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.*

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 due: February 15, 2023 APPLY

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

HI-SURF Summer 2023 Projects

Block Lab

Comparative Cardiac Physiology in Teleost Fishes

Internship available at the Tuna Research and Conservation Center (TRCC) located at Hopkins Marine Station utilizing cutting edge biologging tags to compare the cardiac physiology of various teleost fishes housed at the location. These biologging techniques will be used across various species housed at the TRCC, where the student will develop and execute controlled experiments within the facility to elucidate the differences in cardiac physiology at different temperatures and if possible under variations in environmental conditions (Oxygen). A background and experience with major programming languages (Python, Matlab, IGor Pro, or R) and experience working in a lab with animals is preferred but not required. Additional research may involve examining structure and function of various fishes present as it relates to heart function and circulation. PI: Barbara Block; Research Supervisors: Jonathan Dale, Ted Reimer

Designing Technology for White Shark Morphometrics

Work with the Block Lab at Hopkins Marine Station to design and implement noninvasive pathways to measure white shark body length and girth. The student will use laser altimetry and paired underwater laser designs, with room given to create alternative methods, for high-accuracy photogrammetric measurements of shark morphology. These technologies will be tested locally at Hopkins Marine Station to quantify error and uncertainty using basic computing and statistics. This student will then implement these designs to measure juvenile white sharks in Santa Cruz, assisting with land and boat-based field work for the summer field season. Engineering background and experience with major programming languages (Python, Matlab, or R) and 3D printing preferred. PI: Barbara Block; Research Supervisor: Alexandra DiGiacomo

De Leo Lab

Predicting Hotspots of Abalone Withering Syndrome along the California Coast

Abalones are marine organisms of ecological and economic interest present along the Pacific coast. Many species of abalones suffered from heavy mortality over the last few decades from abalone withering disease. This disease is caused by a bacterial pathogen that infects the digestive tract of abalones, often resulting in starvation and the death of the animal. While infection can occur anytime, symptoms appear when abalones are exposed to high temperatures. In this project, the student will use an existing model of withering syndrome to predict disease risk based on temperature data along the California coast. Depending on previous experience and interest, the student will work on a wide array of tasks, such as an online literature and data search, spatial representation and modeling, model development and analysis, and visualization. Coding experience is strongly recommended, with experience in R and GIS preferred but optional. PI: Giulio De Leo; Research Supervisor: Julie Pourtois

Assessing the Toxicity of Traditional and Virus-Based Sunscreens on Marine Larvae

Despite recent progress and improved formulations, most sunscreens still contain ingredients that are harmful to marine life. In collaboration with the Bollyky lab in the Immunology department, we are working on the development of virus-based sunscreens that rely on UV absorption by DNA from inactive bacteriophages. Bacteriophages are specific viruses that only infect certain bacteria and are thus hypothesized to be safe both for humans and for marine life. In this project, the student will be conducting toxicology experiments on marine larvae in the lab to establish that bacteriophages are safe for key marine organisms. Previous experience with laboratory experiments and animal husbandry is welcome. PI: Giulio De Leo; Research Supervisor: Julie Pourtois

The Effect of Climate Change on Schistosomiasis Dynamics, a Debilitating Parasitic Disease of Poverty

Schistosomiasis is one of the most important of the so called neglected tropical diseases. With more than 200 million people infected, the vast majority school age children in Africa, schistosomiasis is second only to malaria for cumulated disease burden. This student will assist in developing thermal sensitive models of schistosomiasis dynamics that we will be use to explore how seasonality and climate change will affect the dynamics and persistence of schistosomiasis in tropical and subtropical regions up to the skirts of Europe. PI: Giulio De Leo; Research Supervisor: Ibrahim Aslan

Gilly Lab

Color Changing Behavior of Squid Skin

The chromatophore network in squid skin is responsible for color-changing behavior in the living animal. Descending control of this network by the brain via motor axons is well established, but transmission between chromatophores in the absence of nerve activity also appears to be possible. This project will study peripheral control of the chromatophore network after blocking nerve activity. Study of the effects of environmental stressors on squid color-changing and mating behaviors may also be possible.

Goldbogen Lab

The History of a Whale-Based Ecosystem as Told by Ocean Sediment

The Goldbogen Lab welcomes an intern to support our ongoing work using sediment cores to understand marine ecosystem shifts over the last two centuries. Potential areas of study include biogeochemistry, eDNA, or the option to develop your own art- or engineering-based project. While the Goldbogen Lab is located at Stanford’s Hopkins Marine Station 1.5 hours south of Palo Alto there is the option for the intern to pursue laboratory-based work for this project on main campus. PI: Jeremy Goldbogen; Research Supervisors: Mehr Kumar, Matt Savoca

Unsupervised Behavioral State Classification of Diving Humpback Whales from Kinematic Time Series

