• A Sannigrahi, et al. "Sphingomyelin-Cholesterol Synergy as a Lipid Chaperone Driving Cytolysin A Pore Formation" (2026) https://www.biorxiv.org/content/10.64898/2026.01.27.702101v1

• D Chakraborty, et al. "Membrane Fusion Inhibition, Immune Modulation, and Cholesterol Synthesis Dysregulation During Dengue Virus Inhibition by 25-Hydroxycholesterol" (2025) https://doi.org/10.1101/2025.05.31.657153

35. R Boddepalli, H Chhajer and R Roy "Integrative Modelling of Innate Immune Response Dynamics during Virus Infection" PLoS Computational Biology (2026) 

We built an integrative computational model that couples the viral life cycle with innate immune signaling to dissect virus–host dynamics. It recapitulates bifurcating infection outcomes and dose-dependent interferon desensitization, clusters host factors by temporal expression, and evaluates prophylactic antiviral strategies—showing how systems-level modeling can guide antiviral design.

34. D Chakraborty, Namitha R, R Roy, L Devi, "Transcriptome signature for Host directed antiviral reprogramming by Nimba & Triphala in macrophage Dengue virus infection models" Scientific Reports (2026) 

33. N Ronceray et al. , "Multiplexed lifetime imaging of single molecules with a gated single-photon camera" 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)

We developed PARSEC (PARameter SEnsitivity Clustering), a model-based design-of-experiments framework that overcomes the oversimplified assumptions and heavy computational cost limiting MBDoE adoption. By clustering parameter sensitivities, it identifies the most informative measurable combinations, enabling robust, efficient experimental designs for accurate parameter estimation in complex dynamical systems.

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)

 Analyzing all Indian dengue sequences from 1956–2018, we find the four serotypes evolve in a coupled three-year rhythm rather than independently.

• Cases surge triennially, and each serotype's envelope protein repeatedly diverges from and reverts toward its ancestral sequence over ~3 years.

• These fluctuations are correlated across serotypes, pointing to shifting cross-reactive antibodies as the driver.

• A fast-evolving DENV-4 lineage (DENV-4-Id) emerged in South India amid high DENV-1/DENV-3 seroprevalence, acquiring envelope residues mirroring those strains—a molecular fingerprint of population immunity shaping viral evolution.

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 Chhajer, 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)