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Items: 1 to 50 of 348

1.

Utility of deep learning super-resolution in the context of osteoarthritis MRI biomarkers.

Chaudhari AS, Stevens KJ, Wood JP, Chakraborty AK, Gibbons EK, Fang Z, Desai AD, Lee JH, Gold GE, Hargreaves BA.

J Magn Reson Imaging. 2019 Jul 16. doi: 10.1002/jmri.26872. [Epub ahead of print]

PMID:
31313397
2.

Identification of a novel cluster of PCV2 isolates from Meghalaya, India indicates possible recombination along with changes in capsid protein.

Mukherjee P, Karam A, Chakraborty AK, Baruah S, Pegu R, Das S, Milton AAP, Puro K, Sanjukta R, Ghatak S, Shakuntala I, Laha RG, Sen A.

Infect Genet Evol. 2019 Jul;71:7-15. doi: 10.1016/j.meegid.2019.02.026. Epub 2019 Feb 23.

PMID:
30807843
3.

Evolution of weak cooperative interactions for biological specificity.

Gao A, Shrinivas K, Lepeudry P, Suzuki HI, Sharp PA, Chakraborty AK.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):E11053-E11060. doi: 10.1073/pnas.1815912115. Epub 2018 Nov 7.

4.

Hyperechoic Abdominal Fat: A Sentinel Sign of Inflammation.

Chakraborty AK, Olcott EW, Jeffrey BR.

Ultrasound Q. 2019 Jun;35(2):186-194. doi: 10.1097/RUQ.0000000000000387.

PMID:
30300322
5.

Evidence of BVDV in Pigs from North Eastern Part of India- Genetic Profiling and Characterisation.

Chakraborty AK, Mukherjee P, Karam A, Das S, Barkalita L, Puro K, Sanjukta R, Ghatak S, Sakuntala I, Laha RG, Borah P, Ngachan SV, Sharma I, Sen A.

Open Virol J. 2018 Aug 31;12:110-120. doi: 10.2174/1874357901812010110. eCollection 2018.

6.

The low spike density of HIV may have evolved because of the effects of T helper cell depletion on affinity maturation.

Amitai A, Chakraborty AK, Kardar M.

PLoS Comput Biol. 2018 Aug 30;14(8):e1006408. doi: 10.1371/journal.pcbi.1006408. eCollection 2018 Aug.

7.

Detail Photophysical Studies of Sulfonated Polyaniline in Aqueous Medium.

Khatun R, Majhi K, Meriga V, Chakraborty AK, Sinha S.

J Phys Chem A. 2018 Sep 6;122(35):7089-7098. doi: 10.1021/acs.jpca.8b06640. Epub 2018 Aug 23.

PMID:
30101586
8.

The central nervous system manifestations of localized craniofacial scleroderma: a study of 10 cases and literature review.

Maloney E, Menashe SJ, Iyer RS, Ringold S, Chakraborty AK, Ishak GE.

Pediatr Radiol. 2018 Oct;48(11):1642-1654. doi: 10.1007/s00247-018-4177-x. Epub 2018 Jul 3. Review.

PMID:
29971479
9.

Coactivator condensation at super-enhancers links phase separation and gene control.

Sabari BR, Dall'Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, Abraham BJ, Hannett NM, Zamudio AV, Manteiga JC, Li CH, Guo YE, Day DS, Schuijers J, Vasile E, Malik S, Hnisz D, Lee TI, Cisse II, Roeder RG, Sharp PA, Chakraborty AK, Young RA.

Science. 2018 Jul 27;361(6400). pii: eaar3958. doi: 10.1126/science.aar3958. Epub 2018 Jun 21.

10.

How nonuniform contact profiles of T cell receptors modulate thymic selection outcomes.

Chen H, Chakraborty AK, Kardar M.

Phys Rev E. 2018 Mar;97(3-1):032413. doi: 10.1103/PhysRevE.97.032413.

