Rishi De-Kayne

@wes-larsonak.bsky.social

Check out some new work from our team here at @arcadiascience.com on dissecting the evolutionary signal captured by Evo2 (gLM) latent spaces thestacks.org/publications...

Rishi De-Kayne reposted

Wes Larson

24 June

We're hiring a genetics lab manager position at NOAA in Juneau, Alaska! The successful candidate will oversee day-to-day laboratory operations and contribute to the development of new molecular methods. Salary is $75-145k/yr. Email wes.larson@noaa.gov with questions www.usajobs.gov/GetJob/ViewD...

usajobs.govBiologist (Omics)This position is located in the National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS). Vacancies may be available in each listed location. Additional duty lo...

jobs.lever.coArcadia Science - Platform Scientist: Comparative Protein EvolutionA Bit About Us: We're Arcadia Science, an evolutionary biology company founded and led by scientists. Our mission is to turn natural innovations into real-world solutions by developing systematic and ...

22 June

🚨 #Evol2026 attendees - our team at @arcadiascience.com is hiring! We're looking to hire a computational evolutionary biologist interested in asking how and why protein sequences/structures/functions differ across the tree of life 🧬 jobs.lever.co/arcadiascien... Please share widely!

12 June

🚨 We're hiring computational evolutionary biologists! 🚨 Boosting this - industry evolutionary biology jobs don't come along often, so if you're excited to apply your computational evolutionary biology skills to cutting-edge problems, let's talk! 🧪🧬💻

Rishi De-Kayne@rishidekayne.bsky.social

Our team at @arcadiascience.com is hiring! We're looking to hire a computational evolutionary biologist interested in asking how and why protein sequences/structures/functions differ across the tree of life 🧬 jobs.lever.co/arcadiascien... Please share widely!

thestacks.orgArcadia ScienceTo read more on our publishing experiment, browse our collection of iced pubs, and for other insights into our research, visit https://research.arcadiascience.com/.

12 June

To get a sense for what we're working on, check out our website: www.arcadiascience.com and our latest pubs: thestacks.org/organization...

8 June

thestacks.orgAgentic PyMOL: Structural analysis in PyMOL through natural languageAgentic PyMOL is an MCP server that gives language-model agents discoverable, two-way access to a user's live PyMOL session, letting agents both manipulate molecular visualizations and read structured...

8 June

If you use PyMOL in your work, but find its command-driven workflow a bottleneck to getting from an idea to cool analyses, check out Evan's pub: thestacks.org/publications... - Agentic PyMOL is an MCP server that allows you to carry out PyMOL analyses quickly and intuitively using natural language!

Rishi De-Kayne reposted

Integration of Speciation (ESEB Special Topic Network)

@speciation-network.bsky.social

5 May

Happening today: the final "Early Career Researchers in Speciation" seminar! This session features talks by Aryeh Miller on Anolis lizards 🦎 and @rishidekayne.bsky.social on speciation research in industry 📊 + we'll hear from Dr Mariana Braga in the careers Q&A ✋ 👉 find the link on our website

Rishi De-Kayne reposted

Integration of Speciation (ESEB Special Topic Network)

@speciation-network.bsky.social

14 Apr

The final "Early Career Researchers in Speciation"-themed seminar is coming up on the 5th of May! This session features talks by Aryeh Miller on Anolis lizards 🦎 and @rishidekayne.bsky.social on speciation research in industry 📊 + we'll hear from Dr Mariana Braga about her career in the Q&A ✋

Rishi De-Kayne reposted

Claire Mérot

@clairemerot.bsky.social

13 Apr

Looking forward to kicking off the seminar series of our special topic network on structural variants #SV in evolutionary biology. @eseb.bsky.social Join us in listening to Pr. Rieseberg on April 29

STRIVE@strivestn.bsky.social

🌻 Next STRiVE seminar: Loren Rieseberg (UBC) explores SVs, adaptation & speciation—from wild sunflowers to 1000+ species! 🗓️ Apr 29 | 9am PDT / 6pm CEST ✉️ Zoom link via mailing list: groupes.renater.fr/sympa/subscr... ℹ️ Info: structuralvariantsstn.github.io/about/

thestacks.orgAssembly and annotation artifacts can lead to problematic protein structural inferencesProtein structures inferred by protein structure prediction algorithms have incredible potential, but can contain errors stemming from incorrect input sequences. Here, we investigate one such case in ...

