Bay Area RaMP

Bay Area RaMP Program in Microbiome Sciences

Network Labs

Labs Participating in the 2025-26 Cohort

To ensure scholars have the support and resources they need to be successful during the program, lab participation varies from year to year based on mentor and project availability. For the upcoming cohort, there are 10 labs with openings for a scholar. Begin to get to know our lab options below (listed in alphabetical order), and visit their respective websites for more information.

Almeida Lab, California State University - East Bay

About the Lab

As part of the Green Biome Institute, the Almeida lab is a welcoming and relaxed environment where you will have access to cutting edge technologies for the study of plant microbiomes. We are a primarily undergraduate group, with a few masters students, dedicated to our mission to help preserve California's endangered native plants through conservation, genomic profiling, and research into rare plant's beneficial traits in medicine and agriculture. We also investigate the microbiome community exiting in the plants, and study how the community could potentially help in the conservation. Almeida Lab projects are frequently integrative and will provide you with ample opportunities to learn from a variety of approaches and techniques.

What to Expect

While investigating the leaf microbiome of endangered California plant species, such as manzanitas, scholars would have an opportunity to participate in the whole process of the project, from DNA extraction to analyzing sequencing data. Scholars will:

Design and perform experiments based on the use of molecular and microbiological tools to interrogate the plant microbiome;
Analyze large datasets of sequence data to identify and evaluate the diversity of microbes associated with California endangered plant species;
Collaborate with other student researchers during the various stages of development of a research project;
Practice presentation, networking, and science communication at local (e.g. lab meetings, CSUEB events) and national scientific meetings.

For more information, visit https://www.csueastbay.edu/csci/green-biome-institute/

Advisor: Ana Almeida (she/her)

Associated Professor and Chair, Department of Biological Sciences, CSUEB

I strive to be a very approachable and accessible advisor, focused on community and collaboration, rather than competition. I am passionate about all things research and science teaching, and I love to share knowledge, experience and excitement with others.

Mentor: Weilun Tan

Lab Manager

I highly encourage mentees to communicate openly to express their interest and develop new ideas for a project. Sometimes, the experiments do not work as expected, but I believe people can also learn more from troubleshooting and mistakes. Thus, I will mainly guide mentees through real-world scientific challenges and give them opportunities for critical thinking and developing confidence in solving problems with reasonable support.

de la Torre Lab, San Francisco State University

About the Lab

Our research group combines field work, laboratory experiments and computational (bioinformatic) approaches to address questions of microbial ecology and evolution. Much of our work has focused on understanding microbial communities in high temperature environments such as terrestrial hot springs, with a particular interest in how microorganisms drive the nitrogen cycle. Our recent work has centered on understanding how populations of microorganisms living in hot springs in the Nevada desert and in Yellowstone National Park adapt and evolve over time. Students in my lab are involved in a long-term series, collecting hot springs sediment samples monthly over the course of the year. Samples are then used to cultivate representative organisms as well as for metagenomic sequencing. These paired approaches allow us to see how natural populations evolve in response to changing environmental conditions, as well as in response to biological factors such as viral predation.

Areas of interest include:

Using metagenomes to assess genomic diversity of natural microbial populations
Discovery of novel viruses and their hosts using cultivation-independent approaches
Using new sequencing technologies (e.g. long-read metagenomics) to discover novel microbial lineages, sometimes referred to as microbial dark matter
Reconstucting microbially driven geochemical cycles (e.g. nitrogen)

For more information, visit https://biology.sfsu.edu/faculty/delatorre.

Advisor/Mentor: José de la Torre (he/him)

Professor, Biology, San Francisco State University

Koskella Lab, University of California - Berkeley

About the Lab

The Koskella Lab focuses on how bacterial pathogens and their interactions within microbiomes shape human and plant health. We utilize experimental evolution techniques to address questions such as how hosts and microbiomes co-evolve and how microbiomes shape the evolution of pathogenicity. We are also curious about bacteriophages' roles in microbiomes and disease dynamics. The lab has a very friendly atmosphere and is full of welcoming scientists who are excited about mentorship broadly.

