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Arcadia Science

@arcadiascience.com
1.6K followers 16 following 74 posts

Research and development company leveraging the biology of diverse organisms. Read about our science: research.arcadiascience.com

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Arcadia Science @arcadiascience.com · 09/07/2026
Assembly and annotation artifacts can lead to problematic protein structural inferences
doi.org
Assembly and annotation artifacts can lead to problematic protein structural inferences
Protein 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...
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Arcadia Science @arcadiascience.com · 20/05/2026
Morphological transformation of Chlamydomonas smithii grown in Marine Broth medium
doi.org
Morphological transformation of Chlamydomonas smithii grown in Marine Broth medium
Marine Broth induces extreme morphological transformation in C. smithii: Cells shift from typical ellipsoid shape to amorphous forms with thin wisp-like appendages containing mitochondria, revealing...
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Arcadia Science @arcadiascience.com · 30/04/2026
#ICYMI
bsky.app
Rishi De-Kayne (@rishidekayne.bsky.social)
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...
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Arcadia Science @arcadiascience.com · 09/04/2026
#PubDrop bsky.app/profile/rish...
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Arcadia Science @arcadiascience.com · 13/03/2026
#ICYMI
bsky.app
Cameron Dale MacQuarrie (@cdmacquarrie.bsky.social)
New pub from @ArcadiaScience 🧵 We found that C. smithii — a freshwater green alga — undergoes wild morphological transformations when grown on Marine Broth. Huge cells with mysterious wisp-like...
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Arcadia Science @arcadiascience.com · 20/02/2026
#PubDrop
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Cameron Dale MacQuarrie (@cdmacquarrie.bsky.social)
New pub from @ArcadiaScience 🧵 We found that C. smithii — a freshwater green alga — undergoes wild morphological transformations when grown on Marine Broth. Huge cells with mysterious wisp-like...
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Arcadia Science @arcadiascience.com · 30/01/2026
7/6 As always, this study is end-to-end reproducible (arcadia-science.github.io/2025-phyloge...)
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Arcadia Science @arcadiascience.com · 30/01/2026
6/6 As the field shifts toward MSA-based architectures, the quality of input alignments becomes paramount. MSA Pairformer encodes evolutionary signal well, but future architectures might benefit from learning when to trust that signal.
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Arcadia Science @arcadiascience.com · 30/01/2026
5/6 We traced this to layers 5-11, which integrate sequence weights blindly, regardless of whether they help or hurt. When they hurt prediction, we could progressively rescue performance by shuffling weights at earlier layers, saving the model from its own bad intuition.
Box plot of normalized P@L delta across shuffling start layers showing positive cohort recovers performance as shuffling stops while negative cohort degrades.
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Arcadia Science @arcadiascience.com · 30/01/2026
4/6 But surprisingly, encoding phylogeny ≠ leveraging it. Comparing learned weights against uniform averaging for contact prediction, the aggregate improvement was marginal. Per-MSA, uniform averaging outperformed learned weights about half the time, sometimes by a large margin.
Histogram of delta P@L showing roughly symmetric distribution around zero with slight positive mean.
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Arcadia Science @arcadiascience.com · 30/01/2026
3/6 The model consistently upweights evolutionarily close sequences and downweights distant ones, despite never being trained on this. There's also a division of labor across layers: layer 11 acts as a strong phylogenetic filter, while others contribute more modestly.
Unrooted tree for LytTR query with leaves colored by median sequence weight showing gradient of attention from query.
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Arcadia Science @arcadiascience.com · 30/01/2026
2/6 Their key innovation is query-biased attention, where the model weights MSA sequences by relevance to the query. We tested whether "relevance" maps onto phylogenetic distance by correlating sequence weights with evolutionary distances across thousands of protein families.
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Arcadia Science @arcadiascience.com · 30/01/2026
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... 🧪🧬 🖥️
Screenshot of pub title, "MSA-based pLMs encode evolutionary distance but don't reliably exploit it"
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Arcadia Science @arcadiascience.com · 29/12/2025
A free, open-access library of high-quality organism illustrations for science communication
doi.org
A free, open-access library of high-quality organism illustrations for science communication
We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to...
