Publications

For up-to-date information, please visit the Google Scholar page of Prof. Narendra M Dixit

Advances in the mathematical modeling of posttreatment control of HIV-1 B Vemparala, J Guedj, NM Dixit Current Opinion in HIV and AIDS 20 (1), 92-98	2025
Trade-off between the antiviral and vaccinal effects of antibody therapy in the humoral response to HIV S Mittal, AK Garg, R Desikan, NM Dixit Journal of the Royal Society Interface 21 (221), 20240535	2024
Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection: Learning in vivo dynamics using ex vivo data B Vemparala, V Madelain, C Passaes, A Millet, V Avettand-Fenoel, … PLoS Computational Biology 20 (9), e1012434	2024
Modelling HIV-1 control and remission B Vemparala, S Chowdhury, J Guedj, NM Dixit NPJ Systems Biology and Applications 10 (1), 84	2024
Adjusting for specificity of symptoms reveals higher prevalence of asymptomatic SARS-CoV-2 infections than previously estimated A Tiwari, S Chowdhury, A James, B Chatterjee, NM Dixit medRxiv, 2024.09. 11.24313462	2024
Disentangling competitive and cooperative components of the interactions between microbial species AF Ansari, G Sambamoorthy, TC Alexander, YBS Reddy, J Raut, NM Dixit bioRxiv, 2024.02. 06.579244	2024
Molecular dynamics simulations show how antibodies may rescue HIV-1 mutants incapable of infecting host cells D Rajendra, N Maroli, NM Dixit, PK Maiti Journal of Biomolecular Structure and Dynamics, 1-11	2023
Modelling how increased Cathepsin B/L and decreased TMPRSS2 usage for cell entry by the SARS-CoV-2 Omicron variant may affect the efficacy and synergy of TMPRSS2 and Cathepsin … P Padmanabhan, NM Dixit Journal of Theoretical Biology 572, 111568	2023
Sequestration of histidine kinases by non-cognate response regulators establishes a threshold level of stimulation for bacterial two-component signaling GD Sankhe, R Raja, DP Singh, S Bheemireddy, S Rana, PJ Athira, … Nature Communications 14 (1), 4483	2023
A physical tug-of-war and the evolution of immune cells A Tiwari, NM Dixit Journal of Biosciences 48 (3), 20	2023
Asymptomatic SARS-CoV-2 infections tend to occur less frequently in developed nations S Chowdhury, A Tiwari, A James, B Chatterjee, NM Dixit medRxiv, 2023.12. 14.23299954	2023
An Evolutionary Paradigm Favoring Cross Talk between Bacterial Two-Component Signaling Systems B Vemparala, A Valiya Parambathu, DK Saini, NM Dixit mSystems 7 (6), e00298-22	2022
The extent of antimicrobial resistance due to efflux pump regulation V Barnabas, A Kashyap, R Raja, K Newar, D Rai, NM Dixit, S Mehra ACS Infectious Diseases 8 (11), 2374-2388	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 … B Chatterjee, H Singh Sandhu, NM Dixit PLoS pathogens 18 (6), e1010630	2022
Transmitted HIV-1 is more virulent in heterosexual individuals than men-who-have-sex-with-men A James, NM Dixit PLoS Pathogens 18 (3), e1010319	2022
Modeling how antibody responses may determine the efficacy of COVID-19 vaccines P Padmanabhan, R Desikan, NM Dixit Nature Computational Science 2 (2), 123-131	2022
Increased B Cell Selection Stringency In Germinal Centers Can Explain Improved COVID-19 Vaccine Efficacies With Low Dose Prime or Delayed Boost AK Garg, S Mittal, P Padmanabhan, R Desikan, NM Dixit Frontiers in Immunology 12, 5064	2021
An efficient and scalable top-down method for predicting structures of microbial communities AF Ansari, YBS Reddy, J Raut, NM Dixit Nature Computational Science 1 (9), 619-628	2021
