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

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Items 201–300 of 687

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  2. Single amino acid fingerprinting of the human antibody repertoire with high density peptide arrays
    Laura K. Weber, Andrea Palermo, Jonas Kügler, Olivier Armant, Awale Isse, Simone Rentschler, Thomas Jaenisch, Jürgen J. Hubbuch, Stefan Dübel, Alexander Nesterov‐Mueller et al. · 2017 · Journal of Immunological Methods
  3. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads
    Alexander Shlemov, Sergey Bankevich, Andrey V. Bzikadze, Maria A. Turchaninova, Yana Safonova, Pavel A. Pevzner · 2017 · The Journal of Immunology
  4. High-throughput sequencing insights into T-cell receptor repertoire diversity in aging
    Goronzy, Jörg J., Qi, Qian, Olshen, Richard A., Weyand, Cornelia M. · 2015 · Genome Medicine
  5. repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data
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  6. Antibodyomics: bioinformatics technologies for understanding B‐cell immunity to HIV ‐1
    Peter D. Kwong, Gwo‐Yu Chuang, Brandon J. DeKosky, Tatyana S. Gindin, Ivelin S. Georgiev, Thomas Lemmin, Chaim A. Schramm, Zizhang Sheng, Cinque S. Soto, An‐Suei Yang et al. · 2017 · Immunological Reviews
  7. Deep Learning Methods for De Novo Peptide Sequencing
    Wout Bittremieux, Varun Ananth, William E. Fondrie, Carlo Melendez, Marina Pominova, Justin Sanders, Bo Wen, Melih Yilmaz, William Stafford Noble · 2024 · Mass Spectrometry Reviews
  8. Accurate prediction of antibody function and structure using bio-inspired antibody language model
    Hongtai Jing, Zhengtao Gao, Sheng Yong Xu, Tao Shen, Zhangzhi Peng, Shwai He, Tao You, Shuang Ye, Wei Jen Lin, Siqi Sun · 2024 · Briefings in Bioinformatics
  9. Direct high‐throughput amplification and sequencing of immunoglobulin genes from single human B cells
    Rajagopal Murugan, Katharina Imkeller, Christian E. Busse, Hedda Wardemann · 2015 · European Journal of Immunology
  10. VDJviz: a versatile browser for immunogenomics data
    Dmitriy V. Bagaev, Ivan V. Zvyagin, Ekaterina V. Putintseva, Mark Izraelson, Olga V. Britanova, Dmitriy M. Chudakov, Mikhail Shugay · 2016 · BMC Genomics
  11. Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery
    Ufuk Kirik, Lennart Greiff, Fredrik Levander, Mats Ohlin · 2017 · Molecular Immunology
  12. Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq
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  13. Antibody repertoire analysis of mouse immunization protocols using microfluidics and molecular genomics
    Michael A. Asensio, Yoong Wearn Lim, Nicholas P. Wayham, Kacy Stadtmiller, R. C. Edgar, Jackson Leong, Renee Leong, Rena A. Mizrahi, Matthew S. Adams, Jan Fredrik Simons et al. · 2019 · mAbs
  14. Robustification of RosettaAntibody and Rosetta SnugDock
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  15. Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing
    James A. Stapleton, Jeongwoon Kim, John P. Hamilton, Ming Wu, Luiz C. Irber, Rohan Maddamsetti, Bryan S. Briney, Linsey A. Newton, Dennis R. Burton, C. Titus Brown et al. · 2016 · PLoS ONE
  16. High-Throughput Sequencing of Human Immunoglobulin Variable Regions with Subtype Identification
    Merle M. Schanz, Thomas Liechti, Osvaldo Zagordi, Enkelejda Miho, Sai T. Reddy, Huldrych F. Günthard, Alexandra Trkola, Michael Huber · 2014 · PLoS ONE
  17. Genetic background and evolution of relapses in aggressive B-cell lymphomas
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  18. Naïve Human Antibody Libraries for Infectious Diseases
    Soo Khim Chan, Anizah Rahumatullah, Jing Yi Lai, Theam Soon Lim · 2017 · Advances in experimental medicine and biology
  19. Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire
    Rafael Donadelli Melani, Benjamin J. Des Soye, Jared O. Kafader, Eleonora Forte, Michael A. R. Hollas, Voislav Blagojevic, Fernanda Negrão, John P. McGee, Bryon Drown, Cameron Lloyd-Jones et al. · 2021 · Journal of Proteome Research
  20. Delineation of BmSXP antibody V-gene usage from a lymphatic filariasis based immune scFv antibody library
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  21. Principles and application of antibody libraries for infectious diseases
    Bee Nar Lim, Gee Jun Tye, Yee Siew Choong, Eugene Boon Beng Ong, Asma Ismail, Theam Soon Lim · 2014 · Biotechnology Letters
  22. Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages
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  23. Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths
    Ufuk Kirik, Helena Persson, Fredrik Levander, Lennart Greiff, Mats Ohlin · 2017 · Frontiers in Immunology
  24. Synthetic Standards Combined With Error and Bias Correction Improve the Accuracy and Quantitative Resolution of Antibody Repertoire Sequencing in Human Naïve and Memory B Cells
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  25. Landscape of Monoclonal Antibodies Targeting Zika and Dengue: Therapeutic Solutions and Critical Insights for Vaccine Development
    Vincent Dussupt, Kayvon Modjarrad, Shelly J. Krebs · 2021 · Frontiers in Immunology
  26. Next-generation sequencing in chronic lymphocytic leukemia: recent findings and new horizons
    Ana E. Rodríguez‐Vicente, Vasilis Bikos, María Hernández‐Sánchez, Jitka Malčíková, Jesús María Hernández‐Rivas, Šárka Pospı́šilová · 2017 · Oncotarget
  27. Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VLlibraries from immunized animals
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  28. Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
    Jeffrey A. Ruffolo, Lee‐Shin Chu, Sai Pooja Mahajan, Jeffrey J. Gray · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  29. Human picornaviruses associated with neurological diseases and their neutralization by antibodies
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  30. IgE repertoire and immunological memory: compartmental regulation and antibody function
    Hannah Jane Gould, Yu-Chang Bryan Wu · 2018 · International Immunology
  31. Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans
    Shishi Luo, Jane A. Yu, Heng Li, Yun S. Song · 2019 · Life Science Alliance
  32. Long-read sequencing unveils IGH-DUX4 translocation into the silenced IGH allele in B-cell acute lymphoblastic leukemia
    Liqing Tian, Ying Shao, Stephanie Nance, Jinjun Dang, Beisi Xu, Xiaotu Ma, Yongjin Li, Bensheng Ju, Li Dong, Scott Newman et al. · 2019 · Nature Communications
  33. DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations
    T. Daniel Andrews, Yogesh S. Jeelall, Dipti Talaulikar, Christopher Carl Goodnow, Matthew A. Field · 2016 · PeerJ
  34. Looking for therapeutic antibodies in next generation sequencing repositories
    Krawczyk, Konrad, Raybould, Matthew, Kovaltsuk, Aleksandr, Deane, Charlotte M. · 2019
  35. Epigenetic, Metabolic, and Immune Crosstalk in Germinal-Center-Derived B-Cell Lymphomas: Unveiling New Vulnerabilities for Rational Combination Therapies
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  36. Tracing Antibody Repertoire Evolution by Systems Phylogeny
    Alexander Yermanos, Andreas Dounas, Tanja Stadler, Annette Oxenius, Sai T. Reddy · 2018 · Frontiers in Immunology
  37. Antibody-based nanotechnology
    Yaron Hillman, Dan Lustiger, Yariv Wine · 2019 · Nanotechnology
  38. Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses
    Ganesh E. Phad, Pradeepa Pushparaj, Karen Tran, Viktoriya Dubrovskaya, Mónika Ádori, Paola Martinez-Murillo, Néstor Vázquez Bernat, Suruchi Singh, Gilman Dionne, Sijy J. O'Dell et al. · 2019 · The Journal of Experimental Medicine
  39. High-Throughput Screening for Substrate Specificity-Adapted Mutants of the Nisin Dehydratase NisB