What to Expect

You will use a novel transposon-mutagenesis-based system to experimentally evolve a mobile genetic element (MGE). MGEs like plasmids, integrative and conjugative elements, and phage are extremely small but extremely important parts of microbial ecosystems. By observing them as they evolve in the lab, we can gain a better understanding of natural selection on MGEs in the wild and improve our ability to use MGEs as tools for synthetic and functional microbiology. In your project, you will learn both basic microbiology wet lab skills (for the element isolation and experimental evolution) and basic bioinformatics skills (for analyzing sequencing data in evolved MGE populations). This is brand new work that we are really excited about!

For more information, visit https://naturesmicrocosm.com/

Advisor: Britt Koskella (she/her)

Associate Professor, Department of Integrative Biology, UC Berkeley

I’m Britt Koskella, an Associate Professor in the Department of Integrative Biology at UC Berkeley where I’ve been running a lab for the last ten years. My favorite moments are when I have the privilege of witnessing someone become a scientist - when they work hard to collect data that ends up being a fair test of a cool hypothesis and suddenly they have their answer! Outside of the lab, I love hanging out with my two kids and large dog.

Co-Mentor: Milo Johnson (he/him)

Postdoc, Koskella Lab (UC Berkeley) and Deutschbauer Lab (Lawrence Berkeley National Lab)

I love working with other researchers, teaching basic wet lab skills (the secret: it’s not that hard if you know what you don’t need to worry about), and especially teaching data analysis through coding (although I think LLMs are doing a good job trying to steal this job from me). Mentoring is exciting for me because I get to introduce someone to new ideas and form a collaborative relationship with them where we can both learn from each other. I would say my mentoring “superpower” is to zoom out on a project with a critical (but friendly) lens and think about big-picture next directions.

Co-Mentor: Darian Doakes

PhD student, Koskella Lab & Boots Lab, UC Berkeley

I enjoy watching mentees make the transition from learning basic wet lab skills to beautifully designing their own thorough experiments! It doesn’t take as long as you’d think to learn microbio skills. I also love reading papers with students to get them acquainted with what the “final product” of lab work looks like and to show them how data can be communicated simply and elegantly (I think figures are pretty to look at). I think my “superpower” as a mentor is helping researchers hone their creativity! I find that when someone delves into a completely new and unfamiliar type of research, they are incredibly capable of coming up with unique and unbiased questions.

Lynch Lab, University of California - San Francisco

About the Lab

Research in the Lynch Lab focuses primarily on the human microbiota in both respiratory and gastrointestinal tracts, environmental microbial exposures that shape its development, and its role in chronic inflammatory diseases. Interdisciplinary research is conducted with all career stages of both wet- and dry-lab scientists and clinicians, thereby enabling problem solving at each facet of the disease. We strive to create an environment in which every lab member is unhampered in achieving their potential – which means that every voice should be heard, that we benefit from the inputs of lab members who are informed by their own experiences, and that all are welcome.

What to Expect

A scholar can expect to learn skills as they relate to the bench (e.g. microbiological/mammalian cell culturing, DNA extraction, PCR amplification and purification, multiplexing experiments, etc.) and to computation (basic skills in R programing, Sanger sequencing analysis, biostatics, etc.). With this, the beauty of tackling broad scientific challenges is the ability to use one’s own expertise and curiosity to guide questioning and experimentation leveraging these newly acquired skills. Therefore, projects can focus on anything from determining which nutrients enable pathogenic microbes to dominate the airways, to learning new analytic techniques for harmonizing and integrating multi-omic datasets. Each one of these possible projects will be discussed and planned depending on which techniques and skills the mentee wants to continue development.

