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Arandhara, Mrinal ; Kumar, Yogendra ; Dixit, Narendra M. ; Maiti, Prabal K. (2025) Clade-Specific Influences of Glycans on the Interactions between HIV-1 Envelope and Broadly Neutralizing Antibodies Journal of Chemical Information and Modeling . ISSN 1549-9596

Mittal, Soumya ; Garg, Amar K. ; Desikan, Rajat ; Dixit, Narendra M. (2024) Trade-off between the antiviral and vaccinal effects of antibody therapy in the humoral response to HIV Journal of the Royal Society Interface, 21 (221). ISSN 1742-5689

Vemparala, Bharadwaj ; Madelain, Vincent ; Passaes, Caroline ; Millet, Antoine ; Avettand-Fenoel, Véronique ; Djidjou-Demasse, Ramsès ; Dereuddre-Bosquet, Nathalie ; Le Grand, Roger ; Rouzioux, Christine ; Vaslin, Bruno ; Sáez-Cirión, Asier ; Guedj, Jérémie ; Dixit, Narendra M. (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 PLoS Computational Biology, 20 (9). e1012434. ISSN 1553-734X

Vemparala, Bharadwaj ; Chowdhury, Shreya ; Guedj, Jérémie ; Dixit, Narendra M. (2024) Modelling HIV-1 control and remission npj Systems Biology and Applications, 10 (1). ISSN 2056-7189

Rajendra, Dharanish ; Maroli, Nikhil ; Dixit, Narendra M. ; Maiti, Prabal K. (2023) Molecular dynamics simulations show how antibodies may rescue HIV-1 mutants incapable of infecting host cells Journal of Biomolecular Structure and Dynamics, 43 (6). pp. 2982-2992. ISSN 0739-1102

Sankhe, Gaurav D. ; Raja, Rubesh ; Singh, Devendra Pratap ; Bheemireddy, Sneha ; Rana, Subinoy ; Athira, P. J. ; Dixit, Narendra M. ; Saini, Deepak Kumar (2023) Sequestration of histidine kinases by non-cognate response regulators establishes a threshold level of stimulation for bacterial two-component signaling Nature Communications, 14 (1). ISSN 2041-1723

Vemparala, Bharadwaj ; Valiya Parambathu, Arjun ; Saini, Deepak Kumar ; Dixit, Narendra M. (2022) An Evolutionary Paradigm Favoring Cross Talk between Bacterial Two-Component Signaling Systems mSystems, 7 (6). ISSN 2379-5077

Barnabas, Vinay ; Kashyap, Akanksha ; Raja, Rubesh ; Newar, Kapil ; Rai, Deepika ; Dixit, Narendra M. ; Mehra, Sarika (2022) The Extent of Antimicrobial Resistance Due to Efflux Pump Regulation ACS Infectious Diseases, 8 (11). pp. 2374-2388. ISSN 2373-8227

Chatterjee, Budhaditya ; Singh Sandhu, Harshbir ; Dixit, Narendra 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 Pathogens, 18 (6). e1010630. ISSN 1553-7374

James, Ananthu ; Dixit, Narendra M. (2022) Transmitted HIV-1 is more virulent in heterosexual individuals than men-who-have-sex-with-men PLoS Pathogens, 18 (3). e1010319. ISSN 1553-7374

Padmanabhan, Pranesh ; Desikan, Rajat ; Dixit, Narendra M. (2022) Modeling how antibody responses may determine the efficacy of COVID-19 vaccines Nature Computational Science, 2 (2). pp. 123-131. ISSN 2662-8457

Garg, Amar K. ; Mittal, Soumya ; Padmanabhan, Pranesh ; Desikan, Rajat ; Dixit, Narendra M. (2021) Increased B Cell Selection Stringency In Germinal Centers Can Explain Improved COVID-19 Vaccine Efficacies With Low Dose Prime or Delayed Boost Frontiers in Immunology, 12 . ISSN 1664-3224

Ansari, Aamir Faisal ; Reddy, Yugandhar B. S. ; Raut, Janhavi ; Dixit, Narendra M. (2021) An efficient and scalable top-down method for predicting structures of microbial communities Nature Computational Science, 1 (9). pp. 619-628. ISSN 2662-8457

Waturuocha, Uchenna Watson ; Krishna, M. S. ; Malhotra, Vandana ; Dixit, Narendra M. ; Saini, Deepak Kumar (2021) A Low-Prevalence Single-Nucleotide Polymorphism in the Sensor Kinase PhoR in Mycobacterium tuberculosis Suppresses Its Autophosphatase Activity and Reduces Pathogenic Fitness: Implications in Evolutionary Selection Frontiers in Microbiology, 12 . ISSN 1664-302X

