Scaling laws describe memories of host–pathogen riposte in the HIV population by Barton, John P., Kardar, Mehran, Chakraborty, Arup K.

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Large pseudocounts and L[subscript 2]-norm penalties are necessary for the mean-field inference of Ising and Potts models by Cocco, S., De Leonardis, E., Monasson, R., Barton, John P.

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Identification of drug resistance mutations in HIV from constraints on natural evolution by Barton, John P., Kardar, Mehran, Butler, Thomas Charles, Chakraborty, Arup K

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Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable by Barton, John P, Butler, Thomas Charles, Walker, Bruce, Chakraborty, Arup K

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On the Entropy of Protein Families by Cocco, Simona, Jacquin, Hugo, Monasson, Rémi, Chakraborty, Arup K, Barton, John P.

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Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape by Quadeer, Ahmed A, Barton, John P, Chakraborty, Arup K, McKay, Matthew R

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Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies by Karplus, Martin, Ovchinnikov, Victor A, Louveau, Joy E, Barton, John P, Chakraborty, Arup K

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Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes by Shekhar, Karthik, Ruberman, Claire, Ferguson, Andrew L., Kardar, Mehran, Barton, John P., Chakraborty, Arup K

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Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies by Louie, Raymond H. Y., Kaczorowski, Kevin John, Barton, John P, Chakraborty, Arup K, McKay, Matthew

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Adenovirus-vectored vaccine containing multidimensionally conserved parts of the HIV proteome is immunogenic in rhesus macaques by Murakowski, Dariusz K, Barton, John P, Peter, Lauren, Chandrashekar, Abishek, Bondzie, Esther, Gao, Ang, Barouch, Dan H, Chakraborty, Arup K

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The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing by Mann, Jaclyn K., Barton, John P., Ferguson, Andrew L., Omarjee, Saleha, Walker, Bruce D., Ndung'u, Thumbi, Chakraborty, Arup K

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Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease by Zhang, Tian-hao, Dai, Lei, Barton, John P, Du, Yushen, Tan, Yuxiang, Pang, Wenwen, Chakraborty, Arup K, Lloyd-Smith, James O, Sun, Ren

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Modelling and in vitro testing of the HIV-1 Nef fitness landscape by Barton, John P, Rajkoomar, Erasha, Mann, Jaclyn K, Murakowski, Dariusz K, Toyoda, Mako, Mahiti, Macdonald, Mwimanzi, Phillip, Ueno, Takamasa, Chakraborty, Arup K, Ndung’u, Thumbi

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Deconstruction of the Ras switching cycle through saturation mutagenesis by Bandaru, Pradeep, Shah, Neel H, Bhattacharyya, Moitrayee, Barton, John P, Kondo, Yasushi, Cofsky, Joshua C, Gee, Christine L, Chakraborty, Arup K, Kortemme, Tanja, Ranganathan, Rama, Kuriyan, John

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Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA by Lorenzi, Julio C. C., Cohen, Yehuda Z., Cohn, Lillian B., Kreider, Edward F., Learn, Gerald H., Oliveira, Thiago, Lavine, Christy L., Horwitz, Joshua A., Settler, Allison, Jankovic, Mila, Seaman, Michael S., Hahn, Beatrice H., Caskey, Marina, Nussenzweig, Michel C., Barton, John P, Chakraborty, Arup K

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