For more information, visit https://lynchlab.ucsf.edu/

Advisor: Dr. Susan Lynch (she/her)

Professor, Department of Medicine - Gastroenterology; Director, Benioff Center for Microbiome Medicine, UCSF

I am very particularly interested in developing novel prognostics, diagnostics and treatments for allergy and asthma based on observations made in large human microbiome studies and developing new research tools to accelerate discovery in the field. I am also interested in developing new microbiome research, training and education infrastructure at the Parnassus campus of UCSF. Having been in the field for over two decades affords me the capacity to see relationships and guide the research towards testing those theories that sets me apart from others.

Mentor: Dr. Elad Deiss-Yehiely (he/him)

Postdoctoral Researcher, Lynch Lab, UCSF

I firmly believe that excitement and passion drive success, so my job as a mentor is to start by teaching a wide breadth of possibilities and then tailor future work based on learning goals and continuing conversations on what motivates a mentee. I try and define what constitutes a successful experiment or analysis before starting, as there is always something to be learned even if at first glance it may seem like “it did not work.” This affords a broader view of personal growth and development, which I believe should be a goal for any mentee, and not just data collection.

MEEP Lab, San Francisco State University

About the Lab

The Moss Eco-Evo-Physio (MEEP) Lab at San Francisco State University investigates how mosses and their microbiomes survive extreme environmental conditions, such as the intense drought and high solar radiation of deserts. The MEEP Lab aims to create a supportive, collaborative, and inclusive environment, providing trainees with experience in areas such as plant culture, physiology, molecular biology, genomics, data science, bioinformatics, and ecological research.

What to Expect

Scholars in the MEEP Lab may contribute to projects studying microbiomes of biological soil crusts (soil surface communities that stabilize soils, enhance nutrient cycling, and support biodiversity) or the functional roles of moss-associated bacteria. These projects are grounded in computational and data science approaches, with a strong emphasis on bioinformatics and the analysis of metagenomic and transcriptomic datasets. Some opportunities may also include molecular lab techniques, depending on the stage and specific needs of the project. Through these experiences, trainees will build a foundation in microbial genomics and gain transferable skills applicable to ecological, physiological, and microbiome research.

For more information, visit www.meep-lab.com.

Advisor: Jenna Ekwealor (she/her)

Assistant Professor, Department of Biology, San Francisco State University

I’m driven by curiosity and awe at how organisms survive in extreme environments, and how we might apply our understanding of those mechanisms in conservation efforts. My advising superpower is helping trainees realize they’re capable of more than they imagined, whether that’s mastering statistics, writing code, dissecting a moss under the microscope, or presenting their research with confidence.

I believe that mentoring should be collaborative, supportive, and attuned to each mentee’s goals and background. I aim to empower mentees by guiding them through hands-on learning and helping them build confidence in problem-solving, coding, and data analysis and interpretation.

Mentor: Richard Baker-Strader (he/him)

MS Degree Candidate, Department of Biology, SFSU

I think the best part of science is solving puzzles in order to explore the natural world. Mentoring programs like these let us turn science into a collaborative learning activity! We can help each other overcome blocks and hurdles, complement one another's strengths, and build scientific community.

Nayak Lab, University of California - San Francisco

About the Lab

The Nayak Lab seeks to understand the mechanisms by which the gut microbiome impacts the treatment of rheumatic disease. We use multiple state-of-the-art technologies, including metabolomics, anaerobic microbiology, bacterial genetics, gnotobiotic animal models, and studies of patient cohorts to elucidate the mechanisms by which gut microbiota impact patient response to treatment of rheumatic disease. This quote from Helen Keller represents the lab culture: “Alone we can do so little; together we can do so much.” Our lab values respect, integrity, good lab citizenship, kindness, scientific rigor, creativity, diversity, professionalism, and scientific excellence.

What to Expect

In the Nayak lab, the scholar will be trained to several techniques related to drug-microbiome-host interactions. The scholar will be trained for anaerobic bacterial culture to do experiments involving bacterial growth and drug metabolism follow-up. They will learn how to extract samples to run them on a HPLC/LCMS machine. We also have access to a gnotobiotic mouse facility, where we perform mouse experiments. The scholar could thus gain skills in mouse handling, in planing and doing experiments, in collecting samples, etc.

