Models trained on harder antibody binding tasks learned deeper biological rules + generalized better. New NatureMachIntel paper by CTO @victorgreiff.bsky.social shows training on hard negatives (weak vs strong binders) boosts antibody ML generalization. Read the paper: doi.org/10.1038/s422...

Deadline extended - last chance, second edition!

Earlier this year, Imprint came out of stealth on the TED Mainstage to share our vision: What if the immune system holds the key to curing chronic diseases—and we just need the tools to read it? We’re building those tools. Our TED talk is now live 👉 go.ted.com/beckbrachman

Identifying malignant cells in single-cell transcriptomics data – from first principles to computational solutions, framed around the hallmarks of cancer www.nature.com/articles/s42...

EMBL is back on hiring faculty! Check out the multiple open positions: 3 PIs- 2 in Heidelberg incl. our Molecular Systems Biology Unit, 1 in Grenoble 1 Head of Unit (Cell Biology & Biophysics, Heidelberg). Closing deadlines in Sep! +3 more positions to come out then, stay tuned... @embl.org

📣Major thanks to @faylinphd.bsky.social at GEN News for this lovely piece on IMPRINT! It was a pleasure for our founders — @beckbrachman.bsky.social, @victorgreiff.bsky.social, and Raymond Alvarez — to speak about our mission and research, and being NYC's first FRO. @convergentresearch.bsky.social

Excited to co-found and help lead @imprintlabs.bsky.social —a focused effort to decode the immune system’s memory through cutting-edge computation and experimentation. Grateful to be on this journey with an exceptional team.

We have available a 3-year postdoc position in Bioinformatics in our lab at the University of Oslo focusing on the adaptive immune response in rheumatoid arthritis. Please see details here lds.easycruit.com/vacancy/3490...

Online now: Somatic hypermutation unlocks antibody specificities beyond the primary repertoire

Looking for a job in immunology or biotech research? ✨IMPRINT is #hiring! ✨ Join us to help revolutionize how we decode the body’s immune memory, uncover the causes of chronic diseases, and drive breakthroughs in autoimmunity and neuropsychiatric research. #BiotechJobs #Immunology #sciencejobs

The BioEmu-1 model and inference code are now public under MIT license!!! Please go ahead, play with it and let us know if there are issues. github.com/microsoft/bi...

This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after

@timodonnell.bsky.social @giulioisac.bsky.social @jlimenitakis.bsky.social Beck Brachman Raymond Alvarez @victorgreiff.bsky.social Convergent Research

1/10 Small pre-Christmas #bluetorial on the workshop held by the T-cell Receptor (TR) and Immunoglobulin (IG) Nomenclature Sub-Committee of @iuis-online.bsky.social on policies and procedures for TR/IG gene annotation and nomenclature #immunerepertoire #immunogenetics

A good start into 2025: www.cell.com/cell-reports.... High-resolution mapping of cell cycle dynamics during steady-state T cell development and regeneration in vivo.

In a recent article, my group and I laid out some of the recommendations I have learned over the year about research. In 2025, our lab will double down on following our own advice. pubs.rsc.org/en/content/a...

What an amazing read (h/t Jeff Flier) - esp @michaelmina.bsky.social which felt especially raw. #biosky #medsky www.harvardmagazine.com/2025/01/harv...

A periodic reminder that biologically meaningful conformational changes do not have to be large While textbooks may indicate that relevant motions are large, even the original paper on alternating access makes it clear that atoms just need to move a bit to have an effect. doi.org/10.1038/2119... 🧬🧶

Extremely pleased to share our new work in collaboration with the @bruskolab.bsky.social lab, where we leveraged one of the largest TCRbeta sequencing datasets to identify T1D-associated TCR-based signatures. Paper link and 🧵 are below. Incredible work led by @puneet021192.bsky.social.

Happy to share our new collaborative work! 🚨 We analyzed 2250 TCR repertoires to uncover how HLA risk alleles shape immune autoreactivity in T1D. T1D-specific HLA-motifs were also validated in pancreatic lymph nodes (pLN) & spleen. 🧬🧵 #T1D #Immunology #TCR 1/9

Our massive effort to recontextualize #single #T-cell data is now out in Science Advances! We developed a new system, STEGO, to do a TCR-first analysis, and reanalyzed 12 studies and more than 500 000 individual T-cells. Supported by @cziscience.bsky.social ! doi.org/10.1126/scia...

