{"id":"https://openalex.org/W2330144087","doi":"https://doi.org/10.1371/journal.pcbi.1004844","title":"A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts","display_name":"A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts","publication_year":2016,"publication_date":"2016-04-07","ids":{"openalex":"https://openalex.org/W2330144087","doi":"https://doi.org/10.1371/journal.pcbi.1004844","mag":"2330144087","pmid":"https://pubmed.ncbi.nlm.nih.gov/27054587"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004844","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004844","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004844&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004844&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009017303","display_name":"Andrew G. McDonald","orcid":"https://orcid.org/0000-0003-2727-176X"},"institutions":[{"id":"https://openalex.org/I205274468","display_name":"Trinity College Dublin","ror":"https://ror.org/02tyrky19","country_code":"IE","type":"education","lineage":["https://openalex.org/I205274468"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Andrew G. McDonald","raw_affiliation_strings":["School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland","institution_ids":["https://openalex.org/I205274468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047695717","display_name":"Keith F. Tipton","orcid":"https://orcid.org/0000-0001-8855-5315"},"institutions":[{"id":"https://openalex.org/I205274468","display_name":"Trinity College Dublin","ror":"https://ror.org/02tyrky19","country_code":"IE","type":"education","lineage":["https://openalex.org/I205274468"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Keith F. Tipton","raw_affiliation_strings":["School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland","institution_ids":["https://openalex.org/I205274468"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032729634","display_name":"Gavin P. Davey","orcid":"https://orcid.org/0000-0002-8667-8781"},"institutions":[{"id":"https://openalex.org/I205274468","display_name":"Trinity College Dublin","ror":"https://ror.org/02tyrky19","country_code":"IE","type":"education","lineage":["https://openalex.org/I205274468"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Gavin P. Davey","raw_affiliation_strings":["School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland","institution_ids":["https://openalex.org/I205274468"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5009017303","https://openalex.org/A5032729634"],"corresponding_institution_ids":["https://openalex.org/I205274468"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.0889,"has_fulltext":true,"cited_by_count":41,"citation_normalized_percentile":{"value":0.86880828,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"12","issue":"4","first_page":"e1004844","last_page":"e1004844"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10835","display_name":"Carbohydrate Chemistry and Synthesis","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12387","display_name":"Galectins and Cancer Biology","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/glycosylation","display_name":"Glycosylation","score":0.7549998760223389},{"id":"https://openalex.org/keywords/glycan","display_name":"Glycan","score":0.6968416571617126},{"id":"https://openalex.org/keywords/glycomics","display_name":"Glycomics","score":0.5990275144577026},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5520449876785278},{"id":"https://openalex.org/keywords/gene-knockout","display_name":"Gene knockout","score":0.5309911370277405},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4932376742362976},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.47433724999427795},{"id":"https://openalex.org/keywords/glycosyltransferase","display_name":"Glycosyltransferase","score":0.4723331034183502},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.4644119441509247},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.4440067410469055},{"id":"https://openalex.org/keywords/galactosyltransferase","display_name":"Galactosyltransferase","score":0.4151782989501953},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3342912197113037},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3189910650253296},{"id":"https://openalex.org/keywords/glycoprotein","display_name":"Glycoprotein","score":0.2713867127895355}],"concepts":[{"id":"https://openalex.org/C2777313579","wikidata":"https://www.wikidata.org/wiki/Q898365","display_name":"Glycosylation","level":2,"score":0.7549998760223389},{"id":"https://openalex.org/C206212055","wikidata":"https://www.wikidata.org/wiki/Q2553138","display_name":"Glycan","level":3,"score":0.6968416571617126},{"id":"https://openalex.org/C106686826","wikidata":"https://www.wikidata.org/wiki/Q741206","display_name":"Glycomics","level":4,"score":0.5990275144577026},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5520449876785278},{"id":"https://openalex.org/C77957584","wikidata":"https://www.wikidata.org/wiki/Q1133550","display_name":"Gene