A Low-Prevalence Single-Nucleotide Polymorphism in the Sensor Kinase PhoR in Mycobacterium tuberculosis Suppresses Its Autophosphatase Activity and … UW Waturuocha, MS Krishna, V Malhotra, NM Dixit, DK Saini Frontiers in microbiology 12, 724482	2021
The within-host fitness of HIV-1 increases with age in ART-naïve HIV-1 subtype C infected children P Nagaraja, BP Gopalan, RR D’Souza, D Sarkar, N Rajnala, NM Dixit, … Scientific reports 11 (1), 2990	2021
Mechanistic insights into the effects of key mutations on SARS-CoV-2 RBD–ACE2 binding A Aggarwal, S Naskar, N Maroli, B Gorai, NM Dixit, PK Maiti Physical Chemistry Chemical Physics 23 (46), 26451-26458	2021
Physical ‘strength’of the multi‐protein chain connecting immune cells: Does the weakest link limit antibody affinity maturation? R Desikan, R Antia, NM Dixit BioEssays, 2000159	2021
Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection P Padmanabhan, R Desikan, N Dixit PLoS Computational Biology 16 (12), e1008461	2020
Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection A Saha, NM Dixit PLOS Computational Biology 16 (11), e1008434	2020
City-scale agent-based simulators for the study of non-pharmaceutical interventions in the context of the COVID-19 epidemic: IISc-TIFR COVID-19 city-scale simulation team S Agrawal, S Bhandari, A Bhattacharjee, A Deo, NM Dixit, P Harsha, … Journal of the Indian Institute of Science 100, 809-847	2020
Early exposure to broadly neutralizing antibodies may trigger a dynamical switch from progressive disease to lasting control of SHIV infection R Desikan, R Raja, NM Dixit PLoS Computational Biology 16 (8), e1008064	2020
Bistability in virus–host interaction networks underlies the success of hepatitis C treatments P Padmanabhan, R Raja, NM Dixit Phenotypic Switching, 131-156	2020
Concerted interactions between multiple gp41 trimers and the target cell lipidome may be required for HIV-1 entry B Gorai, AK Sahoo, A Srivastava, NM Dixit, PK Maiti Journal of Chemical Information and Modeling 61 (1), 444-454	2020
Preferential presentation of high-affinity immune complexes in germinal centers can explain how passive immunization improves the humoral response AK Garg, R Desikan, NM Dixit Cell reports 29 (12), 3946-3957. e5	2019
110th Anniversary: High-Order Interactions Can Eclipse Pairwise Interactions in Shaping the Structure of Microbial Communities AF Ansari, NIS Acharya, S Kumaran, K Ravindra, YBS Reddy, NM Dixit, … Industrial & Engineering Chemistry Research 58 (51), 23508-23518	2019
You cannot have your synergy and efficacy too P Sen, A Saha, NM Dixit Trends in pharmacological sciences 40 (11), 811-817	2019
Strand-specific affinity of host factor hnRNP C1/C2 guides positive to negative-strand ratio in Coxsackievirus B3 infection P Dave, B George, S Balakrishnan, DK Sharma, H Raheja, NM Dixit, … RNA biology 16 (9), 1286-1299	2019
A dynamical motif comprising the interactions between antigens and CD8 T cells may underlie the outcomes of viral infections S Baral, R Antia, NM Dixit Proceedings of the National Academy of Sciences 116 (35), 17393-17398	2019
Towards multiscale modeling of the CD8⁺ T cell response to viral infections S Baral, R Raja, P Sen, NM Dixit Wiley Interdisciplinary Reviews: Systems Biology and Medicine 11 (4), e1446	2019
Mutational pathway maps and founder effects define the within-host spectrum of hepatitis C virus mutants resistant to drugs. RR Rubesh Raja, AP Aditya Pareek, KN Kapil Newar, NM Dixit	2019
Mutational pathway maps and founder effects define the within-host spectrum of hepatitis C virus mutants resistant to drugs R Raja, A Pareek, K Newar, NM Dixit PLoS Pathogens 15 (4), e1007701	2019
