Author

Mark Jay Shlomchik

University of PittsburghORCID 0000-0002-2152-0959Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Organism:mouse· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

Alisa A. OmelchenkoiD· 2 shared Jishnu DasiD· 2 shared Akash PateliD· 1 shared Alok V. JoglekariD· 1 shared Alyson WangiD· 1 shared Amanda C. PoholekiD· 1 shared AnnaElaine RosengartiD· 1 shared Chinmay V. Gadiraju· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersImmunology

Alisa A. OmelchenkoORCID

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

A unified network systems approach uncovers a core novel program underlying T follicular helper cell differentiation

Alisa A. Omelchenko, Syed Ashiqur Rahman, Alyson Wang, Tracy Tabib, Vinay Viswanadham, Grace J. Yuen, Perla M. Del Río Estrada, Valentino D’Onofrio, Yijia Chen, Na Sun, Hamid Mattoo, Swapnil Keshari, Chinmay V. Gadiraju, Gonzalo Salgado Montes de Oca, Maribel Soto-Nava, , Jishnu Das

This study identifies a core gene program underlying Tfh cell differentiation using a multi-scale network systems approach, revealing a novel role for IL-12 in regulating Tfh precursor differentiation.

Nature Communications · Jul 22, 2026Peer-reviewedImmunology

Sliding Window INteraction Grammar (SWING): a generalized interaction language model for peptide and protein interactions

Jane C Siwek, Alisa A. Omelchenko, Prabal Chhibbar, Sanya Arshad, AnnaElaine Rosengart, Iliyan Nazarali, Akash Patel, Kiran Nazarali, Javad Rahimikollu, Jeremy S. Tilstra, Mark Jay Shlomchik, David Ryan Koes, Alok V. Joglekar, Jishnu Das

SWING is a novel interaction language model that predicts peptide:MHC interactions and protein-protein interaction disruptions using sequence data.

Nature Methods · Jul 28, 2025Peer-reviewedSystems Biology