The promise and challenge of high-throughput sequencing of the antibody repertoire

Antibody therapy of cancer

Scott, A. M., Wolchok, J. D., & Old, L. J. (2012) · Nature reviews. Cancer · doi:10.1038/nrc3236 · Cited by 2,244

Predominant Autoantibody Production by Early Human B Cell Precursors

Wardemann, H., Yurasov, S., Schaefer, A., Young, J. W., Meffre, E., & Nussenzweig, M. C. (2003) · Science · doi:10.1126/science.1086907 · Cited by 2,088

Germinal Centers

Victora, G. D., & Nussenzweig, M. C. (2012) · Annual Review of Immunology · doi:10.1146/annurev-immunol-020711-075032 · Cited by 1,878

Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target

Walker, L., Phogat, S., Chan-hui, P., Wagner, D., Pham, P., Goss, J. L., Wrin, T., Simek, M., Fling, S., Mitcham, J., et al. (2009) · Science · doi:10.1126/science.1178746 · Cited by 1,849

Prevalence of monoclonal gammopathy of undetermined significance

Kyle, R. A., Therneau, T. M., Rajkumar, S. V., Larson, D. R., Plevak, M. F., Offord, J. R., Dispenzieri, A., Katzmann, J. A., & Melton, L. J. (2006) · New England Journal of Medicine · doi:10.1056/nejmoa054494 · Cited by 1,423

Performance comparison of benchtop high-throughput sequencing platforms

Loman, N. J., Misra, R., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J. R., & Pallen, M. J. (2012) · Nature Biotechnology · doi:10.1038/nbt.2198 · Cited by 1,383

A Neutralizing Antibody Selected from Plasma Cells That Binds to Group 1 and Group 2 Influenza A Hemagglutinins

Corti, D., Voss, J., Gamblin, S. J., Codoni, G., Macagno, A., Jarrossay, D., Vachieri, S. G., Pinna, D., Minola, A., Vanzetta, F., et al. (2011) · Science · doi:10.1126/science.1205669 · Cited by 1,203

Human Immunoglobulin (Ig)M+IgD+ Peripheral Blood B Cells Expressing the CD27 Cell Surface Antigen Carry Somatically Mutated Variable Region Genes: CD27 as a General Marker for Somatically Mutated (Memory) B Cells

Klein, U., Rajewsky, K., & Küppers, R. (1998) · The Journal of Experimental Medicine · doi:10.1084/jem.188.9.1679 · Cited by 1,161

Detection and quantification of rare mutations with massively parallel sequencing

Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K. W., & Vogelstein, B. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105422108 · Cited by 1,144

Detection of ultra-rare mutations by next-generation sequencing

Schmitt, M. W., Kennedy, S. R., Salk, J. J., Fox, E. J., Hiatt, J. B., & Loeb, L. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208715109 · Cited by 1,047

Rapid cloning of high-affinity human monoclonal antibodies against influenza virus

Wrammert, J., Smith, K., Miller, J., Langley, W. A., Kokko, K. E., Larsen, C. P., Zheng, N., Mays, I., Garman, L., Helms, C., et al. (2008) · Nature · doi:10.1038/nature06890 · Cited by 1,026

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

Liao, H., Lynch, R. M., Zhou, T., Gao, F., Alam, S. M., Boyd, S. D., Fire, A. Z., Roskin, K. M., Schramm, C. A., Zhang, Z., et al. (2013) · Nature · doi:10.1038/nature12053 · Cited by 986

Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals

Scheid, J. F., Mouquet, H., Feldhahn, N., Seaman, M. S., Velinzon, K., Pietzsch, J., Ott, R. G., Anthony, R. M., Zebroski, H. A., Hurley, A., et al. (2009) · Nature · doi:10.1038/nature07930 · Cited by 855

Therapeutic antibodies for autoimmunity and inflammation

Chan, A. C., & Carter, P. J. (2010) · Nature reviews. Immunology · doi:10.1038/nri2761 · Cited by 846

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

Wu, X., Zhou, T., Zhu, J., Zhang, B., Georgiev, I. S., Wang, C., Chen, X., Longo, N. S., Louder, M. K., McKee, K., et al. (2011) · Science · doi:10.1126/science.1207532 · Cited by 797

Diversity in the CDR3 Region of VH Is Sufficient for Most Antibody Specificities

Xu, J. L., & Davis, M. M. (2000) · Immunity · doi:10.1016/s1074-7613(00)00006-6 · Cited by 779

An efficient method to make human monoclonal antibodies from memory B cells: potent neutralization of SARS coronavirus

Traggiai, E., Becker, S., Subbarao, K., Kolesnikova, L., Uematsu, Y., Gismondo, M. R., Murphy, B. R., Rappuoli, R., & Lanzavecchia, A. (2004) · Nature Medicine · doi:10.1038/nm1080 · Cited by 697

Tracing B cell development in human germinal centres by molecular analysis of single cells picked from histological sections.

