Cleavage-intermediate Lassa virus trimer elicits neutralizing responses, identifies neutralizing nanobodies, and reveals an apex-situated site-of-vulnerability

Authors: Jason Gorman, Crystal Sao-Fong Cheung, Zhijian Duan, Li Ou, Maple Wang, Xuejun Chen, Cheng Cheng, Andrea Biju, Yaping Sun, Pengfei Wang, Yongping Yang, Baoshan Zhang, Jeffrey C. Boyington, Tatsiana Bylund, Sam Charaf, Steven J. Chen, Haijuan Du, Amy R. Henry, Tracy Liu, Edward K. Sarfo, Chaim A. Schramm, Chen-Hsiang Shen, Tyler Stephens, I-Ting Teng, John-Paul Todd, Yaroslav Tsybovsky, Raffaello Verardi, Danyi Wang, Shuishu Wang, Zhantong Wang, Cheng-Yan Zheng, Tongqing Zhou, Daniel C. Douek, John R. Mascola, David D. Ho, Mitchell Ho, Peter D. Kwong

Source: Nature Communications, Vol 15, Iss 1, Pp 1-16 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/83f13599c74f445ebfcd24f0985fef96

Interaction dynamics between innate and adaptive immune cells responding to SARS-CoV-2 vaccination in non-human primates

Authors: Chaim A. Schramm, Damee Moon, Lowrey Peyton, Noemia S. Lima, Christian Wake, Kristin L. Boswell, Amy R. Henry, Farida Laboune, David Ambrozak, Samuel W. Darko, I-Ting Teng, Kathryn E. Foulds, Andrea Carfi, Darin K. Edwards, Peter D. Kwong, Richard A. Koup, Robert A. Seder, Daniel C. Douek

Source: Nature Communications, Vol 14, Iss 1, Pp 1-17 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/5c17ee640e21465b8f13ef277281b87f

High frequency of HIV precursor-target-specific B cells in sub-Saharan populations

Authors: Flavio Matassoli, Alberto Cagigi, Chen-Hsiang Shen, Amy R. Henry, Timothy S. Johnston, Chaim A. Schramm, Christopher A. Cottrell, Oleksandr Kalyuzhniy, Abby Spangler, Leigh Eller, Merlin Robb, Michael Eller, Prossy Naluyima, Peter D. Kwong, Daniel C. Douek, William R. Schief, Sarah F. Andrews, Adrian B. McDermott

Source: Cell Reports, Vol 42, Iss 12, Pp 113450- (2023)

Subject Terms: CP: Immunology, CP: Microbiology, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124723014626; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/eb4e28b80f1b4f7e8299b3bde7fa669f

Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones

Authors: Noemia S. Lima, Maryam Musayev, Timothy S. Johnston, Danielle A. Wagner, Amy R. Henry, Lingshu Wang, Eun Sung Yang, Yi Zhang, Kevina Birungi, Walker P. Black, Sijy O’Dell, Stephen D. Schmidt, Damee Moon, Cynthia G. Lorang, Bingchun Zhao, Man Chen, Kristin L. Boswell, Jesmine Roberts-Torres, Rachel L. Davis, Lowrey Peyton, Sandeep R. Narpala, Sarah O’Connell, Leonid Serebryannyy, Jennifer Wang, Alexander Schrager, Chloe Adrienna Talana, Geoffrey Shimberg, Kwanyee Leung, Wei Shi, Rawan Khashab, Asaf Biber, Tal Zilberman, Joshua Rhein, Sara Vetter, Afeefa Ahmed, Laura Novik, Alicia Widge, Ingelise Gordon, Mercy Guech, I-Ting Teng, Emily Phung, Tracy J. Ruckwardt, Amarendra Pegu, John Misasi, Nicole A. Doria-Rose, Martin Gaudinski, Richard A. Koup, Peter D. Kwong, Adrian B. McDermott, Sharon Amit, Timothy W. Schacker, Itzchak Levy, John R. Mascola, Nancy J. Sullivan, Chaim A. Schramm, Daniel C. Douek

Source: Nature Communications, Vol 13, Iss 1, Pp 1-14 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b6d4d09b5933465b8ae8f4b440a22b6a

The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons

Authors: Scott Christley, Ademar Aguiar, George Blanck, Felix Breden, Syed Ahmad Chan Bukhari, Christian E. Busse, Jerome Jaglale, Srilakshmy L. Harikrishnan, Uri Laserson, Bjoern Peters, Artur Rocha, Chaim A. Schramm, Sarah Taylor, Jason Anthony Vander Heiden, Bojan Zimonja, Corey T. Watson, Brian Corrie, Lindsay G. Cowell

