PUBLICATIONS
2022
• Vemparala, B., Parambathu, A.V., Saini, D.K. & Dixit, N.M. (2022). An evolutionary paradigm favoring crosstalk between bacterial two-component signaling systems. mSystems 7 (6) 2022. link
Article was recommended to Faculty Opinions by Prof. Ann Stock, Rutgers - Robert Wood Johnson Medical School, USA: link
• Barnabas, V., Kashyap, A., Raja, R., Newar, K., Rai, D., Dixit, N.M., & Mehra, S. (2022). The Extent of Antimicrobial Resistance Due to Efflux Pump Regulration. ACS Infect Dis 8 (11), 2022. link
• Chatterjee, B., Sandhu, H. S., & Dixit, N. M. (2022). Modeling recapitulates the heterogeneous outcomes of SARS-CoV-2 infection and quantifies the differences in the innate immune and CD8 T-cell responses between patients experiencing mild and severe symptoms. PLoS Pathog 18 (6), 2374-2388, 2022. link
• James, A., & Dixit, N. M. (2022). Transmitted HIV-1 is more virulent in heterosexual individuals than men-who-have-sex-with-men. PLoS Pathog 18 (3), 2022. link
News coverage: Healthline AJMC MedicalNewsToday Medical Xpress Galileu Outrage SciTech Daily
... and many more
• Padmanabhan, P., Desikan, R., & Dixit, N. M. (2022). Modeling how antibody responses may determine the efficacy of COVID-19 vaccines. Nat Comput Sci 2 (2), 123-131. link
News coverage: News and Views - Nature Computational Science The Hindu Hindustan Times Times of India ET Health Xinhua Net Nature India Outlook India The Indian Express The Hans India ... and many more
• Popular science article Dixit, N. M. (2022). A Dynamical Systems View of the Outcomes of Viral Infections. SIAM News. Link
• Padmanabhan, P., & Dixit, N. M. (2022). Evidence of increased Cathepsin B/L and decreased TMPRSS2 usage for cell entry by the SARS-CoV-2 Omicron variant. biorXiv. link
2021
• Ansari, A. F., Reddy, Y. B. S., Raut, J. et al. (2021). An efficient and scalable top-down method for predicting structures of microbial communities. Nat Comput Sci 1, 619–628. pdf
• Garg, A. K., Mittal, S., Padmanabhan, P., Desikan, R., & Dixit, N. M. (2021). Low dose prime and delayed boost can improve COVID-19 vaccine efficacies by increasing B cell selection stringency in germinal centres. medRxiv. pdf (Update: Published in Frontiers in Immunology - link to the article)
News coverage: The Hindu
• Chatterjee, B., Sandhu, H. S., & Dixit, N. M. (2021). The relative strength and timing of innate immune and CD8 T-cell responses underlie the heterogeneous outcomes of SARS-CoV-2 infection. medRxiv. pdf
• Desikan, R., Antia, R., & Dixit, N. M. (2021). Physical ‘strength’of the multi‐protein chain connecting immune cells: Does the weakest link limit antibody affinity maturation? The weakest link in the multi‐protein chain facilitating antigen acquisition by B cells in germinal centres limits antibody affinity maturation. BioEssays, 43(4), 2000159. pdf
• Padmanabhan, P., Desikan, R., & Dixit, N. M. (2021). Modelling the population-level protection conferred by COVID-19 vaccination. medRxiv. pdf (Published in Nat Comput Sci link)
• Nagaraja, P., Gopalan, B. P., D’Souza, R. R., Sarkar, D., Rajnala, N., Dixit, N. M., & Shet, A. (2021). The within-host fitness of HIV-1 increases with age in ART-naïve HIV-1 subtype C infected children. Scientific reports, 11(1), 1-10. pdf
2020
• Gorai, B., Sahoo, A. K., Srivastava, A., Dixit, N. M., & Maiti, P. K. (2020). Concerted interactions between multiple gp41 trimers and the target cell lipidome may be required for HIV-1 entry. Journal of Chemical Information and Modeling. pdf
• Padmanabhan, P., Raja, R., & Dixit, N. M. (2020). Bistability in virus–host interaction networks underlies the success of hepatitis C treatments. In Phenotypic Switching (pp. 131-156). Academic Press.
