🔬 Exciting News! Our manuscript, "scGPT: toward building a foundation model for single-cell multi-omics using generative AI" is now finally published in Nature Methods (@NatureMethods) 🎉 !!! (Re-)Introducing scGPT: A transformative foundation model engineered for single-cell

Read the associated Research Briefing here: nature.com/articles/s4159…

Thanks a lot Nature Methods for highlighting SLIDE, our flagship #ML approach to identify significant latent factors from multi-omic datasets. Across a range of biological contexts, these latent factors provide inference beyond prediction.

What would happen if you got vaccinated against the same antigen over and over again? In The Lancet Infectious Diseases, we now report on a hypervaccinated individual from Magdeburg (HIM) who received 217 vaccinations within 29 months against SARS-CoV-2. 👇 1/19 thelancet.com/journals/lanin…

Thanks Nature Methods for highlighting our work! Cell segmentation is moving forward fast Rita Strack 🔥🔥🙌🙌

Congratulations to Ariadna Soto receiving the 2024 AAI Intersect fellowship and amazing Co-PI mentor Jishnu Das to study protist immune interactions. Also congrats to Elaine Kouame PhD (she/her) ;Laura Rachel Gottschalk and others #ProudPI #WomenInScience aai.org/Careers/Fellow…

Happy to co-organize Special session on Computational and Systems Immunology at #ISMB2024 with Ferhat Ay Jishnu Das Hatice Ülkü Osmanbeyoglu . Please join us Tue July 16 in Montreal! iscb.org/ismb2024/submi…

ISMB is the premier computational biology conference, and we will have a great mix of invited and contributed talks in this session. It is not too late to submit abstracts for talks or posters, deadline this Friday April 19.

Many thanks to HIRN dkNET NIDDK NIH HRHR program @JDRF for their support; our collaborators Vignali Lab Mark Anderson Jishnu Das Paul G Thomas Nick Borcherding Rahul Satija for analysis tools And a huge thanks to our editor Madhura Mukhopadhyay at Nature Methods ! 🧵5/5

Thrilled to showcase our latest work: biorxiv.org/content/10.110… This was in collaboration with Jishnu Das who had the brilliant idea of generating 'interaction language models' (iLMs) as a way of looking at protein-protein interactions, and developed SWING as a result 🧵1/5

This was exciting interdisciplinary and collaborative work done with Alok Joglekar - would not have been possible without their expertise and amazing antigen discovery and immunopeptidomics pipelines!

SLIDE is an interpretable ML-based method for identification of latent factors across multiomics datasets, developed by Jishnu Das and colleagues. nature.com/articles/s4159…

#ISMB 2024 off to a great start. Excited to share my lab's recent work in 3 talks - Javad Rahimik presenting endotype discovery in RA at TransMed COSI at ISMB/ECCB, Jane Siwek presenting SWING (biorxiv.org/content/10.110…) at CSI, and me talking about SLIDE (nature.com/articles/s4159…) at MLCSB

The party (conference?) continues!! #ISMB2024 Ferhat Ay Jishnu Das Saurabh Sinha

At #ISMB2024 Grégoire AltanBonnet kicks off the Computational and Systems Immunology special session. Excited to have put this session together with co-chairs Ferhat Ay, Yuri Pritykin and Hatice Ülkü Osmanbeyoglu.

After an amazing keynote from Gregoire Altan-Bonnet of NIH, our Computational Systems Immunology Session (CSI) continues with Duygu Ucar, PhD from The Jackson Laboratory talking about modeling immune aging and vaccine response #ISMB2014 Jishnu Das Yuri Pritykin Hatice Ülkü Osmanbeyoglu

Now Jane Siwek from Jishnu Das lab: Sliding Window INteraction Grammar (SWING): a generalized interaction language model for peptide and protein interactions #ISMB2024 Yuri Pritykin Hatice Ülkü Osmanbeyoglu

Jane Siwek, a graduate student from my lab in the CPCB program, presenting SWING at the CSI session at #ISMB2024. Full house!

We are moving on to short talks at CSI session now. Very happy to have a strong representation from industry: Evaxion Biotech, IBM Research, Pfizer. Please check out the program for details #ISMB204 Jishnu Das Yuri Pritykin Hatice Ülkü Osmanbeyoglu iscb.org/ismb2024/progr…

A new publication from our lab: How aberrant mitochondrial DNA synthesis in macrophages affects inflammation and atherosclerosis. rdcu.be/dR2ei by Niranjana Natarajan Jonathan Florentin, and many collaborators- Jishnu Das Sruti Shiva Krithika Rao Yingze Zhang, Sina Tavakoli