Dave Moi
@steg0s4urus
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🔬 Postdoctoral Researcher working at the @dbc_unil for the @DessimozLab | Bridging Borders | #Bioinformatics & #MachineLearning 🤖 |
hyperspace
Joined September 2012
In a post #AlphaFold world, we can use protein structures in ways we never could before. Can we build phylogenies with them? Are they any good? Yes! Foldtree ( https://t.co/GarG48Y21B) surpasses traditional sequence-based methods, even for closely related proteins.👇
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@DessimozLab representation at #ISMB2025 * Phylogenies with protein structures, #FoldTree - @steg0s4urus * Ancestral genome reconstruction: #EdgeHOG - Charles Bernard * Gene duplications and functional evolution @the_alexwv and @IreneJulca
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Fantastic #Sinergia retreat on #animalorigins! A day packed with insights into #multicellularity, #ichthyosporeans, #choanoflagellates & more—capped with a Swiss-style finale. Huge thanks to @dirk_fasshauer @Pahskahrailly @steg0s4urus @cdessimoz @pedrobeltrao @merimonas
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Have you checked out our behind-the-paper blog post on FastOMA? Read it here https://t.co/qaOj4xsBR8 I’ll give you a quick intro to orthology, a bit of history of orthology methods, and the story of how FastOMA came to life—and how it works!
communities.springernature.com
FastOMA was just published in Nature Methods! In this post, we’ll give you a quick intro to orthology, a bit of history of orthology methods, and the story of how FastOMA came to life—and how it...
From @SinaMajidian, @DessimozLab and colleagues, FastOMA achieves fast and accurate orthology inference, with linear scalability. https://t.co/dgYgwg8Qpj
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FastOMA is out now in Nature Methods 🎉: https://t.co/6nNVfbCVqr A new orthology inference algorithm that scales linearly and is highly accurate. FastOMA can process all >2000 eukaryotic UniProt ref proteomes <24 hours 🚀. Try it out at https://t.co/QUPiRx33J9
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Today OpenAI announced o3, its next-gen reasoning model. We've worked with OpenAI to test it on ARC-AGI, and we believe it represents a significant breakthrough in getting AI to adapt to novel tasks. It scores 75.7% on the semi-private eval in low-compute mode (for $20 per task
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This is a foundational achievement. MMseqs2-GPU virtually *erases* the bottleneck of homology search in many workflows, including structure prediction. @sacdallago @milot_mirdita @thesteinegger, Felix, Bertil, and Alejandro too! https://t.co/audMlo0oIh
developer.nvidia.com
The ability to compare the sequences of multiple related proteins is a foundational task for many life science researchers. This is often done in the form of a multiple sequence alignment (MSA)…
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Free scientific illustrations for biologists! 😍 @NIH has released a library of 500+ free scientific illustrations to create figures, presentations, and illustrations! all freely available in the public domain. Retweet and spread the message! https://t.co/p1bD1kxO7H
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Here’s our human protein-protein interactome. We mined the SRA, devised a new distillation dataset for protein complexes, trained a new version of RF2 to screen millions of protein pairs, and identify > 18k binary interactions. https://t.co/rfEOJIlW1x
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7/ In particular, we showcase gLM2's ability to directly learn coevolutionary signal in protein-protein interfaces with no supervision! The learned contact maps can be extracted using @ZhidianZ et al's categorial Jacobian method.
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Super excited to introduce ESM3, a 1.4B, 7B, and 98B(!) series of multimodal generative models for proteins. It's been an incredible journey working on this for the past 7 months at EvolutionaryScale. Check out the blog post and paper!
We have trained ESM3 and we're excited to introduce EvolutionaryScale. ESM3 is a generative language model for programming biology. In experiments, we found ESM3 can simulate 500M years of evolution to generate new fluorescent proteins. Read more: https://t.co/iAC3lkj0iV
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Companies like Deepmind do not have any requirements to make their research available. I signed the letter below because they chose to publish their work and different standards were applied to the Alphafold 3 publication as those applied to others.
We were incredibly disappointed with the lack of code or executable accompanying the publication of AF3 in @Nature . This contradicts scientific principles of the ability to evaluate, use, and build upon existing work.
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A nitrogen-fixing organelle, or “nitroplast,” has been identified in a marine alga. This discovery sheds light on the evolutionary transition from endosymbiont to organelle. Learn more from a recent issue of Science: https://t.co/a1UsC0hlXb
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🧬🔬 Nice dive into how #metagenomics & single-cell genomics are revolutionizing our understanding of the tree of life by @eme_laura & @DanielTamarit 🧬 #MicrobialDiversity #genomics #singlecell #biodiversity #protists
The next Perspective in our 40th anniversary series is Microbial Diversity and Open Questions about the Deep Tree of Life by @eme_laura and @DanielTamarit
https://t.co/ibvQLUHrMd
#science #evolution #biology #genome
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Amazing! the choanoflagellate Choanoeca flexa blurs the lines between clonal and aggregative multicellularity, adapting to extreme salinity with a unique life cycle! A leap forward in understanding animal origins and multicellular evolution. 🌊🔬 Thrilled also by this week's
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https://t.co/kWX1askBGy Have a look at the article I reposted by @BallouxFrancois, @cedriccstan and @LucyvanDorp if you're interested in viruses and their evolutionary signature when jump hosts. I had the pleasure of writing a news and views piece about this work with @cdessimoz
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New open access paper out in @NatureEcoEvo TLDR: - Humans pass on more viruses to other vertebrates than they do to us - Generalist viruses (with broad host range) require fewer mutations to infect a novel host 1/ https://t.co/ixdTgY0cJx
nature.com
Nature Ecology & Evolution - Analysis of publicly available viral genomes shows that humans may give more viruses to animals than they give to us, and reveals evolutionary mechanisms...
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Capping a 10-year-long adventure, in today's @CellCellPress we unveil the molecular mechanism whereby the fertilized egg permanently blocks polyspermy, a lethal condition for the embryo: https://t.co/T0MNqBJ6FU
#structuralbiology #reproduction #fertilization #infertility
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Evo: a foundation model for genomics! Using a well suited architecture, Evo learns from billions of bp of genomic sequence and performs well on several zero-shot prediction tasks on RNA, DNA and protein. Beautiful paper from @BrianHie & @pdhsu at @arcinstitute
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