Küppers, R., Zhao, M., Hansmann, M., & Rajewsky, K. (1993) · The EMBO Journal · doi:10.1002/j.1460-2075.1993.tb06189.x · Cited by 662

The Human Immune Response to Dengue Virus Is Dominated by Highly Cross-Reactive Antibodies Endowed with Neutralizing and Enhancing Activity

Beltramello, M., Williams, K. L., Simmons, C. P., Macagno, A., Simonelli, L., Quyen, N. T. H., Sukupolvi-Petty, S., Navarro-Sánchez, E., Young, P. R., de Silva, A. M., et al. (2010) · Cell Host & Microbe · doi:10.1016/j.chom.2010.08.007 · Cited by 593

Beyond natural antibodies: the power of in vitro display technologies

Bradbury, A. M., Sidhu, S. S., Dübel, S., & McCafferty, J. (2011) · Nature Biotechnology · doi:10.1038/nbt.1791 · Cited by 548

Early Restriction of the Human Antibody Repertoire

Schroeder, H. W., Hillson, J., & Perlmutter, R. M. (1987) · Science · doi:10.1126/science.3118465 · Cited by 543

B-cell–lineage immunogen design in vaccine development with HIV-1 as a case study

Haynes, B. F., Kelsoe, G. H., Harrison, S. C., & Kepler, T. B. (2012) · Nature Biotechnology · doi:10.1038/nbt.2197 · Cited by 481

Autoreactivity in Human IgG+ Memory B Cells

Tiller, T., Tsuiji, M., Yurasov, S., Velinzon, K., Nussenzweig, M. C., & Wardemann, H. (2007) · Immunity · doi:10.1016/j.immuni.2007.01.009 · Cited by 477

Broadly Neutralizing Antiviral Antibodies

Corti, D., & Lanzavecchia, A. (2013) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032712-095916 · Cited by 469

Human Antibodies that Neutralize HIV-1: Identification, Structures, and B Cell Ontogenies

Kwong, P. D., & Mascola, J. R. (2012) · Immunity · doi:10.1016/j.immuni.2012.08.012 · Cited by 457

Neutralizing antibodies derived from the B cells of 1918 influenza pandemic survivors

Yu, X., Tsibane, T., McGraw, P. A., House, F. S., Keefer, C. J., Hicar, M. D., Tumpey, T. M., Pappas, C., Perrone, L. A., Martinez, O., et al. (2008) · Nature · doi:10.1038/nature07231 · Cited by 457

Molecular programming of B cell memory

McHeyzer-Williams, M., Okitsu, S., Wang, N., & McHeyzer-Williams, L. (2012) · Nature Reviews Immunology · doi:10.1038/nri3128 · Cited by 449

Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire

Glanville, J., Zhai, W., Berka, J., Telman, D., Huerta, G., Mehta, G. R., Ni, I., Mei, L., Sundar, P. D., Day, G. M. R., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909775106 · Cited by 440

High-Throughput Sequencing of the Zebrafish Antibody Repertoire

Weinstein, J. A., Jiang, N. J., White, R. A., III, Fisher, D. S., & Quake, S. R. (2009) · Science · doi:10.1126/science.1170020 · Cited by 432

Deep-sequencing approach for minimal residual disease detection in acute lymphoblastic leukemia

Faham, M., Zheng, J., Moorhead, M., Carlton, V. E. H., Stow, P., Coustan‐Smith, E., Pui, C., & Campana, D. (2012) · Blood · doi:10.1182/blood-2012-07-444042 · Cited by 422

High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire

DeKosky, B. J., Ippolito, G. C., Deschner, R. P., Lavinder, J. J., Wine, Y., Rawlings, B. M., Varadarajan, N., Giesecke, C., Dörner, T., Andrews, S. F., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2492 · Cited by 410

Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing

Boyd, S. D., Marshall, E. L., Merker, J. D., Maniar, J. M., Zhang, L. N., Sahaf, B., Jones, C. D., Simen, B. B., Hanczaruk, B., Nguyen, K. D., et al. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000540 · Cited by 387

A Blueprint for HIV Vaccine Discovery

Burton, D. R., Ahmed, R., Barouch, D. H., Butera, S. T., Crotty, S., Godzik, A., Kaufmann, D., McElrath, M. J., Nussenzweig, M. C., Pulendran, B., et al. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.09.008 · Cited by 385

Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies

Zhou, T., Zhu, J., Wu, X., Moquin, S. A., Zhang, B., Acharya, P., Georgiev, I. S., Altae-Tran, H., Chuang, G., Joyce, M. G., et al. (2013) · Immunity · doi:10.1016/j.immuni.2013.04.012 · Cited by 368

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

Campbell, P. J., Pleasance, E., Stephens, P. J., Dicks, E., Rance, R., Goodhead, I., Follows, G., Green, A. R., Futreal, P. A., & Stratton, M. R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801523105 · Cited by 365

Potassium Channel KIR4.1 as an Immune Target in Multiple Sclerosis

Srivastava, R., Aslam, M., Kalluri, S. R., Schirmer, L., Buck, D., Tackenberg, B., Rothhammer, V., Chan, A., Gold, R., Berthele, A., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1110740 · Cited by 344

Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination

Jiang, N., He, J., Weinstein, J. A., Penland, L., Sasaki, S., He, X.-S., Dekker, C. L., Zheng, N.-Y., Huang, M., Sullivan, M., et al. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3004794 · Cited by 335

