Author

Harsh G. Shukla

University of California, Irvine

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 4 Genetics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Organism:Drosophila· 3 Research Focus:gene regulatory network inference· 3 Approach:experimental assay· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2 Assay:ChIP-seq· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Uma RamakrishnaniD· 2 shared Yuheng HuangiD· 2 shared Anubhab KhaniD· 1 shared Arun Zachariah· 1 shared Awadhesh PanditiD· 1 shared Boney KuriakoseiD· 1 shared Grace Yuh Chwen Lee· 1 shared Ishani Sinha· 1 shared

Activity by Year

2020-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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2 shared papersGenomics

Uma RamakrishnanORCID

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5 papers

Recent·Most cited

Polymorphic 3D genome architecture mediated by transposable elements

Harsh G. Shukla, Yuheng Huang, Yi Zita Gao, Grace Yuh Chwen Lee

The paper shows that transposable elements (TEs) influence 3D genome structure by interacting with pericentromeric heterochromatin (PCH), affecting gene expression and evolution in Drosophila.

bioRxiv · Jan 22, 2026 · PreprintGenomics

Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome

Harsh G. Shukla, Mahul Chakraborty, J. J. Emerson

This study assembles and analyzes repetitive genomic regions in Drosophila melanogaster, revealing structural variation and mechanisms of concerted evolution in histone and Stellate clusters.

Genome Research · Jul 16, 2025Peer-reviewedGenomics

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation

Harsh G. Shukla, Kushal Suryamohan, Anubhab Khan, Krishna Mohan, Rajadurai Chinnasamy Perumal, Oommen K. Mathew, Ramesh Menon, Mandumpala Davis Dixon, Megha Muraleedharan, Boney Kuriakose, Saju Michael, Sajesh Puthenpurackal Krishnankutty, Arun Zachariah, Somasekar Seshagiri, Uma Ramakrishnan

The paper presents high-quality near-chromosomal genome assemblies of Indian tigers and identifies genetic features related to their apex-predator traits and conservation.

GigaScience · Dec 28, 2022Peer-reviewedGenomics

Species-specific chromatin landscape determines how transposable elements shape genome evolution

Yuheng Huang, Harsh G. Shukla, Yuh Chwen G. Lee

The paper investigates how species-specific chromatin landscapes influence transposable element abundance through epigenetic effects across six Drosophila species.

eLife · Jul 26, 2022Peer-reviewedGenomics

Metabarcoding for parallel identification of species, sex and diet: an application to the conservation of globally-threatened Gyps vultures

Mousumi Ghosh‐Harihar, Nehal Gurung, Harsh G. Shukla, Ishani Sinha, Awadhesh Pandit, VIBHU M. PRAKASH, Rhys E. Green, Uma Ramakrishnan

The paper develops a metabarcoding workflow to identify vulture species, sex, and diet from fecal samples, finding domestic livestock dominate the diet.

Conservation Genetics Resources · Sep 23, 2020Peer-reviewedGenetics