Author

Noushin Niknafs

Johns Hopkins UniversityORCID 0000-0002-4852-3674Unclaimed 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· 3 Approach:statistical model· 3 Assay:whole-genome sequencing· 3 Research Focus:clustering· 2 Research Focus:differential expression· 2 Approach:Bayesian inference· 1 Research Focus:cell-cell communication· 1 Assay:DNA methylation· 1

Frequent Co-Authors

Jillian A. PhalleniD· 2 shared Rachel KarchiniD· 2 shared Robert B. ScharpfiD· 2 shared Victor E. VelculescuiD· 2 shared Adrianna L. BartolomucciiD· 1 shared Akshaya Vijaya AnnapragadaiD· 1 shared Akul GoeliD· 1 shared Alessandro LealiD· 1 shared

Activity by Year

2015-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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2 shared papersGenomics

Jillian A. PhallenORCID

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Author profile →

4 papers

Recent·Most cited

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Akshaya Vijaya Annapragada, James White, Hope Orjuela, Adrianna L. Bartolomucci, Alice C. Eastman, Shashikant Koul, Kauí Patrício Lebarbenchon, Daniel C. Bruhm, Sarah Short, Keerti Boyapati, Noushin Niknafs, Carter Norton, Vishruth Girish, Nicholas A. Vulpescu, Sofia Velculescu, , Victor E. Velculescu

The paper identifies widespread mosaic structural variants in normal human tissues and tumors, with repeat-mediated variants impacting functional elements and enabling noninvasive tumor monitoring through cell-free DNA.

bioRxiv · Sep 28, 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

Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors

Lily Zheng, Noushin Niknafs, Laura DeLong Wood, Rachel Karchin, Robert B. Scharpf

This paper introduces PICTograph, a Bayesian model for estimating cancer cell fractions and clone trees from multi-region sequencing data, showing improved accuracy in subclone reconstruction and evolutionary inference.

Bioinformatics · Jun 1, 2022Peer-reviewedBioinformatics

SubClonal Hierarchy Inference from Somatic Mutations: automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing

Noushin Niknafs, Violeta Beleva Guthrie, Daniel Q Naiman, Rachel Karchin

This paper introduces a framework for inferring subclonal hierarchies in cancer using somatic mutations, demonstrating improved power and error control in multi-region tumor sequencing.

bioRxiv · Jul 1, 2015Bioinformatics