JULY 19 – AUG 8, 2026

Functional Biodiversity

Genomics, Genetics, Imaging & AI in Aquatic Invertebrates

Three weeks – three animal groups: Cnidaria, Echinodermata, and Cephalopoda. Hands-on collection & culturing, genetic tools, advanced imaging, and AI-driven genomics. Pioneer RNA-sensing technology in jellyfish, sea urchins, and squid.

What You’ll Do

Design. Culture. Modify. Image. Discover.

For each group: Work with genetic tool genetic lines of a representative lab model. Apply cutting-edge genetic tools using mRNAs or shRNAs in local species for the first time. Test new-to-science RNA-sensing constructs in model or local species. Explore origins of our brain and new models for aging resistance in biodiversity.

You will gain high-level training in 1) AI-based phylogenomics across three major animal groups – cnidarians, echinoderms, and cephalopods – vs. human, 2) computational tools for whole-organism connectomics, 3) modeling behavior using whole-organism whole-nervous system dynamics, 4) design and testing of genetic tools, 5) spawning, fertilization, and culturing new genetically-tractable models and local biodiversity species, 6) creating cell and tissue cultures, 7) microinjecting embryos, 8) transfecting cells, 9) live imaging anatomy and behavior in embryos, larvae, and adults using phone to light sheet microscopy technologies, 10) assessing gene-to-system function in wild-type vs. genetically-modified animals.

The RNA-Sensing Breakthrough

RNA-sensing is a new technology that targets genetic tools to specific cell types based on native gene expression. Genetic tool targeting to cells or tissues is classically achieved through intensive development of specific promoters per target. In contrast, RNA-sensing requires only a single ubiqitous promoter for general use in a species. This is combined with a simple-to-optimize targeting system that uses 200-300 bp of a cell-type-specific transcript. This subsequence is SNP-modified to have an internal stop codon, preventing downstream translation. However, the SNP is corrected in presence of natively-expressed WT transcripts, enabling expression of genetic tool payloads in transcript-targeted cell-types. The simplicity and scalability of RNA-sensing is revolutionizing mouse and human research – and is especially promising for functional studies in biodiversity, where research communities, resources, and knowledge may be limited. RNA-sensing has never been used in marine animals – until now. Workshop participants will test new RNA-sensing constructs across cnidarians, echinoderms, and cephalopods—pioneering this technology in non-model organisms. If successful, the workshop will co-author a research paper. 

Cell Lines For Scalable Functional Assays

Functional research in aquatic invertebrates typically depends on limited numbers of animals. This constrains throughput and makes large-scale functional screening impractical. Cell lines change that equation. By establishing stable cell cultures from embryonic tissues, researchers can test hundreds of genetic constructs, optimize conditions rapidly, and develop standardized functional assays—approaches that are routine in mammalian systems but rare in marine biology. Participants will learn to establish  embryonic cell lines in sea urchin and potentially other species, bridging traditional approaches with scalable assay-based methods. Together, this integration can enable functional genomics at scale in aquatic invertebrates.

Why Functional Biodiversity Matters

Evolution is the ultimate engineer. It has run innumerable experiments for billions of years, innovating, optimizing, and rejecting components, systems, and species. Every genome is a library of tested solutions, its readouts producing ion channel dynamics, ciliary movements, nervous system controls, and adaptive behaviors and plasticity in molecular to ecological systems. Genomic sequencing is exploding. Databases are growing exponentially. Yet genomic data without functional testing is just a parts list. This workshop bridges that gap. You’ll combine cutting-edge genomics, genetic manipulation, advanced imaging, and AI to decode how life actually works—venturing beyond classic genetic models and into the Tree of Life. New insights won’t just advance marine biology. They’ll illuminate principles and components that can enable advances in human biology, biotechnology, and conservation. Evolution has done the R&D. Let’s discover, explore, and test its output!