Aggarwal, Abhishek ; Naskar, Supriyo ; Maroli, Nikhil ; Gorai, Biswajit ; Dixit, Narendra M. ; Maiti, Prabal K. (2021) Mechanistic insights into the effects of key mutations on SARS-CoV-2 RBD–ACE2 binding Physical Chemistry Chemical Physics, 23 (46). pp. 26451-26458. ISSN 1463-9076

Padmanabhan, Pranesh ; Desikan, Rajat ; Dixit, Narendra Madhukar (2020) Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection PLoS Computational Biology, 16 (12). e1008461. ISSN 1553-734X

Saha, Ananya ; Dixit, Narendra M. (2020) Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection PLoS Computational Biology, 16 (11). e1008434. ISSN 1553-734X

Desikan, Rajat ; Raja, Rubesh ; Dixit, Narendra 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. ISSN 1553-734X

Padmanabhan, Pranesh ; Raja, Rubesh ; Dixit, Narendra M. (2020) Bistability in virus–host interaction networks underlies the success of hepatitis C treatments Phenotypic Switching . pp. 131-156.

Ansari, Aamir Faisal ; Acharya, Nagaraja I. S. ; Kumaran, Srikala ; Ravindra, Keerthana ; Reddy, Yugandhar B. S. ; Dixit, Narendra M. ; Raut, Janhavi (2019) 110th Anniversary: High-Order Interactions Can Eclipse Pairwise Interactions in Shaping the Structure of Microbial Communities Industrial & Engineering Chemistry Research, 58 (51). pp. 23508-23518. ISSN 0888-5885

Baral, Subhasish ; Antia, Rustom ; Dixit, Narendra M. (2019) A dynamical motif comprising the interactions between antigens and CD8 T cells may underlie the outcomes of viral infections Proceedings of the National Academy of Sciences of the United States of America, 116 (35). pp. 17393-17398. ISSN 0027-8424

Dave, Pratik ; George, Biju ; Balakrishnan, Sreenath ; Sharma, Divya Khandige ; Raheja, Harsha ; Dixit, Narendra M. ; Das, Saumitra (2019) Strand-specific affinity of host factor hnRNP C1/C2 guides positive to negative-strand ratio in Coxsackievirus B3 infection RNA Biology, 16 (9). pp. 1286-1299. ISSN 1547-6286

Raja, Rubesh ; Pareek, Aditya ; Newar, Kapil ; Dixit, Narendra M. (2019) Mutational pathway maps and founder effects define the within-host spectrum of hepatitis C virus mutants resistant to drugs PLoS Pathogens, 15 (4). e1007701. ISSN 1553-7374

Raja, Rubesh ; Pareek, Aditya ; Newar, Kapil ; Dixit, Narendra M. (2019) Mutational pathway maps and founder effects define the within-host spectrum of hepatitis C virus mutants resistant to drugs PLoS Pathogens, 15 (4). e1007701. ISSN 1553-7374

Venugopal, Vishnu ; Padmanabhan, Pranesh ; Raja, Rubesh ; Dixit, Narendra M. (2018) Modelling how responsiveness to interferon improves interferon-free treatment of hepatitis C virus infection PLoS Computational Biology, 14 (7). e1006335. ISSN 1553-734X

Sankhe, Gaurav D. ; Dixit, Narendra M. ; Saini, Deepak K. (2018) Activation of Bacterial Histidine Kinases: Insights into the Kinetics of the cis Autophosphorylation Mechanism mSphere, 3 (3). ISSN 2379-5042

Baral, Subhasish ; Roy, Rahul ; Dixit, Narendra M (2018) Modeling how reversal of immune exhaustion elicits cure of chronic hepatitis C after the end of treatment with direct‐acting antiviral agents Immunology and Cell Biology, 96 (9). pp. 969-980. ISSN 0818-9641

Gupta, Vipul ; Dixit, Narendra M. (2018) Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents PLoS Computational Biology, 14 (2). e1006004. ISSN 1553-734X

Shet, Anita ; Nagaraja, Pradeep ; Dixit, Narendra M. (2016) Viral Decay Dynamics and Mathematical Modeling of Treatment Response: Evidence of Lower in vivo Fitness of HIV-1 Subtype C JAIDS Journal of Acquired Immune Deficiency Syndromes, 73 (3). pp. 245-251. ISSN 1525-4135

