Publications

33. N Ronceray et al. , "Multiplexed lifetime imaging of single molecules with a gated single-photon camera" accepted in Light: Science & Applications (2025) https://doi.org/10.1101/2024.09.17.613468

32. H Chhajer and R Roy, "Rationalised experiment design for parameter estimation with sensitivity clustering" Scientific Reports (2024)

31. V Hill, et al., "A new lineage nomenclature to aid genomic surveillance of dengue virus" PLoS Biology  (2024)

30. J Panwar and R Roy, "Modified capillary number to standardize droplet generation in suction driven microfluidics" Microfluidics and Nanofluidics  (2024) 

29. A Kulshretha, S. Punnathanam, R Roy, K. Ayappa, "Cholesterol catalyzes unfolding in membrane-inserted motifs of the pore forming protein cytolysin A" Biophysical J (2023)

28. S Jagtap, C Pattabiraman, A Sankaradoss, S Krishna, R Roy, "Evolutionary dynamics of dengue virus in India" PLoS Pathogens (2023)

• Interlinked inter- and intra-serotype evolutionary dynamics of dengue

• Several lines of evidence point to the interlinked dengue evolution driven by the underlying population-level natural immunity in India.

• The emergence of rapidly evolving DENV4 lineage (DENV-4-Id) in South India with higher seroprevalence of DENV-1 and DENV-3.

• DENV-4-Id has acquired residues corresponding to Indian DENV-1 and DENV-3 strains.

27. A Kulshrestha, et al. "Conformational flexibility is a key determinant for the lytic activity of the pore-forming protein, Cytolysin A" Journal of Physical Chemistry B pubs.acs.org/doi/10.1021/acs.jpcb.2c05785 (2022)

26. A Sannigrahi, et al. "A Versatile Suspended Lipid Membrane System for Probing Membrane Remodeling and Disruption" Membranes, www.mdpi.com/2077-0375/12/12/1190 (2022)

25. Priyanka V, and R Roy, "Nucleic acid quantification with amplicon yield in recombinase polymerase amplification" Analytical Chemistry, doi.org/10.1021/acs.analchem.2c02810 (2022)

24. S Maurya, V Rai, A Upasani, S Umrao, D Parwana, R Roy, "Single-molecule Diffusion and Assembly on Polymer-crowded Lipid Membranes", Journal of Visualized Experiments,  https://dx.doi.org/10.3791/64243 (2022)

23. A Sankaradoss, S Jagtap, J Nazir, S Moula, A Modak, J Fialho, M Iyer, J Shastri, M Dias, R Gadepalli, A Aggarwal, M Vedpathak, S Agrawal, A Pandit, A Nisheetha, A Kumar, M Bordoloi, M Shafi, B Shelar, S Balachandra, T Damodar, M Masika, P Mwaura, O Anzala, K Muthumani, R Sowdhamini, G Medigeshi, R Roy, C Pattabiraman, S Krishna, E Sreekumar, "Immune profile and responses of a novel Dengue DNA vaccine encoding EDIII-NS1 consensus design based on Indo-African sequences" Molecular Therapy (2022)

22. H Chajjer, VA Rizvi and R Roy, "Life cycle process dependencies of positive-sense RNA viruses suggest strategies for inhibiting productive cellular infection" Journal of the Royal Society Interface, https://doi.org/10.1098/rsif.2021.0401 (2021)

21. S Jagtap, Ratnasri K, Priyanka V, R Sharma, S Maurya, A Gaigore, C Ardhya, D Biligi, B Desiraju, U Natchu, D Saini, R Roy, "Evaluation of spike protein antigens for SARS-CoV-2 serology" Journal of Virological Methods (2021)

20. J Panwar and R Roy, "Integrated Field's metal microelectrodes based microfluidic impedance cytometry for cell-in-droplet quantification" MicroE Engineering, doi: https://doi.org/10.1016/j.mee.2019.111010 (2019)

19. S Umrao, Anusha S, V Jain, B Chakraborty, R Roy, "Smartphone-based kanamycin sensing with ratiometric FRET" RSC Advances, 9, 6143-6151 https://doi.org/10.1039/C8RA10035G (2019)

 18. M Kar, A Nisheetha, A Kumar, S Jagtap, J Shinde, M Singla, S Marimuthu, A Pandit, A Chandele, SK Kabra, S Krishna, R Roy, R Lodha, C Pattabiraman, G Medegeshi, "Isolation and molecular characterization of Dengue virus clinical isolates from pediatric patients in New Delhi" International Journal of Infectious Diseases (2019)

