Publications

Publications:

68. Egorochkin MG, Mitrov GR, Moiseenko AV, Gupta I, Khan R, Boddapati V, Das S, Kaledhonkar S, Kondabagil K, and Sokolova OS. Cryo-EM Reconstruction of the phiK601 Jumbo Phage Head, Microscopy and Microanalysis, Volume 31, Issue Supplement_1, July 2025, ozaf048.375, https://doi.org/10.1093/mam/ozaf048.375

67. Shukla A*, Kashyap S*, Patil S, Varma A, Ghosh SK and Kondabagil K. The putative packaging ATPase of Acanthamoeba polyphaga mimivirus is an essential protein that interacts with the genome segregation and packaging machinery. FASEB J. Accepted.  2025.

66. Lad S*, Mandal S*, and Kondabagil K. The evolutionary landscape of modern-day replicases and archaeo-eukaryotic primases may have giant viral interventions. Virology, Volume 607: 110524, 2025.

65. Salunke P, Kondabagil K, and Karpe Y. Recombinant protein expression in Acanthamoeba castellanii. Front. Bioeng. Biotechnol. Sec. Bioprocess Engineering, Volume 13 | doi: 10.3389/fbioe.2025.1524405, 2025.

64. J. Mishra, T. Suryawanshi, N. Redkar, R. Kumar Das, S. Saxena, A. Majumder, K. Kondabagil, S. Shukla. Toxicological Effects of Metal-Doped Carbon Quantum Dots. ChemSusChem, e202402056. https://doi.org/10.1002/cssc.202402056, 2025.

63. Monika, Damle EA, Kondabagil K#, and Kunawar A#. Comparative study of inactivation efficacy of far-UVC (222 nm) and germicidal UVC (254 nm) radiation against virus-laden aerosols of artificial human saliva. Photochemistry and Photobiology,  2025. https://doi.org/10.1111/php.14062, 

62. Ahuja S, Kulkarni A, Pandey R, Kondabagil K, and Tallur S. Practical considerations for DNA sensing using Faradaic electrochemical impedance spectroscopy on ENIG PCB electrodes. Biosensors and Bioelectronics: X, 22:100569, 2025.

61. Monika, Madugula SK, Kondabagil K, and Kunwar A. Far-UVC (222 nm) Irradiation Effectively Inactivates ssRNA, dsRNA, ssDNA, and dsDNA Viruses as Compared to Germicidal UVC (254 nm). Photochemistry and Photobiology, 101:147-156, 2025.

60. Bagale SS Deshmukh PU, Mandal S, Malvi M, Kondabagil K, and Pradeepkumar PI. Synthesis of N6-dA Damaged DNAs to Probe the Replication Ability of Human Translesion Polymerases. Journal of Organic Chemistry, 90: 1159-1166, 2025.

59. Ramakrishnan U, Aggarwal T, and Kondabagil K. Sequence and biochemical analysis of vaccinia virus A32 protein: Implications for in vitro stability and coiled-coil motif mediated regulation of the DNA-dependent ATPase activity. PLoS ONE 20(1): e0316818. 2025. https://doi.org/10.1371/journal.pone.0316818. 

58. The life history traits of phages in a cocktail determine coinfection dynamics and efficacy

Khan R, Chaudhari H, Inamdar MM, and Kondabagil K. bioRxiv doi: https://doi.org/10.1101/2024.10.26.620386, 2024. 

57. Cui L, Kiga K, Kondabagil, K, and  Alicja Węgrzyn. Current and future directions in bacteriophage research for developing therapeutic innovations. Sci Rep 14, 24404, 2024.

56. Aggarwal T and Kondabagil K. Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins. Archives of Virology, 169:222, 2024.

55. Bagale SS Deshmukh PU, Lad SB, Sudarsan A, Sudhakar S, Mandal S, Kondabagil K#, Pradeepkumar PI# Synthesis of carcinogenic N2 -trans-iso-safrole-dG-adduct bearing DNAs and the bypass studies with human TLS polymerases k and n. Journal of Organic Chemistry, 89: 7680-7691, 2024.

54. Kant P, Petersen B, Sicheritz-Pontén T and Kondabagil K. The low abundance of antimicrobial resistance genes (ARGs) in bacteriophages and their transfer bottlenecks limit the ability of phages to contribute to the spread of ARGs. bioRxiv.  https://doi.org/10.1101/2024.04.02.587543, 2024. 

53. Upadhyay M, Nair D, Moseley GW, Srivastava S#, and Kondabagil K#. Giant Virus Global Proteomics Innovation: Comparative Evaluation of In-Gel and In-Solution Digestion Methods  OMICS: A Journal of Integrative Biology, 18(4): 170-181, 2024.  