Padmanabhan, P ; Dixit, NM (2015) Modeling Suggests a Mechanism of Synergy Between Hepatitis C Virus Entry Inhibitors and Drugs of Other Classes CPT: Pharmacometrics & Systems Pharmacology, 4 (8). pp. 445-453. ISSN 2163-8306

Agrawal, Ruchi ; Pandey, Akancha ; Rajankar, Mayooreshwar P. ; Dixit, Narendra M. ; Saini, Deepak K. (2015) The two-component signalling networks of Mycobacterium tuberculosis display extensive cross-talk in vitro Biochemical Journal, 469 (1). pp. 121-134. ISSN 0264-6021

Padmanabhan, Pranesh ; Garaigorta, Urtzi ; Dixit, Narendra M. (2014) Emergent properties of the interferon-signalling network may underlie the success of hepatitis C treatment Nature Communications, 5 (1). ISSN 2041-1723

Krishnan, Sheeja M ; Dixit, Narendra M (2012) A Formula to Estimate the Optimal Dosage of Ribavirin for the Treatment of Chronic Hepatitis C: Influence of Itpa Polymorphisms Antiviral Therapy, 17 (8). pp. 1581-1592. ISSN 1359-6535

Dixit, Narendra M. ; Srivastava, Piyush ; Vishnoi, Nisheeth K. (2012) A Finite Population Model of Molecular Evolution: Theory and Computation Journal of Computational Biology, 19 (10). pp. 1176-1202. ISSN 1066-5277

Tripathi, Kushal ; Balagam, Rajesh ; Vishnoi, Nisheeth K. ; Dixit, Narendra M. (2012) Stochastic Simulations Suggest that HIV-1 Survives Close to Its Error Threshold PLoS Computational Biology, 8 (9). e1002684. ISSN 1553-734X

Padmanabhan, Pranesh ; Dixit, Narendra M. (2012) Viral Kinetics Suggests a Reconciliation of the Disparate Observations of the Modulation of Claudin-1 Expression on Cells Exposed to Hepatitis C Virus PLoS One, 7 (4). e36107. ISSN 1932-6203

Padmanabhan, Pranesh ; Dixit, Narendra M. (2011) Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry PLoS Computational Biology, 7 (12). e1002307. ISSN 1553-734X

Mulampaka, Shiva Naresh ; Dixit, Narendra M. (2011) Estimating the Threshold Surface Density of Gp120-CCR5 Complexes Necessary for HIV-1 Envelope-Mediated Cell-Cell Fusion PLoS One, 6 (5). e19941. ISSN 1932-6203

Krishnan, Sheeja M. ; Dixit, Narendra M. (2011) Ribavirin-Induced Anemia in Hepatitis C Virus Patients Undergoing Combination Therapy PLoS Computational Biology, 7 (2). e1001072. ISSN 1553-734X

Balagam, Rajesh ; Singh, Vasantika ; Sagi, Aparna Raju ; Dixit, Narendra M. (2011) Taking Multiple Infections of Cells and Recombination into Account Leads to Small Within-Host Effective-Population-Size Estimates of HIV-1 PLoS One, 6 (1). e14531. ISSN 1932-6203

Gadhamsetty, Saikrishna ; Dixit, Narendra M. (2010) Estimating Frequencies of Minority Nevirapine-Resistant Strains in Chronically HIV-1-Infected Individuals Naïve to Nevirapine by Using Stochastic Simulations and a Mathematical Model Journal of Virology, 84 (19). pp. 10230-10240. ISSN 0022-538X

Arora, Pankhuri ; Dixit, Narendra M. (2009) Timing the Emergence of Resistance to Anti-HIV Drugs with Large Genetic Barriers PLoS Computational Biology, 5 (3). e1000305. ISSN 1553-734X

Dixit, Narendra M (2008) Modeling HIV Infection Dynamics: The Role of Recombination in the Development of Drug Resistance Future HIV Therapy, 2 (4). pp. 375-388. ISSN 1746-9600

Mohanty, Utkala ; Dixit, Narendra M. (2008) Mechanism-based model of the pharmacokinetics of enfuvirtide, an HIV fusion inhibitor Journal of Theoretical Biology, 251 (3). pp. 541-551. ISSN 0022-5193

Suryavanshi, Gajendra W ; Dixit, Narendra M (2007) Emergence of Recombinant Forms of HIV: Dynamics and Scaling PLoS Computational Biology, 3 (10). e205. ISSN 1553-734X