• James, A., & Dixit, N. M. (2020). Transmitted HIV-1 is more pathogenic in heterosexual individuals than homosexual men. medRxiv. pdf
• Padmanabhan, P., Desikan, R., & Dixit, N. M. (2020). The quantitative landscape of the neutralizing antibody response to SARS-CoV-2. medRxiv. pdf
• Desikan, R., Raja, R., & Dixit, N. M. (2020). Early exposure to broadly neutralizing antibodies may trigger a dynamical switch from progressive disease to lasting control of SHIV infection. PLoS computational biology, 16(8), e1008064. pdf
• Agrawal, S., Bhandari, S., Bhattacharjee, A., Deo, A., Dixit, N. M., Harsha, P., ... & Yasodharan, S. (2020). City-Scale Agent-Based Simulators for the Study of Non-Pharmaceutical Interventions in the Context of the COVID-19 Epidemic. Journal of the Indian Institute of Science, 1-39. pdf
• Saha, A., & Dixit, N. M. (2020). Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection. PLOS Computational Biology, 16(11), e1008434. pdf
• Padmanabhan, P., Desikan, R., & Dixit, N. M. (2020). Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection. PLoS computational biology, 16(12), e1008461. pdf
2019
• Ansari et al., 110th Anniversary: High-order interactions can eclipse pairwise interactions in shaping the structure of microbial communities: the case of a synthetic oral microbial community containing Actinomyces viscosus, Industrial and Engineering Chemistry Research. pdf
• Garg et al., Preferential presentation of high-affinity immune complexes in germinal centers can explain how passive immunization improves the humoral response. Cell Reports. pdf
• Sen et al., You Cannot Have Your Synergy and Efficacy Too, Trends in Pharmacological Sciences. pdf
• Baral et al., A dynamical motif comprising the interactions between antigens and CD8 T cells may underlie the outcomes of viral infections, PNAS. pdf
• Dave et al., Strand-specific affinity of host factor hnRNP C1/C2 guides positive to negative-strand ratio in Coxsackievirus B3 infection, RNA Biology. pdf
• Raja et al., Mutational pathway maps and founder effects define the within-host spectrum of hepatitis C virus mutants resistant to drugs, PLoS Pathogens. pdf
• Baral S, Raja R, Sen P, Dixit NM. Towards multiscale modeling of the CD8+ T cell response to viral infections. WIREs Syst Biol Med. pdf
2018
• Raja R, Baral S, Dixit NM. Interferon at the cellular, individual, and population level in hepatitis C virus infection: Its role in the interferon-free treatment era. Immunol Rev. 2018; 285: 55 –71. pdf
• Venugopal V, Padmanabhan P, Raja R, Dixit NM. Modelling how responsiveness to interferon improves interferon-free treatment of hepatitis C virus infection. PLoS Comput Biol. 2018; 14: e1006335. pdf
• Sankhe GD, Dixit NM, Saini DK. Activation of bacterial histidine kinases: insights into the kinetics of the cis autophosphorylation mechanism. mSphere. 2018; 3: e00111-18. pdf
• Baral S, Roy R, Dixit NM. Modeling how reversal of immune exhaustion elicits cure of chronic hepatitis C after the end of treatment with direct-acting antiviral agents. Immunol Cell Biol. 2018; 96: 969-980 pdf
• Gupta V, Dixit NM. Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents. PLOS Comput Biol. 2018; 14: e1006004. pdf
2017
• Gogoi M, Ravikumar V, Dixit NM, Chakravortty D. Salmonella escapes K63 ubiquitination mediated MHC II endosomal proteolysis via modulation of endosomal acidification in dendritic cells. Pathog Dis. 2017; doi:10.1093/femspd/ftx125
• Padmanabhan P, Dixit NM. Inhibitors of hepatitis C virus entry may be potent ingredients of optimal drug combinations. Proc Natl Acad Sci. 2017; 201704531. doi:10.1073/pnas.1704531114 - Featured in The Hindu
2016
• Shet A, Nagaraja P, Dixit NM. Viral decay dynamics and mathematical modeling of treatment response: Evidence of lower in vivo fitness of HIV-1 subtype C. J Acq Immun Def Synd 2016; 73:245-251. pdf
• Nagaraja P, Alexander HK, Bonhoeffer S, Dixit NM. Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1. Epidemics. Elsevier B.V.; 2016;14: 11–25. pdf