Despite being the planet’s largest mammals and important ocean sentinels, cetaceans are difficult to study because they regularly dive underwater where they cannot be observed directly by researchers. Biologging tags fill this gap by collecting kinematic data that enables the remote study of cetacean behavior based on a priori assumptions about the types of behavior these animals exhibit and the movement features that define these behavioral states. Traditional methods for behavioral classification are limited, however, as they may overlook behaviors that are unknown to researchers. For this project, the student will use acceleration and gyroscope data recorded by biologging tags to develop unsupervised statistical learning models for classifying behavioral patterns of humpback whales. The student will derive movement spectra from kinematic time series and explore the use of principal component analysis and clustering methods for characterizing and discriminating behaviors. This work will inform an understanding of how humpback whales budget high- and low-activity behaviors across dive cycles and has the potential to reveal previously unrecognized behaviors in a difficult-to-study, free-ranging cetacean. A potential extension of this project could include the development of semi-supervised models for behavioral classification of humpback whales using biologger video data to validate known behavioral events. The student should be comfortable working in MATLAB, Python, and/or R and ideally would have experience with signal processing and statistical learning. PI: Jeremy Goldbogen; Research Supervisor: Ashley Blawas

Micheli Lab

Impacts of Ocean Acidification on Algal Nutritional Content

Ocean acidification (OA) has been shown to have significant impacts on properties of seaweeds such as growth and C:N content. Changes to algal nutrition and defenses could have significant indirect effects on sea urchin feeding behavior, influencing the structure and diversity of benthic marine communities under OA. Laboratory studies have found shifts in nutritional content such as changes in protein and carbohydrates, but these studies typically expose algae to OA for short periods of time (1-3 months). For this project, the student will examine nutritional/ chemical properties of seaweeds collected at an underwater CO2 vent in Ischia, Italy, such as C:N ratios, protein and carbohydrate content, or concentration of defensive chemicals. The student will work with the mentor to perform protein/carbohydrate extractions or C:N analysis using an element analyzer, to determine how palatability changes across a CO2 gradient. PI: Fio Micheli; Research Supervisor: Melissa Palmisciano

Design for Ocean Solutions

Escalating pressures on coastal and ocean ecosystems require increasing the speed and scale of solutions. Design offers concepts and tools to develop, prototype and test solutions, but it is rarely applied in the ocean realm. The internship will draw on design and ocean science to identify opportunities for designing and prototyping solutions. Examples could include 'do-it-yourself', low cost technologies for monitoring ocean change to supporting sustainable aquatic food production. PI: Fio Micheli; Research Supervisor: Carissa Carter

Palumbi Lab

Environmental DNA for Biodiversity Monitoring

Learn lab techniques and bioinformatic resources for analyzing biodiversity data from environmental samples in the Chumash Heritage National Marine Sanctuary. Help train teachers and students from the Chumash community, and participate in sampling coastal intertidal and kelp forest areas. PI: Steve Palumbi; Research Supervisor: Marilla Lippert

Lowe Lab

Early Development in Hemichordate Worms

Hemichordates are a group of worm-like marine animals that are related to vertebrate chordates like humans. The Lowe lab studies these animals to understand more about chordate evolution. Some hemichordates have a life history strategy called indirect development, when they have larval stage before they metamorphose into their adult form. Other hemichordate species immediately develop into their adult body plan, which is called direct development. This project would compare direct and indirect developing hemichordates to better understand early development in hemichordates across life history strategies. The undergraduate student would learn confocal microscopy, molecular biology techniques such as in situ hybridization, and larval rearing of hemichordates and echinoderms. PI: Chris Lowe; Research Supervisor: Lauren Lubeck

Description and Molecular Characterization of the Metamorphosis in a Brittle Star

Echinoderms are a group of marine invertebrates including sea stars, sea urchins, sea cucumbers and lesser known groups such as sea lilies and brittle stars. These animals typically exhibit a bi-phasic life cycle with a pelagic larva and a benthic adult. The transformation from the larva to the adult in echinoderms is one of most spectacular metamorphosis in the animal kingdom and involves a dramatic change in the body plan of the animal, with a switch from a bilateral larva to a pentaradial adult. Among echinoderms, the metamorphosis of brittle stars has not been described in details and is a missing link to understand the evolution of the phylum. This project aims to describe the metamorphosis of the brittle star Ophiotrix spiculata using live imaging, immunohistochemistry stainings and gene expression profiling using HCR in situ hybridization. Imaging of immunohistochemistry and HCRs will be done using a confocal microscope. Adult Ophiotrix spiculata typically spawn between June and July, which will also allow the intern to be involved in rearing the animals through the larval stages and the metamorphosis. The laboratory has an extensive stock of fixed tissues to be used for immunohistochemistry and HCRs, so the success of the internship will not rely upon the success of the spawning and animal rearing only. The lab will welcome any student motivated by a project related to macroevolution, evo-devo and work with non-model animals. PI: Chris Lowe; Research Supervisor: Laurent Formery

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.

Proposals are due March 3, 2023. APPLY

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