing faculty research projects. Internships are open only to current Stanford undergraduates. Funding: $7500 stipend

Summer 2024 Projects

Block Lab

Image Analysis for White Shark Behavior

Work with the Block Lab at Hopkins Marine Station to analyze the morphology and behavior of Northeast Pacific white sharks. This student will review underwater footage of white sharks at local field sites and create a classification and labeling structure for unique morphological and behavioral traits. Specifically, this student will classify patterns such as tag presence, presence of claspers (indicating sex), scarring, unique swimming patterns, and presence of conspecifics. This labeling process can be manual, or assisted with computer vision solutions. This student will also be responsible for assisting with boat-based field work during the summer Block Lab juvenile white shark field season. Experience with major programming languages (Python, Matlab, or R) preferred, but not required.

Epigenetic Aging of Highly Migratory Fishes

We are developing novel techniques for non-invasive aging of fish (bluefin tuna and white sharks), an approach termed epigenetic aging, using DNA methylation techniques. An intern will help design primers, perform DNA extractions and methylation, as well as conduct sequencing and analyses.

De Leo Lab

Automated Identification and Monitoring of Seasonal Water Bodies for Schistosomiasis Snail Habitat

In West Africa, millions of people suffer from schistosomiasis, a debilitating disease caused by parasitic worms infecting peoples’ blood vessels. This disease is spread via small freshwater snails which are ubiquitous across the small, shallow water bodies used by rural villages for everyday tasks. Fertilizer run-off from farm inputs fuels the rapid growth of aquatic vegetation and phytoplankton, which provides forage and refuge for snail populations. Resources for testing and treating at-risk populations are limited, and management of the snails themselves is necessary to effect long-term control of disease transmission. Transmission dynamics occur on a scale smaller than is observable by Landsat or Sentinel satellite platforms, since the water access areas where people become infected are typically only a few tens of meters wide at most. Planet Labs, Inc, has launched hundreds of small satellites which now provide imagery worldwide at 0.5 - 300 cm/pixel, allowing the observation of schistosomiasis contact sites. These satellites provide near daily imagery data, enabling researchers to track factors key to transmission and gauge its potential intensity, such as area of water, area of aquatic vegetation and aquatic plant health, a proxy for potential snail forage. Integrating these variables across time, we can estimate relative risk for individual villages at different times of the year, providing information on where and when to target limited resources allocated for people infected with schistosomiasis. We are looking for 1 or 2 summer interns to help develop a prototype machine learning image classification model on Planet Labs satellite imagery. Students should have an interest in remote sensing, disease ecology, freshwater ecology, and/or epidemiology. Beginner level or better experience in GIS, Python, and/or Google Earth Engine is desired. The primary objective will be the development and evaluation of an image classification model for surface water, aquatic vegetation, and rural village location in an area of Northern Senegal.

Boosting K-12 education in Disease Ecology and Parasitic Diseases of Poverty

We are looking for highly motivated students passionate about improving k-12 education in disease ecology, vector borne diseases and parasitic diseases of poverty in the USA and in the Global South. Specifically, we intend to design age- and cultural-appropriate, educational programs, in collaboration with partners from Cote d’Ivoire, Madagascar, Senegal and Brazil, to engage school age children and help them to gain a deeper understanding of parasites, a too-often neglected component of biodiversity with a significant conservation, veterinary and public health importance. The education activities will tentatively include traditional teaching modules and also use of Foldscope Paper Microscopes and class games. With reference to the latter, we recently developed “Parasite Pioneers'', a prototype bingo game inspired by a traditional Mexican lotería game. The game has tiles depicting 54 human, animal, and environmental parasites with their corresponding host information. The graphic format maintains a balance between simplicity and necessary details on parasites’ life cycle. The present game includes parasites across a range of domains and spanning a variety of different transmission pathways. In addition to the lotería cards and accompanying pin buttons for interactive gameplay, we also compiled flashcards, guidelines, and fact sheets for school instructors to facilitate the administration of the game in the classrooms also when teachers don’t have a specific background in parasite ecology. One or more students will develop region-specific versions of the game for Africa, Latin America, and North America. Other students will collaborate with our country partners to develop age-appropriate and country specific teaching modules.

Development of Shiny Apps for Population Dynamics in Disease Ecology and Fishery Management

Professor De Leo has developed a series of R scripts for his courses in population dynamics, disease ecology and fishery management. He is looking for a highly motivated student with documented experience in R programming, preferably also good knowledge of ggplot2 and, ideally, experience in the development of Shiny App. Basic knowledge of ecology and/or disease dynamics is welcome but not necessary. Project involves developing a Shiny App based on his course R scripts to allow attendants with little or no knowledge of R and programming to be able to run simulations, explore the consequence of alternatives hypotheses on model parameters, and run simple sensitivity analyses; the app will help them manage fisheries in terms of disease ecology and population dynamics.

Gilly Lab

Control of Neuromuscular Systems and Behavior in Invertebrates

The Gilly lab is seeking 1 or 2 students to work on a variety of experimental research on invertebrates, including:

Control of color changing in the skin of squid and octopus by a network of neuromuscular chromatophores.
Comparison of the basic elements of feeding behavior in invertebrates with vast differences in their nervous systems --- cephalopods versus echinoderms.
Control of locomotion, feeding, and spawning by excitable epithelia and nerve nets in jellyfish.

