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Laurence Jn, Varadarajan Navin, Meyer Daniel D", "reference": { "type": "PubMed", "id": "35297693", "url": "https://pubmed.ncbi.nlm.nih.gov/35297693" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.35297693", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", 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respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.35371042", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", 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"glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit.", "journal": "Communications 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human coronaviruses and presented by common HLA alleles.", "journal": "Cell reports", "date": "2022-06-14", "authors": "Becerra-Artiles Aniuska, Calvo-Calle J Mauricio, Co Mary Dawn, Nanaware Padma P, Cruz John, Weaver Grant C, Lu Liying, Forconi Catherine, Finberg Robert W, Moormann Ann M, Stern Lawrence J", "reference": { "type": "PubMed", "id": "35675811", "url": "https://pubmed.ncbi.nlm.nih.gov/35675811" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.35675811", "abstract": "", "glycosylation": 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"count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Longitudinal Assessment of SARS-CoV-2-Specific T Cell Cytokine-Producing Responses for 1 Year Reveals Persistence of Multicytokine Proliferative Responses, with Greater Immunity Associated with Disease Severity.", "journal": "Journal of virology", "date": 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"count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": 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"field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 1 }, { "field": "exact_o_linked_sites", "count": 1 }, { "field": "fuzzy_sites", "count": 0 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_pos", "start_aa", "end_pos", "end_aa", "residue", "site_lbl", "mining_tool", "filter_code", "uniprot_canonical_ac" ] } ] }, { "title": "Pathogen-sugar interactions 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"o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Exosomal Vaccine Loading T Cell Epitope Peptides of SARS-CoV-2 Induces Robust CD8+ T Cell Response in HLA-A Transgenic Mice.", "journal": "International journal of nanomedicine", "date": "2022", "authors": "Shen An-Ran, Jin Xiao-Xiao, Tang Tao-Tao, Ding Yan, Liu Xiao-Tao, Zhong Xin, Wu Yan-Dan, Han Xue-Lian, Zhao Guang-Yu, Shen Chuan-Lai, Lv Lin-Li, Liu Bi-Cheng", "reference": { "type": "PubMed", "id": "35937077", "url": "https://pubmed.ncbi.nlm.nih.gov/35937077" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC4-1", "protein_name": "Envelope small membrane protein", "gene_name": "E", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC5-1", "protein_name": "Membrane protein", "gene_name": "M", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC9-1", "protein_name": "Nucleoprotein", "gene_name": "N", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTD1-1", "protein_name": "Replicase polyprotein 1ab", "gene_name": "rep", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": 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T cells specific for SARS-CoV-2 in individuals who received the BNT162b2 mRNA vaccine.", "journal": "Nature communications", "date": "2022-09-06", "authors": "Kuse Nozomi, Zhang Yu, Chikata Takayuki, Nguyen Hung The, Oka Shinichi, Gatanaga Hiroyuki, Takiguchi Masafumi", "reference": { "type": "PubMed", "id": "36068240", "url": "https://pubmed.ncbi.nlm.nih.gov/36068240" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.36068240", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], 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Horowitz Joseph J, Samet Ron E, Zyskind Israel, Rosenberg Avi Z, Schneck Jonathan P", "reference": { "type": "PubMed", "id": "36134660", "url": "https://pubmed.ncbi.nlm.nih.gov/36134660" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC3-1", "protein_name": "ORF3a protein", "gene_name": "3a", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC9-1", "protein_name": "Nucleoprotein", "gene_name": "N", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.36134660", "abstract": "", 