Thank you @PittHealthSci for highlighting our recent @NIAIDFunding DP2 award ( https://t.co/5lXIPpCPR2), @NIH_CommonFund DP2 awards for awesome Pitt colleagues @DKemaladewi @YinanGong @GuangLiPitt and the Transformative Research Award for the fantastic @donnelly_lab (1/2).

SpaceTravLR learns these functional microniches from spatial transcriptomics without perturbation data for training. Our interpretable ML approach provides testable hypotheses that were experimentally validated. SpaceTravLR generalizes across tissues, species & platforms. (2/2)

Excited to present SpaceTravLR, a new framework to uncover functional spatial microniches across contexts. We learn how individual & combinatorial genetic changes rewire regulation & cell-intrinsic + cell-extrinsic signaling across space in tissues. https://t.co/kqTguEOUik (1/2)

Thrilled to share my promotion to Associate Professor with tenure at @pitt_immunology! Huge thanks to my incredible lab, collaborators, department, colleagues, family & friends. Science is a team effort, and I'm so proud of our work & excited for what's next! Stay tuned!

Today our @NCI funded #COWG Computational Oncology Working Group monthly meetings welcome my dear colleague @jishnu1729 @compbiopitt - On his lab's amazing work in pushing the boundary of #deeplearning, #systembio, and #compImmunology!!! #GRN #networkbiology #machinelearning

Thank you very much @naturemethods for this Research Highlight describing our new interaction language model, SWING, that learns the lexicon of protein and peptide interactions.

Read the Research Briefing on SWING, here! https://t.co/MFnMVuZfqP

Pittsburgh group presenting at the 19th International Workshop on Scleroderma Research! @PittRheum @PittDeptofMed @jishnu1729

Thanks a lot @naturemethods for highlighting SWING, a generalizable biologically-inspired interaction #language_model that learns that lexicon of peptide and protein interactions & the impact of #genetic #variation on these interactions. #ML

Today in @naturemethods, we define a new lexicon for protein/peptide interactions. SWING is a generalizable zero-shot interaction #language_model that outperforms pLMs in multi-context predictions of the impact of genetic variation on interactions. #ML

Full house to start the new #CSI COSI at ISMB 2025 that @ferhatay and I are co-chairing. Looking forward to a great set of talks!

For CSI COSI, I am very thankful to my co-chair @jishnu1729 and steering committee @YuriPritykin , @haticeulku, Aly Azeem Khan. And everyone who submitted their for consideration for this session

I came to the US in 2010 as a PhD student & it transformed my life. Privileged to lead (since 2020) a #systems #immunology lab comprising an incredible group of men & women. This country gave me opportunities I couldn't have dreamed of elsewhere. Proud #US citizen. Happy 4th all!

Check out our recent review in @MolTherapy about how machine learning approaches enable the discovery of therapeutics across domains https://t.co/OokmxOxQM8. We cover a range of #ML techniques with wide applications to #cellulartherapy.

Check out our recent paper in @JCI_insight where we use interpretable #ML to uncover signatures of pathogenesis in localized #scleroderma (#morphea).

Thank you @JCI_insight for highlighting our collaborative work with @corrine_kliment using interpretable #ML approaches to uncover a novel role for GSN in #COPD. We used a range of approaches including a recent flagship method from our lab - SLIDE ( https://t.co/OuFUPiQFZB).

RT @JCI_insight: Can machine learning provide new insight into COPD? https://t.co/C4SZswYRaz Justin Sui, Hanxi Xiao et al use this approa…

If you're at @ASTMH #TropMed24 do add our Systems Immunology of Tropical Diseases symposium (138) to your schedule for Sat Nov 16th. Speakers include @nadegenziza, Dr Elizabeth Aitken & my co-chair @jishnu1729. Exciting talks across AI/ML, Malaria, TB & NTDs incl Schistosomiasis.

Thank you @CellReports for highlighting our work showing how #protein #networks with structural resolution can identify #immunomodulatory variants in infectious disease. Key coding variants often missed by conventional #GWAS can be picked up by our approach.

Uncovering cell-type-specific immunomodulatory variants and molecular phenotypes in COVID-19 using structurally resolved protein networks

Super fun collaboration with @poholeklab now out in Nature Immunology - https://t.co/anFtkycBMH . We use interpretable #machine_learning to help identify spatial microniches of IL2 in a murine model of allergic #asthma.