List of publication involving Next Generation Genomics Facility (NGGF) services:
2024
 
1. Tyagi, A, Yadav, N, Pandit, A and Ramakrishnan, U (2024) On the road to losing connectivity: Fecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India. Molecular Ecology,  https://doi.org/10.1111/mec.17461
 
2. Kamat A, Tran NT, Sharda M, Sontakke N, Le TBK, Badrinarayanan A (2024) Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria. PLoS Biol 22(3): e3002540. https://doi.org/10.1371/journal.pbio.3002540
 
3. Meel, S., Mishra,S., Mann, R., Najar, A. H., Singh, A. K., & Notani, D. (2024). Compaction of Active Chromatin Domains and Promoters by H3S10 Phosphorylation during Mitosis Preserves Interphase-Specific Chromatin Structure and Function. bioRxiv 2024.05.20.595059;  https://doi.org/10.1101/2024.05.20.595059
 
4. Chhattani, H., Harihar, A., Dean, R., Yadav, A., Patel, K., Rana, D., Pandit, A., Shukla, S.K., Rahim, V. and Ramakrishnan, U., (2024) Trace DNA from kill sites identifies predating tigers. bioRxiv, pp.2024-04. doi: https://doi.org/10.1101/2024.04.11.589017
 
5. Ghosh-Harihar M, Yadav N, Gurung N, CS D, CK V, Prakash V, Green RE, Ramakrishnan U (2024) Spatial patterns in the diet of Gyps vultures in India and their implications for conservation. Biological Conservation, 292 (110551)https://doi.org/10.1016/j.biocon.2024.110551
 
6. Ansil, BR, Vishwanathan, A, Ramachandran, V, Yeshwanth, HM, Sanyal, A and Ramakrishnan, U. (2024) Host-pathogen-vector continuum in a changing landscape: potential transmission pathways for Bartonella in a small mammal community doi: https://doi.org/10.1101/2023.09.25.559241
 
7. Ansil, BR, Sanyal, A, Sreenivas, D, Garg, KM, Ramakrishnan, U and Chattopadhyay, B. (2024) Identification of distinct rodent-associated adenovirus lineages from a mixed-use landscape in the Western Ghats biodiversity hotspot  https://doi.org/10.1101/2024.05.18.594665
 
8. Rana, D, Boyer, F, Barba, MD, Taberlet, P and Ramakrishnan, U. (2024) From single species to communities: microsatellite amplicon sequencing to monitor felids using Feliplex doi: https://doi.org/10.1101/2024.10.20.619303
 
9. Pal, A.K., Gandhivel, V.HS., Nambiar, A.B., Shivaprasad PV (2024) Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler. Nat Commun 15, 7807. https://doi.org/10.1038/s41467-024-52239-z 
 
10. Chitthavalli Y. Harshith, Avik Pal, Monoswi Chakraborty, Ashwin Nair, Steffi Raju, Padubidri V. Shivaprasad (2024). Wound-induced small-peptide-mediated signaling cascade, regulated by OsPSKR, dictates balance between growth and defense in rice. Cell reports. 43(7): 114515. DOI: 10.1016/j.celrep.2024.114515
 
11. Dewan A, Jain C, Das M, Tripathi A, Sharma AK, Singh H, Malhotra N, Seshasayee ASN, Chakrapani H, Singh A. (2024) Intracellular peroxynitrite perturbs redox balance, bioenergetics, and Fe-S cluster homeostasis in Mycobacterium tuberculosis. Redox Biol. 75: 103285 https://doi.org/10.1016/j.redox.2024.103285
 
12. Garushyants SK, Sane M, Selifanova MV, Agashe D, Bazykin GA and Gelfand MS (2024). Mutational signatures in wild type Escherichia coli strains reveal dominance of DNA polymerase errors. Genome Biology and Evolution 16(4):evae035 https://doi.org/10.1093/gbe/evae035
 
13. M Sreepadmanabh, Ganesh M, Sanjenbam P, Kurzthaler C, Agashe D and Bhattacharjee T (2024). Cell shape affects bacterial colony growth under physical confinement. Nature Communications 15:9561 https://doi.org/10.1038/s41467-024-53989-6
 
14. Singhal S, Choudhary C, Basu DN, Seal S, Khan I, Shukla JN and Agashe D . (2024) Genome assembly and annotation of the red flour beetle (Tribolium castaneum) from India.doi: https://doi.org/10.1101/2024.05.20.594914
 
15. Y Sharma, P Bhatia, G Rangappa, S Saha, P Raghu (2024) Enhanced Notch dependent gliogenesis and delayed physiological maturation underlie neurodevelopmental defects in Lowe syndrome bioRxiv, 2024.11. 25.625332 https://doi.org/10.1101/2024.11.25.625332
 
16. Sankhanil Saha, Harini Krishnan, Padinjat Raghu (2024) IMPA1 dependent regulation of plasma membrane phosphatidylinositol 4,5-bisphosphate turnover and calcium signalling by lithium doi: https://doi.org/10.1101/2022.10.14.512101
 
17. A Naik, R PADINJAT (2024) The accessory domains of Phospholipase D regulate its localization and activity in Drosophila photoreceptors bioRxiv, 2024.09. 22.614390 doi: https://doi.org/10.1101/2024.09.22.614390
 
18. Namita Mukundan, Nivedita Hariharan, Vidyanand Sasidharan, Vairavan Lakshmanan, Dasaradhi Palakodeti, Colin Jamora  (2024)Poly (A) binding protein 2 is critical for stem cell differentiation during regeneration in the planarian Schmidtea mediterranea Front. Cell Dev. Biol.,Volume 12 - 2024 | https://doi.org/10.3389/fcell.2024.1433142
 