knockout","level":3,"score":0.5309911370277405},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4932376742362976},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.47433724999427795},{"id":"https://openalex.org/C161019410","wikidata":"https://www.wikidata.org/wiki/Q67201373","display_name":"Glycosyltransferase","level":3,"score":0.4723331034183502},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.4644119441509247},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.4440067410469055},{"id":"https://openalex.org/C2780895608","wikidata":"https://www.wikidata.org/wiki/Q5517847","display_name":"Galactosyltransferase","level":3,"score":0.4151782989501953},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3342912197113037},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3189910650253296},{"id":"https://openalex.org/C108625454","wikidata":"https://www.wikidata.org/wiki/Q187126","display_name":"Glycoprotein","level":2,"score":0.2713867127895355}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003412","descriptor_name":"Cricetulus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003412","descriptor_name":"Cricetulus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003412","descriptor_name":"Cricetulus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003412","descriptor_name":"Cricetulus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009077","descriptor_name":"Mucins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009077","descriptor_name":"Mucins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009077","descriptor_name":"Mucins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009077","descriptor_name":"Mucins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009077","descriptor_name":"Mucins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009077","descriptor_name":"Mucins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009077","descriptor_name":"Mucins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009077","descriptor_name":"Mucins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016466","descriptor_name":"CHO Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016466","descriptor_name":"CHO Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016466","descriptor_name":"CHO Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016466","descriptor_name":"CHO Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000172","qualifier_name":"deficiency","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000172","qualifier_name":"deficiency","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000172","qualifier_name":"deficiency","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000172","qualifier_name":"deficiency","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055786","descriptor_name":"Gene Knockout Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055786","descriptor_name":"Gene Knockout Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055786","descriptor_name":"Gene Knockout Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055786","descriptor_name":"Gene Knockout Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1004844","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004844","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004844&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:27054587","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27054587","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:3314a631db01409badcdcea91fbe8408","is_oa":true,"landing_page_url":"https://doaj.org/article/3314a631db01409badcdcea91fbe8408","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 12, Iss 4, p e1004844 (2016)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3808940","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4824424","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/3952065","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/A_Knowledge-Based_System_for_Display_and_Prediction_of_i_O_i_-Glycosylation_Network_Behaviour_in_Response_to_Enzyme_Knockouts/3952065","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:tara.tcd.ie:2262/76782","is_oa":false,"landing_page_url":"http://hdl.handle.net/2262/76782","pdf_url":null,"source":{"id":"https://openalex.org/S4306400387","display_name":"Trinity's Access to Research Output (TARA) (Trinity College Dublin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205274468","host_organization_name":"Trinity College Dublin","host_organization_lineage":["https://openalex.org/I205274468"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004844","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004844","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004844&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1990351228","display_name":null,"funder_award_id":"SSPC/I2893","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G4352723470","display_name":null,"funder_award_id":"13/SP SSPC/I2893","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G4917922675","display_name":null,"funder_award_id":"SFI-13/SP SSPC/I2893","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G8774772663","display_name":null,"funder_award_id":"SFI-13/SP","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"}],"funders":[{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"},{"id":"https://openalex.org/F4320320864","display_name":"Trinity College