Expressed Murine and Human CDR-H3 Intervals of Equal Length Exhibit Distinct Repertoires that Differ in their Amino Acid Composition and Predicted Range of Structures

Zemlin, M., Klinger, M., Link, J. M., Zemlin, C., Bauer, K., Engler, J. A., Schroeder, H. W., & Kirkham, P. M. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.10.007 · Cited by 329

Maximum entropy models for antibody diversity

Mora, T., Walczak, A. M., Bialek, W., & Callan, C. G. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001705107 · Cited by 328

Broadly neutralizing antibodies and the search for an HIV-1 vaccine: the end of the beginning

Kwong, P. D., Mascola, J. R., & Nabel, G. J. (2013) · Nature reviews. Immunology · doi:10.1038/nri3516 · Cited by 325

Evidence for a Large Compartment of IgM-Expressing Memory B Cells in Humans

Klein, U., Küppers, R., & Rajewsky, K. (1997) · Blood · doi:10.1182/blood.v89.4.1288 · Cited by 320

B-cell tolerance checkpoints in health and autoimmunity

Meffre, E., & Wardemann, H. (2008) · Current Opinion in Immunology · doi:10.1016/j.coi.2008.09.001 · Cited by 304

Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells

Reddy, S. T., Ge, X., Miklos, A. E., Hughes, R. A., Kang, S. H., Hoi, K. H., Chrysostomou, C., Hunicke-Smith, S. P., Iverson, B. L., Tucker, P. W., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1673 · Cited by 292

Advances in Human B Cell Phenotypic Profiling

Kaminski, D. A., Wei, C., Yu, Q., Rosenberg, A. F., & Sanz, I. (2012) · Frontiers in Immunology · doi:10.3389/fimmu.2012.00302 · Cited by 291

High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations

Wu, Y.-C. B., Kipling, D., Leong, H. S., Martin, V., Ademokun, A., & Dunn‐Walters, D. K. (2010) · Blood · doi:10.1182/blood-2010-03-275859 · Cited by 289

Microbial colonization influences early B-lineage development in the gut lamina propria

Wesemann, D. R., Portuguese, A. J., Meyers, R. M., Gallagher, M. P., Cluff-Jones, K., Magee, J. M., Panchakshari, R. A., Rodig, S. J., Kepler, T. B., & Alt, F. W. (2013) · Nature · doi:10.1038/nature12496 · Cited by 286

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

Shiroguchi, K., Jia, T. Z., Sims, P. A., & Xie, X. S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118018109 · Cited by 276

Convergent Antibody Signatures in Human Dengue

Parameswaran, P., Liu, Y., Roskin, K. M., Jackson, K., Dixit, V. P., Lee, J.-Y., Artiles, K. L., Zompì, S., Vargas, M. J., Simen, B. B., et al. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.05.008 · Cited by 261

Analysis of the B-cell progenitor compartment at the level of single cells

Ehlich, A., Martin, V. M., Müller, W., & Rajewsky, K. (1994) · Current Biology · doi:10.1016/s0960-9822(00)00129-9 · Cited by 237

B cell exchange across the blood-brain barrier in multiple sclerosis

von Büdingen, H. ‐., Kuo, T. C., Sirota, M., van Belle, C. J., Apeltsin, L., Glanville, J., Cree, B., Gourraud, P., Schwartzburg, A., Huerta, G., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci63842 · Cited by 237

Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements

Boyd, S. D., Gaëta, B. A., Jackson, K., Fire, A. Z., Marshall, E. L., Merker, J. D., Maniar, J. M., Zhang, L. N., Sahaf, B., Jones, C. D., et al. (2010) · The Journal of Immunology · doi:10.4049/jimmunol.1000445 · Cited by 234

Age, microbiota, and T cells shape diverse individual IgA repertoires in the intestine

Lindner, C., Wahl, B., Föhse, L., Suerbaum, S., Macpherson, A. J., Prinz, I., & Pabst, O. (2012) · The Journal of Experimental Medicine · doi:10.1084/jem.20111980 · Cited by 234

Rep‐Seq: uncovering the immunological repertoire through next‐generation sequencing

Benichou, J. I. C., Ben‐Hamo, R., Louzoun, Y., & Efroni, S. (2011) · Immunology · doi:10.1111/j.1365-2567.2011.03527.x · Cited by 233

Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation

Watson, C. T., Steinberg, K. M., Huddleston, J., Warren, R. M., Malig, M., Schein, J. E., Willsey, A. J., Joy, J. B., Scott, J. K., Graves, T., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.03.004 · Cited by 229

Evolutionary implications of a third lymphocyte lineage in lampreys

Hirano, M., Guo, P., McCurley, N., Schorpp, M., Das, S., Boehm, T. L. J., & Cooper, M. D. (2013) · Nature · doi:10.1038/nature12467 · Cited by 224

Reshaping Antibody Diversity

Wang, F., Ekiert, D. C., Ahmad, I., Yu, W., Zhang, Y., Bazirgan, O. A., Torkamani, A., Raudsepp, T., Mwangi, W., Criscitiello, M. F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.049 · Cited by 224