PMID:
29776088
11.

Amelioration of CCl4 induced liver injury in swiss albino mice by antioxidant rich leaf extract of Croton bonplandianus Baill.

Dutta S, Chakraborty AK, Dey P, Kar P, Guha P, Sen S, Kumar A, Sen A, Chaudhuri TK.

PLoS One. 2018 Apr 30;13(4):e0196411. doi: 10.1371/journal.pone.0196411. eCollection 2018.

12.

Detection of classical swine fever virus E2 gene in cattle serum samples from cattle herds of Meghalaya.

Chakraborty AK, Karam A, Mukherjee P, Barkalita L, Borah P, Das S, Sanjukta R, Puro K, Ghatak S, Shakuntala I, Sharma I, Laha RG, Sen A.

Virusdisease. 2018 Mar;29(1):89-95. doi: 10.1007/s13337-018-0433-9. Epub 2018 Feb 17.

13.

Seroprevalence of selected viral pathogens in pigs reared in organized farms of Meghalaya from 2014 to 16.

Mukherjee P, Karam A, Singh U, Chakraborty AK, Huidrom S, Sen A, Sharma I.

Vet World. 2018 Jan;11(1):42-47. doi: 10.14202/vetworld.2018.42-47. Epub 2018 Jan 20.

14.

Porcine circovirus 2 in the North Eastern region of India: Disease prevalence and genetic variation among the isolates from areas of intensive pig rearing.

Mukherjee P, Karam A, Barkalita L, Borah P, Chakraborty AK, Das S, Puro K, Sanjukta R, Ghatak S, Shakuntala I, Laha RG, Sen A, Sharma I.

Acta Trop. 2018 Jun;182:166-172. doi: 10.1016/j.actatropica.2018.02.025. Epub 2018 Feb 19.

PMID:
29470945
15.

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.

16.

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.

17.

A Population Dynamics Model for Clonal Diversity in a Germinal Center.

Amitai A, Mesin L, Victora GD, Kardar M, Chakraborty AK.

Front Microbiol. 2017 Sep 12;8:1693. doi: 10.3389/fmicb.2017.01693. eCollection 2017.

18.

Continuous immunotypes describe human immune variation and predict diverse responses.

Kaczorowski KJ, Shekhar K, Nkulikiyimfura D, Dekker CL, Maecker H, Davis MM, Chakraborty AK, Brodin P.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):E6097-E6106. doi: 10.1073/pnas.1705065114. Epub 2017 Jul 10.

19.

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.

20.

A Phase Separation Model for Transcriptional Control.

Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA.

Cell. 2017 Mar 23;169(1):13-23. doi: 10.1016/j.cell.2017.02.007. Review.

21.

A Perspective on the Role of Computational Models in Immunology.

Chakraborty AK.

Annu Rev Immunol. 2017 Apr 26;35:403-439. doi: 10.1146/annurev-immunol-041015-055325. Epub 2017 Feb 6. Review.

PMID:
28226229
22.

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
23.

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;:.

24.

Optimal immunization cocktails can promote induction of broadly neutralizing Abs against highly mutable pathogens.

Shaffer JS, Moore PL, Kardar M, Chakraborty AK.

Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):E7039-E7048. doi: 10.1073/pnas.1614940113. Epub 2016 Oct 24.

25.

Sustained antigen availability during germinal center initiation enhances antibody responses to vaccination.

Tam HH, Melo MB, Kang M, Pelet JM, Ruda VM, Foley MH, Hu JK, Kumari S, Crampton J, Baldeon AD, Sanders RW, Moore JP, Crotty S, Langer R, Anderson DG, Chakraborty AK, Irvine DJ.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):E6639-E6648. Epub 2016 Oct 4.

26.

Phosphorylation of a Tyrosine Residue on Zap70 by Lck and Its Subsequent Binding via an SH2 Domain May Be a Key Gatekeeper of T Cell Receptor Signaling In Vivo.

