Search Results - "Kleinstein, Steven H."

A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data by Nouri, Nima, Kleinstein, Steven H

“…Abstract Motivation B cells derive their antigen-specificity through the expression of Immunoglobulin (Ig) receptors on their surface. These receptors are…”
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Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data by Gupta, Namita T, Vander Heiden, Jason A, Uduman, Mohamed, Gadala-Maria, Daniel, Yaari, Gur, Kleinstein, Steven H

“…Advances in high-throughput sequencing technologies now allow for large-scale characterization of B cell immunoglobulin (Ig) repertoires. The high germline and…”
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Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles by Gadala-Maria, Daniel, Yaari, Gur, Uduman, Mohamed, Kleinstein, Steven H.

“…Individual variation in germline and expressed B-cell immunoglobulin (Ig) repertoires has been associated with aging, disease susceptibility, and differential…”
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Phylogenetic analysis of migration, differentiation, and class switching in B cells by Hoehn, Kenneth B, Pybus, Oliver G, Kleinstein, Steven H

“…B cells undergo rapid mutation and selection for antibody binding affinity when producing antibodies capable of neutralizing pathogens. This evolutionary…”
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Quantifying selection in high-throughput Immunoglobulin sequencing data sets by Yaari, Gur, Uduman, Mohamed, Kleinstein, Steven H

“…High-throughput immunoglobulin sequencing promises new insights into the somatic hypermutation and antigen-driven selection processes that underlie B-cell…”
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Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses by Ho, Ping-Chih, Bihuniak, Jessica Dauz, Macintyre, Andrew N., Staron, Matthew, Liu, Xiaojing, Amezquita, Robert, Tsui, Yao-Chen, Cui, Guoliang, Micevic, Goran, Perales, Jose C., Kleinstein, Steven H., Abel, E. Dale, Insogna, Karl L., Feske, Stefan, Locasale, Jason W., Bosenberg, Marcus W., Rathmell, Jeffrey C., Kaech, Susan M.

“…Activated T cells engage aerobic glycolysis and anabolic metabolism for growth, proliferation, and effector functions. We propose that a glucose-poor tumor…”
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Language model-based B cell receptor sequence embeddings can effectively encode receptor specificity by Wang, Meng, Patsenker, Jonathan, Li, Henry, Kluger, Yuval, Kleinstein, Steven H

“…Abstract High throughput sequencing of B cell receptors (BCRs) is increasingly applied to study the immense diversity of antibodies. Learning biologically…”
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Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders by Brioschi, Simone, Wang, Wei-Le, Peng, Vincent, Wang, Meng, Shchukina, Irina, Greenberg, Zev J, Bando, Jennifer K, Jaeger, Natalia, Czepielewski, Rafael S, Swain, Amanda, Mogilenko, Denis A, Beatty, Wandy L, Bayguinov, Peter, Fitzpatrick, James A J, Schuettpelz, Laura G, Fronick, Catrina C, Smirnov, Igor, Kipnis, Jonathan, Shapiro, Virginia S, Wu, Gregory F, Gilfillan, Susan, Cella, Marina, Artyomov, Maxim N, Kleinstein, Steven H, Colonna, Marco

“…The meninges contain adaptive immune cells that provide immunosurveillance of the central nervous system (CNS). These cells are thought to derive from the…”
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Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data by Nouri, Nima, Kleinstein, Steven H

“…Adaptive immune receptor repertoire sequencing (AIRR-Seq) offers the possibility of identifying and tracking B cell clonal expansions during adaptive immune…”
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Migrant memory B cells secrete luminal antibody in the vagina by Oh, Ji Eun, Iijima, Norifumi, Song, Eric, Lu, Peiwen, Klein, Jonathan, Jiang, Ruoyi, Kleinstein, Steven H., Iwasaki, Akiko

“…Antibodies secreted into mucosal barriers serve to protect the host from a variety of pathogens, and are the basis for successful vaccines 1 . In type I mucosa…”
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Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation by Di Niro, Roberto, Lee, Seung-Joo, Vander Heiden, Jason A., Elsner, Rebecca A., Trivedi, Nikita, Bannock, Jason M., Gupta, Namita T., Kleinstein, Steven H., Vigneault, Francois, Gilbert, Tamara J., Meffre, Eric, McSorley, Stephen J., Shlomchik, Mark J.