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Arcadia Science @arcadiascience.com · 16/09/2025
All hardware designs, software, and documentation are open-source and available on GitHub. We'd love your feedback on what features would make AutoOpenRaman more useful for your research! [8/8] research.arcadiascience.com/pub/resource...
research.arcadiascience.com
AutoOpenRaman: Low-cost, automated Raman spectroscopy
We developed AutoOpenRaman, an automated, inexpensive microscope for Raman spectroscopy. We recapitulated many features of expensive commercial Raman spectroscopy systems using economical hardware and...
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Arcadia Science @arcadiascience.com · 16/09/2025
This resource is perfect for scientists who want to try Raman spectroscopy without committing to expensive commercial systems, or current OpenRAMAN users who want to add automation to their experiments. [7/8]
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Arcadia Science @arcadiascience.com · 16/09/2025
We demonstrated AutoOpenRaman's capabilities by automatically collecting 200 Raman spectra from Chlamydomonas reinhardtii colonies in 68 minutes across a 96-well plate format. The system successfully detected β-carotene signatures in the algae. [6/8]
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Arcadia Science @arcadiascience.com · 16/09/2025
The software is designed for non-programmers to install and use, built on µManager (micro-manager.org) for broad device support. Users can swap hardware components as long as µManager supports them — no code changes needed [5/8]
Diagram of AutoOpenRaman software flow and user interface
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Arcadia Science @arcadiascience.com · 16/09/2025
On the hardware side, we added a motorized XY stage, microscope objective, laser shutter, and neon light source for quick calibration. [4/8]
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Arcadia Science @arcadiascience.com · 16/09/2025
Our solution: AutoOpenRaman adds automation to OpenRAMAN while keeping it open-source and relatively inexpensive (~$8k in total). [3/8]
Diagrams of the AutoOpenRaman spectrometer setup
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Arcadia Science @arcadiascience.com · 16/09/2025
The problem: Commercial Raman systems offer automation, but cost $200k+. #OpenRAMAN (open-raman.org) is a powerful, inexpensive DIY alternative, but it doesn't support automation. [2/8]
open-raman.org
OpenRAMAN
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Arcadia Science @arcadiascience.com · 16/09/2025
Introducing AutoOpenRaman, an automated, inexpensive microscope setup for Raman spectroscopy! We recapitulated many features of expensive commercial systems using economical hardware and open-source software 🧵 [1/8] research.arcadiascience.com/pub/resource...
research.arcadiascience.com
AutoOpenRaman: Low-cost, automated Raman spectroscopy
We developed AutoOpenRaman, an automated, inexpensive microscope for Raman spectroscopy. We recapitulated many features of expensive commercial Raman spectroscopy systems using economical hardware and...
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Arcadia Science @arcadiascience.com · 01/09/2025
Chlamydomonas cpc1-1 mutant exhibits unexpected growth phenotypes
doi.org
Chlamydomonas cpc1-1 mutant exhibits unexpected growth phenotypes
Comparative analysis of <i>Chlamydomonas </i>strains revealed that a <i>cpc1-1</i> mutant has three unexpected growth phenotypes across different media types, suggesting possible genetic background contributions...
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Reposted by Arcadia Science
Seemay Chou @seemaychou.bsky.social · 05/08/2025
After many yrs building internally @arcadiascience.com we're now able to partner more with others on cool organisms. You won't hurt my feelings if you don't read my post, but don't miss out on our first organismal spotlight animation featuring sea squirts -- just skip to the bottom! 🧵
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Arcadia Science @arcadiascience.com · 05/08/2025
Our blog is now on Substack! Check out our first post there, which includes a fun video we made about why you might want to study sea squirts open.substack.com/pub/arcadias...
open.substack.com
Zoogle Suggested We Try a Sea Squirt, So We Did
It’s true that no model is perfect, but how can we find ones that are less wrong? We’re excited to announce two research partnerships investigating predicted matches between diseases and research orga...
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Arcadia Science @arcadiascience.com · 04/08/2025
AI laboratory for lit review
doi.org
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Arcadia Science @arcadiascience.com · 01/08/2025
New website who dis www.arcadiascience.com
arcadiascience.com
Arcadia Science
Developing better ways to predict and test therapeutics.