Thill PA, Weiss A, Chakraborty AK.

Mol Cell Biol. 2016 Aug 26;36(18):2396-402. doi: 10.1128/MCB.00165-16. Print 2016 Sep 15.

27.

Hydrophobic CDR3 residues promote the development of self-reactive T cells.

Stadinski BD, Shekhar K, Gómez-Touriño I, Jung J, Sasaki K, Sewell AK, Peakman M, Chakraborty AK, Huseby ES.

Nat Immunol. 2016 Aug;17(8):946-55. doi: 10.1038/ni.3491. Epub 2016 Jun 27.

28.

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.

29.

Enhanced clearance of HIV-1-infected cells by broadly neutralizing antibodies against HIV-1 in vivo.

Lu CL, Murakowski DK, Bournazos S, Schoofs T, Sarkar D, Halper-Stromberg A, Horwitz JA, Nogueira L, Golijanin J, Gazumyan A, Ravetch JV, Caskey M, Chakraborty AK, Nussenzweig MC.

Science. 2016 May 20;352(6288):1001-4. doi: 10.1126/science.aaf1279. Epub 2016 May 5.

30.

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
31.

An overview of physico-chemical mechanisms of biogas production by microbial communities: a step towards sustainable waste management.

Goswami R, Chattopadhyay P, Shome A, Banerjee SN, Chakraborty AK, Mathew AK, Chaudhury S.

3 Biotech. 2016 Jun;6(1):72. doi: 10.1007/s13205-016-0395-9. Epub 2016 Feb 16. Review.

32.

Affinity Inequality among Serum Antibodies That Originate in Lymphoid Germinal Centers.

Kang M, Eisen TJ, Eisen EA, Chakraborty AK, Eisen HN.

PLoS One. 2015 Oct 7;10(10):e0139222. doi: 10.1371/journal.pone.0139222. eCollection 2015.

33.

In vitro and in vivo studies of the combination of IGF1R inhibitor figitumumab (CP-751,871) with HER2 inhibitors trastuzumab and neratinib.

Chakraborty AK, Zerillo C, DiGiovanna MP.

Breast Cancer Res Treat. 2015 Aug;152(3):533-44. doi: 10.1007/s10549-015-3504-2. Epub 2015 Jul 21.

PMID:
26195122
34.

Theory, models and biology.

Shou W, Bergstrom CT, Chakraborty AK, Skinner FK.

Elife. 2015 Jul 14;4:e07158. doi: 10.7554/eLife.07158.

35.

The catalytic activity of the kinase ZAP-70 mediates basal signaling and negative feedback of the T cell receptor pathway.

Goodfellow HS, Frushicheva MP, Ji Q, Cheng DA, Kadlecek TA, Cantor AJ, Kuriyan J, Chakraborty AK, Salomon A, Weiss A.

Sci Signal. 2015 May 19;8(377):ra49. doi: 10.1126/scisignal.2005596.

36.

Complete genome sequence of emerging porcine circovirus types 2a and 2b from India.

Bhattacharjee U, Ahuja A, Sharma I, Karam A, Chakraborty AK, Ghatak S, Puro K, Das S, Shakuntala I, Giri S, Pegu RK, Laha R, Pattanayak A, Ngachan SV, Sen A.

Genome Announc. 2015 Mar 12;3(2). pii: e00087-15. doi: 10.1128/genomeA.00087-15.

37.

Co-targeting ER and HER family receptors induces apoptosis in HER2-normal or overexpressing breast cancer models.

Chakraborty AK, Mehra R, Digiovanna MP.

Anticancer Res. 2015 Mar;35(3):1243-50.

PMID:
25750271
38.

Herman N. Eisen, M.D. (1918-2014): Scholar, Gentleman, and AAI President (1968-1969).

Chakraborty AK, Unanue ER.

