1/n Using snRNAseq we identify a previously undiscovered population of alveolar epithelial cells in IPF - Alveolar Intermediate (ATi) cells - they share features of ATI, ATII and Aberrant Basaloid cells but also have their own distinct features. #ATi biorxiv.org/content/10.110…

2/n Using PAGA we define distinct trajectories among ATII, ATI, Aberrant basaloid cells & ATi cells that allow identifying specific markers for intermediate states & then validate and localize the presence of ATi populations in human IPF tissue #CTSE biorxiv.org/content/10.110…

3/n To understand emergence of aberrant basaloid cells in human PCLS we did time course analysis. Untreated PCLS -> ⬆️ alveolar epithelial diversity and proliferation suggesting FC treated PCLS -> ⬇️ proliferation & disease like aberrant basaloid cells biorxiv.org/content/10.110…

4/n 10x Genomics Multiome analysis allowed us to establish Aberrant Basaloid Cells as a distinct lung cell population. It is different from all other lung cells and characterized by ⬆️⬆️ AP1 accessibility reminiscent of Injury memory retention #Multiome biorxiv.org/content/biorxi…

5/n Taken together, our results shift the paradigmatic view of alveolar epithelial cells in IPF from ‘innocent bystanders’ to 'drivers of disease' - maybe positioning Aberrant Basaloid Cells as potential targets for cell-based therapies biorxiv.org/content/10.110…

6/n Deeply grateful to all contributors; Current or former #KaminskiLab members; generous collaborators: Takis, Ivan, Melanie, Jun, the FORMIDABLE KU Leuven team - Wim and Bart; and special 👏🏽👏🏽 to #SuperDuo : Schupp & Adams‼️ Fin. #SchuppAndAdams biorxiv.org/content/biorxi…

The new European Respiratory Journal impact factor is 21. Ranked #2 across all resp journals Thank you to the incredible Don Sin , all authors, our outstanding editors and journal staff ♥️ ERS publications ERS IF for selected respiratory journals below

1/n Happy to share our new single-cell+unsupervised AI drug discovery method is now published in Nature Biomedical Engineering!🚀 Huge thanks to Jun Ding, Naftali Kaminski and all collaborators. 🎉 We hope UNAGI can accelerate the discovery of new drugs. doi.org/10.1038/s41551…

2/n We applied UNAGI to a time-series snRNA-seq Idiopathic Pulmonary Fibrosis (IPF) dataset and successfully reconstructed (1) the temporal dynamics graph (panel A) to describe the IPF progression (2) cellular dynamics (panel B and C) of individual cell tracks. #singlecell #IPF

3/n UNAGI can conduct perturbation on the pathway and drug/compound levels. When applied to the IPF data, we identify a full spectrum of pathways drug/compounds from well established to less studied ones. e.g. We re-identified Nintedanib, the FDA approved drug for IPF.

4/n Thanks to Naftali Kaminski and his team, we validated one of the UNAGI's prediction, Nifedipine, a common medication to treat high blood pressure, has the similar anti-fibrotic effects as Nintedanib in the human Precision-Cut Lung Slices. #ipf #singlecell

5/n We evaluated the generalizability of UNAGI using a COVID-19 dataset. And UNAGI successfully 1) reconstructed the cellular dynamics of COVID19 and 2) re-discovered some compounds that have anti-COVID19 effects supported by existing literatures. #covid19

6/n We benchmarked UNAGI against both conventional DL methods (e.g., scVI) and single-cell foundation models (scGPT, Geneformer). UNAGI outperformed them in cell-embedding generation, disease-associated marker/pathway identification, and in-silico drug perturbation.

The Unagi paper is FINALLY out! We present the first application. of a novel AI tool to human pulmonary fibrosis snRNAseq data to identify cellular trajectories & reversak perturbations with proteomics & PCLS validations!! See 🧵 👇🏼 and paper here nature.com/articles/s4155…

🙏🏼👏🏼🙏🏼 Drs Zheng, Schupp, Adams, Clair, Justet, Ahangari, Yan, Hansen, Carlon, Cortesi, Vermant, Vos, De Sadeleer, Rosas, Pineda, Sembrat, Königshoff, McDonough,Vanaudenaerde, Wuyts & Ding for this amazing #AI2CureIPF collaboration!! nature.com/articles/s4155… and 🧵below 👇🏼

AI Learns Lung Disease Progression, Proposes Drug to Block Fibrosis A new #AImodel called UNAGI pinpoints drivers of idiopathic #pulmonaryfibrosis and identifies possible treatments Naftali Kaminski Jun Ding Yale School of Medicine McGill University #scSeq #drugdiscovery hubs.li/Q03tnvmt0

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As one of the authors of this perspective, I can only say: I wish there was no need to write it. But sadly, there was. I'm grateful NEJM broke the American Medical Establishment's wall of silence and published two perspectives about Gaza. Let's hope more action follows 👇🏼

Dr. Naftali Kaminski is stepping down as Yale PCCSM section chief in 2026. Under his leadership, clinical programs, research funding & educational programs have expanded substantially in size, scope & impact. Learn more about Naftali Kaminski & his tenure. medicine.yale.edu/internal-medic…