Genetic measurement of memory B-cell recall using antibody repertoire sequencing

Vollmers, C., Sit, R. V., Weinstein, J. A., Dekker, C. L., & Quake, S. R. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1312146110 · Cited by 222

High abundance of plasma cells secreting transglutaminase 2–specific IgA autoantibodies with limited somatic hypermutation in celiac disease intestinal lesions

Niro, R. D., Mesin, L., Zheng, N., Stamnæs, J., Michael, M., Lee, J.-H., Huang, M., Iversen, R., du Pré, M. F., Qiao, S., et al. (2012) · Nature Medicine · doi:10.1038/nm.2656 · Cited by 211

Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing

Mohr, S., Ghanem, E., Smith, W., Sheeter, D. A., Qin, Y., King, O., Polioudakis, D., Iyer, V. R., Hunicke‐Smith, S., Swamy, S., et al. (2013) · RNA · doi:10.1261/rna.039743.113 · Cited by 209

High-Resolution Description of Antibody Heavy-Chain Repertoires in Humans

Arnaout, R., Lee, W., Cahill, P., Honan, T., Sparrow, T., Weiand, M., Nusbaum, C., Rajewsky, K., & Koralov, S. B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022365 · Cited by 203

Teleost Fish Mount Complex Clonal IgM and IgT Responses in Spleen upon Systemic Viral Infection

Castro, R., Jouneau, L., Pham, H., Bouchez, O., Giudicelli, V., Lefranc, M., Quillet, E., Benmansour, A., Cazals, F., Six, A., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003098 · Cited by 201

Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies

Muellenbeck, M. F., Ueberheide, B. M., Amulic, B., Epp, A., Fenyö, D., Busse, C. E., Esen, M., Theisen, M., Mordmüller, B. G., & Wardemann, H. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20121970 · Cited by 199

Quantifying selection in high-throughput Immunoglobulin sequencing data sets

Yaari, G., Uduman, M., & Kleinstein, S. H. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks457 · Cited by 189

A proteomics approach for the identification and cloning of monoclonal antibodies from serum

Cheung, W. C., Beausoleil, S. A., Zhang, X., Sato, S., Schieferl, S. M., Wieler, J. S., Beaudet, J. G., Ramenani, R. K., Popova, L., Comb, M. J., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2167 · Cited by 182

Limiting dilution analysis of the B cell compartment in human bone marrow

Hibi∥, T., & Dosch, H. (1986) · European Journal of Immunology · doi:10.1002/eji.1830160206 · Cited by 177

Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation

Glanville, J., Kuo, T. C., von Büdingen, H. ‐., Guey, L. T., Berka, J., Sundar, P. D., Huerta, G., Mehta, G. R., Oksenberg, J. R., Hauser, S. L., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1107498108 · Cited by 177

Addressing challenges in the production and analysis of illumina sequencing data

Kircher, M., Heyn, P. C., & Kelso, J. F. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-382 · Cited by 172

By-passing in vitro screening—next generation sequencing technologies applied to antibody display and in silico candidate selection

Ravn, U., Gueneau, F., Bærlocher, L., Østerås, M., Desmurs, M., Malinge, P., Magistrelli, G., Farinelli, L., Kosco‐Vilbois, M. H., & Fischer, N. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq789 · Cited by 172

High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment

Logan, A. C., Gao, H., Wang, C., Sahaf, B., Jones, C. D., Marshall, E. L., Buño, I., Armstrong, R. J., Fire, A. Z., Weinberg, K. I., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118357109 · Cited by 167

Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing

Larimore, K., McCormick, M. W., Robins, H. S., & Greenberg, P. D. (2012) · The Journal of Immunology · doi:10.4049/jimmunol.1201303 · Cited by 157

Similarity and divergence in the development and expression of the mouse and human antibody repertoires

Schroeder, H. W. (2005) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2005.06.006 · Cited by 151

Tools to therapeutically harness the human antibody response

Wilson, P. C., & Andrews, S. F. (2012) · Nature reviews. Immunology · doi:10.1038/nri3285 · Cited by 149

NCBI GEO standards and services for microarray data

Edgar, R., & Barrett, T. (2006) · Nature Biotechnology · doi:10.1038/nbt1206-1471 · Cited by 148

Next generation sequencing for TCR repertoire profiling: Platform‐specific features and correction algorithms

Bolotin, D. A., Mamedov, I. Z., Britanova, O. V., Zvyagin, I. V., Shagin, D. A., Ustyugova, S. V., Turchaninova, M. A., Lukyanov, S., Lebedev, Y. B., & Chudakov, D. M. (2012) · European Journal of Immunology · doi:10.1002/eji.201242517 · Cited by 147

Antigen Receptor Allelic Exclusion: An Update and Reappraisal

Brady, B. L., Steinel, N. C., & Bassing, C. H. (2010) · The Journal of Immunology · doi:10.4049/jimmunol.1001158 · Cited by 147

Unifying immunology with informatics and multiscale biology

Kidd, B. A., Peters, L. A., Schadt, E. E., & Dudley, J. T. (2014) · Nature Immunology · doi:10.1038/ni.2787 · Cited by 145