New pub! We analyzed protein structures across 36 Drosophila species and found something unexpected: tandem dimers and even trimers lurking in protein structure databases that likely aren't real proteins at all. 🧵 thestacks.org/publications... [1/9]

This matters because protein structure prediction is increasingly being run on sequences from non-model organisms where we have little prior knowledge. Erroneous sequences from genome misassembly can silently percolate through prediction models into structure databases. [8/9]

7 Apr

All code and data are available on GitHub: github.com/Arcadia-Scie.... We hope this work helps others think about quality control of input sequences before running structure prediction at scale. @arcadiascience.com [9/9]

github.comgithub.com

Most tandem dimers turned out to comprise two different genes, Jhbp7 and takeout, which sit next to each other in the genome. The domain order in every dimer matched the gene order in the D. melanogaster genome, strongly suggesting misassembly or misannotation rather than real biology. [6/9]

Our phylogenetic analysis shows this clearly: split domains from tandem proteins land in the same clusters as their separately annotated counterparts, not together as you'd expect if they shared a single evolutionary origin. [7/9]

Here's what these look like: a normal single-domain Takeout structure alongside tandem dimers and trimers from different Drosophila species. [4/9]

To figure out what was going on, we built a pipeline to split tandem-domain proteins into their constituent parts using HMM profiles, then used phylogenetics and BLASTp to identify what each domain actually was. [5/9]

We were exploring structural conservation in Takeout proteins using the TIPS insect structure database (tips.shenxlab.com) when we hit a roadblock: some sequences were 2-3x longer than others, creating huge gaps in our alignments. [2/9]

tips.shenxlab.comTIPS

Digging in, we found these long sequences were tandem dimers and trimers of the conserved domain. These structures had been inferred from what appear to be erroneous input sequences. [3/9]

lnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn

30 Mar

Are you an evolutionary biologist who thinks about the evolution of protein sequences/structure/function across scales? Do you want to implement your skills in industry? We’ve opened a full-time role on our platform team (think computational research group)! lnkd.in/gVE2NGaV

thestacks.orgThe StacksAn experimental new publishing platform. Browse the latest research.

30 Mar

You can see some of the many ways we are leveraging evolutionary biology in our pubs here: thestacks.org

jobs.lever.coArcadia Science - Platform Scientist: Protein EvolutionA Bit About Us: We're Arcadia Science, an evolutionary biology company founded and led by scientists. Our mission is to turn natural innovations into real-world solutions by developing systematic and ...

24 Mar

We have an opportunity to join our team at @arcadiascience.com jobs.lever.co/arcadiascien... We're looking for an evolutionary biologist who thinks a lot about protein evolution. If you have experience investigating genomic and amino acid sequence evolution and protein structural evolution, apply!

Rishi De-Kayne reposted

STRIVE

@strivestn.bsky.social

12 Mar

🧬 Join the STRiVE kick-off conference (TiBE-STRiVE) July 8-10, 2026 near Porto! Registration & abstracts open: 🔹 Members: Feb 25-Apr 7 🔹 Non-members: Mar 16-Apr 7 Info: structuralvariantsstn.github.io/porto_about/ #Evolution #Genomics #Biology

Rishi De-Kayne reposted

STRIVE

@strivestn.bsky.social

20 Feb

🧬We are launching STRiVE, a @eseb.bsky.social Special Topic Network on the evolutionary role of structural genomic variation. 🗓️Std: 29/04: Online seminar w/ L. Rieseberg 8-10/07: Kick-off in Porto Join us: structuralvariantsstn.github.io #Evolution #Genomics #StructuralVariants #Biology #PopGen

structuralvariantsstn.github.ioStructural Variants ESEB Special Topic NetworkESEB Special Topic Network

thestacks.orgStrategizing the search for bio-utility: A framework for evolution-integrated in silico bioprospectingTo accurately and efficiently identify instances of useful biological variation, we must establish an evolution-integrated bioprospecting framework. This will enable us to better interpret biological ...

Really excited to share my first pub from my work at @arcadiascience.com - Strategizing the search for bio-utility: A framework for evolution-integrated in silico bioprospecting thestacks.org/publications... [1/8] 🧵

Evolution tells us not just what's useful, but where to look next, highlighting lineages that might harbor untapped potential for biotechnology applications. [7/8]

This framework could help us move from serendipitous discovery toward predictive identification of bio-utility across the tree of life. Read the full perspective for the details. [8/8]

The key? Identifying indicators of bio-utility from protein variation itself: • Proteins with extreme properties (like extremophile polymerases) • Proteins with discrete novel functions (like different proteases) • Proteins showing conserved or convergent functions (like antifreeze proteins) [5/8]

But protein data alone isn't enough. Integrating evolutionary relationships between species with this protein information helps us understand where useful functions evolved, distinguish conservation from convergence, and spot breakthrough novelty in constrained protein families. [6/8]

thestacks.orgBiology needs to become prospectiveSince biological data are often non-independent, more data doesn't always mean more insight. We argue that a prospective approach is needed to uncover the deepest principles of life.

