Barton lab UCR Physics


See Google Scholar for the most recent and complete list of publications.

= equal contributions
c co-corresponding authors


MPF-BML: a standalone GUI-based package for maximum entropy model inference
Quadeer AA, McKay MR, Barton JP, Louie RH
Bioinformatics [journal link] [pdf] [si] [code]

Inference of compressed Potts graphical models
Rizzato F, Coucke A, de Leonardis E, Barton JPc, Tubiana J, Monasson R, Cocco S
Physical Review E [journal link] [pdf]

Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape
Quadeer AA, Barton JP, Chakraborty AK, McKay MR
Nature Communications [journal link] [pdf] [si]


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 [journal link] [pdf] [code]

Resolving genetic linkage reveals patterns of selection in HIV-1 evolution
Sohail MS=, Louie RH=, McKay MRc, Barton JPc
bioRxiv [journal link] [code]

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 [journal link] [pdf]


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 [journal link] [pdf] [si]

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 [journal link] [pdf] [si]

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 [journal link] [pdf] [code]

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 [journal link] [pdf] [si]


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 [journal link] [pdf]

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 [journal link] [pdf]


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 [journal link] [pdf] [si]

ACE: adaptive cluster expansion for maximum entropy graphical model inference
Barton JPc, De Leonardis E, Coucke A, Cocco Sc
Bioinformatics [journal link] [pdf] [si] [code]

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 [journal link] [pdf] [si]

Identification of drug resistance mutations in HIV from constraints on natural evolution
Butler TC=, Barton JP=, Kardar M, Chakraborty AK
Physical Review E [journal link] [pdf]

On the entropy of protein families
Barton JP, Chakraborty AK, Cocco S, Jacquin H, Monasson R
Journal of Statistical Physics [journal link] [pdf]


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 [journal link] [pdf] [si]


Remarks on the energy costs of insulators in enzymatic cascades
Barton JP, Sontag ED
arXiv [preprint] [pdf]

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 [journal link] [pdf] [si]

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 [journal link] [pdf]


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 [journal link] [pdf] [si]

The energy costs of insulators in biochemical networks
Barton JP, Sontag ED
Biophysical Journal [journal link] [pdf] [si]

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 [journal link] [pdf]


Phase diagram of a generalized ABC model on the interval
Barton J, Lebowitz JL, Speer ER
Journal of Statistical Physics [journal link] [pdf]

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 [journal link] [pdf]