Author

Nirmish Singla

Johns Hopkins UniversityORCID 0000-0001-9495-6983Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:differential expression· 4 Organism:human· 3 Approach:statistical model· 3 Research Focus:drug response / drug discovery· 2 Approach:experimental assay· 2 Organism:mouse· 2 Assay:spatial transcriptomics· 2 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Ezra G. BarabaniD· 2 shared Huili Li· 2 shared James BrugarolasiD· 2 shared Roy Elias· 2 shared Yasser M. A. GediD· 2 shared Adam K. AragakiiD· 1 shared Adrianna Amaral· 1 shared Akinaru Yamamoto· 1 shared

Activity by Year

2020-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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2 shared papersCancer Biology

Ezra G. BarabanORCID

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Author profile →

4 papers

Recent·Most cited

Epithelial to mesenchymal transition and M2 macrophages drive aggressiveness in murine and human sarcomatoid urothelial carcinoma.

Yujiro Hayashi, Roy Elias, Eugene Douglass, Akinaru Yamamoto, Matthew Schuler, Mingxiao Feng, Ekatherina Y. Batourina, Anne E. Geller, Woonyoung Choi, Gabriela Colocho, Alyssa G. Arbuiso, Samuel Jin, Adam K. Aragaki, Charles Ruland, Stanley Rapiey, , Burles Avner Johnson

The paper develops a murine model of sarcomatoid urothelial carcinoma (SUC) and finds it shares molecular and immunological features with human SUC, suggesting its use for therapeutic research.

bioRxiv · Oct 2, 2026 · PreprintCancer Biology

TFE3 fusions drive expression of CD44 and SPP1 in Translocation Renal Cell Carcinoma

Kaushal V. Asrani, Juhyung Woo, Thiago Vidotto, Kewen Feng, Alan Lorenzetti, Eddie L. Imada, Huili Li, Rajan Singh, Anand K Thotakura, Sangeeta Ray, Lia Oliveira, Adrianna Amaral, Vikrant Palande, Ravi Kumar Anchoori, Jayaprakash Mandal, , Tamara Lotan

The paper shows TFE3 fusions upregulate CD44 and SPP1 in tRCC, with potential therapeutic implications.

bioRxiv · Sep 22, 2026 · PreprintCancer Biology

Clear cell renal cell carcinoma consensus transcriptomic programs reveal converging trajectories towards aggressive disease

Roy M. Elias, Vivek Nimgaonkar, Bingrui Emily Xie, Yuqi Zhang, Archana Balan, Kathleen Noller, Nirmish Singla, Yasser M. A. Ged, Ezra G. Baraban, Payal Kapur, James Brugarolas, Genevieve Stein-O’Brien, Michael F. Ochs, Elana Judith Fertig, Atul J Deshpande, Srinivasan Yegnasubramanian

The paper identifies 17 consensus transcriptomic programs in ccRCC using NMF and links them to cellular sources and clinical outcomes, revealing converging trajectories toward aggressive disease.

The Oncologist · Sep 1, 2026Peer-reviewedCancer Biology

Tumor Neoantigenicity Assessment with CSiN Score Incorporates Clonality and Immunogenicity to Predict Immunotherapy Outcomes

Tianshi Lu, Shidan Wang, Lin Xu, Qinbo Zhou, Nirmish Singla, Jianjun Gao, Subrata Manna, Laurentiu M. Pop, Zhiqun Xie, Mingyi Chen, Jason J. Luke, James Brugarolas, Raquibul Hannan, Tao Wang

The paper introduces the CSiN score to predict immunotherapy outcomes by assessing tumor neoantigen quality through clonality and immunogenicity, showing improved performance over existing methods.

Science Immunology · Feb 14, 2020Peer-reviewedBioinformatics