• Padmanabhan P, Dixit NM. Models of Viral Population Dynamics. In: Domingo E, Schuster P, editors. Quasispecies: From Theory to Experimental Systems. Cham: Springer International Publishing; 2016. pp. 277–302. doi:10.1007/82_2015_458
2015
• Nandy B, Saurabh S, Sahoo AK, Dixit NM, Maiti PK. The SPL7013 dendrimer destabilizes the HIV-1 gp120–CD4 complex. Nanoscale. Royal Society of Chemistry; 2015;7:44. pdf
• Gupta V, Dixit NM. Scaling law characterizing the dynamics of the transition of HIV-1 to error catastrophe. Phys Biol. 2015;12(5):054001. pdf - Featured in The Indian Express
• Padmanabhan P, Dixit NM. Modelling suggests a mechanism of synergy between hepatitis C virus entry inhibitors and drugs of other classes. CPT: Pharmacometrics & Systems Pharmacology 2015. pdf - Featured in The Hindu and Bangalore Mirror
• Agrawal R, Pandey A, Rajankar MP, Dixit NM, Saini DK.The Two Component Signaling Networks of Mycobacterium tuberculosis Display Extensive Crosstalk In Vitro. Biochemical Journal 2015; 469: 121-134. pdf
2014
• Padmanabhan P, Garaigorta U, Dixit NM. Emergent properties of the interferon signaling network may underlie the success of hepatitis C treatment. Nat Commun 2014; 5:3872. pdf - Featured in IndiaBioscience and Bangalore Mirror - F1000Prime Recommended
• Thangavelu PU, Gupta V, Dixit NM. Estimating the fraction of progeny virions that must incorporate APOBEC3G for suppression of productive HIV-1 infection. Virology 2014; 449:224-228. pdf - Featured article in Virology Highlights
2013
• Nandy B, Bindu DH, Dixit NM, Maiti PK. Simulations reveal that HIV-1 gp120-CD4 complex dissociates via complex pathways and is a potential target of the polyamidoamine (PANAM) dendrimer. J Chem Phys 2013; 139:024905. pdf
2012
• Tripathi K, Balagam R, Vishnoi NK, Dixit NM. Stochastic simulations suggest that HIV-1 survives close to its error threshold. PLoS Comput Biol 2012; 8(9):e1002684. pdf
• Dixit NM, Srivastava P, Vishnoi NK. A finite population size model of molecular evolution: theory and computation. J Comput Biol 2012; 19:1176-1202. pdf
• Krishnan SM, Dixit NM. A formula to estimate the optimal dosage of ribavirin for the treatment of chronic hepatitis C: influence of ITPA polymorphisms. Antivir Ther 2012; 17:1581-92. pdf
• Padmanabhan P, Dixit NM. Viral kinetics suggests a reconcilation of the disparate observations of the modulation of claudin-1 expression on cells exposed to hepatitis C virus. PLoS ONE 2012; 7(4):e36107. pdf
2011
• Padmanabhan P, Dixit NM. Mathematical model of viral kinetics in vitro estimates the number of E2-CD81 complexes necessary for hepatitis C virus entry. PLoS Comput Biol 2011; 7(12):e1002307. pdf
• Mulampaka SN , Dixit NM. Estimating the threshold surface density of Gp120-CCR5 complexes necessary for HIV-1 envelope-mediated cell-cell fusion. PLoS ONE 2011; 6(5):e19941. pdf
• Krishnan SM, Dixit NM. Ribavirin-induced anemia in Hepatitis C virus patients undergoing combination therapy. PLoS Comput Biol 2011; 7(2):e1001072. pdf
• Balagam R, Singh V, Sagi AR, Dixit NM. Taking multiple infections of cells and recombination into account leads to small within-host effective-population-size estimates of HIV-1. PLoS One 2011; 6(1): e14531. pdf
2010
• Gadhamsetty S, Dixit NM. Estimating frequencies of minority nevirapine resistant strains in chronically HIV-1 infected individuals naive to nevirapine using stochastic simulations and a mathematical model. J Virol 2010; 84:10230-40. pdf
2009
• Krishnan SM, Dixit NM. Estimation of red blood cell lifespan from alveolar carbon monoxide measurements. Transl Res 2009; 154(1):15-7. pdf
• Eswarappa SM, Janice J, Balasundaram SV, Dixit NM, Chakravortty D . Host-specificity of Salmonella enterica serovar Gallinarum: insights from comparative genomics. Infect Genet Evol 2009; 9(4):468-73. pdf
• Arora P and Dixit NM . Timing the emergence of resistance to anti-HIV drugs with large genetic barriers. PLoS Comput Biol 2009; 5(3):e1000305. pdf
2008
