jeroen.vangoey.be - Profile | ThreadSky | a Reddit-style client for Bluesky

Inexplicably, US administration has launched an unprecedented assault on science, on research institutions & on vital international organizations & initiatives. An assault on science anywhere is an assault on science everywhere; the global community must unite 🧪 www.nature.com/articles/d41...

submitted 1 day ago • 12 comments

Introducing π-PrimeNovo, a non-autoregressive model revolutionizing de novo peptide sequencing! Faster, more accurate with deep learning, it outperforms autoregressive methods! 🚀🔬 #Proteomics PMID:39747823, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-024-55021-3

submitted 7 days ago • 0 comments

A transformer-based semi-autoregressive framework for high-speed and accurate de novo peptide sequencing www.nature.com/artic... --- #proteomics #prot-paper

submitted 13 days ago • 0 comments

🔬 Interesting read: MARLOWE enables taxonomic characterization of unknown samples using de novo peptide sequencing & „strong“ peptides! Applied to forensic proteomics, it identifies contributors with high accuracy. New Paper out in JPR: doi.org/10.1021/acs.... #Proteomics #Forensics

submitted 18 days ago • 0 comments

A long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it. www.science.org/content/blog...

submitted 22 days ago • 21 comments

Can AI really help with literature reviews? 🧐 Meet Ai2 ScholarQA, an experimental solution that allows you to ask questions that require multiple scientific papers to answer. It gives more in-depth and contextual answers with table comparisons and expandable sections 💡 Try it now: scholarqa.allen.ai

submitted 36 days ago • 1 comment

🧪AI-designed proteins can neutralize deadly snake venoms, offering hope for modern, low-cost snakebite therapies. These proteins may overcome the limits of century-old antivenoms, saving lives globally. 🩺 🧬💻

submitted 40 days ago • 1 comment

🎉Looking for an exciting opportunity in proteomics and data science?🎉 Join DTU Bioengineering as a #Data #Science Specialist in #Proteomics! Based at our state-of-the-art DTU Proteomics Core. You'll also collaborate with me and the DTU Bioengineering Data Science Hub. lnkd.in/d2zHaMys

submitted 44 days ago • 0 comments

Applications are open for the GeoAI Hackathon at #AIActionSummit 2025! 🗓️ 5-6 Feb 2025 Tackle global challenges with AI-powered geospatial solutions! 🌍✨ 👩‍💻Open to Python & ML enthusiasts 🌟The winners will be presented during the AI Action Summit in #Paris! 👉Apply by 26 Jan 2025: geoaihack.com

submitted 50 days ago • 0 comments

π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing www.nature.com/artic... --- #proteomics #prot-paper

submitted 54 days ago • 1 comment

New paper led by Ismael Rodriguez, with @yc386.bsky.social, @rbharathkumar91.bsky.social, @mirandaevans.bsky.social, @jaadekker.bsky.social, @jespervolsen.bsky.social on benchmarking a single degraded protein out in @PCI Mathematical & Computational Biology doi.org/10.24072/pcj... #teammasspec

submitted 76 days ago • 1 comment

2024 saw another record for bioRxiv postings. Thanks to all the CSHL staff, affiliates, authors, funders, and everyone who advocates for the project. Happy New Year and #letsmakethisthenorm ! 🧪

submitted 57 days ago • 7 comments

NovoRank: Refinement for De Novo Peptide Sequencing Based on Spectral Clustering and Deep Learning pubs.acs.org/doi/10.... --- #proteomics #prot-paper

submitted 57 days ago • 0 comments

NovoRank: Refinement for De Novo Peptide Sequencing Based on Spectral Clustering and Deep Learning #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

submitted 57 days ago • 0 comments

Really glad we got this opinion piece by Kelly Chibale in @cenmag.bsky.social #chemsky #biotech

submitted 163 days ago • 2 comments

Last week, David Baker, alongside John Jumper and Demis Hassabis, received the #Nobel Prize in #Chemistry🏆. It was incredibly special to see our group's and collaborators' work highlighted in the Nobel speech, along with the vital issue of #snakebite #envenoming🎉.

submitted 72 days ago • 0 comments

Three BioML starter packs now! Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc Pack 3: go.bsky.app/NAKYUok DM if you want to be included (or nominate people who should be!)

submitted 86 days ago • 15 comments

In one year, I genetically engineered the boring Arabidopsis into a beautiful ornamental flower 🧬🌹 Here is how and why I gave this model organism a visual upgrade 🧵(1/7)

submitted 77 days ago • 23 comments

A really nice paper, talking about Open Source and what it means for #Proteomics , one for #teamMassSpec and #chemsky to check out. chemrxiv.org/engage/chemr...