In silico bioprospecting tries to fix this by mining existing databases. But those databases are taxonomically biased (see another one of our pubs dropping today: thestacks.org/publications...), and the methods often require knowing what you're looking for upfront. [3/8]

We propose an evolution-integrated framework that combines the best of both worlds: expanding sampling breadth while more deeply interrogating existing data through an evolutionary lens. [4/8]

Bioprospecting has given us incredible discoveries, from life-saving drugs to agricultural innovations. But traditional approaches rely heavily on serendipity and are hard to scale. [2/8]

30 Jan

Interested in whether protein language models can learn about evolution and leverage this to predict protein structures? Check out the pub!

Arcadia Science@arcadiascience.com

1/6 What does MSA Pairformer learns about evolutionary relationships? @yoakiyama.bsky.social et al achieved impressive contact & variant-fitness predictions w a fraction of ESM2's parameters; we wanted to better understand the mechanism arcadia-science.github.io/2025-phyloge... 🧪🧬 🖥️

Genome Biology and Evolution

31 Oct 2025

I'm very excited to share that today is my last day working at UC Berkeley before I start my new position at @arcadiascience.com next week! It has been a pleasure working as a postdoc in so many amazing labs along side amazing scientists, and I can't wait to start this new chapter!

Rishi De-Kayne reposted

Blair Perry

@bwperry.bsky.social

8 July 2025

I am recruiting PhD students to join my lab at MSU starting Fall 2026! Please spread the word and reach out if you are interested and/or want to learn more!

Rishi De-Kayne reposted

@genomebiolevol.bsky.social

25 June 2025

Ryan, @rishidekayne.bsky.social et al. present six new chromosome-level genome assemblies for Poeciliidae, providing a foundation for studies on convergent evolution, repeat content, and demographic history. 🔗 academic.oup.com/gbe/article/17/6/evaf111/8169767 #genome #evolution

academic.oup.comNew Genome Assemblies for Poeciliidae: A Foundation for Adaptation StudiesAbstract. Multiple lineages in the family Poeciliidae have independently adapted to hydrogen-sulfide-rich springs. The independent colonizations of such sp

Rishi De-Kayne reposted

PLOS Biology

@plosbiology.org

3 Mar 2025

Dynamics of a supergene. A study of the BC supergene in wing color morphs of the African monarch #butterfly by @rishidekayne.bsky.social &co reveals dynamic evolution of #supergene haplotypes, fueled by incomplete recombination suppression 🧪 @plosbiology.org plos.io/3DiFhnL

Rishi De-Kayne reposted

Dmitri Petrov

@petrovadmitri.bsky.social

14 Jan 2025

Happy that this paper - www.biorxiv.org/content/10.1... - was accepted at Mol Ecol Res and excited about the promise of this technology to measure pop sizes for such elusive species as snow leopards + learn about at least 1st-degree relationships + beyond? Congrats to Katie Solari and other authors!

biorxiv.orgNext-generation snow leopard population assessment tool: multiplex-PCR SNP panel for individual identification from fecesSnow leopards, Panthera uncia , are under threat from numerous pressures and are the focus of a great deal of conservation efforts. However, their elusive nature makes it difficult to estimate populat...

academic.oup.comEvolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid FishesAbstract. Adaptation to extreme environments often involves the evolution of dramatic physiological changes. To better understand how organisms evolve thes

28 May 2024

Very excited to share our latest paper "Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes" 🐟 academic.oup.com/gbe/article/...

Rishi De-Kayne reposted

Molly Schumer

@mollyschumer.bsky.social

15 May 2024

Thrilled to share a new lab pre-print from graduate student Tris Dodge! Tris & co elegantly uncover the genetic underpinnings and fitness consequences of a sexual mimicry polymorphism in Xiphophorus birchmanni: www.biorxiv.org/content/10.1...

biorxiv.orgComplex structural variation and behavioral interactions underpin a balanced sexual mimicry polymorphismbioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

6 May 2024

Excited to share our review paper "Why Do Some Lineages Radiate While Others Do Not? Perspectives for Future Research on Adaptive Radiations" which is now online here: cshperspectives.cshlp.org/content/earl... Check it out for all things adaptive radiation! 🐟🦎🌿🦋