Dublin","ror":"https://ror.org/02tyrky19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2330144087.pdf","grobid_xml":"https://content.openalex.org/works/W2330144087.grobid-xml"},"referenced_works_count":87,"referenced_works":["https://openalex.org/W241210763","https://openalex.org/W993338644","https://openalex.org/W1485881041","https://openalex.org/W1492512703","https://openalex.org/W1500816652","https://openalex.org/W1517564457","https://openalex.org/W1527012508","https://openalex.org/W1549233174","https://openalex.org/W1553871308","https://openalex.org/W1820870565","https://openalex.org/W1825657610","https://openalex.org/W1870511442","https://openalex.org/W1911267965","https://openalex.org/W1965346959","https://openalex.org/W1969718019","https://openalex.org/W1973353128","https://openalex.org/W1976484683","https://openalex.org/W1983217234","https://openalex.org/W1985310505","https://openalex.org/W1988138737","https://openalex.org/W1990365018","https://openalex.org/W1995662039","https://openalex.org/W1997302006","https://openalex.org/W1997315604","https://openalex.org/W1997576977","https://openalex.org/W2004125187","https://openalex.org/W2014865312","https://openalex.org/W2015986985","https://openalex.org/W2018978714","https://openalex.org/W2020525459","https://openalex.org/W2034162787","https://openalex.org/W2040713190","https://openalex.org/W2044434705","https://openalex.org/W2048507302","https://openalex.org/W2049474907","https://openalex.org/W2049974202","https://openalex.org/W2050153157","https://openalex.org/W2050625315","https://openalex.org/W2052250572","https://openalex.org/W2057049168","https://openalex.org/W2059379158","https://openalex.org/W2062406664","https://openalex.org/W2063368033","https://openalex.org/W2069616255","https://openalex.org/W2070329791","https://openalex.org/W2076258083","https://openalex.org/W2085256683","https://openalex.org/W2088305283","https://openalex.org/W2091988137","https://openalex.org/W2093205346","https://openalex.org/W2094937489","https://openalex.org/W2099343635","https://openalex.org/W2101543964","https://openalex.org/W2112090702","https://openalex.org/W2115236215","https://openalex.org/W2116130065","https://openalex.org/W2117672117","https://openalex.org/W2118672858","https://openalex.org/W2119861230","https://openalex.org/W2120533079","https://openalex.org/W2124450302","https://openalex.org/W2124637492","https://openalex.org/W2129817935","https://openalex.org/W2134294354","https://openalex.org/W2137440674","https://openalex.org/W2137489365","https://openalex.org/W2138605813","https://openalex.org/W2148298538","https://openalex.org/W2148918528","https://openalex.org/W2153310334","https://openalex.org/W2154258517","https://openalex.org/W2154472706","https://openalex.org/W2155181356","https://openalex.org/W2163480486","https://openalex.org/W2164374470","https://openalex.org/W2169015768","https://openalex.org/W2169026128","https://openalex.org/W2170416222","https://openalex.org/W2184464034","https://openalex.org/W2246321819","https://openalex.org/W2312972213","https://openalex.org/W2345317863","https://openalex.org/W2799049976","https://openalex.org/W4299313888","https://openalex.org/W6629114846","https://openalex.org/W6638546981","https://openalex.org/W6664675307"],"related_works":["https://openalex.org/W2344851944","https://openalex.org/W4386770953","https://openalex.org/W4391748392","https://openalex.org/W2076975212","https://openalex.org/W2586793552","https://openalex.org/W2051926957","https://openalex.org/W1965354942","https://openalex.org/W1997293204","https://openalex.org/W2909198132","https://openalex.org/W2028136243"],"abstract_inverted_index":{"O-linked":[0],"glycosylation":[1],"is":[2,59,62],"an":[3],"important":[4,14],"post-translational":[5],"modification":[6],"of":[7,16,21,24,48,69,95,99,101,113,133,151,161,168,192],"mucin-type":[8,172],"protein,":[9],"changes":[10],"to":[11,76,86,105,149,180,187,190],"which":[12,154,184],"are":[13],"biomarkers":[15],"cancer.":[17],"For":[18],"this":[19],"study":[20,94],"the":[22,56,70,88,123,131,152,158,176,182,193],"enzymes":[23,103],"O-glycosylation,":[25],"we":[26],"developed":[27],"a":[28,35,42,93],"shorthand":[29],"notation":[30],"for":[31,37,52],"representing":[32],"GalNAc-linked":[33],"oligosaccharides,":[34],"method":[36],"their":[38],"graphical":[39],"interpretation,":[40],"and":[41,61,119,142,200],"pattern-matching":[43],"algorithm":[44],"that":[45],"generates":[46],"networks":[47,73],"enzyme-catalysed":[49],"reactions.":[50],"Software":[51],"generating":[53],"glycans":[54],"from":[55,175,198],"enzyme":[57],"activities":[58],"presented,":[60],"also":[63],"available":[64],"online.":[65],"The":[66],"degree":[67],"distributions":[68],"resulting":[71,89],"enzyme-reaction":[72],"were":[74,84,145],"found":[75],"be":[77,106],"Poisson":[78],"in":[79,108,126,147],"nature.":[80],"Simple":[81],"graph-theoretic":[82],"measures":[83],"used":[85,179],"characterise":[87],"reaction":[90],"networks.":[91],"From":[92],"in-silico":[96],"single-enzyme":[97],"knockouts":[98,150],"each":[100],"25":[102],"known":[104],"involved":[107],"mucin":[109],"O-glycan":[110,128],"biosynthesis,":[111],"six":[112],"them,":[114],"\u03b2-1,4-galactosyltransferase":[115],"(\u03b24Gal-T4),":[116],"four":[117],"glycosyltransferases":[118],"one":[120],"sulfotransferase,":[121],"play":[122],"dominant":[124],"role":[125],"determining":[127],"heterogeneity.":[129],"In":[130],"absence":[132],"\u03b24Gal-T4,":[134],"all":[135],"Lewis":[136,140],"X,":[137,139],"sialyl-Lewis":[138],"Y":[141],"Sda/Cad":[143],"glycoforms":[144],"eliminated,":[146],"contrast":[148],"N-acetylglucosaminyltransferases,":[153],"did":[155],"not":[156],"affect":[157],"relative":[159],"abundances":[160],"O-glycans":[162,173],"expressing":[163],"these":[164],"epitopes.":[165],"A":[166],"set":[167],"244":[169],"experimentally":[170],"determined":[171],"obtained":[174,197],"literature":[177],"was":[178,185],"validate":[181],"method,":[183],"able":[186],"predict":[188],"up":[189],"98%":[191],"most":[194],"common":[195],"structures":[196],"human":[199],"engineered":[201],"CHO":[202],"cell":[203],"glycoforms.":[204]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}