For more information: https://gillylab.stanford.edu/

Goldbogen Lab

Using Biologging tags and Remote Sensing to Study the Integrative Biology of Large Whales

Gigantic marine filter feeders evolved in several independent lineages of mammals and fish. The most recent and largest radiation of this guild are represented by baleen whales (Mysticeti). Mysticetes evolved gigantic body sizes only several million years ago after the onset of intensified upwelling along coastal ecosystems, where modern whale ecosystems feature seasonally abundant and densely patched prey. We are therefore fortunate to not only be living in a time of giants but also at a time where biologging tags and remote sensing methods allow us to study life at the upper extreme of body mass. Projects may be available to use some combination of these methods to ask different questions about the form, function, and evolution of baleen whales and their prey.

Micheli Lab

Assessing the Effect of Declining Seagrass Health on Vertebrates of Higher Trophic Levels in the Republic of Palau

Nearshore seagrass environments, one of the most widespread coastal ecosystems on the planet, perform countless ecosystem services including their contribution to cultural significance, acting as fish nursery habitat, and enhancing coastal biodiversity. However, the threats to and value of seagrass ecosystems is severely understudied in the tropics, despite this region being home to the most seagrass species. In the Republic of Palau, a small island nation in the tropical Pacific with a long history of stewardship of their natural resources, they have found their seagrasses to be particularly vulnerable to decline. Therefore, in collaboration with Palau International Coral Reef Center (PICRC), we plan to uncover the impacts of seagrass decline on the many fish species that rely on them. We are looking for a student interested in analyzing video data of fish from several seagrass sites in Palau. They would help identify species, densities, and life stages of fish at several varying sites. The work also consists of analyzing seagrass blades for disease and/or grazer marks and working with precent cover, blade length, and plant density data to assess seagrass bed health. With these sets of data, we will be able to look at the relationship between health of a seagrass bed and the biodiversity, density, and size and age structure of fishes.

Investigating the Effects of Ocean Acidification and Warming on Herbivore-algal Interactions

Marine herbivores exhibit affinities for food types that ultimately enhance their fitness and survival, but these preferences may shift under future climate change scenarios due to impacts on both herbivores and their foods. This project will explore the effects of two climate change stressors, ocean acidification and warming, on the palatability of juvenile giant kelp, Macrocystis pyrifera. Using controlled laboratory experiments, the mentee will grow kelp under different pH and temperature combinations and measure responses such as growth rates, nutritional quality (carbon to nitrogen ratios), and caloric content over time. Three pH treatments, including control (8.1 pH), moderate (7.5 pH) and extreme (7.3 pH) and three treatments (12 °C, 18 °C, 24 °C) will be utilized for a total of six treatments. The mentee will prepare samples of algae for processing in an elemental analyzer to measure C:N ratios. The mentee will then evaluate if bottom-up changes to kelp characteristics impact palatability and grazer-algal interactions through feeding preference trials with invertebrates (sea urchins and snails). The student will graph and analyze their results statistically using R. Disentangling the mechanisms for how rising oceanic CO2 causes shifts in species interactions will be valuable for understanding and predicting ecosystem-scale change under future OA.

Global patterns in crustose coralline algae carbonate production

Crustose coralline algae (CCA) are ubiquitous components of temperate benthic habitats and critical contributors to their diversity and structural complexity. The precipitation of calcium carbonate (CaCO3) by CCA also supports numerous essential geo-ecological functions, such as the production of reef framework, the creation of habitat complexity, and the generation of sediment. While in situ carbonate production rates of coralline algae have been quantified in tropical ecosystems and rhodolith beds, estimates in temperate reefs are scarce. This knowledge gap hampers our understanding of the functions CCA performs and how those functions may be affected in response to environmental change. This project will quantify the recruitment and carbonate production of CCA in temperate reefs across the globe. In July 2023, we deployed PVC cards at three different sites in Monterey Bay to recruit CCA under the kelp canopy. These cards will be recovered in July 2024 for further sample preparation and analysis. The cards will be photographed for encruster composition and analysed for their total mass of carbonate production.

BSURP Projects based at Hopkins

For more information and application: Click Here

Voskoboynik Lab

Studying the Evolution of Chordate Regeneration Through Comparative Studies

Many invertebrates can regenerate their entire bodies, while vertebrates can regenerate only certain tissues and organs. To better understand why some animals can regenerate lost or damaged organs while others cannot, we study, the stem cell biology and regeneration capacity of ascidians, invertebrate chordates with highly diverse development and regeneration. In this project, we will study short- and long-term changes in the cellular and molecular dynamics of regeneration in ascidian species with different regeneration capacities. We will use this valuable data in a comparative analysis to identify regeneration-specific factors that distinguish the two groups of species.

Major Grants

For students who want to design their own research projects, grants are available through Stanford's undergraduate Research and Independent Study program; priority is given to juniors. Unlike VPUE grants, where a student joins a pre-existing effort, these grants require students to draw up a research proposal in collaboration with a member of the Hopkins faculty.

Applications are now closed; they will reopen in spring 2024.

Academic Year

While studying at Hopkins, you can also work on a research project under the supervision of one of the Hopkins faculty—and get additional academic credit in BIOHOPK 199 Guided Research. Our faculty is available to help you identify appropriate research opportunities—before you arrive or after you get here.

To see what we are working on, explore our Faculty Research Page.