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Items: 38

1.

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 Evol. 2019 Aug 5;5(2):vez029. doi: 10.1093/ve/vez029. eCollection 2019 Jul.

2.

Characterization of Intact Proviruses in Blood and Lymph Node from HIV-Infected Individuals Undergoing Analytical Treatment Interruption.

Vibholm LK, Lorenzi JCC, Pai JA, Cohen YZ, Oliveira TY, Barton JP, Garcia Noceda M, Lu CL, Ablanedo-Terrazas Y, Del Rio Estrada PM, Reyes-Teran G, Tolstrup M, Denton PW, Damsgaard T, S√łgaard OS, Nussenzweig MC.

J Virol. 2019 Apr 3;93(8). pii: e01920-18. doi: 10.1128/JVI.01920-18. Print 2019 Apr 15.

3.

Relationship between latent and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117.

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, Shimeliovich I, Gulick RM, Seaman MS, Jankovic M, Caskey M, Nussenzweig MC.

J Exp Med. 2018 Sep 3;215(9):2311-2324. doi: 10.1084/jem.20180936. Epub 2018 Aug 2.

4.

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. 2018 Feb 14;7. pii: e33038. doi: 10.7554/eLife.33038.

5.

Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies.

Louie RHY, Kaczorowski KJ, Barton JP, Chakraborty AK, McKay MR.

Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):E564-E573. doi: 10.1073/pnas.1717765115. Epub 2018 Jan 8.

6.

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. 2017 Jul 7;6. pii: e27810. doi: 10.7554/eLife.27810.

7.

Rational design of vaccine targets and strategies for HIV: a crossroad of statistical physics, biology, and medicine.

Chakraborty AK, Barton JP.

Rep Prog Phys. 2017 Mar;80(3):032601. doi: 10.1088/1361-6633/aa574a. Epub 2017 Jan 6. Review.

PMID:
28059778
8.

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.

Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):E7908-E7916. Epub 2016 Nov 21. Erratum in: Proc Natl Acad Sci U S A. 2017 Jan 17;:.

9.

ACE: adaptive cluster expansion for maximum entropy graphical model inference.

Barton JP, De Leonardis E, Coucke A, Cocco S.

Bioinformatics. 2016 Oct 15;32(20):3089-3097. Epub 2016 Jun 21.

PMID:
27329863
10.

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.

Nat Commun. 2016 May 23;7:11660. doi: 10.1038/ncomms11660.

11.

Identification of drug resistance mutations in HIV from constraints on natural evolution.

Butler TC, Barton JP, Kardar M, Chakraborty AK.

Phys Rev E. 2016 Feb;93(2):022412. doi: 10.1103/PhysRevE.93.022412. Epub 2016 Feb 19.

PMID:
26986367
12.

Scaling laws describe memories of host-pathogen riposte in the HIV population.

Barton JP, Kardar M, Chakraborty AK.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):1965-70. doi: 10.1073/pnas.1415386112. Epub 2015 Feb 2.

13.

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.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jul;90(1):012132. Epub 2014 Jul 28.

PMID:
25122276
14.

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 Comput Biol. 2014 Aug 7;10(8):e1003776. doi: 10.1371/journal.pcbi.1003776. eCollection 2014 Aug.

15.

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.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Dec;88(6):062705. Epub 2013 Dec 4.

16.

The energy costs of insulators in biochemical networks.

Barton JP, Sontag ED.

Biophys J. 2013 Mar 19;104(6):1380-90. doi: 10.1016/j.bpj.2013.01.056. Epub 2013 Mar 19.

17.

Actual focal length of a symmetric biconvex microlens and its application in determining the transmitted beam waist position.

Wang J, Barton JP.

Appl Opt. 2010 Oct 20;49(30):5828-36. doi: 10.1364/AO.49.005828.

PMID:
20962947
18.
20.

Excitation localization principle for spherical microcavities.

Lin HB, Eversole JD, Campillo AJ, Barton JP.

Opt Lett. 1998 Dec 15;23(24):1921-3.

PMID:
18091956
21.
22.

Electromagnetic field for a focused light sheet incident on a plane surface.

Barton JP.

J Opt Soc Am A Opt Image Sci Vis. 2005 May;22(5):978-83.

PMID:
15898558
23.

Near-field calculations for a rigid spheroid with an arbitrary incident acoustic field.

Barton JP, Wolff NL, Zhang H, Tarawneh C.

J Acoust Soc Am. 2003 Mar;113(3):1216-22.

PMID:
12656356
24.
25.

Electromagnetic fields for a spheroidal particle with an arbitrary embedded source.

Barton JP.

J Opt Soc Am A Opt Image Sci Vis. 2000 Mar;17(3):458-64.

PMID:
10708026
28.

Electromagnetic-field calculations for irregularly shaped, axisymmetric layered particles with focused illumination.

Barton JP.

Appl Opt. 1996 Jan 20;35(3):532-41. doi: 10.1364/AO.35.000532.

PMID:
21069037
29.

Internal and near-surface electromagnetic fields for an absorbing spheroidal particle with arbitrary illumination.

Barton JP.

Appl Opt. 1995 Dec 20;34(36):8472-3. doi: 10.1364/AO.34.008472.

PMID:
21068967
30.

Internal and near-surface electromagnetic fields for a spheroidal particle with arbitrary illumination.

Barton JP.

Appl Opt. 1995 Aug 20;34(24):5542-51. doi: 10.1364/AO.34.005542.

PMID:
21060377
31.

Theoretical analysis of the effects of particle trajectory and structural resonances on the performance of a phase-Doppler particle analyzer.

Schaub SA, Alexander DR, Barton JP.

Appl Opt. 1994 Jan 20;33(3):473-83. doi: 10.1364/AO.33.000473.

PMID:
20862039
32.

Theoretical model of the laser imaging of small aerosols: applications to aerosol sizing.

Schaub SA, Alexander DR, Barton JP.

Appl Opt. 1991 Nov 20;30(33):4777-84. doi: 10.1364/AO.30.004777.

PMID:
20717280
33.

Electromagnetic field for a beam incident on two adjacent spherical particles.

Barton JP, Ma W, Schaub SA, Alexander DR.

Appl Opt. 1991 Nov 20;30(33):4706-15. doi: 10.1364/AO.30.004706.

PMID:
20717273
34.

Nonlinear interaction of KrF laser radiation with small water droplets.

Alexander DR, Barton JP, Schaub SA, Holtmejer GM.

Appl Opt. 1991 Apr 20;30(12):1455-60. doi: 10.1364/AO.30.001455.

PMID:
20700304
35.

Scattering of incident KrF laser radiation resulting from the laser-induced breakdown of H(2)O droplets.

Alexander DR, Schaub SA, Zhang J, Poulain DE, Barton JP.

Opt Lett. 1989 Jun 1;14(11):548-50.

PMID:
19752892
36.

Focused laser beam interactions with methanol droplets: effects of relative beam diameter.

Schaub SA, Alexander DR, Barton JP, Emanuel MA.

Appl Opt. 1989 May 1;28(9):1666-9. doi: 10.1364/AO.28.001666.

PMID:
20548723
37.

RADIOGRAPHY WITH RESONANCE ENERGY NEUTRONS.

BARTON JP.

Phys Med Biol. 1965 Apr;10:209-12. No abstract available.

PMID:
14332802
38.

SOME POSSIBILITIES OF NEUTRON RADIOGRAPHY.

BARTON JP.

Phys Med Biol. 1964 Jan;9:33-42. No abstract available.

PMID:
14108130

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