Immunoglobulin G4+ clones identified by next-generation sequencing dominate the B cell receptor repertoire in immunoglobulin G4 associated cholangitis

Wenniger, L. J. M. D. B., Doorenspleet, M. E., Klarenbeek, P. L., Verheij, J., Baas, F., Elferink, R. P. J. O., Tak, P. P., de Vries, N., & Beuers, U. H. (2013) · Hepatology · doi:10.1002/hep.26232 · Cited by 145

Counting individual DNA molecules by the stochastic attachment of diverse labels

Fu, G. K., Hu, J., Wang, P., & Fodor, S. P. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017621108 · Cited by 142

Vaccination‐induced changes in human B‐cell repertoire and pneumococcal IgM and IgA antibody at different ages

Ademokun, A., Wu, Y., Martin, V., Mitra, R., Sack, U., Baxendale, H., Kipling, D., & Dunn‐Walters, D. K. (2011) · Aging Cell · doi:10.1111/j.1474-9726.2011.00732.x · Cited by 139

Prize-based contests can provide solutions to computational biology problems

Lakhani, K. R., Boudreau, K. J., Loh, P., Bäckström, L., Baldwin, C. Y., Lonstein, E., Lydon, M., MacCormack, A., Arnaout, R., & Guinan, E. C. (2013) · Nature Biotechnology · doi:10.1038/nbt.2495 · Cited by 137

Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response

Wine, Y., Boutz, D. R., Lavinder, J. J., Miklos, A. E., Hughes, R. A., Hoi, K. H., Jung, S. T., Horton, A. P., Murrin, E. M., Ellington, A. D., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1213737110 · Cited by 135

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, M. K., Lu, G., McKee, K., Pancera, M., Skinner, J., Zhang, Z., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219320110 · Cited by 135

Isolation of Human Antibody Repertoires with Preservation of the Natural Heavy and Light Chain Pairing

Meijer, P., Andersen, P. S., Hansen, M. H., Steinaa, L., Jensen, A. D., Lantto, J., Oleksiewicz, M. B., Tengbjerg, K., Poulsen, T. R., Coljee, V. W., et al. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.02.040 · Cited by 127

Massive evolution of the immunoglobulin heavy chain locus in children with B precursor acute lymphoblastic leukemia

Gawad, C., Pepin, F., Carlton, V. E. H., Klinger, M., Logan, A. C., Miklos, D. B., Faham, M., Dahl, G. V. H., & Lacayo, N. J. (2012) · Blood · doi:10.1182/blood-2012-05-429811 · Cited by 123

Single‐cell based high‐throughput sequencing of full‐length immunoglobulin heavy and light chain genes

Busse, C. E., Czogiel, I., Braun, P., Arndt, P. F., & Wardemann, H. (2014) · European Journal of Immunology · doi:10.1002/eji.201343917 · Cited by 121

Deep sequencing of phage display libraries to support antibody discovery

Ravn, U., Didelot, G., Venet, S., Ng, K.-T., Gueneau, F., Rousseau, F., Calloud, S., Kosco‐Vilbois, M. H., & Fischer, N. (2013) · Methods · doi:10.1016/j.ymeth.2013.03.001 · Cited by 115

Determinism and stochasticity during maturation of the zebrafish antibody repertoire

Jiang, N. J., Weinstein, J. A., Penland, L., White, R. A., III, Fisher, D. S., & Quake, S. R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1014277108 · Cited by 107

Targeting TLRs Expands the Antibody Repertoire in Response to a Malaria Vaccine

Wiley, S. R., Raman, V. S., Desbien, A. L., Bailor, H. R., Bhardwaj, R., Shakri, A. R., Reed, S. G., Chitnis, C. E., & Carter, D. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3002135 · Cited by 97

New tools for classification and monitoring of autoimmune diseases

Maecker, H. T., Lindstrom, T. M., Robinson, W. H., Utz, P. J., Hale, M., Boyd, S. D., Shen-Orr, S. S., & Fathman, C. G. (2012) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2012.66 · Cited by 95

Variable Region Sequences of Five Human Immunoglobulin Heavy Chains of the V H III Subgroup: Definitive Identification of Four Heavy Chain Hypervariable Regions

Capra, J. D., & Kehoe, J. M. (1974) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.71.3.845 · Cited by 93

Regulation of the B Cell Receptor Repertoire and Self-Reactivity by BAFF

Ota, M., Duong, B. H., Torkamani, A., Doyle, C., Gavin, A. L., Ota, T., & Nemazee, D. A. (2010) · The Journal of Immunology · doi:10.4049/jimmunol.1002176 · Cited by 91

Forced usage of positively charged amino acids in immunoglobulin CDR-H3 impairs B cell development and antibody production

Ippolito, G. C., Schelonka, R. L., Zemlin, M., Ivanov, I. I., Kobayashi, R., Zemlin, C., Gartland, G. L., Nitschke, L., Pelkonen, J., Fujihashi, K., et al. (2006) · The Journal of Experimental Medicine · doi:10.1084/jem.20052217 · Cited by 89

