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Raju, Steffi ; Swetha, Chenna ; Harshith, Chitthavalli Y. ; Shivaprasad, P.V. (2025) Copper-sensitive OsSPL9 TF regulates expression of indica rice domestication-associated miRNAs and phenotypes bioRxiv . 2025.03-27.645634.

Gandhivel, Vivek Hari-Sundar ; Sotelo-Parrilla, Paula ; Raju, Steffi ; Jha, Shaileshanand ; Gireesh, Anjitha ; Harshith, Chitthavalli Y. ; Gut, Fabian ; Vinothkumar, Kutti R. ; Berger, Frédéric ; Jeyaprakash, A. Arockia ; Shivaprasad, P. V. (2025) An Oryza-specific histone H4 variant predisposes H4 lysine 5 acetylation to modulate salt stress responses Nature Plants, 11 (4). pp. 790-807. ISSN 2055-0278

Prasad, Melvin ; Shetty, Prateek ; Pal, Avik Kumar ; Rigó, Gábor ; Kant, Kamal ; Zsigmond, Laura ; Nagy, István ; Shivaprasad, Padubidri V ; Szabados, László ; Probst, Aline (2025) Transcriptional and epigenomic changes in response to polyethylene glycol-triggered osmotic stress in Brassica napus L. Journal of Experimental Botany, 17 (9). pp. 2535-2556. ISSN 0022-0957

Vivek Hari Sundar, G. ; Madhu, Aravind ; Archana, A. ; Shivaprasad, P.V. (2024) Plant histone variants at the nexus of chromatin readouts, stress and development Biochimica et Biophysica Acta (BBA) - General Subjects, 1868 (2). p. 130539. ISSN 0304-4165

Pal, Avik Kumar ; Gandhivel, Vivek Hari-Sundar ; Nambiar, Amruta B. ; Shivaprasad, P. V. (2024) Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler Nature Communications, 15 (1). ISSN 2041-1723

Harshith, Chitthavalli Y. ; Pal, Avik ; Chakraborty, Monoswi ; Nair, Ashwin ; Raju, Steffi ; Shivaprasad, Padubidri V. (2024) Wound-induced small-peptide-mediated signaling cascade, regulated by OsPSKR, dictates balance between growth and defense in rice Cell Reports, 43 (7). p. 114515. ISSN 2211-1247

Nair, Ashwin ; Harshith, Chitthavalli Y. ; Narjala, Anushree ; Shivaprasad, Padubidri V. (2023) Begomoviral βC1 orchestrates organellar genomic instability to augment viral infection The Plant Journal, 114 (4). pp. 934-950. ISSN 0960-7412

Tripathi, Abhinandan Mani ; Singh, Rajneesh ; Verma, Ashwani Kumar ; Singh, Akanksha ; Mishra, Parneeta ; Dwivedi, Varun ; Narayan, Shiv ; Gandhivel, Vivek Hari Sundar ; Shirke, Pramod Arvind ; Shivaprasad, Padubidri V. ; Roy, Sribash (2023) Indian Himalayan natural Arabidopsis thaliana accessions with abolished miR158 levels exhibit robust miR173‐initiated trans‐acting cascade silencing The Plant Journal, 114 (4). pp. 855-874. ISSN 0960-7412

Nair, Ashwin ; Shivaprasad, P V (2023) Novel regulators of mitochondrial genome integrity Journal of Biosciences, 48 (4). ISSN 0250-5991

Vivek, Hari Sundar G ; Sotelo-Parrilla, Paula ; Raju, Steffi ; Jha, Shaileshanand ; Gireesh, Anjitha ; Gut, Fabian ; Vinothkumar, K.R. ; Berger, Frédéric ; Jeyaprakash, A. Arockia ; Shivaprasad, P.V. (2023) Oryza genera-specific novel Histone H4 variant predisposes H4 Lysine5 Acetylation marks to modulate salt stress responses BioRxiv . 2023.07-31.551207.

Hari Sundar G, Vivek ; Swetha, Chenna ; Basu, Debjani ; Pachamuthu, Kannan ; Raju, Steffi ; Chakraborty, Tania ; Mosher, Rebecca A. ; Shivaprasad, P.V. (2023) Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains Genome Research, 33 (5). pp. 715-728. ISSN 1088-9051

Jaganathan, Deepa ; Rajakani, Raja ; Doddamani, Dadakhalandar ; Saravanan, Divya ; Pulipati, Shalini ; Hari Sundar G, Vivek ; Sellamuthu, Gothandapani ; Jayabalan, Shilpha ; Kumari, Kumkum ; Parthasarathy, Pavithra ; S., Punitha ; Ramalingam, Sivaprakash ; Shivaprasad, Padubidri V. ; Venkataraman, Gayatri (2023) A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance Scientific Reports, 13 (1). ISSN 2045-2322

Tirumalai, Varsha ; Narjala, Anushree ; Swetha, Chenna ; Sundar, G. Vivek Hari ; Sujith, T. N. ; Shivaprasad, P. V. (2022) Cultivar-specific miRNA-mediated RNA silencing in grapes Planta, 256 (1). ISSN 0032-0935

