Items where Author is "Dixit, Narendra M."

Article

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

Gorai, Biswajit ; Sahoo, Anil Kumar ; Srivastava, Anand ; Dixit, Narendra M. ; Maiti, Prabal K. (2021) Concerted Interactions between Multiple gp41 Trimers and the Target Cell Lipidome May Be Required for HIV-1 Entry Journal of Chemical Information and Modeling, 61 (1). pp. 444-454. ISSN 1549-9596

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

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

Agrawal, Shubhada ; Bhandari, Siddharth ; Bhattacharjee, Anirban ; Deo, Anand ; Dixit, Narendra M. ; Harsha, Prahladh ; Juneja, Sandeep ; Kesarwani, Poonam ; Swamy, Aditya Krishna ; Patil, Preetam ; Rathod, Nihesh ; Saptharishi, Ramprasad ; Shriram, Sharad ; Srivastava, Piyush ; Sundaresan, Rajesh ; Vaidhiyan, Nidhin Koshy ; Yasodharan, Sarath (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, 100 (4). pp. 809-847. ISSN 0970-4140

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

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

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

Nandy, Bidisha ; Saurabh, Suman ; Sahoo, Anil Kumar ; Dixit, Narendra M. ; Maiti, Prabal K. (2015) The SPL7013 dendrimer destabilizes the HIV-1 gp120–CD4 complex Nanoscale, 7 (44). pp. 18628-18641. ISSN 2040-3364

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

Nandy, Bidisha ; Hima Bindu, D. ; Dixit, Narendra M. ; Maiti, Prabal K. (2013) Simulations reveal that the HIV-1 gp120-CD4 complex dissociates via complex pathways and is a potential target of the polyamidoamine (PAMAM) dendrimer Journal of Chemical Physics, 139 (2). Article ID 024905. ISSN 0021-9606

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

Eswarappa, Sandeepa M. ; Janice, Jessin ; Balasundaram, Sudhagar V. ; Dixit, Narendra M. ; Chakravortty, Dipshikha (2009) Host-specificity of Salmonella enterica serovar Gallinarum: Insights from comparative genomics Infection, Genetics and Evolution, 9 (4). pp. 468-473. ISSN 1567-1348

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

Ahmed, Niyaz ; Eswarappa, Sandeepa M. ; Janice, Jessin ; Nagarajan, Arvindhan G. ; Balasundaram, Sudhagar V. ; Karnam, Guruswamy ; Dixit, Narendra M. ; Chakravortty, Dipshikha (2008) Differentially Evolved Genes of Salmonella Pathogenicity Islands: Insights into the Mechanism of Host Specificity in Salmonella PLoS One, 3 (12). e3829. ISSN 1932-6203

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. ; Layden-Almer, Jennifer E. ; Layden, Thomas J. ; Perelson, Alan S. (2004) Modelling how ribavirin improves interferon response rates in hepatitis C virus infection Nature, 432 (7019). pp. 922-924. ISSN 0028-0836

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. ; 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

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