The Inference of Phased Haplotypes for the Immunoglobulin H Chain V Region Gene Loci by Analysis of VDJ Gene Rearrangements

Kidd, M. J., Chen, Z., Wang, Y., Jackson, K., Zhang, L., Boyd, S. D., Fire, A. Z., Tanaka, M. M., Gaëta, B. A., & Collins, A. M. (2011) · The Journal of Immunology · doi:10.4049/jimmunol.1102097 · Cited by 88

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. J., Soto, C. S., Zhou, T., Casazza, J. P., Program, N. C. S., Mullikin, J. C., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1306262110 · Cited by 87

Fundamental Characteristics of the Immunoglobulin VH Repertoire of Chickens in Comparison with Those of Humans, Mice, and Camelids

Wu, L., Oficjalska, K., Lambert, M. A., Fennell, B. J., Darmanin-Sheehan, A., Shúilleabháin, D. N., Autin, B., Cummins, E., Tchistiakova, L., Bloom, L., et al. (2011) · The Journal of Immunology · doi:10.4049/jimmunol.1102466 · Cited by 87

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Krause, J. C., Tsibane, T., Tumpey, T. M., Huffman, C. J., Briney, B. S., Smith, S. A., Basler, C. F., & Crowe, J. E. (2011) · The Journal of Immunology · doi:10.4049/jimmunol.1101823 · Cited by 86

Differential regulation of self-reactivity discriminates between IgG + human circulating memory B cells and bone marrow plasma cells

Scheid, J. F., Mouquet, H., Kofer, J., Yurasov, S., Nussenzweig, M. C., & Wardemann, H. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113395108 · Cited by 83

Sequencing antibody repertoires

Fischer, N. (2011) · mAbs · doi:10.4161/mabs.3.1.14169 · Cited by 79

Antibody Repertoires in Humanized NOD-scid-IL2Rγnull Mice and Human B Cells Reveals Human-Like Diversification and Tolerance Checkpoints in the Mouse

Ippolito, G. C., Hoi, K. H., Reddy, S. T., Carroll, S. M., Ge, X., Rogosch, T., Zemlin, M., Shultz, L. D., Ellington, A. D., Berg, C. L. V. D., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035497 · Cited by 79

Antibody isolation from immunized animals: comparison of phage display and antibody discovery via V gene repertoire mining

Saggy, I., Wine, Y., Shefet-Carasso, L., Nahary, L., Georgiou, G., & Benhar, I. (2012) · Protein Engineering Design and Selection · doi:10.1093/protein/gzs060 · Cited by 78

High-throughput antibody sequencing reveals genetic evidence of global regulation of the naïve and memory repertoires that extends across individuals

Briney, B. S., Willis, J. R., McKinney, B. A., & Crowe, J. E. (2012) · Genes and Immunity · doi:10.1038/gene.2012.20 · Cited by 76

Location and length distribution of somatic hypermutation-associated DNA insertions and deletions reveals regions of antibody structural plasticity

Briney, B. S., Willis, J. R., & Crowe, J. E. (2012) · Genes and Immunity · doi:10.1038/gene.2012.28 · Cited by 75

Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

Nguyen, P., Ma, J., Pei, D., Obert, C. A., Cheng, C., & Geiger, T. L. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-106 · Cited by 73

Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium

Brusić, V., Gottardo, R., Kleinstein, S. H., Davis, M. M., Davis, M. M., Hafler, D. A., Quill, H., Palucka, A. K., Poland, G. A., Pulendran, B., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2777 · Cited by 69

Frequency and genetic characterization of V(DD)J recombinants in the human peripheral blood antibody repertoire

Briney, B. S., Willis, J. R., Hicar, M. D., Thomas, J. W., & Crowe, J. E. (2012) · Immunology · doi:10.1111/j.1365-2567.2012.03605.x · Cited by 67

IgH gene rearrangements as plasma biomarkers in Non-Hodgkin's Lymphoma patients

He, J., Wu, J., Jiao, Y., Wagner‐Johnston, N. D., Ambinder, R. F., Diaz, L. A., Kinzler, K. W., Vogelstein, B., & Papadopoulos, N. (2011) · Oncotarget · doi:10.18632/oncotarget.235 · Cited by 66

Human lymphocyte repertoires in ageing

Boyd, S. D., Liu, Y., Wang, C., Martin, V., & Dunn‐Walters, D. K. (2013) · Current Opinion in Immunology · doi:10.1016/j.coi.2013.07.007 · Cited by 61

Somatic populations of PGT135–137 HIV-1-neutralizing antibodies identified by 454 pyrosequencing and bioinformatic

Zhu, J. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00315 · Cited by 60

Proteomics-directed cloning of circulating antiviral human monoclonal antibodies

Sato, S., Beausoleil, S. A., Popova, L., Beaudet, J. G., Ramenani, R. K., Zhang, X., Wieler, J. S., Schieferl, S. M., Cheung, W. C., & Polakiewicz, R. D. (2012) · Nature Biotechnology · doi:10.1038/nbt.2406 · Cited by 58

Genomic screening by 454 pyrosequencing identifies a new human IGHV gene and sixteen other new IGHV allelic variants

