Author

Anindya Dutta

University of VirginiaORCID 0000-0002-3559-2574Unclaimed ORCID profile · follow to get notified of new preprints

Additional preprints under this name without ORCID

Anindya Dutta2 papers · University of Alabama

Biology Disciplines

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Molecular Biology· 3 Bioinformatics· 1 Genetic & Genomic Medicine· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:human· 6 Approach:experimental assay· 3 Research Focus:gene regulatory network inference· 3 Approach:statistical model· 3 Research Focus:differential expression· 2 Assay:DNA methylation· 2 Assay:ATAC-seq· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Pankaj KumariD· 4 shared Etsuko Shibata· 3 shared Shekhar SahaiD· 3 shared Yoshiyuki ShibataiD· 3 shared Zhangli SuiD· 3 shared Ajay ChatrathiD· 2 shared Briana WilsoniD· 2 shared Shashi KiraniD· 2 shared

Activity by Year

2019-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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4 shared papersBioinformatics

Pankaj KumarORCID

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Author profile →

6 papers

Recent·Most cited

Chromatin regulator HELLS mediates SSB repair and responses to DNA alkylation damage.

Joyous T. Joseph, Christine M. Wright, Estanislao Peixoto, Etsuko Shibata, Asad Ullah Khan, Yong Li, Jason Romero Neidigk, Bo-Ruei Chen, Saba Tufail, Aaiyas Mujawar, Olivia Decker, Krishna Reethika Kadali, Azait Imtiaz, Brianna A Jones, Yanfeng Zhang, , Wioletta Czaja

This study identifies HELLS as a regulator of SSB repair and DNA alkylation damage response, showing its synthetic lethality with HRD in cancer.

Nucleic Acids Research · Oct 21, 2025Peer-reviewedMolecular Biology

Specific origin selection and excess functional MCM2-7 loading in ORC-deficient cells.

Yoshiyuki Shibata, Mihaela Peycheva, Etsuko Shibata, Daniel Malzl, Rushad Pavri, Anindya Dutta

The paper shows that specific DNA replication origins are still used and excess MCM2-7 is loaded in ORC-deficient human cancer cells.

Nucleic Acids Research · May 30, 2025Peer-reviewedMolecular Biology

tRForest: a novel random forest-based algorithm for tRNA-derived fragment target prediction

R. Parikh, Briana Wilson, Laine Marrah, Zhangli Su, Shekhar Saha, Pankaj Kumar, Fenix W. D. Huang, Anindya Dutta

tRForest improves tRNA fragment target prediction using random forest, validated in cell lines and showing enrichment in neuronal function.

NAR Genomics and Bioinformatics · Mar 31, 2022Peer-reviewedBioinformatics

ATAC-seq identifies thousands of extrachromosomal circular DNA in cancers and cell lines

Pankaj Kumar, Shashi Kiran, Shekhar Saha, Zhangli Su, Teressa Paulsen, Ajay Chatrath, Yoshiyuki Shibata, Etsuko Shibata, Anindya Dutta

The paper shows that ATAC-seq can detect thousands of extrachromosomal circular DNAs in cancer and cell lines without specific enrichment.

Science Advances · May 15, 2020Peer-reviewedGenomics

The Pan-Cancer Landscape of Prognostic Germline Variants in 10,582 Patients

Ajay Chatrath, Róża K. Przanowska, Shashi Kiran, Zhangli Su, Shekhar Saha, Briana Wilson, Takaaki Tsunematsu, Ji‐Hye Ahn, Kyung Yong Lee, Teressa Paulsen, Ewelina Sobierajska, Manjari Kiran, Xiwei Tang, Tianxi Li, Pankaj Kumar, , Anindya Dutta

The paper identifies prognostic germline variants in 10,582 cancer patients using multivariate Cox regression, showing their association with patient outcomes beyond clinical data.

Genome Medicine · Feb 17, 2020Peer-reviewedGenetic & Genomic Medicine

Extrachromosomal circular DNA, microDNA, without canonical promoters produce short regulatory RNAs that suppress gene expression

Teressa Paulsen, Yoshiyuki Shibata, Pankaj Kumar, Laura Williams Dillon, Anindya Dutta

The paper shows that microDNA produces regulatory RNAs that suppress gene expression through miRNA and si-like RNA mechanisms.

bioRxiv · Jan 31, 2019 · PreprintMolecular Biology