Dennis Sun (孙丹)
@Mezarque
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scientist, artist, writer, gamer 🏳️🌈👾🖌 currently @ArcadiaScience @[email protected] mezarque at https://t.co/6VkH405sw5
Ohlone Land (Berkeley, CA)
Joined January 2012
Ever wondered which organisms encode your favorite protein? 🤔 Do you like maps? 🗺️ At @ArcadiaScience, we’re developing “ProteinCartography,” a tool that makes interactive maps of protein space. We'd love your feedback on this early version! 🧵 1/9.
research.arcadiascience.com
The ProteinCartography pipeline identifies proteins related to a query protein using sequence- and structure-based searches, compares all protein structures, and creates a navigable map that can be...
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RT @ArcadiaScience: Happy Darwin Day! Today we’re thinking about how to use evolution to accelerate biomedical research. We think the answe….
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Generate videos in just a few seconds. Try Grok Imagine, free for a limited time.
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RT @NeuroLuebbert: Srinivasan has posted responses to our manuscript documenting data duplication in his papers. They are filled with insul….
github.com
Contribute to pachterlab/LP_2024 development by creating an account on GitHub.
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RT @compbiologist: Join the discussion of our latest review at @askalphaxiv. Check out the great comment (by @Mezarque / @ArcadiaScience)….
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RT @bentbraverman: If you’re a fan of DIY lab equipment, you’ll love the phenotype-o-mat, a customizable DIY 96-well plate imager from @Arc….
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I’m at #TAGC24 to talk about ProteinCartography! Stop by and check out our website for our other events.
Interested in protein structural comparisons and attending #TAGC24?. Join @Mezarque on Fri 3/8 from 11:30–11:45 am in Woodrow Wilson B-D as he discusses the #ProteinCartography pipeline and its role in generating hypotheses for the actin family and polyphosphate proteins!
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RT @Manon_Morin23: At @ArcadiaScience we also share our negative results. Dive into our latest work where we employed trait mapping and evo….
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RT @ArcadiaScience: Can we identify more human-relevant and research-friendly models by unifying various genetic approaches? . Join us at #….
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RT @BiggeBrae: How might structural differences within the actin family lead to insights about its proteins’ functions? I’m excited to shar….
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RT @BiggeBrae: 🚨 An updated version (v0.4.2) of the #ProteinCartography pipeline (our tool for protein comparisons across species) is now a….
github.com
ProteinCartography v0.4.2 Overview This release introduces minor changes that improve the performance of the pipeline. These changes are not breaking changes and do not modify the nature of the fil...
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RT @emilycpierce: In our new pub, we investigate disease-associated repeat expansions (dREs). Expansion of DNA repeats can cause neurodegen….
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RT @BiggeBrae: If you’re attending #CellBio2023, don’t forget to send your favorite proteins (submit on ! Then, com….
ascb2023.arcadiascience.com
Arcadia Science is heading to #cellbio2023! On this page, you can see what we’ll be up to, when/where you can find us, and check out all the science we’re sharing, including poster PDFs and links to...
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RT @ArcadiaScience: We’re heading to #cellbio2023! Check out to see the posters we’re presenting and what else we’l….
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RT @seemaychou: 🧊 Scientists know the importance of failing fast. We wear this like a badge of honor @ArcadiaScience w our published “icebo….
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RT @seemaychou: New job alert: know someone who loves to scale and automate workflows in the lab? We want to apply new tools to onboard a d….
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Come work with us!.
Interested in computationally exploring how proteins are related across species? Join us @ArcadiaScience and engage collaboratively to design, create, and iterate on workflows and tools for comparing proteins in diverse organisms. Check out the job ad ➡️
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RT @lizilla93: The enzymes for polyphosphate formation are present in nearly all bacteria, but only some store large amounts of polyP. Why?….
research.arcadiascience.com
Only some bacteria accumulate substantial amounts of polyphosphate (polyP). We thought that despite sequence divergence, polyP synthesis enzymes in these bacteria might have similar structures. We...
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After stopping this work a few months ago, we applied some of the methods and learnings towards building #ProteinCartography, our pipeline to build interactive maps of protein structural space – check out an explainer thread here:. 5/end.
Ever wondered which organisms encode your favorite protein? 🤔 Do you like maps? 🗺️ At @ArcadiaScience, we’re developing “ProteinCartography,” a tool that makes interactive maps of protein space. We'd love your feedback on this early version! 🧵 1/9.
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Thanks to @ryanayork @AustinHPatton @KiraPoskanzer @_mertcelebi for their advice and contributions to code, methodology, and brainstorming for this project!. 4/n.
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You can find the code to reproduce and explore our preliminary analyses in our GitHub repo. 3/n.
github.com
Evolutionary origins and relationships of glial cell types - Arcadia-Science/glial-origins
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The tl;dr is: our attempts to group genes across species using Foldseek structural clusters did not improve species mixing in scRNA-seq data than when grouping by sequence similarity (in the form of orthogroups). But there's still more to be done in this space! 2/n
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