For more information, visit https://nayak.ucsf.edu.

Advisor: Renuka R. Nayak, PhD (she/her)

Associate Professor, Medicine / Rheumatology Department, San Francisco VA and UCSF

I am a physician-scientist and rheumatologist interested in understanding how the gut microbiome impacts treatment outcomes in patients. My love for science and research was inspired and sustained by good mentors. I would like to provide that opportunity for others now. My advising superpowers include guiding young scientists in scientific communication, data analysis, and grant writing.

Mentor: Alexandra L. Degraeve, PharmD, PhD (she/her)

Postdoctoral Researcher

As a pharmacist, I am very interested by drugs and how to get the most benefit from them. During my PhD, I started to discover the importance of our gut microbiome and I think there is still so much to discover about host-drug-microbiota interactions. It is exciting! My colleagues describe my mentoring "superpower" as being a good teacher: I take the time to explain and I provide valuable feedback. For me, there is no stupid question/mistake as long as you learn.

Okamoto Lab, University of California - Berkeley

About the Lab

We study population dynamics with a focus on exploited species of importance to coastal communities. We are broadly interested in how environment and species interactions regulate fluctuations in population dynamics, physiology, and vital rates (i.e., recruitment and connectivity, metabolism, energy budgets, development, growth, reproduction & mortality), and how such information can lead to more robust, equitable, and just natural resource management. Our research integrates mathematical modeling, Bayesian statistical analysis, field data, & laboratory experiments. We are a collaborative and inclusive lab. The research interests among the members of our lab are disparate, working on systems from abalone and urchin energetics to disease in Daphnia and macroalgal growth and kelp patch persistence.

What to Expect

Skills you can gain: algal culturing, lipid extraction and fatty acid analysis, RNA extraction, animal husbandry, statistics, coding in R, mathematical modeling, data visualization, microscopy, scientific writing.

Possible Projects: Macroalgae associated bacteria culturing and identification and impact on performance, co-infection of Daphnia dentifera and examining disease progression

For more information, visit https://dkokamoto.com/

Advisor: Daniel K. Okamoto (he/him)

Assistant Professor of Global Change Biology, Department of Integrative Biology, University of California-Berkeley

I am a marine ecologist with expertise in ecological modeling, biostatistics, and kelp forest ecology. My group and I study how trophic interactions, climate, and fishing combine to affect individual traits and population dynamics, especially in species like sea urchins, kelp, abalone, and forage fish. My advising style is to work closely with students to generate research projects and experiences that help them pursue their career aspirations, generate excellent and meaningful science, and to seek training, funding, and partners for their journey. I meet regularly with students and aim to integrate them into a productive, inclusive, and collaborative environment.

Mentor: Olivia Ruffins (they/them)

Graduate Student, Integrative Biology Department, UC Berkeley

My mentoring philosophy is to empower my mentees to be confident and independent researchers who feel comfortable asking questions and approach the process of doing research with curiosity. When I am teaching bench skills my approach is to have mentees shadow me and then mirror my technique until they feel confident enough to work on their own. It is important to me that mentees get hands-on experience, as I believe that this is the best way to learn.

Mentor: Grace Westphal (she/they)

Graduate Student, Integrative Biology Department, UC Berkeley

I am excited to support mentees to build skills and confidence as scientists through fostering a strong sense of belonging, collaboration, and critical thinking. I believe all questions are good questions, everyone makes mistakes, and science is a team effort. I am a patient instructor, and enjoy teaching benchwork skills, coding, and scientific writing.

Ott Lab, University of California - San Francisco

About the Lab

The Ott lab focuses on human host factors that restrict or enable viral infections. We build and study sophisticated primary cell systems to model the physiological conditions of viral pathogenesis. By studying multiple pathogens, we hope to identify common host pathways that can be therapeutically targeted to thwart multiple infectious agents.

