Author

Dhirendra Kumar

National Institutes of HealthORCID 0000-0002-4349-3605Unclaimed 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 Assay:DNA methylation· 3 Approach:experimental assay· 3 Approach:statistical model· 3 Research Focus:cell type annotation· 2 Assay:ChIP-seq· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2

Frequent Co-Authors

Andrew OldfieldiD· 4 shared Pengyi YangiD· 4 shared Raja Jothi· 4 shared Senthilkumar Cinghu· 4 shared Rajneesh PathaniaiD· 2 shared Adam BurkholderiD· 1 shared Andrew J. Siladi· 1 shared Anuj Pandey· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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4 shared papersGenomics

Andrew OldfieldORCID

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4 papers

Recent·Most cited

Malignant epithelial diversification and inflammatory neutrophil remodeling define a transitional stage between tumor cell dissemination and overt metastatic outgrowth in breast cancer

Rajneesh Pathania, Brian N. Papas, Justin Kosak, Senthilkumar Cinghu, Dhirendra Kumar, B. Deskin, Andrew Oldfield, Anuj Pandey, Andrew J. Siladi, Saurabh Tiwari, Marie A. Iannone, Maria I. Sifre, Carl D. Bortner, Xin Xu, Rajasekaran Mahalingam, , Raja Jothi

The paper identifies a transitional stage in breast cancer metastasis characterized by malignant epithelial diversification and inflammatory neutrophil remodeling, linking these to poor clinical outcomes.

bioRxiv · Aug 26, 2026 · PreprintCancer Biology

Bivalent chromatin protects reversibly repressed genes from irreversible silencing

Dhirendra Kumar, Senthilkumar Cinghu, Andrew Oldfield, Pengyi Yang, Raja Jothi

The paper shows that bivalent chromatin protects reversibly repressed genes from irreversible silencing by maintaining H3K4me3 at promoters, which prevents de novo DNA methylation in adult cancers.

Genome Research · Dec 1, 2021Peer-reviewedGenomics

NF-Y Controls Fidelity of Transcription Initiation at Gene Promoters Through Maintenance of the Nucleosome-Depleted Region

Andrew Oldfield, Telmo Henriques, Dhirendra Kumar, Adam Burkholder, Senthilkumar Cinghu, Damien Paulet, Brian D. Bennett, Pengyi Yang, Benjamin S. Scruggs, Christopher A. Lavender, Éric Rivals, Karen Adelman, Raja Jothi

This study shows NF-Y maintains nucleosome-depleted regions at promoters to ensure accurate transcription initiation, preventing aberrant gene expression.

Nature Communications · Jul 11, 2019Peer-reviewedGenomics

Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

Pengyi Yang, Sean J. Humphrey, Senthilkumar Cinghu, Rajneesh Pathania, Andrew Oldfield, Dhirendra Kumar, Dinuka Perera, Jean Yee Hwa Yang, David Ernest James, Matthias Mann, Raja Jothi

The paper maps multi-omic changes during mouse pluripotency transition, showing phosphoproteome dynamics precede epigenome and transcriptome changes.

Cell Systems · May 1, 2019Peer-reviewedGenomics