Source: Frontiers in Big Data, Vol 3 (2020)

Subject Terms: community standards, data sharing, immunology, Rep-Seq, repertoire analysis, antibody, Information technology, T58.5-58.64

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fdata.2020.00022/full; https://doaj.org/toc/2624-909X

Access URL: https://doaj.org/article/11a666e9b5fc4c998941829a06ba9514

HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies

Authors: Kimmo Rantalainen, Zachary T. Berndsen, Aleksandar Antanasijevic, Torben Schiffner, Xi Zhang, Wen-Hsin Lee, Jonathan L. Torres, Lei Zhang, Adriana Irimia, Jeffrey Copps, Kenneth H. Zhou, Young D. Kwon, William H. Law, Chaim A. Schramm, Raffaello Verardi, Shelly J. Krebs, Peter D. Kwong, Nicole A. Doria-Rose, Ian A. Wilson, Michael B. Zwick, John R. Yates, III, William R. Schief, Andrew B. Ward

Source: Cell Reports, Vol 31, Iss 4, Pp - (2020)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124720305325; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/d9f16fbf109a4f2f9110c0d89c79dd68

Sequencing HIV-neutralizing antibody exons and introns reveals detailed aspects of lineage maturation

Authors: Erik L. Johnson, Nicole A. Doria-Rose, Jason Gorman, Jinal N. Bhiman, Chaim A. Schramm, Ashley Q. Vu, William H. Law, Baoshan Zhang, Valerie Bekker, Salim S. Abdool Karim, Gregory C. Ippolito, Lynn Morris, Penny L. Moore, Peter D. Kwong, John R. Mascola, George Georgiou

Source: Nature Communications, Vol 9, Iss 1, Pp 1-13 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/a62bf922ef2c4169b0b995d4e2ae1f37

sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation

Authors: Branden J. Olson, Pejvak Moghimi, Chaim A. Schramm, Anna Obraztsova, Duncan Ralph, Jason A. Vander Heiden, Mikhail Shugay, Adrian J. Shepherd, William Lees, Frederick A. Matsen

Source: Frontiers in Immunology, Vol 10 (2019)

Subject Terms: repertoire comparison, model validation, rep-seq, B cell receptor, T cell receptor, summary statistics, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fimmu.2019.02533/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/22073bd60c67415fa63b32924d8b4d9e

Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming

Authors: Mats Ohlin, Cathrine Scheepers, Martin Corcoran, William D. Lees, Christian E. Busse, Davide Bagnara, Linnea Thörnqvist, Jean-Philippe Bürckert, Katherine J. L. Jackson, Duncan Ralph, Chaim A. Schramm, Nishanth Marthandan, Felix Breden, Jamie Scott, Frederick A. Matsen IV, Victor Greiff, Gur Yaari, Steven H. Kleinstein, Scott Christley, Jacob S. Sherkow, Sofia Kossida, Marie-Paule Lefranc, Menno C. van Zelm, Corey T. Watson, Andrew M. Collins

Source: Frontiers in Immunology, Vol 10 (2019)

Subject Terms: immunoglobulin, allelic variation, inference, AIRR-seq, IGHV, V(D)J rearrangement, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fimmu.2019.00435/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/ff5064523d2c4931a175eb46313164cf

Design of Nanoparticulate Group 2 Influenza Virus Hemagglutinin Stem Antigens That Activate Unmutated Ancestor B Cell Receptors of Broadly Neutralizing Antibody Lineages

Authors: Kizzmekia S. Corbett, Syed M. Moin, Hadi M. Yassine, Alberto Cagigi, Masaru Kanekiyo, Seyhan Boyoglu-Barnum, Sky I. Myers, Yaroslav Tsybovsky, Adam K. Wheatley, Chaim A. Schramm, Rebecca A. Gillespie, Wei Shi, Lingshu Wang, Yi Zhang, Sarah F. Andrews, M. Gordon Joyce, Michelle C. Crank, Daniel C. Douek, Adrian B. McDermott, John R. Mascola, Barney S. Graham, Jeffrey C. Boyington

Source: mBio, Vol 10, Iss 1 (2019)

Subject Terms: hemagglutinin, influenza, influenza vaccines, nanoparticle, protein engineering, vaccine design, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/cd997d727dab4f9a9bff7e2660bf416f