 17. P Sathyanarayana, S Maurya, A Behera, M Ravichandran, SS Visweswariah, KG Ayappa, and R Roy, "Cholesterol promotes Cytolysin A activity by stabilizing the intermediates during pore formation" PNAS (USA), 115 (31) E7323-E7330, https://doi.org/10.1073/pnas.1721228115  (2018)

16. S Banerjee, S Maurya and R Roy, “Single-molecule fluorescence imaging: generating insights into molecular interactions in virology” J Biosciences, 43(3), 519-540, doi: 10.1007/s12038-018-9769-y (2018)

15. S Baral, R Roy, NM Dixit, “Modelling how reversal of immune exhaustion elicits cure of chronic hepatitis C after the end of treatment with direct-acting antiviral agents” Immunology & Cell Biology, 96(9), 969-980, doi: 10.1111/imcb.12161 (2018)

14. HR Koh, R Roy, M Sorokina, GQ Tang, D Nandakumar, SS Patel, T Ha, "Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution" Molecular Cell, 70(4): 695-706, doi: 10.1016/j.molcel.2018.04.018 (2018) 

13.  S Umrao, V Jain, Anusha, B Chakraborty, R Roy,  "Protein-induced fluorescence enhancement as aptamer sensing mechanism for thrombin detection." Sensors and Actuators B: Chemical 267: 294-301 doi: https://doi.org/10.1016/j.snb.2018.04.039 (2018)

12. GQ Tang, D Nandakumar, RP Bandwar, KS Lee, R Roy, T Ha and SS Patel, "Relaxed Rotational and Scrunching Changes in P266L Mutant of T7 RNA Polymerase Reduce Short Abortive RNAs while Delaying Transition into Elongation" PLoS One, 9(3): e91859. doi:10.1371/journal.pone.0091859 (2014)                                 

11.  ZW Zhao*, R Roy*, JCM Gebhardt*, DM Suter*, AR Chapman and S Xie, "Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet super-resolution microscopy" PNAS (USA), 111(2):681-6 (2014)  * equal contribution

10.  R Roy, "Next generation optical microscopy" Current Science, 105(11):1524-36 (2013)

9. JCM Gebhardt, DM Suter, R Roy, ZW Zhao, AR Chapman, S Basu, T. Maniatis and S Xie, “Single-molecule imaging of transcription factor binding to DNA in live mammalian cells”  Nature Methods, 10(5): 4216 (2013)                                                                                                  

8.  R Zhou, A Kozlov, R Roy, J Zhang, S Korolev, T Lohman and T Ha, “SSB Functions as a Sliding Platform that Migrates on DNA via Reptation” Cell, 146(2): 222-32 (2011)

• Featured with the issue’s PaperFlick

7.  G Tang, R Roy, T Ha and S Patel, “Kinetics of Transition to Elongation Phase by T7 RNA Polymerase” PNAS (USA), 106(52): 22175-80 (2009)

6. R Roy, A Kozlov, T Lohman and T Ha, “Rolling Migration of SSB Stimulates RecA Filament Formation” Nature, 461(7267): 1092-7 (2009)

• Accompanying Comment in News and Views Nature, 461(7267):1067-8 (2009)

5. W Min, S Lu, S Chong, R Roy, G Holtom and S Xie, “Imaging Chromophores with Non-Detectable Fluorescence by Stimulated Emission Microscopy” Nature, 461(7267): 1105-9 (2009)

•  Featured Article of the Nature issue; Accompanying Comment in News and Views Nature, 461(7267):1069-70 (2009)

•  Eisenstein, Michael, "Seeing in the dark" Nature Methods 6: 866 (2009)

•  Borman, Stu, "Seeing Molecules With A New Light" C&E News (October 21, 2009)

•  ‘Must Read’ Article rating at F1000.com (Ebbinghaus S, Gruebele M: 2009. F1000.com/1166582)

4. G Tang, R Roy, T Ha and S Patel “Transcription initiation in a single-subunit RNA polymeraseproceeds through DNA scrunching and rotation of the N-terminal subdomains” Molecular Cell, 30(5): 567-77 (2008)

3.  R. Roy, S. Hohng and T Ha “A practical guide to single molecule FRET” Nature Methods, 5(6): 507-18 (2008)

• Nature ‘Milestones in Light Microscopy’ Collection Article

2. R Roy, A Kozlov, T Lohman and T Ha, "Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein", Journal of Molecular Biology, 369(5):1244-57 (2007)

1.  V Arluison, S Hohng, R Roy, O Pellegrini, P Regnier and T Ha, "Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA", Nucleic Acids Research, 35(3):999-1006 (2007)

• ‘Recommended’ Article rating at F1000.com (Westhof E: 2007. F1000.com/1071893)