John P Barton
John P Barton
Associate Professor, Department of Computational and Systems Biology, University of Pittsburgh
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Cited by
Cited by
Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA
JCC Lorenzi*, YZ Cohen*, LB Cohn, EF Kreider, JP Barton, GH Learn, ...
Proceedings of the National Academy of Sciences 113 (49), E7908–E7916, 2016
The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing
JK Mann*, JP Barton*, AL Ferguson*, S Omarjee, BD Walker, ...
PLoS Computational Biology 10 (8), e1003776, 2014
Deconstruction of the Ras switching cycle through saturation mutagenesis
P Bandaru, NH Shah, M Bhattacharyya, JP Barton, Y Kondo, JC Cofsky, ...
Elife 6, e27810, 2017
Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies
RHY Louie*, KJ Kaczorowski*, JP Barton, AK Chakraborty, MR McKay
Proceedings of the National Academy of Sciences, 201717765, 2018
Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable
JP Barton, N Goonetilleke, TC Butler, BD Walker, AJ McMichael, ...
Nature Communications 7, 11660, 2016
Relationship between latent and rebound viruses in a clinical trial of anti–HIV-1 antibody 3BNC117
YZ Cohen, JCC Lorenzi, L Krassnig, JP Barton, L Burke, J Pai, CL Lu, ...
Journal of Experimental Medicine 215 (9), 2311-2324, 2018
ACE: adaptive cluster expansion for maximum entropy graphical model inference
JP Barton†, E De Leonardis, A Coucke, S Cocco†
Bioinformatics 32 (20), 3089-3097, 2016
Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies
V Ovchinnikov*, JE Louveau*, JP Barton*, M Karplus, AK Chakraborty
eLife 7, e33038, 2018
Dietary supplements and nutraceuticals under investigation for COVID-19 prevention and treatment
R Lordan, HM Rando, CS Greene
Msystems 6 (3), 10.1128/msystems. 00122-21, 2021
Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes
K Shekhar, CF Ruberman, AL Ferguson, JP Barton, M Kardar, ...
Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 88 (6 …, 2013
Relationship between intact HIV-1 proviruses in circulating CD4+ T cells and rebound viruses emerging during treatment interruption
CL Lu, JA Pai, L Nogueira, P Mendoza, H Gruell, TY Oliveira, J Barton, ...
Proceedings of the National Academy of Sciences 115 (48), E11341-E11348, 2018
Characterization of intact proviruses in blood and lymph node from HIV-infected individuals undergoing analytical treatment interruption
LK Vibholm, JCC Lorenzi, JA Pai, YZ Cohen, TY Oliveira, JP Barton, ...
Journal of Virology 93 (8), 2019
Ising models for neural activity inferred via selective cluster expansion: structural and coding properties
J Barton, S Cocco
Journal of Statistical Mechanics: Theory and Experiment 2013 (03), P03002, 2013
Scaling laws describe memories of host–pathogen riposte in the HIV population
JP Barton, M Kardar, AK Chakraborty
Proceedings of the National Academy of Sciences 112 (7), 1965-1970, 2015
Large pseudocounts and L2-norm penalties are necessary for the mean-field inference of Ising and Potts models
JP Barton, S Cocco, E De Leonardis, R Monasson
Physical Review E 90 (1), 012132, 2014
Pathogenesis, symptomatology, and transmission of SARS-CoV-2 through analysis of viral genomics and structure
HM Rando, AL MacLean, AJ Lee, R Lordan, S Ray, V Bansal, AN Skelly, ...
MSystems 6 (5), 10.1128/msystems. 00095-21, 2021
Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape
AA Quadeer, JP Barton, AK Chakraborty, MR McKay
Nature communications 11 (1), 377, 2020
Identification of drug resistance mutations in HIV from constraints on natural evolution
TC Butler*, JP Barton*, M Kardar, AK Chakraborty
Physical Review E 93 (2), 022412, 2016
MPL resolves genetic linkage in fitness inference from complex evolutionary histories
MS Sohail, RHY Louie, MR McKay, JP Barton
Nature Biotechnology 39 (4), 472-479, 2021
The energy costs of insulators in biochemical networks
JP Barton, ED Sontag
Biophysical Journal 104 (6), 1380-1390, 2013
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