Founded at the peak of the HIV/AIDS epidemic, our lab has since broadened its scope to other endemic viruses as well as to newly emerging ones. Recently, we started to study and design next-generation phage therapies - both to treat and understand life-threatening bacterial infections, as well as to intelligently remodel human microbiomes.

Our lab has a highly collaborative, collegial environment that prides itself on maintaining an inclusive and respectful community. We work thoughtfully and carefully to make sure we get the most out of our research while prioritizing and respecting our lives inside and outside of the lab.

What to Expect

As a RaMP scholar, you would be working with Ivan Zheludev, Ph.D., investigating Obelisk RNAs. Obelisk RNAs are a recently discovered class of mobile genetic elements which persist, colonise, and spread with the bacteria of human (and environmental) microbiomes. Having just been noticed for the first time, almost any question about Obelisks has yet to be asked. Using an isolated microbe-Obelisk system, you will be taught how to identify and then ask such basic science questions. You will have the opportunity to use a wide range of experimental techniques, including: classical biochemical (e.g. molecular cloning, protein purification, etc.), and microbiological experiments (e.g. competition assays, complementation experiments, bacterial phenotyping, etc.), as well as cutting-edge technologies (e.g. next generation sequencing, mass spectrometry, single-cell RNA sequencing). The exact themes of your work will be decided by you and your interests within the first months of the scholarship. Potential projects include: a) isolation of novel Obelisk-host pairs from human/environmental niches, b) construction of a genetic reporter circuit for Obelisk presence, c) investigation into the impact of Obelisk presence in in vitro models of host biology.

For more information, visit https://ottlab.gladstone.org/

Advisor: Melanie Ott, PhD (she/her)

Director and Senior Investigator, Gladstone Institute of Virology; Senior Vice President, Gladstone Institutes; Professor of Medicine, University of California - San Francisco

As Director of the Gladstone Institute of Virology, I lead a lab focused on understanding the pathogenesis of viral diseases—from our foundational work on HIV to our expanded research on SARS-CoV-2, Hepatitis C, Zika, and other emerging viruses. We also translate our molecular understanding of host-pathogen interactions into novel antiviral therapies and diagnostic tools. An area of particular focus is our pioneering work in next-generation phage therapy, an emerging field with many open basic science questions where RaMP scholars can make many fundamental contributions. My greatest joy as a mentor comes from creating a supportive environment where my mentees can develop their unique talents while tackling important questions, allowing them to grow into thoughtful and skilled researchers who push the boundaries of scientific understanding.

Mentor: Ivan Zheludev, PhD (he/him)

Postdoc, Ott Lab, Gladstone Institute of Virology, Gladstone Institutes

Hello! My name is Ivan. I’m originally from England where I did my undergrad studies, but I’ve been in California for a while now, first doing my Ph.D., and now my post-doctoral research. I study a subset of the most dynamic and numerous part of any microbiome - the virome. Specifically, I am interested in “Obelisks,” mysterious bacteria-associated genetic agents which I discovered during my Ph.D. We have pretty much no clue what Obelisks do on a molecular, cellular, or ecological level and so I am incredibly excited about mentoring a RaMP scholar (you!) with Obelisks as a pedagogical backdrop, because I expect we will discover lots of interesting and new biology!

I am a biochemist by training, so I love trying to understand the molecular nuts and bolts of living processes. I’ve been doing it for over a decade. My particular expertise is in nucleic acid (DNA and RNA) molecular biology. I truly believe that being able to generate and analyze your own sequencing data these days is a super-power, and I take immense pride in teaching folks how to do this. My goal as a mentor is to transfer full intellectual “ownership” of a project to my mentees - to have them critically understand both the hows and the whys of their work.

