Author

Archana Balan

Johns Hopkins UniversityORCID 0000-0003-1283-577XUnclaimed 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· 3 Organism:human· 3 Approach:statistical model· 3 Research Focus:clustering· 2 Research Focus:trajectory inference· 2 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Assay:DNA methylation· 1

Frequent Co-Authors

Elana Judith FertigiD· 2 shared Kathleen NolleriD· 2 shared Akul GoeliD· 1 shared Alessandro LealiD· 1 shared Ali Hussainy ZaidiiD· 1 shared Atul J Deshpande· 1 shared Benjamin Philip LevyiD· 1 shared Benny WeksleriD· 1 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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2 shared papersCancer Biology

Elana Judith FertigORCID

Mutual co-authors in cluster

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3 papers

Recent·Most cited

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

Reconstructing clone-resolved transcriptional programs from bulk tumor sequencing

Jiaying Lai, Yi Yang, Kathleen Noller, YunZhou Liu, Archana Balan, Prathima B. Nagendra, Luciane Tsukamoto Kagohara, Elana Judith Fertig, Laura DeLong Wood, Rachel Karchin

PICTographPlus infers clone-resolved transcriptional programs from bulk RNA-seq by integrating clonal phylogenies and proportions, achieving high accuracy in recovering clone-level expression and localizing pathway changes.

bioRxiv · Jun 5, 2026 · PreprintGenomics

Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

Joseph Christopher Murray, Lavanya Sivapalan, Karlijn Hummelink, Archana Balan, James Robert White, Noushin Niknafs, Lamia Rhymee, Gavin Pereira, Nisha Rao, Benny Weksler, Nathan Bahary, Jillian A. Phallen, Alessandro Leal, David L. Bartlett, Kristen Ashley Marrone, , Valsamo Anagnostou

This study tracks ctDNA and immune cell changes in lung cancer patients on immunotherapy to identify molecular responses and immune-related toxicities.

Clinical Cancer Research · Nov 8, 2023Peer-reviewedGenomics