52. Aggrawal T and Kondabagil K. Assembly and Evolution of poxviruses.  Advances in Experimental Medicine and Biology (AEMB, Volume 1451; Chapter 3)  https://link.springer.com/book/9783031571640, 2024. [Book Chapter]

51. A. Patnaik, G. P, S. S. Palli, M. S. Kumar, K. Kondabagil and T. Kundu, "Protocol development for specific detection of SARS CoV-2 variants using a U-bent fiber optic probe," 2024 IEEE Applied Sensing Conference (APSCON), Goa, India, 2024, pp. 1-4, doi: 10.1109/APSCON60364.2024.10466063. [Conference]

50. Sharma D, Coulibaly F, and Kondabagil K. Mimivirus encodes an essential MC1-like non-histone architectural protein involved in DNA condensation. bioRxiv,  https://www.biorxiv.org/content/10.1101/2024.02.22.580433v1  2024. 

49. Kuruwa S, Zade A, Shah S, Moidu R, Lad S, Chande C, Joshi A, Hirani N, Nikam C, Bhattacharya S, Poojari A, Kapoor M, Kondabagil K and Chatterjee A. An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG, Journal of Applied Microbiology, lxae037, 2024. 

48. Ahuja S, Tallur S#, and Kondabagil K#. Simultaneous microbial capture and nucleic acid extraction from wastewater with minimal pre-processing and high recovery efficiency. Science of the Total Environment, 170347, 2024. 

47. Deshmukh PU, Lad SB, Sudarsan A, Sudhakar S, Aggarwal T, Mandal S, Bagale SS, Kondabagil K* and P. I. Pradeepkumar*. Human Translesion Synthesis Polymerases polκ and polη Perform Error-Free Replication across N2-dG Methyleugenol and Estragole DNA Adducts. Biochemistry, 62, 16, 2391–2406, 2023.

46. Lad SB, Upadhyay M, Thorat P, Nair D, Moseley GW, Srivastava S, Pradeepkumar PI and Kondabagil K. Biochemical reconstitution of the mimiviral base excision repair pathway. J. Mol. Biol. 168188, 2023. Cover page article. 

45. Nandeshwar R, Kulkarni A, Shuja S, Kumar MS, Paul D, Kondabagil K and Tallur S. Portable absorbance platform for sensing of viral and bacterial nucleic acid leveraging intercalation with methylene blue: Application for wastewater-based epidemiology. Biosensors and Bioelectronics: X. 100373, 2023.

44. Goyal N, Barai A, Sen S and Kondabagil K. Amoebal Tubulin Cleavage Late during Infection is a Characteristic Feature of Mimivirus but not of Marseillevirus. Microbiology Spectrum, 10(6):e0275322, 2022. 

43. Lad SB, Roy S, George ES, Chakraborti H, Lalsare S, Barik B, Singh A, Zade A, Agrawal A, Shastri J, Chatterjee A, Gupta KD, Paul D* and Kondabagil K*. Development of a PNA-DiSc2 based portable absorbance platform for the detection of pathogen nucleic acids. Analyst, 147:5306-5313, 2022. 

42. Zade A, Shah S, Hirani N, Kondabagil K, Joshi A, Chatterjee A. Whole-genome sequencing of presumptive MDR-TB isolates from a tertiary healthcare setting in Mumbai. J Global Antimicrobial Res, 31: 256-2062; 2022.

41. Ahuja S, Kumar MS, Nandeshwar R,  Kondabagil K*, Tallur S*. Longer amplicons provide better sensitivity for electrochemical sensing of viral nucleic acid in water samples using PCB electrodes. Scientific Reports, 12:8814, 2022. 

40. Sthanam LK, Patwardhan S, Shukla A, Sharma A, Roy T, Shinde PV, Kale HT, Chandra Shekhar P, Kondabagil K, and Sen S. MMP modulated differentiation of mouse embryonic stem cells on engineered cell derived matrices. Biomaterials. 121268, 2022.

39. Nandeshwar R, Kumar MS, Kondabagil K and Tallur S. Electrochemical Immunosensor Platform Using Low-Cost ENIG PCB Finish Electrodes: Application For SARS-CoV-2 Spike Protein Sensing. IEEE Access,  9: 154368-154377, 2021. 

38. Wangchuk J, Chatterjee A, Patil S, Kumar MS, Kondabagil K. The Coevolution of Large and Small Terminases of Bacteriophages is a Result of Purifying Selection Leading to Phenotypic Stabilization. Virology, 564:13-25, 2021. 