submitted 79 days ago • 0 comments

For years, Hunt lab members were tasked with de novo sequencing a notebook full of MS/MS spectra upon joining (still have mine!). This provided a firm foundation for many careers in MS-based proteomics. Thanks to L.Anderson et al for making the “blue book” available to #teammassspec in honor of DFH:

submitted 77 days ago • 1 comment

🧪🧬🖥️ Nucleotide Transformer is now published in Nature Methods! A foundational models for genomics, with up to 2.5 billion parameters, that are trained on genomes from 800+ species and 3000+ human individuals. 📄 www.nature.com/articles/s41... 💻 github.com/instadeepai/... #Genomics #BioML #MLSky

submitted 84 days ago • 3 comments

An advertorial from Bruker Daltonics about using the de novo peptide sequencing algorithm Novor 2.0 for immunopeptidomics. www.labcompare.com/10-Featured-...

submitted 84 days ago • 0 comments

Reposting two starter packs with researchers working on AI4Science for those who are newly joining 🦋. So many wonderful folks on these lists, help me add more by sending names (including your own 😊). Starter Pack 2: go.bsky.app/GnFTUM6 Starter Pack 1: go.bsky.app/JeFdryY

submitted 85 days ago • 18 comments

Friends, it's fun to see the #immunology community continue to grow! I created a 4th Starter Pack to help folks find each other. If you're an immunologist and you don't see yourself on the lists, let me know 🧪 go.bsky.app/PY5tCas go.bsky.app/FmERUoD go.bsky.app/6aT6qDS go.bsky.app/QSEPDoj

submitted 89 days ago • 41 comments

Protein Sequence Modelling with Bayesian Flow Networks ProtBFN, a 650M parameter Bayesian Flow Network (BFN), generates diverse, structurally sound proteins, outperforming autoregressive and diffusion models. It excels in both unconditional and conditional generation.

submitted 87 days ago • 1 comment

Deep Learning Methods for De Novo Peptide Sequencing #MassSpectromRev analyticalsciencejournals.onlinelibrary.wiley.com/doi/full/10....

submitted 89 days ago • 0 comments

Recently stumbled upon these talks from the 2024 Genome Sciences Symposium at the University of Washington. #bioinformatics youtube.com/playlist?lis...

submitted 95 days ago • 0 comments

Here's another youtube channel with a bunch of talks on the intersection of deep learning/ml and bio www.youtube.com/@valence_lab.... #bioinformatics

submitted 89 days ago • 0 comments

New blogpost: The ABCs of Alphafold 3, Boltz and Chai-1 blog.booleanbiotech.com/alphafold3-b...

submitted 88 days ago • 9 comments

Congratulations @isma-rgz.mastodon.social.ap.brid.gy et al. on the recent publication in @peercommunityin.bsky.social: Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins! If you missed the corresponding talk: youtu.be/YJ9OKRR0Tj8

submitted 93 days ago • 1 comment

Let's get connected on 🦋. With this starter pack we want to highlight immunology research done by Belgians and/or in #Belgium. go.bsky.app/PZ9BgQM #Immunosky Help us to expand this list.

submitted 91 days ago • 0 comments

My first Skeetorial! 💻🧬TCR-TRANSLATE - A new framework for thinking about the TCR:pMHC specificity problem. TLDR: We pretrained LLMs on ~8M TCR & pMHC seqs Finetuned on sparse pMHC->TCR pair data Validated CDR3b sequences to unseen antigens >> random performance on IMMREP2023 "private" antigens

submitted 99 days ago • 1 comment

Any chance of getting Biology+AI Daily in here? Biggest X pull factor left for me tbh

submitted 101 days ago • 1 comment

I work for company number 9 on this list, InstaDeep, and can confirm that we are using AlphaFold internally. We're actively hiring in London, Paris and Kigali: www.instadeep.com/careers (filter on BioAI department)

submitted 92 days ago • 0 comments

Chiang and Collins making a fun Casanovo + Sage (w/Mokapot et al.) metaproteomics pipeline (Bittremieux, @michaellazear.bsky.social @willfondrie.com) … and an exceptional TOC graphic.

submitted 103 days ago • 1 comment

RankNovo: A Universal Reranking Approach for Robust De Novo Peptide Sequencing openreview.net/forum?id=87B...

submitted 92 days ago • 0 comments