Ever wanted to assemble specific genes out of raw sequence reads? Try sharkmer, a tool for in silico PCR (sPCR) developed with @shchurch.bsky.social - academic.oup.com/bioinformati.... Feed it raw reads and primer sequences, it gives you amplicon sequences. Can work on a laptop in minutes.

Sharkmer: repurposing PCR primers for targeted genome assembly using in silico PCR

AbstractSummary. We introduce an in silico PCR (sPCR) method for the assembly of specific genomic regions spanned by PCR primers using raw sequence reads.

academic.oup.com

Our eLetter github.com/caseywdunn/s... responding to a recent Science paper was just posted. The paper found more genes with consistent support for sponge-sister than ctenophore-sister. We found several technical issues that, when corrected, reverse the conclusions and recover ctenophore-sister.

It has been wonderful to teach Invertebrate Zoology in the field - youtu.be/cPqdVsxsnSs?...

Serene Learning: Hands-on course on Horse Island

YouTube video by Yale University

youtu.be

Interested in joining our lab (dunnlab.org) as a postdoc to work on siphonophores, processes that structure diversity in the open ocean, or natural history? If so, please reach out to discuss a nomination for the Donnelley Postdoctoral Fellowship - yibs.yale.edu/donnelley-fe...

I hope to take a PhD student in 2026 to study siphonophores. Please reach out if you are interested in applying this fall. For examples of recent lab projects see www.sciencedirect.com/science/arti... and academic.oup.com/gbe/article/...

Population genomics of a sailing siphonophore reveals genetic structure in the open ocean

The open ocean is a vast, highly connected environment, and the organisms found there have been hypothesized to represent massive, well-mixed populati…

sciencedirect.com

Casey Dunn@caseywdunn.bsky.social · last yr.

I hope to take a PhD student in the coming application cycle. Please reach out if you are interested in joining our lab in EEB at Yale, especially if interested in working on the natural history/ phylogenetics/ morphology/ population biology/ development/ genomics of siphonophores. dunnlab.org

As the Gulf Stream carries man o’ war colonies north, winds push them on shore 🏖️, causing strandings along the U.S. East Coast - from Florida in the winter to New England in the summer.

Check out our preprint 🧪 on the origin & dispersal dynamics of a sailing ⛵ #siphonophore! We use #iNaturalist and particle tracking simulations to show that juvenile man o' war surface in the Gulf of Mexico & Straits of FL and disperse rapidly along the Gulf Stream 🌊 www.biorxiv.org/content/10.1...

From surfacing to stranding: The origins and dispersal dynamics of a neustonic siphonophore

The siphonophore Physalia physalis regularly strands along the US East Coast, yet the dynamics driving its seasonal and geographic distribution in this region remain poorly understood. Building on a n...

biorxiv.org

Our new paper on structure and growth of Porpita porpita - rdcu.be/etcY6 . Like Velella and Physalia, this is a colonial cnidarian that floats at the surface of the Ocean. The whole colony arises form a single embryo through clonal growth that gives rise to many specialized bodies.

Excited to share our study on sailing siphonophores, AKA bluebottles or man-o'-war! 🌊 we received hundreds of samples from scientists around the world, part of a huge effort to sequence genomes and test for multiple species 🧬 out today in @currentbiology.bsky.social doi.org/10.1016/j.cu... 🦑🧪📌

I wrote this essay a few years ago with general background and advice for anyone applying to start a PhD in Biology - medium.com/@caseywdunn/... . If that is you, now is the time to start the process (reading literature, reaching out to possible advisors, ...) ahead of fall deadlines.

Applying to Biology PhD programs

Each year I advise undergraduate students who are applying to grad school, help evaluate grad school applications, and talk with…

medium.com

I hope to take a PhD student in the coming application cycle. Please reach out if you are interested in joining our lab in EEB at Yale, especially if interested in working on the natural history/ phylogenetics/ morphology/ population biology/ development/ genomics of siphonophores. dunnlab.org

Postdoc job opportunity! We're looking for ECR in evolutionary genomics to study the relation between intra-specific gene expression variability, polymorphism, and macro-evolutionary rates. We have the data in 3 fishes & amphioxus, just waiting for your expertise and enthusiasm! tinyurl.com/3aewk286

Our chromosome-scale genome assembly of Nanomia septata, a siphonophore - doi.org/10.1101/2025... . Much larger than many other cnidarian genomes, fewer chromosomes, and highly rearranged. No smoking gun for how they achieve complex colony-level organization. Great work Namrata Ahuja and friends!

Yale Department of Ecology and Evolutionary Biology is running an assistant professor search for a Global Change Ecologist - apply.interfolio.com/164677 . Please consider applying.

This paper provides now solid evidence that the xenacoelomorph male gonopore is homologous to the bilaterian hindgut. www.biorxiv.org/content/10.1...

The xenacoelomorph gonopore is homologous to the bilaterian anus

The bilaterian through gut with an anal opening is a key invention in animals, since it facilitates effective food processing, which allows animals to grow to a larger body size. However, because non-...

biorxiv.org

Even on a dive boat, sometimes the most spectacular displays are above water. This was from when @caseywdunn.bsky.social and I were on a small liveaboard off Komodo, Indonesia. I like the offset paths of the double-flash on the right.

Try our new in silico PCR (sPCR) tool sharkmer- github.com/caseywdunn/s.... You give it primers and fastq reads, it gives you sequences that would be amplified by PCR. Works in minutes on a laptop for high copy regions like rRNA, great for species id etc. Feedback welcome. #bioinformatics #ngs

GitHub - caseywdunn/sharkmer

Contribute to caseywdunn/sharkmer development by creating an account on GitHub.

github.com

Recent PhD interested in deep-sea ecology, genomics, biochemistry, or bioluminescence? Apply for a postdoctoral fellowship at MBARI. Check out the sponsor list & e-mail me to discuss projects in my lab. Grad student position soon too. www.mbari.org/about/careers/postdoc-fellowships/how-to-apply