Wang, Y., Jackson, K., Gaëta, B. A., Pomat, W. S., Siba, P., Sewell, W. A., & Collins, A. M. (2011) · Immunogenetics · doi:10.1007/s00251-010-0510-8 · Cited by 56

History of immunology

Silverstein, A. M. (1979) · Cellular Immunology · doi:10.1016/0008-8749(79)90215-6 · Cited by 54

Skewed Primary Igκ Repertoire and V–J Joining in C57BL/6 Mice: Implications for Recombination Accessibility and Receptor Editing

Aoki-Ota, M., Torkamani, A., Ota, T., Schork, N. J., & Nemazee, D. A. (2012) · The Journal of Immunology · doi:10.4049/jimmunol.1103484 · Cited by 52

Comprehensive Interrogation of a Minimalist Synthetic CDR-H3 Library and Its Ability to Generate Antibodies with Therapeutic Potential

Mahon, C. M., Lambert, M. A., Glanville, J., Wade, J. M., Fennell, B. J., Krebs, M. R. H., Armellino, D. C., Yang, S., Liu, X., O'Sullivan, C. M., et al. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.02.015 · Cited by 50

Wrestling with the repertoire: The promise and perils of next generation sequencing for antigen receptors

Baum, P. D., Venturi, V., & Price, D. A. (2012) · European Journal of Immunology · doi:10.1002/eji.201242999 · Cited by 50

High‐Throughput Multiplex Sequencing of miRNA

Vigneault, F., Ter‐Ovanesyan, D., Alon, S., Eminaga, S., Christodoulou, D. C., Seidman, J. G., Eisenberg, E., & Church, G. M. (2012) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1112s73 · Cited by 48

Divergent human populations show extensive shared IGK rearrangements in peripheral blood B cells

Jackson, K., Wang, Y., Gaëta, B. A., Pomat, W. S., Siba, P., Rimmer, J., Sewell, W. A., & Collins, A. M. (2011) · Immunogenetics · doi:10.1007/s00251-011-0559-z · Cited by 43

Construction of a rationally designed antibody platform for sequencing-assisted selection

Larman, H. B., Xu, G. J., Pavlova, N. N., & Elledge, S. J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1215549109 · Cited by 41

Intrinsic bias and public rearrangements in the human immunoglobulin Vλ light chain repertoire

Hoi, K. H., & Ippolito, G. C. (2013) · Genes and Immunity · doi:10.1038/gene.2013.10 · Cited by 37

Onset of Immune Senescence Defined by Unbiased Pyrosequencing of Human Immunoglobulin mRNA Repertoires

Rubelt, F., Sievert, V., Knaust, F., Diener, C., Lim, T. S., Skriner, K., Klipp, E., Reinhardt, R., Lehrach, H., & Konthur, Z. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049774 · Cited by 37

Clustering-based identification of clonally-related immunoglobulin gene sequence sets

Chen, Z., Collins, A. M., Wang, Y., & Gaëta, B. A. (2010) · Immunome Research · doi:10.1186/1745-7580-6-s1-s4 · Cited by 37

IgE Sequences in Individuals Living in an Area of Endemic Parasitism Show Little Mutational Evidence of Antigen Selection

Wang, Y., Jackson, K., Chen, Z., Gaëta, B. A., Siba, P. M., Pomat, W. S., Walpole, E., Rimmer, J., Sewell, W. A., & Collins, A. M. (2011) · Scandinavian Journal of Immunology · doi:10.1111/j.1365-3083.2011.02525.x · Cited by 36

Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing

Prabakaran, P., Zhu, Z., Chen, W., Gong, R., Feng, Y., Streaker, E. D., & Dimitrov, D. S. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00277 · Cited by 35

Models and methods for analysis of lymphocyte repertoire generation, development, selection and evolution

Mehr, R., Sternberg‐Simon, M., Michaeli, M., & Pickman, Y. (2012) · Immunology Letters · doi:10.1016/j.imlet.2012.08.002 · Cited by 35

Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire

Larsen, P. A., & Smith, T. P. L. (2012) · BMC Immunology · doi:10.1186/1471-2172-13-52 · Cited by 35

Rapid construction and characterization of synthetic antibody libraries without DNA amplification

Ge, X., Mazor, Y., Hunicke‐Smith, S., Ellington, A. D., & Georgiou, G. (2010) · Biotechnology and Bioengineering · doi:10.1002/bit.22712 · Cited by 33

The Restricted DH Gene Reading Frame Usage in the Expressed Human Antibody Repertoire Is Selected Based upon its Amino Acid Content

Benichou, J. I. C., Glanville, J., Prak, E. T. L., Azran, R., Kuo, T. C., Pons, J., Desmarais, C., Tsaban, L., & Louzoun, Y. (2013) · The Journal of Immunology · doi:10.4049/jimmunol.1201929 · Cited by 31

Clues to pathogenesis of Waldenström macroglobulinemia and immunoglobulin M monoclonal gammopathy of undetermined significance provided by analysis of immunoglobulin heavy chain gene rearrangement and clustering of B-cell receptors

