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Need a break from EVERYTHING?? Come join our free public talk this evening, where NYU professor Dr. Samuel Church will tell us all about his hunt for new blue bottle (man-o-war) species 🪼🧪🌊🦑 7:30 PM (EST) Zoom link: u-tokyo-ac-jp.zoom.us/j/8337406906... Meeting ID: 833 7406 9068 Passcode: 430292
@caseywdunn.bsky.social and I have a new tool for "in silico PCR" out in Bioinformatics: 🦈 sharkmer 🦈 With a subsample of raw reads and a few minutes, you can assemble your favorite barcode sequences! Try it out and let us know how we can make it better: github.com/caseywdunn/s...
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.
So cool to see our work highlighted here! Thanks @botany.one ! And, re: the question “were you one of the observers in our dataset,” besides in the paper supplement, there’s a full list of them here: github.com/pmckenz1/mon...
Quick plug for our new resource, the Drosophila Species Stock Exchange. This is a database and mailing list that documents species currently in culture and the labs holding them. If you want to know more or sign up then please get in touch. See attached for more info and please share!
The Church Evolution Lab (CEL@NYU) is hiring a postdoc! We have several new projects to study the genomic basis of biodiversity in model clades – especially Hawaiian Drosophila. apply.interfolio.com/179354 Come join our new group, you can study bugs and live in NYC! Feel free to share widely!
Applications are now open for the 2026 Workshop on Molecular Evolution (MOLE)! www.mbl.edu/education/ad... Claudia Solis-Lemus and I will be holding an informational session on Zoom next Wed (1/21) from 10:30-11:30 AM Central for those interested: lsu.zoom.us/j/4968115684 Deadline to apply: 1/26
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 was amazing to be part of this cool natural history project led by @patrickmckenzie.bsky.social, and I’m so happy I can now say I have worked on plants!
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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
Sharkmer: repurposing PCR primers for targeted genome assembly using in silico PCR
The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetic...
www.mbl.edu
Workshop on Molecular Evolution | Marine Biological Laboratory
Contribute to caseywdunn/sharkmer development by creating an account on GitHub.
github.com
Ben Hopkins
Casey Dunn
Patrick McKenzie
Casey Dunn
Jeremy M. Brown
GitHub - caseywdunn/sharkmer
How Thousands of Phone Snapshots Solved a Flower Colour Mystery www.botany.one/how-thousand... Nearly 10,000 People Helped Confirm a Botanical Hunch. Were You One of Them? #Botany #PlantScience
Available now in @asn-amnat.bsky.social ! Taking on some big-scale natural history: processed >40k @inaturalist.bsky.social images of Monarda fistulosa using computer vision to query for flower presence and phenotype flower color: doi.org/10.1086/739413
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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.
1mo
Nearly 10,000 People Helped Confirm a Botanical Hunch. Were You One of Them?
www.botany.one
How Thousands of Phone Snapshots Solved a Flower Colour Mystery
doi.org
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
Sharkmer: repurposing PCR primers for targeted genome assembly using in silico PCR
High-throughput iNaturalist image analysis reveals flower color divergence in Monarda fistulosa | The American Naturalist: Vol 0, No ja
Patrick McKenzie
Botany One
Casey Dunn
Super excited to have been part of the project using participatory science to study flower color variation, led by @patrickmckenzie.bsky.social!
New preprint out today! A really fun collaboration with @shchurch.bsky.social and Robin Hopkins in which we study flower color variation in Monarda fistulosa using iNaturalist data. We process >40,000 images and use them to phenotype flower color in >16,000 observations: doi.org/10.1101/2025...
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May 27, 2025
Patrick McKenzie
Samuel Church
Samuel Church
Samuel Church
Samuel Church
Rebecca R Helm
McKenzie et al. applied a novel pipeline to automate floral color phenotyping from community science photographs, supporting anecdotal evidence that Monarda fistulosa is deeper purple in western vs. eastern North America. Read now ahead of print! www.journals.uchicago.edu/doi/10.1086/...
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American Naturalist / ASN 🐌