37. Mehner-Breitfeld D, Schwarzkopf J-MF, Young RF, Kondabagil K, Brüser T. The phage T4 antiholin RI has a cleavable signal peptide, not a SAR domain. Front. Microbiology, 12:712460, 2021. 

36. Halkare, P,  Punjabi N, Wangchuk J, Kumar MS, Kondabagil K, Mukherji S. Label-Free Detection of Escherichia coli from Mixed Bacterial Cultures Using Bacteriophage T4 on Plasmonic Fiber-Optic Sensor. ACS Sensors, 6(7): 2720-2727, 2021.

35. Kumar MS, Nandeshwar R, Lad SB, Megha K, Mangat M, Butterworth A, Knapp CW, Knapp M, Hoskisson PA, Corrigan DK, Ward AC, Kondabagil K*, and Tallur S*. Electrochemical sensing of SARS-CoV-2 amplicons with PCB electrodes. Sensors and Actuators B: Chemical. 343: 130169, 2021. 

34. Chaudhari HV, Inamdar MM*, and Kondabagil K*. Scaling relation between genome length and particle size of viruses provides insights into viral life history. iScience. 24:102452, 2021.  

33. Patil S and Kondabagil K. Coevolutionary and phylogenetic analysis of Mimiviral replication machinery suggest the cellular origin of Mimiviruses. Molecular Biology and Evolution. 38(5): 2014-2029, 2021.

32. Sharma S*, Kumari V*, Kumbhar B, Mukherjee A, Pandey R, and Kondabagil K. Immunoinformatics approach for a novel multi-epitope subunit vaccine design against various subtypes of Influenza A virus. Immunobiology, 226(2): 152053, 2021. 

31. Kondabagil K*, Sicheritz-Pontén T*, and Clokie MRJ*. inPhocus: A local perspective on phage-based biocontrol in agriculture and aquaculture in India. PHAGE 1 (4), 169-173, 2020. 

30. Sadani K, Muthuraj L, Nag P, Fernandes M, Kondabagil K, Mukhopadhyay C, and Mukherji S. A point of use of sensor assay for detecting purely virus versus viral-bacterial samples. Sensors and Actuators: B. Chemical, 322: 128562, 2020. 

29. Sharma S, Chatterjee A, Kumar P, Lal S, and Kondabagil K. Upregulation of miR-101 during Influenza A Virus Infection Abrogates Viral Life Cycle by Targeting mTOR Pathway. Viruses, 12(4):444, 2020.

28. Chatterjee A and Kondabagil K. Giant viral genomic signatures in the previously reported gut metagenomes of pre-school children in rural India. Arch Virol. 164:2819-2822. 2019. 

27. Gupta A*, Lad SB*, Ghodke PP, Pradeepkumar PI, and Kondabagil K. Mimivirus encodes a multifunctional primase with DNA/RNA polymerase, terminal transferase and translesion synthesis activities, Nucleic Acids Research, 47:6932–6945, 2019. Cover page article

26. Chatterjee A, Sicheritz-Pontén T, Yadav R, and Kondabagil K. Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India. Scientific Rep 9, 1: 3690. 2019.

25. Halkare P, Punjabi N, Wangchuk J, Nair A, Kondabagil K, and Mukherji S. Bacteria functionalized gold nanoparticle matrix fibre-optic sensor for monitoring heavy metal pollution in water. Sensors & Actuators: B Chemical 281: 643-651, 2019.

24. Wangchuk J, Prakash P, Bhaumik P, and Kondabagil K. Bacteriophage N4 large terminase: expression, purification and X-ray crystallographic analysis. Acta Cryst. F74: 198–204, 2018.

23. Shukla A, Chatterjee A, and Kondabagil K. The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses. Virus Evolution, 4(1): vex039, 2018.

22. Gupta A*, Patil S*, Vijaykumar R*, and Kondabagil K. The Polyphyletic Origins of Primase-Helicase Bifunctional Proteins. J. Mol. Evol. 85:188-204, 2017. 

21. Chatterjee A and Kondabagil K. Complete genome sequence of Kurlavirus, a novel member of the family Marseillviridae isolated from Mumbai India, Arch Virol. 162:3243-3245, 2017.

20. Poonia VS, Kondabagil K, Saha D, and Ganguly S. On the functional window of avian campass. Phys Rev E, 95:052417, 2017.

19. Chatterjee A, Ali F, Bhange D, and Kondabagil K. Complete genome sequence of a new Megavirus family member isolated from an inland water lake for the first time in India. Genome Announcements. 4(3). pii: e00402-16. doi: 10.1128/genomeA.00402-16, 2016.