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Arcadia Science @arcadiascience.com · 22/07/2025
Want to give input to help your fellow scientists? We’ve updated our list of preprints in need of feedback: bit.ly/preprintrequests We’re having our own preprint commenting event next Friday. We’ll consider reading your work if you add it to the list: bit.ly/submitpreprint
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Arcadia Science @arcadiascience.com · 24/06/2025
Two Arcadia talks today! 11:15 am — Athena CD — George Sandler “The potential of machine learning for genomic prediction in a quantitative genetics framework” 11:45 am — Athena F — Ryan York “Evolution determines what machines can learn”
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Arcadia Science @arcadiascience.com · 23/06/2025
#ICYMI
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Cameron Dale MacQuarrie (@cdmacquarrie.bsky.social)
Discovered some unexpected growth phenotypes in Chlamydomonas flagellar mutants! The cpc1-1 strain (with central pair complex defects) shows surprising metabolic traits that might be independent of its...
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Arcadia Science @arcadiascience.com · 23/06/2025
Calling all scientists! 🚨 Share feedback on preprints that need it! Check out our updated list: bit.ly/preprintrequests We’re hosting our next internal preprint commenting party this Friday, and might review your work! Submit it here: bit.ly/submitpreprint
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Arcadia Science @arcadiascience.com · 22/06/2025
As #Evol2025 talks wrap up for the day, our mixer begins! Come upstairs at The Globe any time til 7:30 to learn about opportunities at Arcadia over charcuterie & drinks 🍷🧀 We’re looking for a Computational Evolutionary Biologist, Evolutionary Cell Biologist, and more…
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Arcadia Science @arcadiascience.com · 22/06/2025
📢 Hey #Evol2025 attendees, we’re hiring! If you’re interested in #careers at Arcadia, swing by our free mixer upstairs at The Globe today from 5:30 to 7:30. It’s a 7-minute walk from the Classic Center and drinks are free 🍻 jobs.lever.co/arcadiascience
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Arcadia Science @arcadiascience.com · 22/06/2025
First Arcadia talk at @evolmtg.bsky.social‬! #Evol2025 Today — 3 pm — Athena CD Austin Patton presents “Graph neural networks: A unifying predictive model architecture for evolutionary applications”
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Arcadia Science @arcadiascience.com · 21/06/2025
We’re at ‪@evolmtg.bsky.social‬! Follow us for updates on talks as the conference unfolds. We’re also hosting a free careers mixer 🍺 at The Globe tomorrow @ 5:30 pm — join us! #Evol2025
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Arcadia Science @arcadiascience.com · 29/05/2025
#PubDrop bsky.app/profile/cdma...
bsky.app
Cameron Dale MacQuarrie (@cdmacquarrie.bsky.social)
Discovered some unexpected growth phenotypes in Chlamydomonas flagellar mutants! The cpc1-1 strain (with central pair complex defects) shows surprising metabolic traits that might be independent of its...
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Arcadia Science @arcadiascience.com · 26/05/2025
#ICYMI
bsky.app
Arcadia Science (@arcadiascience.com)
One of our scientists whipped up a lit review terminal program where AI agents with different expertise collaboratively discuss #biorxiv and #arxiv preprints 🤖🧪📚 https://github.com/Arcadia-Science/agent-literature-review...
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Reposted by Arcadia Science
Ubadah Sabbagh @ubadahsabbagh.com · 03/05/2025
>march 10 @arcadiascience.com announces new form of rapid publishing >apr 18 team reads a preprint, finds it interesting >9 work days later, team publishes results validating and extending model this is how science should be. open, rapid, with the community arcadia-science.github.io/2025-geno-ph...
arcadia-science.github.io
Cross-trait learning with a canonical transformer tops custom attention in genotype-phenotype mapping –
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Reposted by Arcadia Science
Ubadah Sabbagh @ubadahsabbagh.com · 30/04/2025
Not only do we do cool science but we have a badass illustrator for our pubs
Graphical abstract depicting diverse types of ticks on a phylogenetic tree
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Arcadia Science @arcadiascience.com · 30/04/2025
And the artist, Audrey Bell! www.aebellillustration.com
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Arcadia Science @arcadiascience.com · 21/04/2025
One of our scientists whipped up a lit review terminal program where AI agents with different expertise collaboratively discuss #biorxiv and #arxiv preprints 🤖🧪📚 github.com/Arcadia-Scie... Anyone here using an agent-based research tool you recommend?
github.com
GitHub - Arcadia-Science/agent-literature-review
Contribute to Arcadia-Science/agent-literature-review development by creating an account on GitHub.