Modeling how reversal of immune exhaustion elicits cure of chronic hepatitis C after the end of treatment with direct‐acting antiviral agents S Baral, R Roy, NM Dixit Immunology and cell biology 96 (9), 969-980	2018
Interferon at the cellular, individual, and population level in hepatitis C virus infection: Its role in the interferon‐free treatment era R Raja, S Baral, NM Dixit Immunological reviews 285 (1), 55-71	2018
Modelling how responsiveness to interferon improves interferon-free treatment of hepatitis C virus infection V Venugopal, P Padmanabhan, R Raja, NM Dixit PLoS Computational Biology 14 (7), e1006335	2018
Activation of Bacterial Histidine Kinases: Insights into the Kinetics of the cis Autophosphorylation Mechanism GD Sankhe, NM Dixit, DK Saini Msphere 3 (3), 10.1128/msphere. 00111-18	2018
Salmonella escapes antigen presentation through K63 ubiquitination mediated endosomal proteolysis of MHC II via modulation of endosomal acidification in … M Gogoi, V Ravikumar, NM Dixit, D Chakravortty Pathogens and disease 76 (2), ftx125	2018
Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents V Gupta, NM Dixit PLoS computational biology 14 (2), e1006004	2018
Inhibitors of hepatitis C virus entry may be potent ingredients of optimal drug combinations P Padmanabhan, NM Dixit Proceedings of the National Academy of Sciences 114 (23), E4524-E4526	2017
Viral decay dynamics and mathematical modeling of treatment response: Evidence of lower in vivo fitness of HIV-1 subtype C A Shet, P Nagaraja, NM Dixit JAIDS Journal of Acquired Immune Deficiency Syndromes 73 (3), 245-251	2016
Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1. PN Pradeep Nagaraja, HK Alexander, S Bonhoeffer, NM Dixit	2016
Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1 P Nagaraja, HK Alexander, S Bonhoeffer, NM Dixit Epidemics 14, 11-25	2016
Viral decay dynamics and mathematical modeling of treatment response: evidence of lower in vivo fitness of HIV-1 subtype C. AS Anita Shet, PN Pradeep Nagaraja, NM Dixit	2016
Scaling law characterizing the dynamics of the transition of HIV-1 to error catastrophe V Gupta, NM Dixit Physical biology 12 (5), 054001	2015
Modeling suggests a mechanism of synergy between hepatitis C virus entry inhibitors and drugs of other classes P Padmanabhan, NM Dixit CPT: pharmacometrics & systems pharmacology 4 (8), 445-453	2015
Models of viral population dynamics P Padmanabhan, NM Dixit Quasispecies: From Theory to Experimental Systems, 277-302	2015
The two-component signalling networks of Mycobacterium tuberculosis display extensive cross-talk in vitro R Agrawal, A Pandey, MP Rajankar, NM Dixit, DK Saini Biochemical Journal 469 (1), 121-134	2015
The SPL7013 dendrimer destabilizes the HIV-1 gp120–CD4 complex B Nandy, S Saurabh, AK Sahoo, NM Dixit, PK Maiti Nanoscale 7 (44), 18628-18641	2015
Emergent properties of the interferon-signalling network may underlie the success of hepatitis C treatment P Padmanabhan, U Garaigorta, NM Dixit Nature Communications 5 (1), 3872	2014
Estimating the fraction of progeny virions that must incorporate APOBEC3G for suppression of productive HIV-1 infection PU Thangavelu, V Gupta, NM Dixit Virology 449, 224-228	2014
Simulations reveal that the HIV-1 gp120-CD4 complex dissociates via complex pathways and is a potential target of the polyamidoamine (PAMAM) dendrimer B Nandy, DH Bindu, NM Dixit, PK Maiti The Journal of chemical physics 139 (2)	2013