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Sall Amadou Alpha, Seydi Moussa, Noirel Josselin, Moreau Gabriel, Simon Arnaud, Holenya Pavlo, Meyniel Jean-Philippe, Zagury Jean-Fran\u00e7ois, Schoenhals Matthieu", "reference": { "type": "PubMed", "id": "36646780", "url": "https://pubmed.ncbi.nlm.nih.gov/36646780" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC5-1", "protein_name": "Membrane protein", "gene_name": "M", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC9-1", "protein_name": "Nucleoprotein", "gene_name": "N", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome 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"total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Antibody isotype epitope mapping of SARS-CoV-2 Spike RBD protein: Targets for COVID-19 symptomatology and disease control.", "journal": "European journal of immunology", "date": "2023-04", "authors": "Contreras Marinela, Vicente Joaqu\u00edn, Cer\u00f3n Jos\u00e9 Joaqu\u00edn, Martinez Subiela Silvia, Urra Jos\u00e9 Miguel, Rodr\u00edguez-Del-R\u00edo Francisco J, Ferreras-Colino Elisa, Vaz-Rodrigues Rita, de Fern\u00e1ndez de Mera Isabel G, Antunes Sandra, Domingos Ana, Gort\u00e1zar Christian, de la Fuente Jos\u00e9", "reference": { "type": "PubMed", "id": "36658749", "url": "https://pubmed.ncbi.nlm.nih.gov/36658749" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": 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}, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "SARS-CoV-2 Omicron BA.4/BA.5 Mutations in Spike Leading to T Cell Escape in Recently Vaccinated Individuals.", "journal": "Viruses", "date": "2022-12-29", "authors": "Emmelot Maarten E, Vos Martijn, Boer Mardi C, Rots Nynke Y, van Els C\u00e9cile A C M, Kaaijk Patricia", "reference": { "type": "PubMed", "id": "36680141", "url": "https://pubmed.ncbi.nlm.nih.gov/36680141" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.36680141", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, 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Beatriz, Rosa Daniela Santoro, Schechtman Deborah, Nakaya Helder I, Cunha-Neto Edecio, Gadermaier Gabriele, Kalil Jorge, Coelho Ver\u00f4nica, Santos Keity Souza", "reference": { "type": "PubMed", "id": "36685521", "url": "https://pubmed.ncbi.nlm.nih.gov/36685521" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.36685521", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ 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Annalisa, Abolhassani Hassan, Jarrossay David, Uguccioni Mariagrazia, Medaglini Donata, Pan-Hammarstr\u00f6m Qiang, Calzolai Luigi, Fernandez Daniel, Baldanti Fausto, Franzetti-Pellanda Alessandra, Garzoni Christian, Sedlacek Radislav, Ruzek Daniel, Varani Luca, Cavalli Andrea, Barnes Christopher O, Robbiani Davide F", "reference": { "type": "PubMed", "id": "36701425", "url": "https://pubmed.ncbi.nlm.nih.gov/36701425" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.36701425", "abstract": "", 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"journal": "Journal of virology", "date": "2023-02-28", "authors": "Wang Xinxin, Wen Zhiyuan, Cao Huizhen, Luo Jie, Shuai Lei, Wang Chong, Ge Jinying, Wang Xijun, Bu Zhigao, Wang Jinliang", "reference": { "type": "PubMed", "id": "36779763", "url": "https://pubmed.ncbi.nlm.nih.gov/36779763" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P02786-1", "protein_name": "Transferrin receptor protein 1", "gene_name": "TFRC", "tax_name": "Human" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.36779763", "abstract": "", 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"count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "A novel mAb broadly neutralizes SARS-CoV-2 VOCs in vitro and in vivo, including the Omicron variants.", "journal": "Journal of medical virology", "date": "2023-03", "authors": "Kan Qiuqi, Lin Xian, Li Tuofan, Ke Xianliang, Jian Xiaoqin, Hou Lidan, Zhang Wenyuan, Wan Zhimin, Xie Quan, Shao Hongxia, Ye Lilin, Ye Jianqiang, Qin Aijian, Zou Zhong, Chen Quanjiao", "reference": { "type": "PubMed", "id": "36912367", "url": "https://pubmed.ncbi.nlm.nih.gov/36912367" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.36912367", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], 