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Arcadia Science @arcadiascience.com · 09/04/2025
Help advance science by giving feedback! #SharingIsCaring Browse our list of preprints that need feedback: bit.ly/preprintrequests We’re hosting a #preprint commenting event this Friday — submit your work for consideration: bit.ly/submitpreprint
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Arcadia Science @arcadiascience.com · 24/03/2025
Early update on Arcadia publishing 2.0: Scientists are in charge, speed is an issue
buff.ly
Early update on Arcadia publishing 2.0: Scientists are in charge, speed is an issue · Reimagining scientific publishing
Since starting v2 of our publishing model to restore scientist agency, pub “quality” has been similar, and this approach is more efficient overall. The major downside is that pubs take longer. We’re...
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Arcadia Science @arcadiascience.com · 24/03/2025
Rescuing Chlamydomonas Motility in Mutants Modeling Spermatogenic Failure
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Rescuing Chlamydomonas motility in mutants modeling spermatogenic failure · Genetics: Decoding evolutionary drivers across biology
We used Chlamydomonas reinhardtii motility mutants with disrupted genes homologous to human SPEF2 or DNALI1 to model spermatogenic failure disorders SPGF43 and SPGF83, respectively. We recovered aspects...
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Arcadia Science @arcadiascience.com · 19/03/2025
Researchers often use a compound called 48/80 to activate mast cells for degranulation assays... But it's toxic ☠️ in the two cell lines we tested: HMC1.2 (human mast cells) and RBL-2H3 (rat basophils) This could confound many studies — please share! 🧪 research.arcadiascience.com/pub/result-4...
research.arcadiascience.com
Compound 48/80 is toxic in HMC1.2 and RBL-2H3 cells
We found that compound 48/80, an MRGPRX2 agonist and commonly used in vitro mast cell activator, is toxic in HMC1.2 (human mast cells) and RBL-2H3 (rat basophils). Researchers should use caution and i...
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Arcadia Science @arcadiascience.com · 18/03/2025
Check out our first two notebook pubs to see what we mean... 1️⃣ One is about a counterintuitive pattern we noticed in the ESM2 model: arcadia-science.github.io/2024-paired-... 2️⃣ The other compares several Raman spectroscopy instruments head-to-head: arcadia-science.github.io/2025-raman-s...
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Arcadia Science @arcadiascience.com · 18/03/2025
We're trying a new publication format — the notebook pub! By turning our Jupyter Notebooks into publishable artifacts, we hope to share faster, reduce the effort to convert analysis ➡️ pub, and make our work more reproducible. Weigh in on our commentary: research.arcadiascience.com/pub/perspect...
Diagram comparing processes for creating standard vs. notebook pubs where notebook pubs cut out significant manual, irreproducible editing steps.
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Arcadia Science @arcadiascience.com · 04/03/2025
Scientists: Share your expertise with your peers! #GiveFeedback Check out our updated list of preprints seeking valuable input: bit.ly/preprintrequests Have a preprint that needs feedback? Add it to our list: bit.ly/submitpreprint
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Arcadia Science @arcadiascience.com · 12/02/2025
Check out our first validation study here: research.arcadiascience.com/pub/result-c...
research.arcadiascience.com
Rescuing Chlamydomonas motility in mutants modeling spermatogenic failure
We used Chlamydomonas reinhardtii motility mutants with disrupted genes homologous to human SPEF2 or DNALI1 to model spermatogenic failure disorders SPGF43 and SPGF83, respectively. We recovered aspec...
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Arcadia Science @arcadiascience.com · 12/02/2025
Dive into our methods here: research.arcadiascience.com/pub/result-e...
research.arcadiascience.com
Leveraging evolution to identify novel organismal models of human biology
Researching just a handful of organisms limits biological discovery. We developed an approach pairing organisms with biological questions to expand research biodiversity.
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