{ "bcoid": "GLY_000470", "title": "SARS-CoV2 Protein Citations (UniProtKB)", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Protein Citations dataset contains publication information ...", "filename": "sarscov2_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)", "molecule": "Protein", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P0DTD2-1...", "A new corona..." ], [ "P0DTD2-1...", "SARS-CoV-2 O..." ] ], "headers": [ "uniprotkb_ca...", "title..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "P0DTD2-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTD2" ], [ "P0DTD2-1", "SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70.", "Cell. 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Immunol.", "2020", "Li Y., Zhang J., Chen H., Xie J., Han Z.G., Qi H., Wang X.N., Jiang H.W., Meng Q.F., Tao S.C., Wang P.H., Zhang H.N., Zheng Y.X.", "protein_xref_pubmed", "32728199", "protein_xref_uniprotkb", "P0DTD2" ], [ "P0DTD1-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTD1" ], [ "P0DTD1-1", "Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.", "Science", "2020", "Sun X., Zhang L., Lin D., Becker S., Drosten C., Hilgenfeld R., Curth U., Rox K., Sauerhering L.", "protein_xref_pubmed", "32198291", "protein_xref_uniprotkb", "P0DTD1" ], [ "P0DTD1-1", "Structure of Mpro from COVID-19 virus and discovery of its inhibitors.", "Nature", "2020", "Jiang H., Jin Z., Li X., Liu H., Liu M., Liu X., Wang L., Xu W., Yang H., Yang X., Yu J., Zhang L., Zhao Y., Bai F., Xu Y., Peng C., Yang K., Zhang B., Deng Y., Guddat L.W., Liu F., Rao Z., Jiang R., Xiao G., Liu X.', Duan Y., Shi Z., Du X., Qin C., Yang X.', You T.", "protein_xref_pubmed", "32272481", "protein_xref_uniprotkb", "P0DTD1" ], [ "P0DTD1-1", "Structure of replicating SARS-CoV-2 polymerase.", "Nature", "2020", "Cramer P., Farnung L., Hillen H.S., Dienemann C., Kokic G., Tegunov D.", "protein_xref_pubmed", "32438371", "protein_xref_uniprotkb", "P0DTD1" ], [ "P0DTD1-1", "Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.", "Cell", "2020", "Gao Y., Wang H., Wang Q., Wu J., Xu W., Yang H., Yang X., Zhu Y., Ge J., Huang Y., Liu Z., Yan L., Guddat L.W., Liu Q., Liu F., Rao Z., Zhu C., Gao H., Ji W., Sun Q., Fang X., Jiang B., Lou Z., Gong P., Mu A., Yang X.'", "protein_xref_pubmed", "32526208", "protein_xref_uniprotkb", "P0DTD1" ], [ "P0DTD1-1", "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", "Science", "2020", "Cheng J., Becker T., Kirchhoff F., Froehlich T., Beckmann R., Berninghausen O., Sparrer K.M.J., Ameismeier M., Buschauer R., Kratzat H., Mackens-Kiani T., Koepke L., Denk T., Hayn M., Hirschenberger M., Straub J.H., Stuerzel C.M., Thoms M.", "protein_xref_pubmed", "32680882", "protein_xref_uniprotkb", "P0DTD1" ], [ "P0DTD1-1", "Activation and evasion of type I interferon responses by SARS-CoV-2.", "Nat. 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Chem.", "2020", "Lavillette D., Cosset F.L., Zhou B., Mathieu C., Boson B., Denolly S., Legros V., Siret E.", "protein_xref_pubmed", "33229438", "protein_xref_uniprotkb", "P0DTC4" ], [ "P0DTC3-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC3" ], [ "P0DTC3-1", "beta-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway.", "Cell", "2020", "Hsu V.W., Fisher M., Perlman S., Qiu Q., Ghosh S., Pak E., Altan-Bonnet N., Fehr A.R., Kehrl J., Whittaker G.R., Achar S.R., Altan-Bonnet G., Bleck C., Dellibovi-Ragheb T.A., Kerviel A., Straus M.R., Takvorian P.M., de Haan C.A.M.", "protein_xref_pubmed", "33157038", "protein_xref_uniprotkb", "P0DTC3" ], [ "P0DTC3-1", "ORF3a of the COVID-19 virus SARS-CoV-2 blocks HOPS complex-mediated assembly of the SNARE complex required for autolysosome formation.", "Dev. 