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cell-based vaccine protects against SARS-CoV-2 infection in a preclinical animal model.", "journal": "JCI insight", "date": "2023-04-10", "authors": "Tada Takuya, Peng Ju-Yi, Dcosta Belinda M, Landau Nathaniel R", "reference": { "type": "PubMed", "id": "37036004", "url": "https://pubmed.ncbi.nlm.nih.gov/37036004" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC9-1", "protein_name": "Nucleoprotein", "gene_name": "N", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTD1-1", "protein_name": "Replicase polyprotein 1ab", "gene_name": "rep", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", 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"glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Large libraries of single-chain trimer peptide-MHCs enable antigen-specific CD8+ T cell discovery and analysis.", "journal": "Communications biology", "date": "2023-05-16", "authors": "Chour William, Choi Jongchan, Xie Jingyi, Chaffee Mary E, Schmitt Thomas M, Finton Kathryn, DeLucia Diana C, Xu Alexander M, Su Yapeng, Chen Daniel G, Zhang Rongyu, Yuan Dan, Hong Sunga, Ng Alphonsus H C, Butler Jonah Z, Edmark Rick A, Jones Lesley C, Murray Kim M, Peng Songming, Li Guideng, Strong Roland K, Lee John K, Goldman Jason D, Greenberg Philip D, Heath James R", "reference": { "type": "PubMed", "id": "37193826", "url": "https://pubmed.ncbi.nlm.nih.gov/37193826" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTD1-1", "protein_name": "Replicase polyprotein 1ab", "gene_name": "rep", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P78358-1", "protein_name": "Cancer/testis antigen 1", "gene_name": "CTAG1A; CTAG1B", "tax_name": "Human" } ], "species": 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"Frontiers in immunology", "date": "2023", "authors": "Lie-Andersen Olivia, H\u00fcbbe Mie Linder, Subramaniam Krishanthi, Steen-Jensen Daniel, Bergmann Ann Christina, Justesen Daniel, Holmstr\u00f6m Morten Orebo, Turtle Lance, Justesen Sune, Lan\u00e7a Telma, Hansen Morten", "reference": { "type": "PubMed", "id": "37275886", "url": "https://pubmed.ncbi.nlm.nih.gov/37275886" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.37275886", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], 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Garner Lee, Wang Beibei, Yao Xuan, Felce Suet Ling, Peng Yanchun, Moore Shona, Peeters Bas W A, Rei Margarida, Canto Gomes Joao, Tomas Ana, Davidson Andrew, Semple Malcolm G, Turtle Lance C W, Openshaw Peter J M, Baillie J Kenneth, Mentzer Alexander J, Klenerman Paul, , Borrow Persephone, Dong Tao, McKeating Jane A, Gillespie Geraldine M, McMichael Andrew J", "reference": { "type": "PubMed", "id": "37390223", "url": "https://pubmed.ncbi.nlm.nih.gov/37390223" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTD1-1", "protein_name": "Replicase polyprotein 1ab", "gene_name": "rep", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": 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"sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry.", "journal": "Cell", "date": "2023-08-03", "authors": "Baggen Jim, Jacquemyn Maarten, Persoons Leentje, Vanstreels Els, Pye Valerie E, Wrobel Antoni G, Calvaresi Valeria, Martin Stephen R, Roustan Chlo\u00eb, Cronin Nora B, Reading Eamonn, Thibaut Hendrik Jan, Vercruysse Thomas, Maes Piet, De Smet Frederik, Yee Angie, Nivitchanyong Toey, Roell Marina, Franco-Hernandez Natalia, Rhinn Herve, Mamchak Alusha Andre, Ah Young-Chapon Maxime, Brown Eric, Cherepanov Peter, Daelemans Dirk", "reference": { "type": "PubMed", "id": "37421949", "url": "https://pubmed.ncbi.nlm.nih.gov/37421949" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "Q9NUM4-1", "protein_name": "Transmembrane protein 106B", "gene_name": "TMEM106B", "tax_name": "Human" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ 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"o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection.", "journal": "Nature", "date": "2023-08", "authors": "Augusto Danillo G, Murdolo Lawton D, Chatzileontiadou Demetra S M, Sabatino Joseph J, Yusufali Tasneem, Peyser Noah D, Butcher Xochitl, Kizer Kerry, Guthrie Karoline, Murray Victoria W, Pae Vivian, Sarvadhavabhatla