Swetha, Chenna ; Narjala, Anushree ; Pandit, Awadhesh ; Tirumalai, Varsha ; Shivaprasad, P. V. (2022) Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs BMC Genomics, 23 (1). ISSN 1471-2164

Prasad, Melvin ; Kataria, Priyanka ; Ningaraju, Sunayana ; Buddidathi, Radhika ; Bankapalli, Kondalarao ; Swetha, Chenna ; Susarla, Gautam ; Venkatesan, Radhika ; D'Silva, Patrick ; Shivaprasad, Padubidri V. (2022) Double DJ‐1 domain containing Arabidopsis DJ‐1D is a robust macromolecule deglycase New Phytologist, 236 (3). pp. 1061-1074. ISSN 0028-646X

Sanjenbam, Pratibha ; Shivaprasad, P. V. ; Agashe, Deepa ; Hom, Erik F. Y. ; Calatrava, Victoria ; Kolb, Steffen (2022) Impact of Phyllosphere Methylobacterium on Host Rice Landraces Microbiology Spectrum, 10 (4). ISSN 2165-0497

Sundar G, Vivek Hari ; Swetha, Chenna ; Basu, Debjani ; Pachamuthu, Kannan ; Raju, Steffi ; Chakraborty, Tania ; Mosher, Rebecca A. ; Shivaprasad, P. V. (2022) Investigation of Transposon DNA Methylation and Copy Number Variation in Plants Using Southern Hybridisation Bio-Protocol, 12 (11). e4432-e4432. ISSN 2331-8325

Pachamuthu, Kannan ; Hari Sundar, Vivek ; Narjala, Anushree ; Singh, Rahul R ; Das, Soumita ; Avik Pal, Harshith C Y ; Shivaprasad, Padubidri V ; Sunkar, Ramanjulu (2022) Nitrate-dependent regulation of miR₄₄₄-O_sMADS₂₇ signalling cascade controls root development in rice Journal of Experimental Botany, 73 (11). pp. 3511-3530. ISSN 0022-0957

Lakshmanan, Vairavan ; Sujith, T.N. ; Bansal, Dhiru ; Shivaprasad, Padubidri V. ; Palakodeti, Dasaradhi ; Krishna, Srikar (2021) Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs) RNA Biology, 27 (4). pp. 477-495. ISSN 1547-6286

Jha, Vikram ; Narjala, Anushree ; Basu, Debjani ; T. N., Sujith ; Pachamuthu, Kannan ; Chenna, Swetha ; Nair, Ashwin ; Shivaprasad, Padubidri V. (2021) Essential role of γ‐clade RNA‐dependent RNA polymerases in rice development and yield‐related traits is linked to their atypical polymerase activities regulating specific genomic regions New Phytologist, 232 (4). pp. 1674-1691. ISSN 0028-646X

Pachamuthu, Kannan ; Swetha, Chenna ; Basu, Debjani ; Das, Soumita ; Singh, Indira ; Sundar, Vivek Hari ; Sujith, T. N. ; Shivaprasad, Padubidri V. (2021) Rice-specific Argonaute 17 controls reproductive growth and yield-associated phenotypes Plant Molecular Biology, 105 (1-2). pp. 99-114. ISSN 0167-4412

Vinoth Kumar, R. ; Shivaprasad, P. V. (2020) Plant-virus-insect tritrophic interactions: insights into the functions of geminivirus virion-sense strand genes Proceedings of the Royal Society B: Biological Sciences, 287 (1936). p. 20201846. ISSN 0962-8452

Vinoth Kumar, R. ; Shivaprasad, P. V. (2020) Plant-virus-insect tritrophic interactions: insights into the functions of geminivirus virion-sense strand genes Proceedings of the Royal Society B: Biological Sciences, 287 (1936). p. 20201846. ISSN 0962-8452

Shivaprasad, P. V. ; Prasad, Melvin ; Tirumalai, Varsha (2020) RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs Journal of Visualized Experiments (161). ISSN 1940-087X

Nair, Ashwin ; Chatterjee, Kiran Sankar ; Jha, Vikram ; Das, Ranabir ; Shivaprasad, P. V. (2020) Stability of Begomoviral pathogenicity determinant βC1 is modulated by mutually antagonistic SUMOylation and SIM interactions BMC Biology, 18 (1). ISSN 1741-7007

Walavalkar, Kaivalya ; Saravanan, Bharath ; Singh, Anurag Kumar ; Jayani, Ranveer Singh ; Nair, Ashwin ; Farooq, Umer ; Islam, Zubairul ; Soota, Deepanshu ; Mann, Rajat ; Shivaprasad, Padubidri V. ; Freedman, Matthew L. ; Sabarinathan, Radhakrishnan ; Haiman, Christopher A. ; Notani, Dimple (2020) A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer Nature Communications, 11 (1). ISSN 2041-1723