John P Barton

john.barton@ucr.edu
bartonlab.ucr.edu

Employment

Assistant Professor
2018 -
Department of Physics and Astronomy
University of California, Riverside
Postdoctoral Fellow
2012 - 2017
Massachusetts Institute of Technology
Ragon Institute of MGH, MIT & Harvard
Adviser: Arup K Chakraborty

Education

PhD, Physics
2006 - 2012
Rutgers, The State University of New Jersey
Adviser: Joel L Lebowitz
BS, Physics & Mathematics
2002 - 2006
Duke University
Magna cum laude
Honors thesis adviser: M Ronen Plesser

Research Interests

I use methods from statistical mechanics and machine learning to study pathogen evolution and human immunity. I am particularly interested in highly mutable pathogens such as HIV, and the dynamical interactions between microbes and the immune system.

Publications

= equal contributions, c co-corresponding authors
2020
MPF-BML: a standalone GUI-based package for maximum entropy model inference
Quadeer AA, McKay MR, Barton JP, Louie RH
Bioinformatics 36 (7): 2278-2279
Inference of compressed Potts graphical models
Rizzato F, Coucke A, de Leonardis E, Barton JPc, Tubiana J, Monasson R, Cocco S
Physical Review E 101 (1): 12309
Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape
Quadeer AA, Barton JP, Chakraborty AK, McKay MR
Nature Communications 11 (1): 13-Jan
2019
Modelling and in vitro testing of the HIV-1 Nef fitness landscape
Barton JP=, Rajkoomar E=, Mann JK, Murakowski DK, Toyoda M, Mahiti M, Mwimanzi P, Ueno T, Chakraborty AK, Ndung'u T
Virus Evolution 5 (2): vez029
Resolving genetic linkage reveals patterns of selection in HIV-1 evolution
Sohail MS=, Louie RH=, McKay MRc, Barton JPc
bioRxiv 711861
Characterization of intact proviruses in blood and lymph node from HIV-infected individuals undergoing analytical treatment interruption
Vibholm LK, Lorenzi JC, Pai JA, Cohen YZ, Oliveira TY, Barton JP, Garcia Noceda M, Lu C, Ablanedo-Terrazas Y, Estrada PMDR, Teran GR, Tolstrup M, Denton PW, Damsgaard T, Sogaard OS, Nussenzweig MC
Journal of Virology 93 (8): e01920-18
2018
Relationship between intact HIV-1 proviruses in circulating CD4+ T cells and rebound viruses emerging during treatment interruption
Lu C, Pai JA, Nogueira L, Mendoza P, Gruell H, Oliveira TY, Barton J, Lorenzi JC, Cohen YZ, Cohn LB, Klein F, Caskey M, Nussenzweig MC, Jankovic M
Proceedings of the National Academy of Sciences 115 (48): E11341-E11348
Relationship between latent and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117
Cohen YZ, Lorenzi JC, Krassnig L, Barton JP, Burke L, Pai J, Lu C, Mendoza P, Oliveira TY, Sleckman C, Millard K, Butler AL, Dizon JP, Belblidia SA, Witmer-Pack M, Shimeliovich I, Gulick RM, Seaman MS, Jankovic M, Caskey M, Nussenzweig MC
Journal of Experimental Medicine 215 (9): 2311-2324
Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies
Ovchinnikov V=, Louveau JE=, Barton JP=, Karplus M, Chakraborty AK
eLife 7: e33038
Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies
Louie RH=, Kaczorowski KJ=, Barton JP, Chakraborty AK, McKay MR
Proceedings of the National Academy of Sciences 115 (4): E564-E573
2017
Deconstruction of the Ras switching cycle through saturation mutagenesis
Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J
eLife 6: e27810
Rational design of vaccine targets and strategies for HIV: a crossroad of statistical physics, biology, and medicine
Chakraborty AK, Barton JP
Reports on Progress in Physics 80 (3): 32601
2016
Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA
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, Nussenzweig MC
Proceedings of the National Academy of Sciences 113 (49): E7908-E7916
ACE: adaptive cluster expansion for maximum entropy graphical model inference
Barton JPc, De Leonardis E, Coucke A, Cocco Sc
Bioinformatics 32 (20): 3089-3097
Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable
Barton JP, Goonetilleke N, Butler TC, Walker BD, McMichael AJ, Chakraborty AK
Nature Communications 7: 11660
Identification of drug resistance mutations in HIV from constraints on natural evolution
Butler TC=, Barton JP=, Kardar M, Chakraborty AK
Physical Review E 93 (2): 22412
On the entropy of protein families
Barton JP, Chakraborty AK, Cocco S, Jacquin H, Monasson R
Journal of Statistical Physics 162 (5): 1267-1293
2015
Scaling laws describe memories of host-pathogen riposte in the HIV population
Barton JP, Kardar M, Chakraborty AK
Proceedings of the National Academy of Sciences 112 (7): 1965-1970
2014
The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing
Mann JK=, Barton JP=, Ferguson AL=, Omarjee S, Walker BD, Chakraborty A, Ndung'u T
PLoS Computational Biology 10 (8): e1003776
Large pseudocounts and L2-norm penalties are necessary for the mean-field inference of Ising and Potts models
Barton JP, Cocco S, De Leonardis E, Monasson R
Physical Review E 90 (1): 12132
2013
Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes
Shekhar K, Ruberman CF, Ferguson AL, Barton JP, Kardar M, Chakraborty AK
Physical Review E 88 (6): 62705
The energy costs of insulators in biochemical networks
Barton JP, Sontag ED
Biophysical Journal 104 (6): 1380-1390
Ising models for neural activity inferred via selective cluster expansion: structural and coding properties
Barton Jc, Cocco Sc
Journal of Statistical Mechanics: Theory and Experiment 2013 (3): P03002
2011
Phase diagram of a generalized ABC model on the interval
Barton J, Lebowitz JL, Speer ER
Journal of Statistical Physics 145 (3): 763-784
The grand canonical ABC model: a reflection asymmetric mean-field Potts model
Barton J, Lebowitz JL, Speer ER
Journal of Physics A: Mathematical and Theoretical 44 (6): 65005

