Arcadia Science

doi.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...

9 July

Assembly and annotation artifacts can lead to problematic protein structural inferences

doi.orgMorphological transformation of Chlamydomonas smithii grown in Marine Broth mediumMarine 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...

20 May

Morphological transformation of Chlamydomonas smithii grown in Marine Broth medium

bsky.appRishi 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...

30 Apr

#ICYMI

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 ...

9 Apr

#PubDrop bsky.app/profile/rish...

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 at all. 🧵 thestacks.org/publications... [1/9]

bsky.appCameron 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...

13 Mar

#ICYMI

#PubDrop

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... 🧪🧬 🖥️

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.

30 Jan

7/6 As always, this study is end-to-end reproducible (arcadia-science.github.io/2025-phyloge...)

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.

30 Jan

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.

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.

30 Jan

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.

doi.orgA free, open-access library of high-quality organism illustrations for science communicationWe 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...

29 Dec 2025

A free, open-access library of high-quality organism illustrations for science communication

research.arcadiascience.comAutoOpenRaman: Low-cost, automated Raman spectroscopyWe developed AutoOpenRaman, an automated, inexpensive microscope for Raman spectroscopy. We recapitulated many features of expensive commercial Raman spectroscopy systems using economical hardware and...

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...

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]

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...

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]

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]

Our solution: AutoOpenRaman adds automation to OpenRAMAN while keeping it open-source and relatively inexpensive (~$8k in total). [3/8]

On the hardware side, we added a motorized XY stage, microscope objective, laser shutter, and neon light source for quick calibration. [4/8]

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.orgOpenRAMAN

doi.orgChlamydomonas cpc1-1 mutant exhibits unexpected growth phenotypesComparative 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...

1 Sept 2025

Chlamydomonas cpc1-1 mutant exhibits unexpected growth phenotypes

open.substack.comZoogle Suggested We Try a Sea Squirt, So We DidIt’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...

5 Aug 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...

arcadiascience.comArcadia ScienceDeveloping better ways to predict and test therapeutics.

4 Aug 2025

AI laboratory for lit review

New website who dis www.arcadiascience.com

22 July 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

24 June 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”

bsky.appCameron 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...

23 June 2025

#ICYMI

23 June 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

22 June 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…

22 June 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

22 June 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”

21 June 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

29 May 2025

#PubDrop bsky.app/profile/cdma...

bsky.appArcadia 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...

26 May 2025

#ICYMI

Arcadia Science reposted

Ubadah Sabbagh

@ubadahsabbagh.com

2 May 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.ioCross-trait learning with a canonical transformer tops custom attention in genotype-phenotype mapping –

Arcadia Science reposted

Ubadah Sabbagh

@ubadahsabbagh.com

30 Apr 2025

Not only do we do cool science but we have a badass illustrator for our pubs

github.comGitHub - Arcadia-Science/agent-literature-reviewContribute to Arcadia-Science/agent-literature-review development by creating an account on GitHub.

21 Apr 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?

9 Apr 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

buff.lyEarly update on Arcadia publishing 2.0: Scientists are in charge, speed is an issue · Reimagining scientific publishingSince 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...

24 Mar 2025

Early update on Arcadia publishing 2.0: Scientists are in charge, speed is an issue

buff.lyRescuing Chlamydomonas motility in mutants modeling spermatogenic failure · Genetics: Decoding evolutionary drivers across biologyWe 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...

24 Mar 2025

Rescuing Chlamydomonas Motility in Mutants Modeling Spermatogenic Failure

research.arcadiascience.comCompound 48/80 is toxic in HMC1.2 and RBL-2H3 cellsWe 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...

19 Mar 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...

18 Mar 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...

18 Mar 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...