Hey academics, what is happening with the preprint sites? 🧪 help.. @bioarxiv : reject (no biological data, no surprise) @arxiv_bio: 3 weeks turnaround! OSF preprint: 1 week, no approval yet 😮 - do they need help?

Curious about generative modeling for T and B cell receptor repertoires and its role in understanding immune system diversity? Watch my talk here youtu.be/HVUYG-UmRH8?.... Thanks to the @airr-community.bsky.social and @victorgreiff.bsky.social for the opportunity to share our work!

We created one of the largest antibody bottom-up proteomics datasets to query the impact of experimental and computational parameters on the reconstruction of antibody sequences. www.biorxiv.org/content/10.1... Brilliant work by @mchernigovskaya.bsky.social, Khang Le Quy and Igor Snapkow.

My last paper with Shuguang Zhang is finally published! We explored QTY (L → Q, I/V → T, F → Y) mutagenesis to make hydrophobic transmembrane proteins more water-soluble. It shows that simple methods, without thousands of GPUs, can be useful and fulfill their tasks. www.nature.com/articles/s41...

⏰ www.antibodysociety.org/the-airr-com... Short talk abstract submission for AIRR Community meeting is January 18! Link to abstract submission form:  docs.google.com/forms/d/e/1F...

Protein Stability Prediction by Fine-tuning a Protein Language Model on a Mega-scale Dataset https://www.biorxiv.org/content/10.1101/2023.11.19.567747v1

Curious about what a blood sample can reveal about humoral immunity? Our latest work combined sequencing methods and mass spectrometry to explore BCR and antibody repertoires and assess their synergistic potential. www.biorxiv.org/content/10.1...

If you're interested in listening to some geeks yammer on about the past, present and future of immunoglobulin and T cell receptor genomics and germline databases: www.podbean.com/ew/pb-nvt5d-...

The updated AIRR-C Governance awaits AIRR-C member vote by November 10th! Version 22 of the AIRR-C Governance doc has passed internal review and the AIRR-C feedback process. It is now ready for formal ratification. All infos and link to vote are here: www.antibodysociety.org/airr-communi...

Really excited that our work on the plasticity of antibody developability is out www.biorxiv.org/content/10.1.... A fantastic collaborative effort led by Habib Bashour, @evasmorodina.bsky.social, Matteo Pariset, and @jahnzhong.bsky.social. All details are in the thread below.

Machine learning on immune receptors/repertoires is an exponentially expanding field, but labeled data to benchmark ML methods are missing. We address this need with our new simulation framework LIgO. www.biorxiv.org/content/10.1... Led by @mchernigovskaya.bsky.social and Milena Pavlović.

Inferring B cell phylogenies from paired heavy and light chain BCR sequences with Dowser www.biorxiv.org/content/10.1...

AIRR-C/TAbS Webinar on Nov 7th on "Quality Control Pipelines for T cell and B cell AIRR-seq" by Encarnita Mariotti-Ferrandiz and Nina Luning Prak. It's free and will be recorded! Register here: webinars-antibodysociety.org/store/semina...

"Community-developed checklists for publishing images and image analyses" Very important resource for #Microscopy coming from Christopher Schmied, Christian Tischer & Helena Klara Jambor et al. 👍 I assume this was edited by @ritastrack.bsky.social? www.nature.com/articles/s41...

This post is long but informative (even if mostly written before the newest paper): The 8 Fallacies of Assembly Theory hectorzenil.medium.com/test-8f0be54...

New work from my lab on "Weakly supervised identification and generation of adaptive immune receptor sequences associated with immune disease status" led by @highvariance.bsky.social and Philippe Robert. Great collaboration with G.K. Sandve and L.M. Sollid. www.biorxiv.org/content/10.1...

The past, present and future of science publishing. New article from me on a history not always told correctly, the reality of the journal world, and choices for the future doi.org/10.1371/jour...

I'm dreaming of AI tools not just for finding interpretable biological insights, but for all the **** we do instead of the actual science, mentoring and teaching. Can someone please steal and implement some of these ideas:

“POP-UP TCR: Prediction of Previously Unseen Paired TCR-pMHC” 🧶🧬 “Models trained only on beta chains give satisfactory predictions” (TCR beta chain is equivalent to Ab/BCR heavy chain) www.biorxiv.org/content/10.1... github.com/NiliTicko/PO...