18. Halkare P, Punjabi N, Wangchuk J, Kondabagil K, and Mukherji S. Detection of bacteria using bacteriophage with hollow gold nanostructures immobilized fiber optic sensor. Proc. SPIE 9899, Optical Sensing and Detection IV, 98992Z, doi: 10.1117/12.2230639. 2016.

17. Chatterjee A, Ali F, Bhange D, and Kondabagil K. Isolation and complete genome sequencing of Mimivirus bombay, a Giant Virus in sewage of Mumbai, India. Genomics Data. 9:1-3, 2016.

16. Halkare P, Punjabi N, Wangchuk J, Kondabagil K, and Mukherji S. LSPR based fiber optic sensor for detection of E.coli using bacteriophage T4. IEEE WRAP, 1570211247. 2015.

15. Zade A, Sengupta M, and Kondabagil K. Extensive in silico analysis of Mimivirus coded Rab GTPase homolog suggests a possible role in virion membrane biogenesis. Front. Microbiol. 6: 929, 2015.

14. Kondabagil K. Bacteriophage mediated Bio-control in wastewater management. In Industrial and Environmental Microbiology, Studium Press, Chapter 30: 473-495, 2014.

13. Chelikani V, Ranjan T, and Kondabagil K. Revisiting the genome packaging in viruses with lessons from the “Giants”. Virology, 466-467:15-26, 2014.

12. Chelikani V*, Ranjan T*, Zade A*, Shukla A, and Kondabagil K. Genome segregation and packaging machinery in Acanthamoeba polyphaga mimivirus is reminiscent of bacterial apparatus J Virol. 88:6069-75. 2014.   

Earlier Publications                      

11. Vafabakhsh R, Kondabagil K, Earnest T, Lee KS, Zhang S, Dai L, Dahmen KA, Rao VB, and Ha T. Single Molecule Packaging Initiation in Real-time by a Viral DNA Packaging Machine from Bacteriophage T4. Proc Natl Acad Sci USA. 111:15096-101, 2014.

10. Kondabagil K, Vafabakhsh R, Ha T, Draper B, and Rao VB. Designing a nine cysteine-less DNA packaging motor from bacteriophage T4 reveals new insights into ATPase structure and function. Virology, 468-470:660-668, 2014. Cover page article. 

9. Sun S*, Gao S*, Kondabagil K*, Xiang Y, Rossmann MG, and Rao VB. Structure and function of the small terminase component of the DNA packaging machine in T4-like bacteriophages. Proc Natl Acad Sci U S A. 109:817-22, 2012.       

8. Kondabagil K, Draper B, and Rao VB. Adenine recognition is a key checkpoint in the energy release mechanism of phage T4 DNA packaging motor. J Mol Biol. 415:329-42. 2012. Cover page article.   

7. Al-Zahrani A*, Kondabagil K*, Gao S, Kelly N, Ghosh-Kumar M, and Rao VB. The Small Terminase, gp16, of Bacteriophage T4 is a Global Regulator of the DNA Packaging Motor. J. Biol. Chem. 284:24490-500, 2009.

6. Sun S*, Kondabagil K*, Draper B, Alam TI, Bowman VD, Zhang Z, Hegde S, Fokine A, Rossmann MG, and Rao VB. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell 135:1251-1262, 2008. Leading Edge Article; previewed, Williams RS, Williams GJ, Tainer JA. A charged performance by gp17 in viral packaging. Cell 135:1169-1171, 2008. 

5. Alam TI, Draper B, Kondabagil K, Rentas FJ, Ghosh-Kumar M, Sun S, Rossmann MG, and Rao VB. The headful packaging nuclease of bacteriophage T4. Mol. Microbiol. 69:1180-1190, 2008.

4. Sun S, Kondabagil K, Gentz P, Rossmann MG, and Rao VB. The structure of the ATPase that powers DNA packaging into bacteriophage T4 procapsids. Mol Cell. 25:943-949, 2007.

3. Kondabagil K, Zhihong Z, and Rao VB. The DNA Translocating ATPase of Bacteriophage T4 Packaging Motor. J.Mol.Biol. 363: 786-799, 2006.

2. Kondabagil K, and Rao VB. A Critical Coiled Coil Motif in the Small Terminase, gp16, from Bacteriophage T4: Insights into DNA Packaging Initiation and Assembly of Packaging Motor. J.Mol.Biol. 358:67-82, 2006.

1. Kanamaru S*, Kondabagil K*, Rossmann MG, and Rao VB. The functional domains of bacteriophage T4 terminase. J. Biol. Chem. 279:40795-40801, 2004. 

*-Contributed equally and shared first authorship.

#-Corresponding authors