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Rep.", "2020", "Bundalovic-Torma C., Eshaghi A., Grana-Miraglia L., Groves H.E., Gubbay J.B., Gutierrez J.M., Guttman D.S., Isabel M.R., Isabel S., Patel S.N., Poutanen S.M., Poutanen T.", "protein_xref_pubmed", "32820179", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition.", "Sci. Rep.", "2020", "Ito K., Montgomery D., Woods R.J., Grant O.C.", "protein_xref_pubmed", "32929138", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Molecular Architecture of the SARS-CoV-2 Virus.", "Cell", "2020", "Chen Y., Li L., Li S., Lu X., Shi Y., Wu Z., Xu J., Zhang J., Zhang Z., Yao H., Song Y., Cheng L., Wu N., Sun C., Shi D., Lei J., Weng T., Crispin M.", "protein_xref_pubmed", "32979942", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity.", "Science", "2020", "Simons M., Helenius A., Osterlund P., Teesalu T., Kallio K., Joensuu M., Meunier F.A., Anastasina M., Balistreri G., Butcher S.J., Cantuti-Castelvetri L., Djannatian M., Franz J., Gokce O., Hepojoki J., Kallio-Kokko H., Kaya T., Kuivanen S., Levanov L., Mollenhauer B., Oesterlund P., Ojha R., Pedro L.D., Smura T., Stadelmann C., Szirovicza L., Tobi A., Vapalahti O., Winkler M.S., van der Meer F.", "protein_xref_pubmed", "33082293", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Neuropilin-1 is a host factor for SARS-CoV-2 infection.", "Science", "2020", "Cullen P.J., Klein K., Collins B.M., Sessions R.B., Matthews D.A., Yamauchi Y., Bauer M., Chen K.E., Helenius A., Teesalu T., Horvath P., Greber U.F., Williamson M.K., Anton-Plagaro C., Daly J.L., Davidson A.D., Hiscox J.A., Hollandi R., Shoemark D.K., Simon-Gracia L., Simonetti B.", "protein_xref_pubmed", "33082294", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection.", "JACC Basic Transl. Sci.", "2021", "Zheng W., Kolls J.K., Beddingfield B.J., Bix G.J., Chapagain P.P., Hu T.Y., Iwanaga N., Roy C.J.", "protein_xref_pubmed", "33102950", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Spike mutation D614G alters SARS-CoV-2 fitness.", "Nature", "2020", "Liu J., Liu Y., Zhang X., Zou J., Xie X., Xia H., Kalveram B., Shi P.Y., Johnson B.A., An Z., Lokugamage K.G., Freiberg A.N., Menachery V.D., Bilello J.P., Mirchandani D., Plante J.A., Plante K.S., Scharton D., Fontes-Garfias C.R., Weaver S.C., Ku Z., Muruato A.E.", "protein_xref_pubmed", "33106671", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "A multibasic cleavage site in the Spike protein of SARS-CoV-2 is essential for infection of human lung cells.", "Mol. Cell", "2020", "Poehlmann S., Hoffmann M., Kleine-Weber H.", "protein_xref_pubmed", "32362314", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Deducing the N- and O- glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2.", "Glycobiology", "2020", "Azadi P., Gleinich A.S., Shajahan A., Supekar N.T.", "protein_xref_pubmed", "32363391", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Site-specific glycan analysis of the SARS-CoV-2 spike.", "Science", "2020", "Watanabe Y., McLellan J.S., Allen J.D., Wrapp D., Crispin M.", "protein_xref_pubmed", "32366695", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.", "Cell", "2020", "Huang W., Li X., Liu H., Liu J., Liu S., Wang Y., Wu J., Zhang L., Zhang Q., Li Q., Lu Q., Wang M., Zhao C., Li X.', Sun Q., Nie J., Hao H., Qin H., Nie L., Zhang L.'", "protein_xref_pubmed", "32730807", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy.", "Science", "2020", "Chen S., Han G., He L., Li J., Li Y., Wang H., Wang X., Wang Y., Yang X., Zhao G., Zhao Z., Zhou X., Zhou Y., Chen Q., Guo Y., He Y., Gu H., Jiang S., Cui Y., Fan H., Li Y.', Yang G., Sun S., Sheng X., Li X.F., Teng Y., Yang X.', Deng Y.Q., Geng S., Luo D.Y., Qin C.F., Zhang N.N.", "protein_xref_pubmed", "32732280", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.", "Science", "2020", "Landry J., Beck M., Hoerner C., Bagola K., Sikora M., Hummer G., Schwarz A., Blanc F.E.C., Covino R., Gecht M., Hagen W.J.H., Krijnse Locker J., Mosalaganti S., Muehlebach M.D., Schuermann C., Turonova B., Welsch S., de Azevedo N.T.D., van Zandbergen G., von Buelow S.", "protein_xref_pubmed", "32817270", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo.", "Science", "2020", "Graham R., Nakajima N., Suzuki T., Takahashi K., Chiba S., Okuda K., Schaefer A., Kuroda M., Boucher R.C., Kawaoka Y., Randell S.H., Gralinski L.E., Hou Y.J., Baric R.S., Bartelt L., Dinnon K.H. III, Edwards C.E., Ehre C., Halfmann P., Lee R.E., Leist S.R., Margolis D.M., Markmann A.J., Mascenik T.M., Tse L.V., de Silva A.", "protein_xref_pubmed", "33184236", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "The SARS-CoV-2 Envelope and Membrane proteins modulate maturation and retention of the Spike protein, allowing assembly of virus-like particles.", "J. Biol. Chem.", "2020", "Lavillette D., Cosset F.L., Zhou B., Mathieu