Turnbaugh Lab, University of California - San Francisco

About the Lab

The Turnbaugh lab is composed of highly talented scientists with diverse backgrounds coming together under a common goal: better living through microbes. We work collaboratively to determine how gut microbes influence human health using a variety of approaches including molecular (biochemistry, bacterial genetics, structural biology), organismal (germ-free/gnotobiotic mice, conventional animals, and human cohorts), and ecological (synthetic microbial communities and metagenomic sequencing). While pursuing cool and novel research projects, everyone in the lab understands the importance of creating a safe and supportive environment where people feel comfortable to share ideas and make mistakes without judgement; this is universally regarded as a core aspect of good scientific research.

What to Expect

This lab is addressing a real-world problem by investigating and leveraging microbial contributions to chemotherapy metabolism for better control of related toxicities within a host. This is being achieved using a multi-faceted approach by 1) determining mechanisms of action for gut microbial metabolism of chemotherapy (i.e. capecitabine or 5-FU) and how that contributes to drug efficacy/toxicity, 2) characterizing chemotherapy-induced toxicity in a genetically deficient host with variable capacity for metabolism, and 3) investigating drug-microbe interactions using commercially available probiotics to determine their utility in future microbe-based interventions. Possible projects for a RaMP scholar include determining metabolic capacity of commercial probiotics of common cancer therapeutics (including chemotherapy), creation of the ultimate “super-probiotic” through bacterial genetic engineering, and modulation of cancer toxicity in vitro and in vivo with microbial metabolites.

For more information, visit https://turnbaughlab.ucsf.edu/better-living-through-gut-microbes.

Advisor: Peter Turnbaugh (he/him)

Professor, Microbiology and Immunology, University of California - San Francisco

I am passionate about discovering new mechanisms through which gut microbes influence the treatment of disease. My advising superpower is nurturing team spirit through our annual lab challenge, a battle of wits and fine motor skills.

Mentor: Taylor Halsey, PhD (she/her)

Postdoctoral Scholar

I find a lot of joy in scientific discovery and I love sharing that joy with others. I am a great team player that thrives when working through big, complex problems with a group of highly motivated and equally excited people, independent of background: curiosity and willingness to learn are the only prerequisites! Mentoring represents an exciting way to add more people to the team, which will only strengthen the research.

Wolf Lab, University of California - Berkeley

About the Lab

The Wolf lab works on diet metabolism and how human gut microbiome protects us from pathogens. We use both experimental and computational methods to understand the molecular basis of gut microbiome-mediated events. Much of our work is collaborative, and the group has tight connections with each other scientifically and personally. Everyone works to learn from each other, provide feedback, and share new techniques and approaches.

What to Expect

We will teach scholars common techniques in microbiome research, including bacterial culture, nucleic acid isolation, sequencing, and computational analysis of metagenomic data. Alongside a mentor starting a new project about antimicrobial resistance, scholars will also learn how to identify a question and search for approaches to tackle the problem. One potential project to work on is the regulation of carbon utilization in gut microbes, which is to identify the key factors (genes, proteins) that affect how gut microbes consume carbon sources in our diet. The other potential project is about gut microbiome-mediated antimicrobial resistance, which is to identify how antimicrobial resistance genes are spread within a bacterial community and other protection mechanisms, such as antibiotic-degrading enzymes.

For more information, visit https://www.awolflab.com.

Advisor: Ashley Wolf (she/her)

Assistant Professor, Division of Infectious Diseases and Vaccinology, School of Public Health Center for Computational Biology, UC Berkeley

Helping lab members achieve their career goals is an extremely rewarding part of my job! I meet regularly with mentees to discuss research progress and goals. I love baking and sharing with the lab like during our recent pi day celebration.

Mentor: Jonathan Chiu-Chun Chou (he/him)

Postdoc

I am a strong believer of unhindered communication. As much as I will set up clear expectations and instructions, mentees are also free to tell me what they expect and how they feel about my mentoring.

Other Network Members

Though not accepting scholars this year, these advisors have hosted RaMP scholars in their labs in previous cohorts and remain an important part of our network. Visit their websites for more information about their exciting research.