A formula to estimate the optimal dosage of ribavirin for the treatment of chronic hepatitis C: influence of ITPA polymorphisms SM Krishnan, NM Dixit Antiviral therapy 17 (8), 1581-1592	2012
A finite population model of molecular evolution: Theory and computation NM Dixit, P Srivastava, NK Vishnoi Journal of Computational Biology 19 (10), 1176-1202	2012
Stochastic simulations suggest that HIV-1 survives close to its error threshold K Tripathi, R Balagam, NK Vishnoi, NM Dixit Public Library of Science 8 (9), e1002684	2012
Viral kinetics suggests a reconciliation of the disparate observations of the modulation of claudin-1 expression on cells exposed to hepatitis C virus P Padmanabhan, NM Dixit PLoS One 7 (4), e36107	2012
Mathematical model of viral kinetics in vitro estimates the number of E2-CD81 complexes necessary for hepatitis C virus entry P Padmanabhan, NM Dixit PLoS computational biology 7 (12), e1002307	2011
Estimating the threshold surface density of Gp120-CCR5 complexes necessary for HIV-1 envelope-mediated cell-cell fusion SN Mulampaka, NM Dixit PloS one 6 (5), e19941	2011
Ribavirin-induced anemia in hepatitis C virus patients undergoing combination therapy SM Krishnan, NM Dixit PLoS computational biology 7 (2), e1001072	2011
Taking multiple infections of cells and recombination into account leads to small within-host effective-population-size estimates of HIV-1 R Balagam, V Singh, AR Sagi, NM Dixit PLoS One 6 (1), e14531	2011
Estimating frequencies of minority nevirapine-resistant strains in chronically HIV-1-infected individuals naive to nevirapine by using stochastic simulations and a mathematical … S Gadhamsetty, NM Dixit Journal of virology 84 (19), 10230-10240	2010
Host-specificity of Salmonella enterica serovar Gallinarum: insights from comparative genomics SM Eswarappa, J Janice, SV Balasundaram, NM Dixit, D Chakravortty Infection, genetics and evolution 9 (4), 468-473	2009
Estimation of red blood cell lifespan from alveolar carbon monoxide measurements SM Krishnan, NM Dixit Translational research 154 (1), 15-17	2009
Timing the emergence of resistance to anti-HIV drugs with large genetic barriers P Arora, NM Dixit PLoS computational biology 5 (3), e1000305	2009
Differentially evolved genes of Salmonella pathogenicity islands: insights into the mechanism of host specificity in Salmonella SM Eswarappa, J Janice, AG Nagarajan, SV Balasundaram, G Karnam, … PLOS one 3 (12), e3829	2008
Modeling HIV infection dynamics: the role of recombination in the development of drug resistance NM Dixit Future Medicine Ltd 2 (4), 375-388	2008
Recombination increases human immunodeficiency virus fitness, but not necessarily diversity NNV Vijay, Vasantika, R Ajmani, AS Perelson, NM Dixit Journal of General Virology 89 (6), 1467-1477	2008
Mechanism-based model of the pharmacokinetics of enfuvirtide, an HIV fusion inhibitor U Mohanty, NM Dixit Journal of theoretical biology 251 (3), 541-551	2008
Advances in the mathematical modelling of hepatitis C virus dynamics NM Dixit Journal of the Indian Institute of Science 88 (1), 37-43	2008
Emergence of recombinant forms of HIV: dynamics and scaling GW Suryavanshi, NM Dixit PLoS Computational Biology 3 (10), e205	2007
Characterizing T cell movement within lymph nodes in the absence of antigen C Beauchemin, NM Dixit, AS Perelson The Journal of Immunology 178 (9), 5505-5512	2007
Viral decay dynamics in HIV-infected patients receiving ritonavir-boosted saquinavir and efavirenz with or without enfuvirtide: a randomized, controlled trial (HIV-NAT 012) MA Boyd, NM Dixit, U Siangphoe, NE Buss, MP Salgo, JMA Lange, … The Journal of infectious diseases 194 (9), 1319-1322	2006