19. Michelle Ninochka D’Souza,  Naveen Kumar Chandappa Gowda,  Nivedita Hariharan,  Syed Wasifa Qadri, Dasaradhi Palakodeti, Ravi S Muddashetty (2024) Altering rRNA 2’O-methylation pattern during neuronal differentiation is regulated by FMRP doi: https://doi.org/10.1101/2024.07.25.605157
 
20. Nataraj N, Mondhe D, Srikantaiah V, Ishtiaq F. (2024) Metagenomic analysis reveals differential effects of sewage treatment on the microbiome and antibiotic resistome in Bengaluru, India. Water Reuse 14 (3): 418–433 https://doi.org/10.2166/wrd.2024.032
 
21. "Prashali Bansal, Roshni Pillai, DB Pooja, Sonia Q Sen (2024) Two neuropeptides that promote blood-feeding in Anopheles stephensi mosquitoes doi: https://doi.org/10.1101/2024.05.15.594342
 
22. Petrauskas A*, Fortunati DL*, Reddy A, Pothapragada SS, Agrawal K, Singh A, Huelsmeier  J, Hillebrand J, Brown G, Chaturvedi D, Lee J, Lim C, Auburger G, VijayRaghavan K, Ramaswami M#, and Bakthavachalu B# (2024) Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation. PLoS Genet. 2024 May 20;20(5):e1011251. https://doi.org/10.1371/journal.pgen.1011251
 
2023
 
1. T Naik, M Sharda, L CP, K Virbhadra, A Pandit* (2023) High-quality single amplicon sequencing method for illumina MiSeq platform using pool of ‘N’(0–10) spacer-linked target specific primers without PhiX spike-in BMC genomics 24 (1), 1-11A https://doi.org/10.1186/s12864-023-09233-4
 
2. JK Dhall*, N Kasturacharya, A Pandit*, CP Lakshminarayanan (2023) Optimized protocol for assay for transposase-accessible chromatin by sequencing (ATAC-seq) from Drosophila melanogaster brain tissue STAR protocols 4 (2), 102153 https://doi.org/10.1016/j.xpro.2023.102153
 
3. Sreenivas, D., Kumar, V., Kathirvel, K., Vadnala, R. N., Mishra, S., Shelar, B., Marate, S., CP, L., K, S. D., Bhardwaj, M., Pandit, A., Mayor, S., Ramakrishnan, U., & Notani, D. (2023). Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru. BioRxiv, 2023.03.14.532352. Link: https://doi.org/10.1101/2023.03.14.532352.
 
4. Islam, Z., Saravanan, B., Walavalkar, K., Farooq, U., Singh, A. K., Radhakrishnan, S., Thakur, J., Pandit, A., Henikoff, S., & Notani, D. (2023). Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries. Genome research, 33(1), 1–17. Link: https://doi.org/10.1101/gr.276643.122
 
5. Faseela, E. E., Notani, D., & Sabarinathan, R. (2023). Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancer. BioRxiv, 2023.10.24.563697. https://doi.org/10.1101/2023.10.24.563697
 
6. Soota, D., Saravanan, B., Mann, R., Kharbanda, T., & Notani, D. (2023). RNA binding limits the ligand induced transcriptional potential of estrogen receptor-alpha (ERα). BioRxiv, 2023.08.10.552751. https://doi.org/10.1101/2023.08.10.552751
 
7. Tyagi, A, Godbole, M, Vanak, A and Ramakrishnan, U (2023) Citizen science facilitates first ever genetic detection of wolf-dog hybridization in Indian savannahs. Ecology and Evolution, https://doi.org/10.1002/ece3.10100
 
8. Vivek Hari Sundar, Chenna Swetha, Debjani Basu, Kannan Pachamuthu, Steffi Raju, Tania Chakraborty, Rebecca A. Mosher and P.V. Shivaprasad (2023). Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains. Genome Research 023. 33:715-728. https://www.genome.org/cgi/doi/10.1101/gr.277353.122. 
 
9. Ashwin Nair, Harshith CY, Anushree N and P.V. Shivaprasad (2023). Begomoviral βC1 orchestrates organellar genomic instability to augment viral infection by hijacking host RecA. The Plant Journal. 114: 934-950 https://doi.org/10.1111/tpj.16186 
 
10. Das M, Sreedharan S, Shee S, Malhotra N, Nandy M, Banerjeee U, Kholi S, Rajmani R, Chandra N, Seshasayee AN, Laxman S and Singh A. Cysteine desulfurase (IscS)–mediated fine- tuning of bioenergetics and SUF expression prevents Mycobacterium tuberculosis Sci Adv. 2023. 15(50): eadh2858 DOI: 10.1126/sciadv.adh2858 
 
11. Sane M, Diwan GD, Bhat BA, Wahl LM and Agashe D (2023). Shifts in mutation spectra enhance access to beneficial mutations. Proceedings of the National Academy of Science 120:e2207355120 https://doi.org/10.1073/pnas.2207355120 
 
12. Vivek Hari Sundar, Chenna Swetha, Debjani Basu, Kannan Pachamuthu, Steffi Raju, Tania Chakraborty, Rebecca A. Mosher and P.V. Shivaprasad (2023). Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains. Genome Research 023. 33:715-728. https://www.genome.org/cgi/doi/10.1101/gr.277353.122.
 
13. Ashwin Nair, Harshith CY, Anushree N and P.V. Shivaprasad (2023). Begomoviral βC1 orchestrates organellar genomic instability to augment viral infection by hijacking host RecA. The Plant Journal. 114: 934-950 https://doi.org/10.1111/tpj.16186