The Instructors

Amro Hamdoun | UC San Diego Echinoderm genetic lines (Remote)

Andrea Bodnar | Gloucester Marine Genomics Institute Cell lines and Aging 

Brandon Weissbourd | MIT Cnidarian neuroscience 

Connor Gibbons | Columbia University Cephalopod culturing 

Eric Edsinger | University of Florida Animal origins and evolution 

Fabian Voigt | Harvard Live tracking microscopy 

Jason Hodin | University of Washington Echinoderm biology & conservation

Josh Huang | Duke University RNA-sensing technology

Shulin Zhang | Stanford Hydra connectomics

Tessa Montague | Columbia University Cephalopod neuroscience

The Animals

Cnidaria: Jellyfish & Polyps

Hydra vulgaris (Polyp – GCaMP genetic line)

Clytia hemisphaerica (Jellyfish – RCaMP genetic line)

Clytia gregaria + Aequorea victoria (Jellyfishes – field-collected)

Echinodermata: Sea Stars, Sea Urchins & Sand Dollars

Lytechinus pictus (Sea urchin – TBD genetic line)

Patiria miniata (Sea star – field-collected Reporters)

Dendraster excentricus (Sand dollar – field-collected)

Cephalopoda: Squid, Cuttlefish & Octopus

Sepia bandensis (Cuttlefish – TBD genetic line)

Doryteuthis pealeii (Squid – field-collected CRISPR)

Doryteuthis opalescens + Octopus rubescens (Squid and Octopus – field-collected)

Training

Genetic Tools

• Fluorescent protein reporters
• RNA-sensing (pioneering work!)
• Vitellotag transfection
• shRNA knockdowns
• CRISPR knockouts
• Biosensors – Calcium / Serotonin

Imaging

• Fluorescence microscopy
• Confocal microscopy
• Live-tracking microscopy
• Phone-based documentation
• TBD – Light-sheet microscopy

Genomics & AI

• Phylogenomic pipeline design with AI
• Species & gene tree construction
• HMM protein annotation
• Orthogroup genomes clustering
• Origin-conservation-loss mapping
• Agentic AI data exploration

Field & Lab Skills

• Salish Sea collection
• Embryo culture & maintenance
• Genetic line husbandry
• Gonad tissue culture
• Embryonic cell lines
• Neurotransmitter pharmacology

AI/ML/Modeling

• Behavior quantification
• TBD Behavior modeling
• Connectomics
• TBD Protein engineering

Program Structure

Duration: Three weeks, intensive hands-on format Location: University of Washington’s Friday Harbor Laboratories, San Juan Island, Washington—a premier marine station with direct access to incredibly rich Salish Sea biodiversity Daily schedule:  Laboratory work with embryos, larvae, adults, and/or cell and tissue cultures of aquatic invertebrates, expert-led instruction, data analysis sessions, field collection, collaborative research. Small group format: Direct mentoring from faculty instructors, working in teams on shared research goals

Who Should Apply

This workshop is designed for graduate students, postdocs, and early-career researchers who want to:

• Add genetic tools and cell-based assays to their research toolkit
• Work across species diversity, not just model organisms
• Combine molecular, cellular, and computational approaches
• Scale up functional genomics in non-model systems
• Apply cutting-edge methods to their own research questions

Prerequisites: Graduate-level training in biology, computer science, or related field. Prior experience with molecular biology, cell culture, or microscopy is helpful but not required—the work is high-level and you’ll learn hands-on.

*Workshop design is ongoing. Details may be updated here through the Spring.

Application Materials Must Include:

• PDF of your Statement of Purpose: write 500 words or more indicating your (1) interest in the chosen training workshop, (2) how the workshop will influence your career path. (3) what aspects of the workshop you are most interested in, (4) a statement of current research or research interests
• PDF of your CV
• Name and contact information for one reference
• PDF of your unofficial transcript if applicant is an undergraduate or not yet in graduate school