C., Boson B., Denolly S., Legros V., Siret E.", "protein_xref_pubmed", "33229438", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2.", "PLoS Pathog.", "2021", "Zhang L., Choe H., Farzan M., Mou H., Ojha A., Ou T.", "protein_xref_pubmed", "33465165", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction.", "Biophys. J.", "2021", "Kim S., Dong C., Cao W., Hou D., Du L., Zhang X.F., Im W., Tai W.", "protein_xref_pubmed", "33607086", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "SARS-CoV-2 spike D614G change enhances replication and transmission.", "Nature", "2021", "Wang L., Beer M., Lin X., Wilson M., Cui D., Wentworth D.E., Hoffmann D., Hoffmann B., Fan X., Keller M., Pozzi B., Zhou B., Dijkman R., King J., Jiang N., Benarafa C., Thiel V., Barnes J.R., Ebert N., Halwe N.J., Hossain J., Jores J., Kelly J.N., Labroussaa F., Pohlmann A., Portmann J., Stalder H., Stark T.J., Steiner S., Taddeo A., Thi Nhu Thao T., Thomann L., Trueeb B.S., Ulrich L., de Brot S.", "protein_xref_pubmed", "33636719", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein.", "Nature", "2021", "Martin D., Davies M.A., Godzik A., Williamson C., Hardie D., Ismail A., Hsiao M., Pillay S., Sewell B.T., Engelbrecht S., Weaver S., Lourenco J., Goedhals D., Abrahams S., Alcantara L.C.J., Alisoltani-Dehkordi A., Allam M., Bhiman J.N., Doolabh D., Fonseca V., Giandhari J., Giovanetti M., Glass A.J., Iranzadeh A., Korsman S., Kosakovsky Pond S.L., Laguda-Akingba O., Lessells R.J., Marais G., Maslo C., Mlisana K., Mohale T., Msomi N., Mudau I., Petruccione F., Preiser W., San E.J., Sigal A., Tegally H., Tyers L., Van Zyl G., Walaza S., Wibmer C.K., Wilkinson E., York D., de Oliveira T., von Gottberg A.", "protein_xref_pubmed", "33690265", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction.", "Cell Rep.", "2021", "Haynes B.F., Edwards R.J., Acharya P., Henderson R., Gobeil S.M., Janowska K., Kopp M.F., Manne K., Mansouri K., McDowell S., Parks R., Stalls V.", "protein_xref_pubmed", "33417835", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7.", "Cell Rep.", "2021", "Cameroni E., Meng B., Collier D.A., Gupta R.K., Bailey D., Mlcochova P., Robertson D.L., James L.C., Mohamed A., Thakur N., Duncan L.M., Matheson N.J., Marelli S., Gallo G., Carabelli A.M., Corti D., Culap K., Datir R., De Marco A., Ferreira I.A.T.M., Harvey W.T., Kemp S.A., Kenyon J.C., Lever A.M., Lytras S., Papa G., Piccoli L., Saliba C.", "protein_xref_pubmed", "34166617", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC1-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC1" ] ] }, "readme": "Name\n - SARS-CoV2 Protein Citations (UniProtKB)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2020-04-19T11:32:35.963024\n\nModified on\n - 2020-04-19T11:33:03.867613\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Protein Citations dataset contains publication information for sarscov2 [taxid:2697049] UniProtKB accessions that includes PMID, journal name, date and author and title. The dataset is derived from 2020-01 UniProt release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - publications\n - PMID\n - journal\n - citations\n - authors\n - UniProtKB\n - PubMed\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB publication data from the triplestore containing triples from nt file to retrieve the publication information associated with the UniProtKB accession and maps it to the UniProtKB canonical accessions. The script also filters out publications of large scale studies, and high frequency publications pertaining to DNA sequencing, cDNA, chromosomes using blacklisted PMIDs file.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: sarscov2_protein_masterlist.csv\n URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/sarscov2_protein_masterlist.csv\n Name: uniprot-proteome-sars-cov-2.nt\n URI: https://data.glygen.org//ln2downloads/ebi/2021_03/uniprot-proteome-sars-cov-2.nt\n Output Subdomain\n Name: sarscov2_protein_citations_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/sarscov2_protein_citations_uniprotkb.csv\n Name: sarscov2_protein_citations_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/sarscov2_protein_citations_uniprotkb.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/sarscov2_protein_citations_uniprotkb.csv" }