Sannidhi, Beltran Fiona, Gill Gurjot S, Lynch Kara L, Yun Cassandra, Maguire Colin T, Peluso Michael J, Hoh Rebecca, Henrich Timothy J, Deeks Steven G, Davidson Michelle, Lu Scott, Goldberg Sarah A, Kelly J Daniel, Martin Jeffrey N, Vierra-Green Cynthia A, Spellman Stephen R, Langton David J, Dewar-Oldis Michael J, Smith Corey, Barnard Peter J, Lee Sulggi, Marcus Gregory M, Olgin Jeffrey E, Pletcher Mark J, Maiers Martin, Gras Stephanie, Hollenbach Jill A", "reference": { "type": "PubMed", "id": "37468623", "url": "https://pubmed.ncbi.nlm.nih.gov/37468623" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC5-1", "protein_name": "Membrane protein", "gene_name": "M", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.37468623", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": 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Elke, Rammensee Hans-Georg, Salih Helmut R, Walz Juliane S", "reference": { "type": "PubMed", "id": "37596280", "url": "https://pubmed.ncbi.nlm.nih.gov/37596280" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC4-1", "protein_name": "Envelope small membrane protein", "gene_name": "E", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC5-1", "protein_name": "Membrane protein", "gene_name": "M", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC8-1", "protein_name": "ORF8 protein", "gene_name": "8", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC9-1", "protein_name": "Nucleoprotein", "gene_name": "N", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": 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"total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "SARS-CoV-2 Spike protein peptides displayed in the Pyrococcus furiosus RAD system preserve epitopes antigenicity, immunogenicity, and virus-neutralizing activity of antibodies.", "journal": "Scientific reports", "date": "2023-10-05", "authors": "Cioffi Victor Bolsanelli, de Castro-Amarante Maria Fernanda, Lulla Aleksei, Andreata-Santos Robert, Cruz Mario Costa, Moreno Ana Carolina Ramos, de Oliveira Silva Mari\u00e2ngela, de Miranda Peres Bianca, de Freitas Junior Lucio Holanda Gondim, Moraes Carolina Borsoi, Durigon Edison Luiz, Gordon Nicola Coker, Hyv\u00f6nen Marko, de Souza Ferreira Lu\u00eds Carlos, Balan Andrea", "reference": { "type": "PubMed", "id": "37798298", "url": "https://pubmed.ncbi.nlm.nih.gov/37798298" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.37798298", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": 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"glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "SARS-CoV-2 spike protein-derived immunogenic peptides that are promiscuously presented by several HLA-class II molecules and their potential for inducing acquired immunity.", "journal": "Heliyon", "date": "2023-09", "authors": "Yajima Yuki, Kosaka Akemi, Ohkuri Takayuki, Hirohashi Yoshihiko, Li Dongliang, Nagasaki Takeshi, Nagato Toshihiro, Torigoe Toshihiko, Kobayashi Hiroya", "reference": { "type": "PubMed", "id": "37809871", "url": "https://pubmed.ncbi.nlm.nih.gov/37809871" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.37809871", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { 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"total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": 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"count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Engineered immunogens to elicit antibodies against conserved coronavirus epitopes.", "journal": "Nature communications", "date": "2023-11-30", "authors": "Kapingidza A Brenda, Marston Daniel J, Harris Caitlin, Wrapp Daniel, Winters Kaitlyn, Mielke Dieter, Xiaozhi Lu, Yin Qi, Foulger Andrew, Parks Rob, Barr Maggie, Newman Amanda, Sch\u00e4fer Alexandra, Eaton Amanda, Flores Justine Mae, Harner Austin, Catanzaro Nicholas J, Mallory Michael L, Mattocks Melissa D, Beverly Christopher, Rhodes Brianna, Mansouri Katayoun, Van Itallie Elizabeth, Vure Pranay, Dunn Brooke, Keyes Taylor, Stanfield-Oakley Sherry, Woods Christopher W, Petzold Elizabeth A, Walter Emmanuel B, Wiehe Kevin, Edwards Robert J, Montefiori David C, Ferrari Guido, Baric Ralph, Cain Derek W, Saunders Kevin O, Haynes Barton F, Azoitei Mihai