Author

Nilam S. Mangalmurti

University of PennsylvaniaORCID 0000-0002-9146-1608Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 2 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Approach:contrastive learning· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

Abhishek Kulkarni· 1 shared Ajinkya PattekariD· 1 shared Alexandra P. TurneriD· 1 shared Allison R. GreenplateiD· 1 shared Benjamin A. Bleiberg· 1 shared Caroline A. G. Ittner· 1 shared Carolyn S. CalfeeiD· 1 shared Corey Jay LangeriD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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1 shared paperCancer Biology

Abhishek Kulkarni

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2 papers

Recent·Most cited

The Red Blood Cell Surface Defines a Distinct Tumor DNA Compartment for Liquid Biopsy

Elias Elias, H Ruger, Jarrod D. Predina, Benjamin A. Bleiberg, Phurin Areesawangkit, Estela Noguera-Ortega, Abhishek Kulkarni, Jeffrey C. Thompson, Michael G. S. Shashaty, Corey Jay Langer, Steven M. Albelda, Nilam S. Mangalmurti

This study identifies RBC-bound tumor DNA as a distinct compartment for liquid biopsy, showing it is more abundant and concordant with tumor tissue than plasma DNA.

bioRxiv · Oct 10, 2026 · PreprintCancer Biology

Cytometry Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper

Jaesik Kim, Matei Ionita, Matthew Lee, Michelle L. McKeague, Ajinkya Pattekar, Mark M. Painter, Joost Wagenaar, Van Truong, Dylan T. Norton, Divij Mathew, Yonghyun Nam, Sokratis A. Apostolidis, Cynthia J. Clendenin, Patryk Orzechowski, Sang‐Hyuk Jung, , Dokyoon Kim

The paper introduces cyMAE, a masked autoencoder for automated immunophenotyping, showing it improves accuracy and interpretability over manual methods in cytometry data analysis.

Cell Reports Medicine · Nov 1, 2024Peer-reviewedBioinformatics