Publications and Presentations

Raja R, Pareek A, Newar K, Dixit NM. Mutational pathway maps and founder effects define the within-host spectrum of hepatitis C virus mutants resistant to drugs. PLoS Pathogens 2019; 15: e1007701


Baral S, Raja R, Sen P, Dixit NM. Towards multiscale modeling of the CD8+ T cell response to viral infections. WIREs Syst Biol Med 2019; 11: e1446


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 


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.

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.


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; doi:


Gupta V, Dixit NM. Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents. PLOS Comput Biol. 2018;14: e1006004.


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 USA 2017; doi:10.1073/pnas.1704531114.

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.


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 2016; 14:11-25.  


Nandy B, Saurabh S, Sahoo AK, Dixit NM, Maiti PK. The SPL7013 dendrimer destabilizes the HIV-1 gp120–CD4 complex. Nanoscale  2015; 7:44. 


Padmanabhan P, Dixit NM (2015) Models of viral population dynamics. In: Current Topics in Microbiology and Immunology. Springer Berlin Heidelberg. DOI: 10.1007/82_2015_458


Gupta V, Dixit NM. Scaling law characterizing the dynamics of the transition of HIV-1 to error catastrophe. Phys Biol 2015; 12(5):054001. 


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; 8:445-453.


Agrawal R, Pandey A, Rajankar MP, Dixit NM, Saini DK.The Two Component Signaling Networks of Mycobacterium tuberculosis Display Extensive Crosstalk In Vitro. Biochem J 2015; 469: 121-134. 


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. 


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. 


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. 


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. 


Dixit NM, Srivastava P, Vishnoi NK. A finite population size model of molecular evolution: theory and computation. J Comput Biol 2012; 19:1176-1202.


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. 


Padmanabhan P, Dixit NM. Viral kinetics suggests a reconcilation of the disparate observations of th e modulation of claudin-1 expression on cells exposed to hepatitis C virus. PLoS ONE 2012; 7(4):e36107. 


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. 


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.


Krishnan SM, Dixit NM. Ribavirin-induced anemia in Hepatitis C virus patients undergoing combination therapy. PLoS Comput Biol 2011; 7(2):e1001072.


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. 


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. 


Krishnan SM, Dixit NM. Estimation of red blood cell lifespan from alveolar carbon monoxide measurements. Transl Res 2009; 154(1):15-7. 


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.


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. 


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. 


Dixit NM . Modelling HIV infection dynamics: The role of recombination in the development of drug resistance. Future HIV Therapy 2008; 2:375-88. 


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; 89:1467-77. 


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. 


Dixit NM , Advances in the mathematical modelling of hepatitis C virus dynamics, J Ind Inst Sci 2008, 88, 37. 


Suryavanshi G W and Dixit NM . Emergence of recombinant forms of HIV: dynamics and scaling. PLoS Comput Biol 2007; 3(10):2003-18. 


Beauchemin C, Dixit NM, Perelson AS. Characterizing T cell movement within lymph nodes in the absence of antigen. J Immunol 2007; 178(9):5505-12.


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. 


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. 


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.


Dixit NM, Perelson AS. HIV dynamics with multiple infections of target cells. Proc Natl Acad Sci USA 2005; 102(23):8198-203. 


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.


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.


Dixit NM, Perelson AS. Multiplicity of human immunodeficiency virus infections in lymphoid tissue. J Virol 2004; 78(16):8942-5. 


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. 


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. 


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. 


Dixit NM and Zukoski CF, Pseudo-steady rates of crystal nucleation in suspensions of charged colloidal particles, J Phys Condens Matter 2003; 15, 1531. 


Dixit NM, Zukoski CF. Competition between crystallization and gelation: a local description. Phys Rev E 2003, 67:061501. 


Kulkarni AM, Dixit NM, Zukoski CF. Ergodic and non-ergodic phase transitions in globular protein suspensions. Faraday Discuss 2003;123:37-50. 


Dixit NM, Zukoski CF. Nucleation rates and induction times during colloidal crystallization: links between models and experiments. Phys Rev E 2002; 66:051602. 


Dixit NM and Zukoski CF, Crystal nucleation rates for particles experiencing anisotropic interactions, J Chem Phys 2002; 117:8540-50. 


Dixit NM, Zukoski CF. Kinetics of crystallization in hard-sphere colloidal suspensions. Phys Rev E 2001; 64:041604.


Dixit NM, Kulkarni AM and Zukoski CF, Comparison of experimental estimates and model predictions of protein crystal nucleation rates, Colloid Surf 2001 . A 190, 47.


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.