L", "reference": { "type": "PubMed", "id": "38036525", "url": "https://pubmed.ncbi.nlm.nih.gov/38036525" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.38036525", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", 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"total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "The HLA-II immunopeptidome of SARS-CoV-2.", "journal": "Cell reports", "date": "2024-01-23", "authors": "Weingarten-Gabbay Shira, Chen Da-Yuan, Sarkizova Siranush, Taylor Hannah B, Gentili Matteo, Hernandez Gabrielle M, Pearlman Leah R, Bauer Matthew R, Rice Charles M, Clauser Karl R, Hacohen Nir, Carr Steven A, Abelin Jennifer G, Saeed Mohsan, Sabeti Pardis C", "reference": { "type": "PubMed", "id": "38117652", "url": "https://pubmed.ncbi.nlm.nih.gov/38117652" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC5-1", "protein_name": "Membrane protein", "gene_name": "M", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC6-1", "protein_name": "ORF6 protein", "gene_name": "6", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC9-1", "protein_name": "Nucleoprotein", "gene_name": "N", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTD1-1", "protein_name": "Replicase polyprotein 1ab", "gene_name": "rep", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTG1-1", 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"total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { 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}, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Ad5-nCoV Vaccination Could Induce HLA-E Restricted CD8+ T Cell Responses Specific for Epitopes on Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein.", "journal": "Viruses", "date": "2023-12-28", "authors": "Wang Yuling, Yang Lu, Tang Kang, Zhang Yusi, Zhang Chunmei, Zhang Yun, Jin Boquan, Zhang Yuan, Zhuang Ran, Ma Ying", "reference": { "type": "PubMed", "id": "38257752", "url": "https://pubmed.ncbi.nlm.nih.gov/38257752" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", 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"CD8+ T\u00a0cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by shifts in clonal dominance.", "journal": "Cell reports", "date": "2024-03-26", "authors": "Aoki Hiroyasu, Kitabatake Masahiro, Abe Haruka, Xu Peng, Tsunoda Mikiya, Shichino Shigeyuki, Hara Atsushi, Ouji-Sageshima Noriko, Motozono Chihiro, Ito Toshihiro, Matsushima Kouji, Ueha Satoshi", "reference": { "type": "PubMed", "id": "38458195", "url": "https://pubmed.ncbi.nlm.nih.gov/38458195" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 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Xu, Shao Jiahao, Wang Kejia", "reference": { "type": "PubMed", "id": "38539271", "url": "https://pubmed.ncbi.nlm.nih.gov/38539271" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC9-1", "protein_name": "Nucleoprotein", "gene_name": "N", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.38539271", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": 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"n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Early acquisition of S-specific Tfh clonotypes after SARS-CoV-2 vaccination is associated with the longevity of anti-S antibodies.", "journal": "eLife", "date": "2024-05-08", "authors": "Lu Xiuyuan, Hayashi Hiroki, Ishikawa Eri, Takeuchi Yukiko, Dychiao Julian Vincent Tabora, Nakagami Hironori, Yamasaki Sho", "reference": { "type": "PubMed", "id": "38716629", "url": "https://pubmed.ncbi.nlm.nih.gov/38716629" }, 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"protein_name": "HLA class I histocompatibility antigen, A alpha chain", "gene_name": "HLA-A", "tax_name": "Human" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.38885041", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { 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[] } ] }, { "title": "T Cell Peptide Prediction, Immune Response, and Host-Pathogen Relationship in Vaccinated and Recovered from Mild COVID-19 Subjects.", "journal": "Biomolecules", "date": "2024-09-26", "authors": "Macchia Iole, La Sorsa Valentina, Ciervo Alessandra, Ruspantini Irene, Negri Donatella, Borghi Martina, De Angelis Maria Laura, Luciani Francesca, Martina Antonio, Taglieri Silvia, Durastanti Valentina, Altavista Maria Concetta, Urbani Francesca, Mancini Fabiola", "reference": { "type": "PubMed", "id": "39456150", "url": "https://pubmed.ncbi.nlm.nih.gov/39456150" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTD1-1", "protein_name": "Replicase polyprotein 1ab", "gene_name": "rep", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.39456150", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { 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"count": 0 } ], "sort_fields": [] } ] }, { "title": "Staggered immunization with mRNA vaccines encoding SARS-CoV-2 polymerase or spike antigens broadens the T cell epitope repertoire.