• Eswarappa SM, Janice J, Nagarajan AG, Balasundaram SV, Karnam G, Dixit NM, Chakravortty D. Differentially evolved genes of Salmonella pathogenicity islands: insights into the mechanism of host specificity in Salmonella. PLoS One 2008; 3(12):e3829. pdf
• Dixit NM . Modelling HIV infection dynamics: The role of recombination in the development of drug resistance. Future HIV Therapy 2008; 2:375-88. pdf
• Vijay N N V, Vasantika, Ajmani R, Perelson AS and Dixit NM . Recombination increases human immunodeficiency virus fitness, but not necessarily diversity. J Gen Virol 2008; 89(Pt 6):1467-77. pdf
• Mohanty U and Dixit NM . Mechanism-based model of the pharmacokinetics of enfuvirtide, an HIV fusion inhibitor. J Theor Biol 2008; 251(3):541-51. pdf
• Dixit NM , Advances in the mathematical modelling of hepatitis C virus dynamics, J Ind Inst Sci 2008, 88, 37. pdf
2006
• Boyd MA, Dixit NM, Siangphoe U, Buss NE, Salgo MP, Lange JM, Phanuphak P, Cooper DA, Perelson AS, Ruxrungtham K. Viral decay dynamics in HIV-infected patients receiving ritonavir-boosted saquinavir and efavirenz with or without enfuvirtide: a randomized, controlled trial (HIV-NAT 012). J Infect Dis 2006; 194(9):1319-22. pdf
• Dixit NM, Perelson AS. The metabolism, pharmacokinetics and mechanisms of antiviral activity of ribavirin against hepatitis C virus. Cell Mol Life Sci 2006; 63(7-8):832-42. pdf
• Ribeiro RM, Dixit NM, Perelson AS (2006) Modelling the in vivo growth rate of HIV: Implications for vaccination. In: Paton R, McNamara LA, editors. Multidisciplinary Approaches to Theory in Medicine. Amsterdam: Elsevier. pp. 231-246.
2005
• Dixit NM, Perelson AS. HIV dynamics with multiple infections of target cells. Proc Natl Acad Sci USA 2005; 102(23):8198-203. pdf
• Dixit NM, Perelson AS (2005) Influence of drug pharmacokinetics on HIV pathogenesis and therapy. In: Wu H, Tan WY, editors. Deterministic and Stochastic Models on AIDS and HIV with Intervention. Singapore: World Scientific Press. pp. 287-311.
2004
• Dixit NM, Layden-Almer JE, Layden TJ, Perelson AS. Modelling how ribavirin improves interferon response rates in hepatitis C virus infection. Nature 2004; 432(7019):922-4. pdf
• Dixit NM, Perelson AS. Multiplicity of human immunodeficiency virus infections in lymphoid tissue. J Virol 2004; 78(16):8942-5. pdf
• Dixit NM, Markowitz M, Ho DD, Perelson AS. Estimates of intracellular delay and average drug efficacy from viral load data of HIV-infected individuals under antiretroviral therapy. Antivir Ther 2004; 9(2):237-46. pdf
• Dixit NM, Perelson AS. Complex patterns of viral load decay under antiretroviral therapy: influence of pharmacokinetics and intracellular delay. J Theor Biol 2004; 226(1):95-109. pdf
2003
• Powers KA, Dixit NM, Ribeiro RM, Golia P, Talal AH, Perelson AS. Modeling viral and drug kinetics: hepatitis C virus treatment with pegylated interferon alfa-2b. Semin Liver Dis 2003; 23 Suppl 1:13-8. pdf
• Zukoski CF, Kulkarni AM, and Dixit NM, Response to: On methods of determination of homogeneous nucleation rates of protein crystals, Colloid Surf 2003: A 215, 137. pdf
• Dixit NM and Zukoski CF, Pseudo-steady rates of crystal nucleation in suspensions of charged colloidal particles, J Phys Condens Matter 2003; 15, 1531. pdf
• Dixit NM, Zukoski CF. Competition between crystallization and gelation: a local description. Phys Rev E 2003, 67:061501. pdf
-Kulkarni AM, Dixit NM, Zukoski CF. Ergodic and non-ergodic phase transitions in globular protein suspensions. Faraday Discuss 2003;123:37-50. pdf
2002
• Dixit NM, Zukoski CF. Nucleation rates and induction times during colloidal crystallization: links between models and experiments. Phys Rev E 2002; 66:051602. pdf
• Dixit NM and Zukoski CF, Crystal nucleation rates for particles experiencing anisotropic interactions, J Chem Phys 2002; 117:8540-50. pdf
2000
• Dixit NM, Zukoski CF. Crystal Nucleation Rates for Particles Experiencing Short-Range Attractions: Applications to Proteins. J Colloid Interface Sci 2000; 228(2):359-371. pdf