“…The B cell response to Salmonella typhimurium (STm) occurs massively at extrafollicular sites, without notable germinal centers (GCs). Little is known in terms…”
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pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires by Vander Heiden, Jason A, Yaari, Gur, Uduman, Mohamed, Stern, Joel N H, O'Connor, Kevin C, Hafler, David A, Vigneault, Francois, Kleinstein, Steven H

“…Driven by dramatic technological improvements, large-scale characterization of lymphocyte receptor repertoires via high-throughput sequencing is now feasible…”
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Dynamic expression profiling of type I and type III interferon‐stimulated hepatocytes reveals a stable hierarchy of gene expression by Bolen, Christopher R., Ding, Siyuan, Robek, Michael D., Kleinstein, Steven H.

“…Despite activating similar signaling cascades, the type I and type III interferons (IFNs) differ in their ability to antagonize virus replication. However, it…”
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Differential Expression of Ly6C and T-bet Distinguish Effector and Memory Th1 CD4 + Cell Properties during Viral Infection by Marshall, Heather D., Chandele, Anmol, Jung, Yong Woo, Meng, Hailong, Poholek, Amanda C., Parish, Ian A., Rutishauser, Rachel, Cui, Weiguo, Kleinstein, Steven H., Craft, Joe, Kaech, Susan M.

“…CD4 + T cells differentiate into multiple effector types, but it is unclear how they form memory T cells during infection in vivo. Profiling virus-specific CD4…”
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Germinal Center B Cell and T Follicular Helper Cell Development Initiates in the Interfollicular Zone by Kerfoot, Steven M., Yaari, Gur, Patel, Jaymin R., Johnson, Kody L., Gonzalez, David G., Kleinstein, Steven H., Haberman, Ann M.

“…We identify the interfollicular (IF) zone as the site where germinal center B cell and T follicular helper (Tfh) cell differentiation initiates. For the first…”
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Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination by Hoehn, Kenneth B., Vander Heiden, Jason A., Zhou, Julian Q., Lunter, Gerton, Pybus, Oliver G., Kleinstein, Steven H.

“…In order to produce effective antibodies, B cells undergo rapid somatic hypermutation (SHM) and selection for binding affinity to antigen via a process called…”
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B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes by Stern, Joel N H, Yaari, Gur, Vander Heiden, Jason A, Church, George, Donahue, William F, Hintzen, Rogier Q, Huttner, Anita J, Laman, Jon D, Nagra, Rashed M, Nylander, Alyssa, Pitt, David, Ramanan, Sriram, Siddiqui, Bilal A, Vigneault, Francois, Kleinstein, Steven H, Hafler, David A, O'Connor, Kevin C

“…Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) characterized by autoimmune-mediated demyelination and…”
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A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures by Newton, Adam J H, Chartash, David, Kleinstein, Steven H, McDougal, Robert A

“…The accelerating pace of biomedical publication has made it impractical to manually, systematically identify papers containing specific information and extract…”
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Two levels of protection for the B cell genome during somatic hypermutation by Schatz, David G, Liu, Man, Duke, Jamie L, Richter, Daniel J, Vinuesa, Carola G, Goodnow, Christopher C, Kleinstein, Steven H

“…Somatic hypermutation introduces point mutations into immunoglobulin genes in germinal centre B cells during an immune response. The reaction is initiated by…”
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Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children by Xu, Qin, Milanez-Almeida, Pedro, Martins, Andrew J., Radtke, Andrea J., Hoehn, Kenneth B., Oguz, Cihan, Chen, Jinguo, Liu, Can, Tang, Juanjie, Grubbs, Gabrielle, Stein, Sydney, Ramelli, Sabrina, Kabat, Juraj, Behzadpour, Hengameh, Karkanitsa, Maria, Spathies, Jacquelyn, Kalish, Heather, Kardava, Lela, Kirby, Martha, Cheung, Foo, Preite, Silvia, Duncker, Patrick C., Kitakule, Moses M., Romero, Nahir, Preciado, Diego, Gitman, Lyuba, Koroleva, Galina, Smith, Grace, Shaffer, Arthur, McBain, Ian T., McGuire, Peter J., Pittaluga, Stefania, Germain, Ronald N., Apps, Richard, Schwartz, Daniella M., Sadtler, Kaitlyn, Moir, Susan, Chertow, Daniel S., Kleinstein, Steven H., Khurana, Surender, Tsang, John S., Mudd, Pamela, Schwartzberg, Pamela L., Manthiram, Kalpana

“…Most studies of adaptive immunity to SARS-CoV-2 infection focus on peripheral blood, which may not fully reflect immune responses at the site of infection…”
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