J Immunol. 2015 Mar 15;194(6):2451-2. doi: 10.4049/jimmunol.1590003. No abstract available.

39.

Herman Eisen (1918-2014).

Chakraborty AK, Unanue ER.

Immunity. 2014 Dec 18;41(6):869-70. No abstract available.

40.

Manipulating the selection forces during affinity maturation to generate cross-reactive HIV antibodies.

Wang S, Mata-Fink J, Kriegsman B, Hanson M, Irvine DJ, Eisen HN, Burton DR, Wittrup KD, Kardar M, Chakraborty AK.

Cell. 2015 Feb 12;160(4):785-797. doi: 10.1016/j.cell.2015.01.027. Epub 2015 Feb 5.

41.

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.

42.

Complete genome sequence of classical Swine Fever virus subgenogroup 2.1 from assam, India.

Ahuja A, Bhattacharjee U, Chakraborty AK, Karam A, Ghatak S, Puro K, Das S, Shakuntala I, Srivastava N, Ngachan SV, Sen A.

Genome Announc. 2015 Jan 22;3(1). pii: e01437-14. doi: 10.1128/genomeA.01437-14.

43.

Understanding immunology: fun at an intersection of the physical, life, and clinical sciences.

Chakraborty AK.

Phys Biol. 2014 Oct 8;11(5):053014. doi: 10.1088/1478-3975/11/5/053014.

PMID:
25292176
44.

Coreceptor scanning by the T cell receptor provides a mechanism for T cell tolerance.

Stepanek O, Prabhakar AS, Osswald C, King CG, Bulek A, Naeher D, Beaufils-Hugot M, Abanto ML, Galati V, Hausmann B, Lang R, Cole DK, Huseby ES, Sewell AK, Chakraborty AK, Palmer E.

Cell. 2014 Oct 9;159(2):333-45. doi: 10.1016/j.cell.2014.08.042. Epub 2014 Oct 2.

45.

Insights into the initiation of TCR signaling.

Chakraborty AK, Weiss A.

Nat Immunol. 2014 Sep;15(9):798-807. doi: 10.1038/ni.2940. Review.

46.

Fabrication of Bi2O3/TiO2 nanocomposites and their applications to the degradation of pollutants in air and water under visible-light.

Chakraborty AK, Hossain ME, Rhaman MM, Sobahan KM.

J Environ Sci (China). 2014 Feb 1;26(2):458-65.

PMID:
25076538
47.

Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics.

Iversen L, Tu HL, Lin WC, Christensen SM, Abel SM, Iwig J, Wu HJ, Gureasko J, Rhodes C, Petit RS, Hansen SD, Thill P, Yu CH, Stamou D, Chakraborty AK, Kuriyan J, Groves JT.

Science. 2014 Jul 4;345(6192):50-4. doi: 10.1126/science.1250373.

48.

Neonatal uterine prolapse - a case report.

Saha DK, Hasan KM, Rahman SM, Majumder SK, Zahid MK, Chakraborty AK, Bari MS.

Mymensingh Med J. 2014 Apr;23(2):401-5.

PMID:
24858176
49.

Statistical linkage analysis of substitutions in patient-derived sequences of genotype 1a hepatitis C virus nonstructural protein 3 exposes targets for immunogen design.

Quadeer AA, Louie RH, Shekhar K, Chakraborty AK, Hsing IM, McKay MR.

J Virol. 2014 Jul;88(13):7628-44. doi: 10.1128/JVI.03812-13. Epub 2014 Apr 23.

50.

Monovalent engagement of the BCR activates ovalbumin-specific transnuclear B cells.

Avalos AM, Bilate AM, Witte MD, Tai AK, He J, Frushicheva MP, Thill PD, Meyer-Wentrup F, Theile CS, Chakraborty AK, Zhuang X, Ploegh HL.

J Exp Med. 2014 Feb 10;211(2):365-79. doi: 10.1084/jem.20131603. Epub 2014 Feb 3.

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