Varettoni, M., Zibellini, S., Capello, D., Arcaini, L., Rossi, D., Pascutto, C., Rattotti, S., Mangiacavalli, S., Pochintesta, L., Gotti, M., et al. (2013) · Leukemia & lymphoma/Leukemia and lymphoma · doi:10.3109/10428194.2013.779689 · Cited by 30

Stereotyped B Cell Receptors in B Cell Leukemias and Lymphomas

Darzentas, N., & Σταματόπουλος, Κ. (2012) · Methods in molecular biology · doi:10.1007/978-1-62703-269-8_8 · Cited by 28

Model for comparative analysis of antigen receptor repertoires

Rempała, G. A., Seweryn, M. T., & Ignatowicz, L. (2010) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.10.001 · Cited by 28

Antibody Vh Repertoire Differences between Resolving and Chronically Evolving Hepatitis C Virus Infections

Racanelli, V., Brunetti, C., Re, V. D., Caggiari, L., Zorzi, M. D., Leone, P., Perosa, F., Vacca, A., & Dammacco, F. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025606 · Cited by 28

VH replacement in mice and humans

Zhang, Z. (2007) · Trends in Immunology · doi:10.1016/j.it.2007.01.003 · Cited by 25

454 antibody sequencing - error characterization and correction

Prabakaran, P., Streaker, E. D., Chen, W., & Dimitrov, D. S. (2011) · BMC Research Notes · doi:10.1186/1756-0500-4-404 · Cited by 24

Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing

Michaeli, M., Noga, H., Tabibian‐Keissar, H., Barshack, I., & Mehr, R. (2012) · Frontiers in Immunology · doi:10.3389/fimmu.2012.00386 · Cited by 18

Correlation of Gene Expression and Genome Mutation in Single B-Cells

Weinstein, J. A., Zeng, X., Chien, Y., & Quake, S. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067624 · Cited by 17

Comprehensive Assessment of Potential Multiple Myeloma Immunoglobulin Heavy Chain V-D-J Intraclonal Variation Using Massively Parallel Pyrosequencing

Tschumper, R. C., Asmann, Y. W., Hossain, A., Huddleston, P. M., Wu, X., Dispenzieri, A. A., Eckloff, B. W., & Jelinek, D. F. (2012) · Oncotarget · doi:10.18632/oncotarget.469 · Cited by 17

B cell receptor light chain repertoires show signs of selection with differences between groups of healthy individuals and SLE patients

Schoettler, N., Ni, D., & Weigert, M. (2012) · Molecular Immunology · doi:10.1016/j.molimm.2012.03.028 · Cited by 16

In Vivo VL-Targeted Microbial Superantigen Induced Global Shifts in the B Cell Repertoire

Grönwall, C., Pond, S. L. K., Young, J. A., & Silverman, G. J. (2012) · The Journal of Immunology · doi:10.4049/jimmunol.1200245 · Cited by 11

Development of therapeutic antibodies for the treatment of diseases

Lu, R., Hwang, Y., Liu, I.-J., Lee, C., Tsai, H.-Z., Li, H., & Wu, H. (2020) · Journal of Biomedical Science · doi:10.1186/s12929-019-0592-z · Cited by 2,235

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

Callahan, B. J., Wong, J., Heiner, C. R., Oh, S. D., Theriot, C. M., Gulati, A., McGill, S., & Dougherty, M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz569 · Cited by 739

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

Shugay, M., Bagaev, D. V., Turchaninova, M. A., Bolotin, D. A., Britanova, O. V., Putintseva, E. V., Pogorelyy, M. V., Nazarov, V. I., Zvyagin, I. V., Kirgizova, V., et al. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004503 · Cited by 608

SERS-Activated Platforms for Immunoassay: Probes, Encoding Methods, and Applications

Wang, Z., Zong, S., Wu, L., Zhu, D., & Cui, Y. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00027 · Cited by 620

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

DeKosky, B. J., Kojima, T., Rodin, A., Charab, W., Ippolito, G. C., Ellington, A. D., & Georgiou, G. (2014) · Nature Medicine · doi:10.1038/nm.3743 · Cited by 358

High-throughput Sequencing and Profiling of Antibody Repertoire and the Promises for Diagnostic and Therapeutic Applications

Getachew, A., & Pandian, M. (2016) · Journal of Advances in Medicine and Medical Research · doi:10.9734/bjmmr/2016/27765

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Tian, X., Li, C., Wu, Y., & Ying, T. (2020) · Small Methods · doi:10.1002/smtd.202000451 · Cited by 6

Next-generation sequencing and protein mass spectrometry for the comprehensive analysis of human cellular and serum antibody repertoires

Lavinder, J. J., Horton, A. P., Georgiou, G., & Ippolito, G. C. (2014) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.11.007 · Cited by 92

Sequencing the functional antibody repertoire—diagnostic and therapeutic discovery

Robinson, W. H. (2014) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2014.220 · Cited by 178

High-Throughput DNA Sequencing Analysis of Antibody Repertoires

Boyd, S. D., & Joshi, S. A. (2015) · ASM Press eBooks · doi:10.1128/9781555817411.ch20 · Cited by 9