Papers

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

⁼ equal contributions
^c co-corresponding authors

2024

popDMS infers mutation effects from deep mutational scanning data
Hong Z⁼, Shimagaki KS⁼, Barton JP
Bioinformatics [journal link] [pdf] [si] [code]

Correlated allele frequency changes reveal clonal structure and selection in temporal genetic data
Li Y, Barton JP
Molecular Biology and Evolution [journal link] [pdf] [si] [code]

2023

An inference model gives insights into innate immune adaptation and repertoire diversity
Qin Y, Mace EM, Barton JP
Proceedings of the National Academy of Sciences [journal link] [pdf] [si] [code]

Small RNA sequencing of field Culex mosquitoes identifies patterns of viral infection and the mosquito immune response
Abel SM, Hong Z, Williams D, Ireri S, Brown MQ, Su T, Hung KY, Henke JA, Barton JP, Le Roch KG
Scientific reports [journal link] [pdf]

Estimating linkage disequilibrium and selection from allele frequency trajectories
Li Y, Barton JP
Genetics [journal link] [pdf] [si] [code]

Bezier interpolation improves the inference of dynamical models from data
Shimagaki K, Barton JP
Physical Review E [journal link] [pdf] [si] [code]

2022

Inferring epistasis from genetic time-series data
Sohail MS, Louie RH, Hong Z, Barton JP^c, McKay MR^c
Molecular Biology and Evolution [journal link] [pdf] [si]

Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data
Lee B, Sohail MS, Finney E, Ahmed SF, Quadeer AA, McKay MR, Barton JP
medRxiv [journal link] [pdf] [code]

2021

Pathogenesis, symptomatology, and transmission of SARS-CoV-2 through analysis of viral genomics and structure
Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L
Msystems [journal link] [pdf]

SARS-CoV-2 and COVID-19: An evolving review of diagnostics and therapeutics
Rando HM, Greene CS, Robson MP, Boca SM, Wellhausen N, Lordan R, Brueffer C, Ray S, Lucy D, McGowan A
Manubot [journal link]

Dietary supplements and nutraceuticals under investigation for COVID-19 prevention and treatment
Lordan R, Rando HM, Greene CS
Msystems [journal link] [pdf]

MPL resolves genetic linkage in fitness inference from complex evolutionary histories
Sohail MS⁼, Louie RH⁼, McKay MR^c, Barton JP^c
Nature Biotechnology [journal link] [pdf] [si] [code]

Studying viral populations with tools from quantum spin chains
Shivam S, Baldwin CL, Barton J, Kardar M, Sondhi S
Journal of Statistical Physics [journal link] [pdf]

Adenovirus-vectored vaccine containing multidimensionally conserved parts of the HIV proteome is immunogenic in rhesus macaques
Murakowski DK, Barton JP, Peter L, Chandrashekar A, Bondzie E, Gao A, Barouch DH, Chakraborty AK
Proceedings of the National Academy of Sciences [journal link] [pdf] [si]

2020

Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease
Zhang T, Dai L, Barton JP, Du Y, Tan Y, Pang W, Chakraborty AK, Lloyd-Smith JO, Sun R
PLoS Genetics [journal link] [pdf]

Cross-serotypically conserved epitope recommendations for a universal T cell-based dengue vaccine
Ahmed SF, Quadeer AA^c, Barton JP^c, McKay MR^c
PLoS Neglected Tropical Diseases [journal link] [pdf] [code]

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 JP, 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]

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 [journal link] [pdf] [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]

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 [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]

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 [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]

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 [journal link] [pdf] [si]

ACE: adaptive cluster expansion for maximum entropy graphical model inference
Barton JP^c, De Leonardis E, Coucke A, Cocco S^c
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]

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 [journal link] [pdf] [si]

2014

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]

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 [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 J^c, Cocco S^c
Journal of Statistical Mechanics: Theory and Experiment [journal link] [pdf]

2011

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]