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  40. Teaching 'big data' analysis to young immunologists
    Joachim Ludwig Schultze · 2015 · Nature Immunology
  41. Analysis of peripheral B cells and autoantibodies against the anti-nicotinic acetylcholine receptor derived from patients with myasthenia gravis using single-cell manipulation tools
    Tomohiro Makino, Ryuichi Nakamura, Maki Terakawa, Satoshi Muneoka, Kazuhiro Nagahira, Yuriko Nagane, Jyoji Yamate, Masakatsu Motomura, Kimiaki Utsugisawa · 2017 · PLoS ONE
  42. Unravelling adverse reactions to NSAIDs using systems biology
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  43. Identification of highly selective MMP‐14 inhibitory Fabs by deep sequencing
    Tyler Lopez, Dong Hyun Nam, Evan Kaihara, Zahid Mustafa, Xin Ge · 2017 · Biotechnology and Bioengineering
  44. Antibody-based therapies for Huntington’s disease: current status and future directions
    Hélèna L. Denis, Linda Suzanne David, Francesca Cicchetti · 2019 · Neurobiology of Disease
  45. Selectivity over coverage in de novo sequencing of IgGs
    Maurits A. den Boer, Jean‐François Greisch, Sem Tamara, Albert Bondt, Albert J. R. Heck · 2020 · Chemical Science
  46. The emerging role of biosensor-based epitope binning and mapping in antibody-based drug discovery
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  47. Comparative Analysis of B-Cell Receptor Repertoires Induced by Live Yellow Fever Vaccine in Young and Middle-Age Donors
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  48. A facile technology for the high-throughput sequencing of the paired VH:VL and TCRβ:TCRα repertoires
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  49. Analysis of microbial community structure and volatile compounds in pit mud used for manufacturing Taorong-type Baijiu based on high-throughput sequencing
    Yanbo Liu, Mengxiao Sun, Pei Hou, Wenya Wang, Xiangkun Shen, Lixin Zhang, Suna Han, Chunmei Pan · 2022 · Scientific Reports
  50. Inference of B cell clonal families using heavy/light chain pairing information
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  51. Secreted autoantibody repertoires in Sjögren's syndrome and systemic lupus erythematosus: A proteomic approach
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  52. Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion
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  53. Enhancing Antibody Language Models with Structural Information
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  58. Application of recombinant antibodies for treatment of Clostridioides difficile infection: Current status and future perspective
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  59. Monitoring Pharmacologically Induced Immunosuppression by Immune Repertoire Sequencing to Detect Acute Allograft Rejection in Heart Transplant Patients: A Proof-of-Concept Diagnostic Accuracy Study
    Christopher Vollmers, Iwijn De Vlaminck, Hannah A. Valantine, Lolita Penland, Helen I. Luikart, Calvin Strehl, Garrett Cohen, Kiran K. Khush, Stephen R. Quake · 2015 · PLoS Medicine
  60. Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads
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  64. Different B cell subpopulations show distinct patterns in their IgH repertoire metrics
    Marie Ghraichy, Valentin von Niederhäusern, Aleksandr Kovaltsuk, Jacob D. Galson, Charlotte Mary Deane, Johannes Trück · 2021 · eLife
  65. Systems integration of innate and adaptive immunity
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  67. IgGM: A Generative Model for Functional Antibody and Nanobody Design
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  98. Computational Approaches and Challenges to Developing Universal Influenza Vaccines
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