Invited Talks

2018
Colloquium: Department of Biochemistry, University of California, Riverside
Statistical Modelling of Protein Sequences: From Fitness to Free Energy Landscapes and Back, Temple University
Colloquium: Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside
2017
Colloquium: Department of Physics, California State University, Fullerton
Covariance Analysis in Biology Workshop, Harvard Center of Mathematical Sciences and Applications
Department of Physics, University of California, Riverside
2016
116th Statistical Mechanics Conference, Rutgers University
Initiative for the Theoretical Sciences, CUNY (declined for family reasons)
Department of Microbiology, University of Pennsylvania School of Medicine
Coevolution in Proteins and RNA, Theory and Experiments Workshop, Institut d'Études Scientifiques de Cargèse
Keystone Systems Immunology Meeting (short talk selected from abstracts)
2015
Monday Meeting, Ragon Institute of MGH, MIT and Harvard
Systems Immunology Workshop, Cincinnati Children’s Hospital Medical Center
Mathematical Physics Seminar, Rutgers University
Keystone HIV Vaccines Meeting (short talk selected from abstracts)
Center for Biophysics and Computational Biology, Temple University
2014
Monday Meeting, Ragon Institute of MGH, MIT and Harvard
Institute for Advanced Study Focused Program on Computational and Experimental Immunology, Hong Kong University of Science and Technology
2013
Harvard Microbial Evolution Group, Harvard University
2012
Massachusetts Institute of Technology

Contributed Presentations

2018
SMBE Meeting
APS March Meeting
2016
Koch Institute Immune Engineering Symposium, MIT
Institute for Medical Engineering and Science Research Progress Meeting, MIT
APS March Meeting
2015
Forecasting Evolution Conference (short talk invitation declined)
APS March Meeting
Third Annual Winter Q-Bio Meeting
2014
112th Statistical Mechanics Conference, Rutgers University
MIT Biophysics Retreat
MIT-MGH Meeting on IBD, Microbiome and Autoimmune Disease
2013
First Annual Winter Q-Bio Meeting
2012
108th Statistical Mechanics Conference, Rutgers University
107th Statistical Mechanics Conference, Rutgers University
2011
106th Statistical Mechanics Conference, Rutgers University

Honors & Awards

eLife Early-Career Reviewer (2016)
Lindau Nobel Laureate Meeting Attendee, Siemens AG Fellow (2015)
MIT Postdoctoral Association Travel Grant (2014)
Rutgers University Departmental Graduate Assistantship (2010, 2012)
GAANN Graduate Fellowship, Rutgers University (declined)
Phi Beta Kappa, National honor society
Sigma Pi Sigma, National physics honor society
Phi Eta Sigma, National honor society
Georgia Regional STAR Student (2002)

Teaching Experience & Certification

Completed MIT Kaufman Teaching Certificate Program (2017)
Teaching assistant: Honors Physics III (Physics 273), Rutgers University (2011)
Teaching assistant: Extended General Physics (Physics 201/202), Rutgers University (2006 - 2010)
Teaching assistant: General Physics I-II (Physics 52L-54L), Duke University (2003)