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Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains.

Zhu J, Ofek G, Yang Y, Zhang B, Louder MK, Lu G, McKee K, Pancera M, Skinner J, Zhang Z, Parks R, Eudailey J, Lloyd KE, Blinn J, Alam SM, Haynes BF, Simek M, Burton DR, Koff WC; NISC Comparative Sequencing Program, Mullikin JC, Mascola JR, Shapiro L, Kwong PD.

Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6470-5. doi: 10.1073/pnas.1219320110. Epub 2013 Mar 27.


De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts.

Zhu J, Wu X, Zhang B, McKee K, O'Dell S, Soto C, Zhou T, Casazza JP; NISC Comparative Sequencing Program, Mullikin JC, Kwong PD, Mascola JR, Shapiro L.

Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):E4088-97. doi: 10.1073/pnas.1306262110. Epub 2013 Oct 8.


Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing.

Wu X, Zhou T, Zhu J, Zhang B, Georgiev I, Wang C, Chen X, Longo NS, Louder M, McKee K, O'Dell S, Perfetto S, Schmidt SD, Shi W, Wu L, Yang Y, Yang ZY, Yang Z, Zhang Z, Bonsignori M, Crump JA, Kapiga SH, Sam NE, Haynes BF, Simek M, Burton DR, Koff WC, Doria-Rose NA, Connors M; NISC Comparative Sequencing Program, Mullikin JC, Nabel GJ, Roederer M, Shapiro L, Kwong PD, Mascola JR.

Science. 2011 Sep 16;333(6049):1593-602. doi: 10.1126/science.1207532. Epub 2011 Aug 11.


N332-Directed broadly neutralizing antibodies use diverse modes of HIV-1 recognition: inferences from heavy-light chain complementation of function.

Pancera M, Yang Y, Louder MK, Gorman J, Lu G, McLellan JS, Stuckey J, Zhu J, Burton DR, Koff WC, Mascola JR, Kwong PD.

PLoS One. 2013;8(2):e55701. doi: 10.1371/journal.pone.0055701. Epub 2013 Feb 19.


Antibodies VRC01 and 10E8 neutralize HIV-1 with high breadth and potency even with Ig-framework regions substantially reverted to germline.

Georgiev IS, Rudicell RS, Saunders KO, Shi W, Kirys T, McKee K, O'Dell S, Chuang GY, Yang ZY, Ofek G, Connors M, Mascola JR, Nabel GJ, Kwong PD.

J Immunol. 2014 Feb 1;192(3):1100-6. doi: 10.4049/jimmunol.1302515. Epub 2014 Jan 3.


Somatic Populations of PGT135-137 HIV-1-Neutralizing Antibodies Identified by 454 Pyrosequencing and Bioinformatics.

Zhu J, O'Dell S, Ofek G, Pancera M, Wu X, Zhang B, Zhang Z; NISC Comparative Sequencing Program, Mullikin JC, Simek M, Burton DR, Koff WC, Shapiro L, Mascola JR, Kwong PD.

Front Microbiol. 2012 Sep 11;3:315. eCollection 2012.


Structural and genetic basis for development of broadly neutralizing influenza antibodies.

Lingwood D, McTamney PM, Yassine HM, Whittle JR, Guo X, Boyington JC, Wei CJ, Nabel GJ.

Nature. 2012 Sep 27;489(7417):566-70. doi: 10.1038/nature11371. Epub 2012 Aug 29.


Viral escape from neutralizing antibodies in early subtype A HIV-1 infection drives an increase in autologous neutralization breadth.

Murphy MK, Yue L, Pan R, Boliar S, Sethi A, Tian J, Pfafferot K, Karita E, Allen SA, Cormier E, Goepfert PA, Borrow P, Robinson JE, Gnanakaran S, Hunter E, Kong XP, Derdeyn CA.

PLoS Pathog. 2013 Feb;9(2):e1003173. doi: 10.1371/journal.ppat.1003173. Epub 2013 Feb 28.


Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method.

Evans MC, Phung P, Paquet AC, Parikh A, Petropoulos CJ, Wrin T, Haddad M.

BMC Bioinformatics. 2014 Mar 19;15:77. doi: 10.1186/1471-2105-15-77.


Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.

Wu X, Zhang Z, Schramm CA, Joyce MG, Kwon YD, Zhou T, Sheng Z, Zhang B, O'Dell S, McKee K, Georgiev IS, Chuang GY, Longo NS, Lynch RM, Saunders KO, Soto C, Srivatsan S, Yang Y, Bailer RT, Louder MK; NISC Comparative Sequencing Program, Mullikin JC, Connors M, Kwong PD, Mascola JR, Shapiro L.

Cell. 2015 Apr 23;161(3):470-85. doi: 10.1016/j.cell.2015.03.004. Epub 2015 Apr 9.


In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire.

DeKosky BJ, Kojima T, Rodin A, Charab W, Ippolito GC, Ellington AD, Georgiou G.

Nat Med. 2015 Jan;21(1):86-91. doi: 10.1038/nm.3743. Epub 2014 Dec 15.


Molecular profile of an antibody response to HIV-1 as probed by combinatorial libraries.

Barbas CF 3rd, Collet TA, Amberg W, Roben P, Binley JM, Hoekstra D, Cababa D, Jones TM, Williamson RA, Pilkington GR, et al.

J Mol Biol. 1993 Apr 5;230(3):812-23.


A binary plasmid system for shuffling combinatorial antibody libraries.

Collet TA, Roben P, O'Kennedy R, Barbas CF 3rd, Burton DR, Lerner RA.

Proc Natl Acad Sci U S A. 1992 Nov 1;89(21):10026-30.


The potential of the human immune system to develop broadly neutralizing HIV-1 antibodies: implications for vaccine development.

Zhang Y, Yuan T, Li J, Zhang Y, Xu J, Shao Y, Chen Z, Zhang MY.

AIDS. 2013 Oct 23;27(16):2529-39. doi: 10.1097/QAD.0000000000000015.


10E8-like neutralizing antibodies against HIV-1 induced using a precisely designed conformational peptide as a vaccine prime.

Yu Y, Tong P, Li Y, Lu Z, Chen Y.

Sci China Life Sci. 2014 Jan;57(1):117-27. doi: 10.1007/s11427-013-4591-0. Epub 2013 Dec 26.


Mouse marginal zone B cells harbor specificities similar to human broadly neutralizing HIV antibodies.

Pujanauski LM, Janoff EN, McCarter MD, Pelanda R, Torres RM.

Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1422-7. doi: 10.1073/pnas.1213713110. Epub 2013 Jan 3.


Molecular characterization of variable heavy and light chain regions of five HIV type 1-specific human monoclonal antibodies.

van der Donk EM, Schutten M, Osterhaus AD, van der Heijden RW.

AIDS Res Hum Retroviruses. 1994 Dec;10(12):1639-49.

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