The metabolism, pharmacokinetics and mechanisms of antiviral activity of ribavirin against hepatitis C virus NM Dixit, AS Perelson Cellular and Molecular Life Sciences CMLS 63, 832-842	2006
HIV dynamics with multiple infections of target cells NM Dixit, AS Perelson Proceedings of the National Academy of Sciences 102 (23), 8198-8203	2005
13 Modelling the in vivo growth rate of HIV: implications for vaccination RM Ribeiro, NM Dixit, AS Perelson Studies in Multidisciplinarity 3, 231-246	2005
Influence of drug pharmacokinetics on HIV pathogenesis and therapy NM Dixit, AS Perelson Deterministic and Stochastic Models of AIDS and HIV with Intervention, 287-311	2005
Modelling how ribavirin improves interferon response rates in hepatitis C virus infection NM Dixit, JE Layden-Almer, TJ Layden, AS Perelson Nature 432 (7019), 922-924	2004
Multiplicity of human immunodeficiency virus infections in lymphoid tissue NM Dixit, AS Perelson Journal of virology 78 (16), 8942-8945	2004
Estimates of intracellular delay and average drug efficacy from viral load data of HIV-infected individuals under antiretroviral therapy NM Dixit, M Markowitz, DD Ho, AS Perelson Antiviral therapy 9 (2), 237-246	2004
Complex patterns of viral load decay under antiretroviral therapy: influence of pharmacokinetics and intracellular delay NM Dixit, AS Perelson Journal of Theoretical Biology 226 (1), 95-109	2004
Competition between crystallization and gelation: a local description NM Dixit, CF Zukoski Physical Review E 67 (6), 061501	2003
Response to: On methods of determination of homogeneous nucleation rates of protein crystals CF Zukoski, AM Kulkarni, NM Dixit Colloids and Surfaces A: Physicochemical and Engineering Aspects 215 (1-3 …	2003
Pseudo-steady rates of crystal nucleation in suspensions of charged colloidal particles NM Dixit, CF Zukoski Journal of Physics: Condensed Matter 15 (10), 1531	2003
Ergodic and non-ergodic phase transitions in globular protein suspensions AM Kulkarni, NM Dixit, CF Zukoski Faraday discussions 123, 37-50	2003
Modeling viral and drug kinetics: hepatitis C virus treatment with pegylated interferon alfa-2b KA Powers, NM Dixit, RM Ribeiro, P Golia, AH Talal, AS Perelson Seminars in liver disease 23 (S 1), 013-018	2003
Nucleation rates and induction times during colloidal crystallization: Links between models and experiments NM Dixit, CF Zukoski Physical Review E 66 (5), 051602	2002
Crystal nucleation rates for particles experiencing anisotropic interactions NM Dixit, CF Zukoski The Journal of chemical physics 117 (18), 8540-8550	2002
Kinetics of crystallization and gelation in colloidal suspensions NM Dixit University of Illinois at Urbana-Champaign	2002
Comparison of experimental estimates and model predictions of protein crystal nucleation rates NM Dixit, AM Kulkarni, CF Zukoski Colloids and Surfaces A: Physicochemical and Engineering Aspects 190 (1-2 …	2001
Kinetics of crystallization in hard-sphere colloidal suspensions NM Dixit, CF Zukoski Physical Review E 64 (4), 041604	2001
Method and an apparatus for the identification and/or separation of complex composite signals into its deterministic and noisy components VR Kumar, BD Kulkarni, NM Dixit, N Vaish US Patent 6,208,951	2001
Crystal nucleation rates for particles experiencing short-range attractions: Applications to proteins NM Dixit, CF Zukoski Journal of colloid and interface science 228 (2), 359-371	2000