{"id":"https://openalex.org/W2229411104","doi":"https://doi.org/10.1093/bib/bbv052","title":"Dynamics of ubiquitin-mediated signalling: insights from mathematical modelling and experimental studies","display_name":"Dynamics of ubiquitin-mediated signalling: insights from mathematical modelling and experimental studies","publication_year":2015,"publication_date":"2015-07-25","ids":{"openalex":"https://openalex.org/W2229411104","doi":"https://doi.org/10.1093/bib/bbv052","mag":"2229411104","pmid":"https://pubmed.ncbi.nlm.nih.gov/26210356"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv052","pdf_url":"https://academic.oup.com/bib/article-pdf/17/3/479/6686575/bbv052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/17/3/479/6686575/bbv052.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040251521","display_name":"Lan K. Nguyen","orcid":"https://orcid.org/0000-0003-4040-7705"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","IE"],"is_corresponding":true,"raw_author_name":"Lan K. Nguyen","raw_affiliation_strings":["Lan K. Nguyen, holds a PhD in computational systems biology and is currently a research fellow at Systems Biology, Ireland. His research interests include modelling and systems analysis of signalling networks; Department of Biochemistry and Molecular Biology, Faculty of Biomedical and Psychological Sciences, Monash University, Clayton, VIC 3800, Australia","University College Dublin"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lan K. Nguyen, holds a PhD in computational systems biology and is currently a research fellow at Systems Biology, Ireland. His research interests include modelling and systems analysis of signalling networks; Department of Biochemistry and Molecular Biology, Faculty of Biomedical and Psychological Sciences, Monash University, Clayton, VIC 3800, Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"University College Dublin","institution_ids":["https://openalex.org/I100930933"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5040251521"],"corresponding_institution_ids":["https://openalex.org/I100930933","https://openalex.org/I56590836"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":null,"fwci":0.6938,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.70530985,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"17","issue":"3","first_page":"479","last_page":"493"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11041","display_name":"Ubiquitin and proteasome pathways","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/T11041","display_name":"Ubiquitin and proteasome pathways","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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.9976999759674072,"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/T10583","display_name":"Cancer-related Molecular Pathways","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ubiquitin","display_name":"Ubiquitin","score":0.9016217589378357},{"id":"https://openalex.org/keywords/deubiquitinating-enzyme","display_name":"Deubiquitinating enzyme","score":0.8488532304763794},{"id":"https://openalex.org/keywords/signalling","display_name":"Signalling","score":0.7577873468399048},{"id":"https://openalex.org/keywords/crosstalk","display_name":"Crosstalk","score":0.7424876689910889},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5320490598678589},{"id":"https://openalex.org/keywords/signalling-pathways","display_name":"Signalling pathways","score":0.47274836897850037},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4725838899612427},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.43673795461654663},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.37892335653305054},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3425758481025696},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.18241769075393677},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09315618872642517}],"concepts":[{"id":"https://openalex.org/C25602115","wikidata":"https://www.wikidata.org/wiki/Q407111","display_name":"Ubiquitin","level":3,"score":0.9016217589378357},{"id":"https://openalex.org/C102658986","wikidata":"https://www.wikidata.org/wiki/Q5266092","display_name":"Deubiquitinating enzyme","level":4,"score":0.8488532304763794},{"id":"https://openalex.org/C39743133","wikidata":"https://www.wikidata.org/wiki/Q3262595","display_name":"Signalling","level":2,"score":0.7577873468399048},{"id":"https://openalex.org/C169822122","wikidata":"https://www.wikidata.org/wiki/Q230187","display_name":"Crosstalk","level":2,"score":0.7424876689910889},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5320490598678589},{"id":"https://openalex.org/C3018449070","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signalling pathways","level":3,"score":0.47274836897850037},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4725838899612427},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.43673795461654663},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.37892335653305054},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3425758481025696},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.18241769075393677},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09315618872642517},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025801","descriptor_name":"Ubiquitin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D025801","descriptor_name":"Ubiquitin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D025801","descriptor_name":"Ubiquitin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbv052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv052","pdf_url":"https://academic.oup.com/bib/article-pdf/17/3/479/6686575/bbv052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26210356","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26210356","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:open-archive.highwire.org:bib:17/3/479","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/3/479","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv052","pdf_url":"https://academic.oup.com/bib/article-pdf/17/3/479/6686575/bbv052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2229411104.pdf"},"referenced_works_count":92,"referenced_works":["https://openalex.org/W23903782","https://openalex.org/W150897306","https://openalex.org/W275852982","https://openalex.org/W1483395792","https://openalex.org/W1535070554","https://openalex.org/W1590553747","https://openalex.org/W1967269362","https://openalex.org/W1969236463","https://openalex.org/W1969761431","https://openalex.org/W1975467795","https://openalex.org/W1985940938","https://openalex.org/W1987028692","https://openalex.org/W1989712725","https://openalex.org/W1991841644","https://openalex.org/W1995952124","https://openalex.org/W2002223631","https://openalex.org/W2005811767","https://openalex.org/W2010658933","https://openalex.org/W2013064021","https://openalex.org/W2013098933","https://openalex.org/W2013339424","https://openalex.org/W2017253785","https://openalex.org/W2021565943","https://openalex.org/W2026873880","https://openalex.org/W2028157992","https://openalex.org/W2032852681","https://openalex.org/W2033398667","https://openalex.org/W2033427788","https://openalex.org/W2033890654","https://openalex.org/W2035542044","https://openalex.org/W2036806530","https://openalex.org/W2039778506","https://openalex.org/W2041652145","https://openalex.org/W2044724807","https://openalex.org/W2044877094","https://openalex.org/W2045223401","https://openalex.org/W2047365291","https://openalex.org/W2056040174","https://openalex.org/W2060867078","https://openalex.org/W2061191702","https://openalex.org/W2062510288","https://openalex.org/W2064639714","https://openalex.org/W2068802700","https://openalex.org/W2069934833","https://openalex.org/W2077494922","https://openalex.org/W2078495108","https://openalex.org/W2078856281","https://openalex.org/W2079397912","https://openalex.org/W2085624021","https://openalex.org/W2086831875","https://openalex.org/W2086928685","https://openalex.org/W2087818316","https://openalex.org/W2090288242","https://openalex.org/W2094374269","https://openalex.org/W2098286150","https://openalex.org/W2098687987","https://openalex.org/W2099998040","https://openalex.org/W2100972952","https://openalex.org/W2101622956","https://openalex.org/W2103059173","https://openalex.org/W2103305337","https://openalex.org/W2103806497","https://openalex.org/W2106969933","https://openalex.org/W2116062594","https://openalex.org/W2118225942","https://openalex.org/W2120376520","https://openalex.org/W2121490181","https://openalex.org/W2131403694","https://openalex.org/W2133797106","https://openalex.org/W2134095164","https://openalex.org/W2135278768","https://openalex.org/W2135535700","https://openalex.org/W2139364069","https://openalex.org/W2140638448","https://openalex.org/W2140697098","https://openalex.org/W2143538182","https://openalex.org/W2143619350","https://openalex.org/W2144114582","https://openalex.org/W2146084258","https://openalex.org/W2149296898","https://openalex.org/W2150091336","https://openalex.org/W2151505861","https://openalex.org/W2152084880","https://openalex.org/W2157989234","https://openalex.org/W2158516169","https://openalex.org/W2162103775","https://openalex.org/W2164001388","https://openalex.org/W2168591052","https://openalex.org/W2171825994","https://openalex.org/W2175715045","https://openalex.org/W2793216206","https://openalex.org/W6610113517"],"related_works":["https://openalex.org/W2611649496","https://openalex.org/W2067364318","https://openalex.org/W2020053069","https://openalex.org/W2056210416","https://openalex.org/W2770653741","https://openalex.org/W1954801073","https://openalex.org/W2159751912","https://openalex.org/W2888617581","https://openalex.org/W3025383677","https://openalex.org/W4367835058"],"abstract_inverted_index":{"Post-translational":[0],"modification":[1],"of":[2,22,32,58,78,80,104,111,162,176,180,190,207],"cellular":[3],"proteins":[4],"by":[5,75],"ubiquitin":[6,81,120,134,163,191,213],"is":[7,26,62,67,200],"a":[8,20,29,68,76],"pivotal":[9],"regulatory":[10,85],"event":[11],"that":[12,65,131,148,193],"controls":[13],"not":[14],"only":[15],"protein":[16],"degradation,":[17],"but":[18,116],"also":[19],"variety":[21],"non-proteolytic":[23],"functions.":[24],"Ubiquitination":[25],"involved":[27],"in":[28,119,128,173],"broad":[30],"array":[31],"physiological":[33],"processes,":[34],"and":[35,48,71,90,93,106,140,153,159,185,188,214],"its":[36],"dysregulation":[37],"has":[38,52],"been":[39],"associated":[40],"with":[41,96],"many":[42],"human":[43],"diseases,":[44],"including":[45],"neuronal":[46],"disorders":[47],"cancers.":[49],"Ubiquitin-mediated":[50],"signalling":[51,113,135,192],"thus":[53],"come":[54],"to":[55,210],"the":[56,102,108,151,177,202,212],"forefront":[57],"biomedical":[59],"research.":[60],"It":[61,199],"increasingly":[63],"apparent":[64],"ubiquitination":[66,105,181],"highly":[69],"complex":[70],"dynamic":[72,109,178],"process,":[73],"evidenced":[74],"myriad":[77],"ways":[79],"chain":[82],"formation,":[83],"tightly":[84],"mechanisms":[86],"involving":[87],"E3":[88],"ligases":[89],"deubiquitinating":[91],"enzymes":[92],"extensive":[94],"crosstalk":[95],"other":[97],"post-translational":[98],"modifications.":[99],"To":[100],"unravel":[101],"complexity":[103,152],"understand":[107],"properties":[110],"ubiquitin-mediated":[112],"are":[114,143],"challenging,":[115],"critical":[117],"topics":[118],"research,":[121],"which":[122],"will":[123,169,205],"undoubtedly":[124],"benefit":[125],"our":[126,174],"effort":[127],"developing":[129],"strategies":[130],"could":[132],"target":[133],"for":[136,157],"therapeutics.":[137],"Computational":[138],"modelling":[139],"model-based":[141],"approaches":[142],"emerging":[144],"as":[145],"promising":[146],"tools":[147],"help":[149],"tackle":[150],"provide":[154],"useful":[155],"frameworks":[156],"quantitative":[158],"dynamical":[160,197],"analysis":[161],"signalling.":[164],"In":[165],"this":[166],"article,":[167],"I":[168],"discuss":[170],"recent":[171],"advances":[172],"understanding":[175],"behaviour":[179],"from":[182],"both":[183,211],"theoretical":[184],"experimental":[186],"studies,":[187],"aspects":[189],"may":[194],"have":[195],"major":[196],"consequences.":[198],"expected":[201],"discussed":[203],"issues":[204],"be":[206],"relevant":[208],"interest":[209],"systems":[215],"biology":[216],"fields.":[217]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