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-12-03", "authors": "Abt Evan R, Lam Alex K, Noguchi Miyako, Rashid Khalid, McLaughlin Jami, Teng Pu-Lin, Tran Wendy, Cheng Donghui, Nesterenko Pavlo A, Mao Zhiyuan, Creech Amanda L, Burton Sojo Giselle, Jeyachandran Arjit Vijey, Tam Ying K, Henley Jill E, Comai Lucio, Pardi Norbert, Arumugaswami Vaithilingaraja, Witte Owen N, Radu Caius G, Wu Ting-Ting", "reference": { "type": "PubMed", "id": "39589869", "url": "https://pubmed.ncbi.nlm.nih.gov/39589869" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC2-1", "protein_name": "Spike glycoprotein", "gene_name": "S", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTD1-1", "protein_name": "Replicase polyprotein 1ab", "gene_name": "rep", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.39589869", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": 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"count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": 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"count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] } ] }, { "title": "Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers.", "journal": "Nat. Struct. Mol. Biol.", "date": "2020", "authors": "Mandala Venkata S, McKay Matthew J, Shcherbakov Alexander A, Dregni Aurelio J, Kolocouris Antonios, Hong Mei", "reference": { "type": "PubMed", "id": "33177698", "url": "https://pubmed.ncbi.nlm.nih.gov/33177698" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC4-1", "protein_name": "Envelope small membrane protein", "gene_name": "E", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC4", "url": "https://www.uniprot.org/uniprotkb/P0DTC4" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.33177698", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "uniprot_canonical_ac", "protein_name", "gene_name", "tax_name" ] }, { "table_id": "referenced_glycans", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": 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Samuels Yardena", "reference": { "type": "PubMed", "id": "34166618", "url": "https://pubmed.ncbi.nlm.nih.gov/34166618" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC4-1", "protein_name": "Envelope small membrane protein", "gene_name": "E", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTD2-1", "protein_name": "ORF9b protein", "gene_name": "9b", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC4", "url": "https://www.uniprot.org/uniprotkb/P0DTC4" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.34166618", "abstract": "", "glycosylation": [], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "section_stats": [ { "table_id": "referenced_proteins", "table_stats": [ { "field": 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L\u00fctgehetmann Marc, Kwok William W, Sidney John, Schulze Zur Wiesch Julian", "reference": { "type": "PubMed", "id": "34529740", "url": "https://pubmed.ncbi.nlm.nih.gov/34529740" }, "referenced_glycans": [], "referenced_proteins": [ { "uniprot_canonical_ac": "P0DTC4-1", "protein_name": "Envelope small membrane protein", "gene_name": "E", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC5-1", "protein_name": "Membrane protein", "gene_name": "M", "tax_name": "2019-nCoV" }, { "uniprot_canonical_ac": "P0DTC9-1", "protein_name": "Nucleoprotein", "gene_name": "N", "tax_name": "2019-nCoV" } ], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC4", "url": "https://www.uniprot.org/uniprotkb/P0DTC4" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "record_id": "pubmed.34529740", "abstract": 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