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John P Barton - Publications

Affiliations: 
Physics and Astronomy University of California, Riverside, Riverside, CA, United States 
Website:
https://profiles.ucr.edu/app/home/profile/johnpb
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Murakowski DK, Barton JP, Peter L, Chandrashekar A, Bondzie E, Gao A, Barouch DH, Chakraborty AK. Adenovirus-vectored vaccine containing multidimensionally conserved parts of the HIV proteome is immunogenic in rhesus macaques. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33514660 DOI: 10.1073/pnas.2022496118  0.572
2020 Zhang TH, Dai L, Barton JP, Du Y, Tan Y, Pang W, Chakraborty AK, Lloyd-Smith JO, Sun R. Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease. Plos Genetics. 16: e1009009. PMID 33085662 DOI: 10.1371/journal.pgen.1009009  0.512
2020 Ahmed SF, Quadeer AA, Barton JP, McKay MR. Cross-serotypically conserved epitope recommendations for a universal T cell-based dengue vaccine. Plos Neglected Tropical Diseases. 14: e0008676. PMID 32956362 DOI: 10.1371/Journal.Pntd.0008676  0.345
2020 Quadeer AA, Barton JP, Chakraborty AK, McKay MR. Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape. Nature Communications. 11: 377. PMID 31953427 DOI: 10.1038/S41467-019-14174-2  0.592
2019 Quadeer AA, McKay MR, Barton JP, Louie RHY. MPF-BML: A standalone GUI-based package for maximum entropy model inference. Bioinformatics (Oxford, England). PMID 31851308 DOI: 10.1093/Bioinformatics/Btz925  0.348
2019 Barton JP, Rajkoomar E, Mann JK, Murakowski DK, Toyoda M, Mahiti M, Mwimanzi P, Ueno T, Chakraborty AK, Ndung'u T. Modelling and testing of the HIV-1 Nef fitness landscape. Virus Evolution. 5: vez029. PMID 31392033 DOI: 10.1093/Ve/Vez029  0.599
2019 Vibholm LK, Lorenzi JCC, Pai JA, Cohen YZ, Oliveira TY, Barton JP, Noceda MG, Lu CL, Ablanedo-Terrazas Y, Del Rio Estrada PM, Reyes Teran G, Tolstrup M, Denton PW, Damsgaard T, Søgaard OS, et al. Characterization of intact proviruses in blood and lymph node from HIV-infected individuals undergoing analytical treatment interruption. Journal of Virology. PMID 30700598 DOI: 10.1128/Jvi.01920-18  0.342
2018 Lu CL, Pai JA, Nogueira L, Mendoza P, Gruell H, Oliveira TY, Barton J, Lorenzi JCC, Cohen YZ, Cohn LB, Klein F, Caskey M, Nussenzweig MC, Jankovic M. Relationship between intact HIV-1 proviruses in circulating CD4 T cells and rebound viruses emerging during treatment interruption. Proceedings of the National Academy of Sciences of the United States of America. PMID 30420517 DOI: 10.1073/Pnas.1813512115  0.4
2018 Cohen YZ, Lorenzi JCC, Krassnig L, Barton JP, Burke L, Pai J, Lu CL, Mendoza P, Oliveira TY, Sleckman C, Millard K, Butler AL, Dizon JP, Belblidia SA, Witmer-Pack M, et al. Relationship between latent and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117. The Journal of Experimental Medicine. PMID 30072495 DOI: 10.1084/Jem.20180936  0.397
2018 Ovchinnikov V, Louveau JE, Barton JP, Karplus M, Chakraborty AK. Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies. Elife. 7. PMID 29442996 DOI: 10.7554/Elife.33038  0.57
2018 Louie RHY, Kaczorowski KJ, Barton JP, Chakraborty AK, McKay MR. Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies. Proceedings of the National Academy of Sciences of the United States of America. PMID 29311326 DOI: 10.1073/Pnas.1717765115  0.618
2018 Ovchinnikov V, Louveau JE, Barton JP, Karplus M, Chakraborty AK. Author response: Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies Elife. DOI: 10.7554/Elife.33038.022  0.479
2017 Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Deconstruction of the Ras switching cycle through saturation mutagenesis. Elife. 6. PMID 28686159 DOI: 10.7554/Elife.27810  0.497
2017 Chakraborty AK, Barton J. Rational design of vaccine targets and strategies for HIV: a crossroad of statistical physics, biology, and medicine. Reports On Progress in Physics. Physical Society (Great Britain). PMID 28059778 DOI: 10.1088/1361-6633/Aa574A  0.498
2017 Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Author response: Deconstruction of the Ras switching cycle through saturation mutagenesis Elife. DOI: 10.7554/Elife.27810.040  0.421
2016 Lorenzi JC, Cohen YZ, Cohn LB, Kreider EF, Barton JP, Learn GH, Oliveira T, Lavine CL, Horwitz JA, Settler A, Jankovic M, Seaman MS, Chakraborty AK, Hahn BH, Caskey M, et al. Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA. Proceedings of the National Academy of Sciences of the United States of America. PMID 27872306 DOI: 10.1073/Pnas.1617789113  0.532
2016 Barton JP, Goonetilleke N, Butler TC, Walker BD, McMichael AJ, Chakraborty AK. Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable. Nature Communications. 7: 11660. PMID 27212475 DOI: 10.1038/Ncomms11660  0.571
2016 Butler TC, Barton JP, Kardar M, Chakraborty AK. Identification of drug resistance mutations in HIV from constraints on natural evolution. Physical Review. E. 93: 022412. PMID 26986367 DOI: 10.1103/Physreve.93.022412  0.579
2016 Butler TC, Barton JP, Kardar M, Chakraborty AK. Identification of drug resistance mutations in HIV from constraints on natural evolution Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 93. DOI: 10.1103/PhysRevE.93.022412  0.507
2016 Barton JP, Chakraborty AK, Cocco S, Jacquin H, Monasson R. On the Entropy of Protein Families Journal of Statistical Physics. 162: 1267-1293. DOI: 10.1007/S10955-015-1441-4  0.502
2015 Barton JP, Kardar M, Chakraborty AK. Scaling laws describe memories of host-pathogen riposte in the HIV population. Proceedings of the National Academy of Sciences of the United States of America. 112: 1965-70. PMID 25646424 DOI: 10.1073/Pnas.1415386112  0.589
2014 Mann JK, Barton JP, Ferguson AL, Omarjee S, Walker BD, Chakraborty A, Ndung'u T. The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing. Plos Computational Biology. 10: e1003776. PMID 25102049 DOI: 10.1371/Journal.Pcbi.1003776  0.592
2013 Shekhar K, Ruberman CF, Ferguson AL, Barton JP, Kardar M, Chakraborty AK. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 062705. PMID 24483484 DOI: 10.1103/Physreve.88.062705  0.598
2011 Barton J, Lebowitz JL, Speer ER. The grand canonical ABC model: A reflection asymmetric mean-field Potts model Journal of Physics a: Mathematical and Theoretical. 44. DOI: 10.1088/1751-8113/44/6/065005  0.436
2011 Barton J, Lebowitz JL, Speer ER. Phase Diagram of a Generalized ABC Model on the Interval Journal of Statistical Physics. 145: 763-784. DOI: 10.1007/S10955-011-0279-7  0.416
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