Boyd, Mark A. ; Dixit, Narendra M. ; Siangphoe, Umaporn ; Buss, Neil E. ; Salgo, Miklos P. ; Lange, Joep M. A. ; Phanuphak, Praphan ; Cooper, David A. ; Perelson, Alan S. ; Ruxrungtham, Kiat (2006) Viral Decay Dynamics in HIV‐Infected Patients Receiving Ritonavir‐Boosted Saquinavir and Efavirenz With or Without Enfuvirtide: A Randomized, Controlled Trial (HIV‐NAT 012) The Journal of Infectious Diseases, 194 (9). pp. 1319-1322. ISSN 0022-1899

Dixit, N. M. ; Perelson, A. S. (2006) The metabolism, pharmacokinetics and mechanisms of antiviral activity of ribavirin against hepatitis C virus Cellular and Molecular Life Sciences, 63 (7-8). pp. 832-842. ISSN 1420-682X

Dixit, Narendra M. ; Perelson, Alan S. (2005) HIV dynamics with multiple infections of target cells Proceedings of the National Academy of Sciences of the United States of America, 102 (23). pp. 8198-8203. ISSN 0027-8424

Ribeiro, Ruy M. ; Dixit, Narendra M. ; Perelson, Alan S. (2005) 13 Modelling the in vivo growth rate of HIV: implications for vaccination Studies in Multidisciplinarity . pp. 231-246. ISSN 1571-0831

Dixit, Narendra M. ; Perelson, Alan S. (2004) Multiplicity of Human Immunodeficiency Virus Infections in Lymphoid Tissue Journal of Virology, 78 (16). pp. 8942-8945. ISSN 0022-538X

Dixit, Narendra M ; Markowitz, Martin ; Ho, David D ; Perelson, Alan S (2004) Estimates of Intracellular Delay and Average Drug Efficacy from Viral Load Data of HIV-Infected Individuals under Antiretroviral Therapy Antiviral Therapy, 9 (2). pp. 237-246. ISSN 1359-6535

Dixit, Narendra M. ; Perelson, Alan S. (2004) Complex patterns of viral load decay under antiretroviral therapy: influence of pharmacokinetics and intracellular delay Journal of Theoretical Biology, 226 (1). pp. 95-109. ISSN 0022-5193

Dixit, Narendra M. ; Zukoski, Charles F. (2003) Competition between crystallization and gelation: A local description Physical Review E - Statistical, Nonlinear and Soft Matter Physics, 67 (6). ISSN 1539-3755

Dixit, Narendra M ; Zukoski, Charles F (2003) Pseudo-steady rates of crystal nucleation in suspensions of charged colloidal particles Journal of Physics: Condensed Matter, 15 (10). pp. 1531-1552. ISSN 0953-8984

Zukoski, C.F. ; Kulkarni, A.M. ; Dixit, N.M. (2003) Response to: On methods of determination of homogeneous nucleation rates of protein crystals Colloids and Surfaces A: Physicochemical and Engineering Aspects, 215 (1-3). pp. 137-140. ISSN 0927-7757

Kulkarni, Amit M. ; Dixit, Narendra M. ; Zukoski, Charles F. (2002) Ergodic and non-ergodic phase transitions in globular protein suspensions Faraday Discussions, 123 . pp. 37-50. ISSN 1359-6640

Dixit, Narendra M. ; Zukoski, Charles F. (2002) Nucleation rates and induction times during colloidal crystallization: Links between models and experiments Physical Review E - Statistical, Nonlinear and Soft Matter Physics, 66 (5). ISSN 1539-3755

Dixit, Narendra M. ; Zukoski, Charles F. (2001) Kinetics of crystallization in hard-sphere colloidal suspensions Physical Review E - Statistical, Nonlinear and Soft Matter Physics, 64 (4). ISSN 1539-3755

Dixit, Narendra M. ; Kulkarni, Amit M. ; Zukoski, Charles F. (2001) Comparison of experimental estimates and model predictions of protein crystal nucleation rates Colloids and Surfaces A: Physicochemical and Engineering Aspects, 190 (1-2). pp. 47-60. ISSN 0927-7757

Dixit, Narendra M. ; Zukoski, Charles F. (2000) Crystal Nucleation Rates for Particles Experiencing Short-Range Attractions: Applications to Proteins Journal of Colloid and Interface Science, 228 (2). pp. 359-371. ISSN 0021-9797