AIRR Community Standardized Representations for Annotated Immune Repertoires

Authors: Jason Anthony Vander Heiden, Susanna Marquez, Nishanth Marthandan, Syed Ahmad Chan Bukhari, Christian E. Busse, Brian Corrie, Uri Hershberg, Steven H. Kleinstein, Frederick A. Matsen IV, Duncan K. Ralph, Aaron M. Rosenfeld, Chaim A. Schramm, The AIRR Community, Scott Christley, Uri Laserson

Source: Frontiers in Immunology, Vol 9 (2018)

Subject Terms: antibody, immunoglobulin, T cell, B cell, immunology, repertoire, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fimmu.2018.02206/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/53c34074047c4f109683661e2d2ed682

Beyond Hot Spots: Biases in Antibody Somatic Hypermutation and Implications for Vaccine Design

Authors: Chaim A. Schramm, Daniel C. Douek

Source: Frontiers in Immunology, Vol 9 (2018)

Subject Terms: somatic hypermutation, hot spot motifs, affinity maturation, substitution profiles, vaccine design, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fimmu.2018.01876/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/6d8cb59c27fe4244ae1462c6dc575f64

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data

Authors: Felix Breden, Eline T. Luning Prak, Bjoern Peters, Florian Rubelt, Chaim A. Schramm, Christian E. Busse, Jason A. Vander Heiden, Scott Christley, Syed Ahmad Chan Bukhari, Adrian Thorogood, Frederick A. Matsen IV, Yariv Wine, Uri Laserson, David Klatzmann, Daniel C. Douek, Marie-Paule Lefranc, Andrew M. Collins, Tania Bubela, Steven H. Kleinstein, Corey T. Watson, Lindsay G. Cowell, Jamie K. Scott, Thomas B. Kepler

Source: Frontiers in Immunology, Vol 8 (2017)

Subject Terms: B-cell receptors, T-cell receptors, data sharing, immunogenetics, community standards, high-throughput sequencing, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: http://journal.frontiersin.org/article/10.3389/fimmu.2017.01418/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/baa46033725a4e99b5a18b8f93cfffdc

Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation

Authors: Zizhang Sheng, Chaim A. Schramm, Rui Kong, NISC Comparative Sequencing Program, James C. Mullikin, John R. Mascola, Peter D. Kwong, Lawrence Shapiro

Source: Frontiers in Immunology, Vol 8 (2017)

Subject Terms: antibodyomics, B cell ontogeny, broadly neutralizing antibody, mutation frequency, repertoire diversity, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: http://journal.frontiersin.org/article/10.3389/fimmu.2017.00537/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/9a95ccfe3d4b48bf82d151153d8360a0

Broad coverage of neutralization-resistant SIV strains by second-generation SIV-specific antibodies targeting the region involved in binding CD4.

Authors: Hugh C Welles, Hannah A D King, Leonard Nettey, Nicole Cavett, Jason Gorman, Tongqing Zhou, Yaroslav Tsybovsky, Renguang Du, Kaimei Song, Richard Nguyen, David Ambrozak, Amy Ransier, Chaim A Schramm, Nicole A Doria-Rose, Adrienne E Swanstrom, James A Hoxie, Celia LaBranche, David C Montefiori, Daniel C Douek, Peter D Kwong, John R Mascola, Mario Roederer, Rosemarie D Mason

Source: PLoS Pathogens, Vol 18, Iss 6, p e1010574 (2022)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/4be5c204019f42f9a419f3dd8f3193f7

SONAR: A high-throughput pipeline for inferring antibody ontogenies from longitudinal sequencing of B cell transcripts

Authors: Chaim A Schramm, Zizhang Sheng, Zhenhai Zhang, John R Mascola, Peter D Kwong, Lawrence Shapiro

Source: Frontiers in Immunology, Vol 7 (2016)

Subject Terms: Next-generation sequencing, Antibody repertoire, antibody maturation, longitudinal analysis, antibody lineage, b cell ontogeny, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: http://journal.frontiersin.org/Journal/10.3389/fimmu.2016.00372/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/ddc58ef0924347eab6870b1952451d0b

Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection.

Authors: Zizhang Sheng, Chaim A Schramm, Mark Connors, Lynn Morris, John R Mascola, Peter D Kwong, Lawrence Shapiro

Source: PLoS Computational Biology, Vol 12, Iss 5, p e1004940 (2016)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004940&type=printable; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/d1cba16dd2ce4ed2a7ec0bab1275cfc9