{"id":"https://openalex.org/W3114658574","doi":"https://doi.org/10.1109/bibe50027.2020.00128","title":"Predicting Kinase-Substrate Interactions in Medulloblastoma Subtypes","display_name":"Predicting Kinase-Substrate Interactions in Medulloblastoma Subtypes","publication_year":2020,"publication_date":"2020-10-01","ids":{"openalex":"https://openalex.org/W3114658574","doi":"https://doi.org/10.1109/bibe50027.2020.00128","mag":"3114658574"},"language":"en","primary_location":{"id":"doi:10.1109/bibe50027.2020.00128","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe50027.2020.00128","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077840174","display_name":"Aparna Krishnan","orcid":null},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aparna Krishnan","raw_affiliation_strings":["Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA"],"affiliations":[{"raw_affiliation_string":"Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA","institution_ids":["https://openalex.org/I1284308235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085161967","display_name":"Kristin Leskoske","orcid":"https://orcid.org/0000-0002-9187-2730"},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kristin Leskoske","raw_affiliation_strings":["Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA"],"affiliations":[{"raw_affiliation_string":"Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA","institution_ids":["https://openalex.org/I1284308235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075336615","display_name":"Krystine Garcia\u2010Mansfield","orcid":null},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Krystine Garcia-Mansfield","raw_affiliation_strings":["Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA"],"affiliations":[{"raw_affiliation_string":"Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA","institution_ids":["https://openalex.org/I1284308235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051330635","display_name":"Ritin Sharma","orcid":"https://orcid.org/0000-0001-8365-9916"},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ritin Sharma","raw_affiliation_strings":["Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA"],"affiliations":[{"raw_affiliation_string":"Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA","institution_ids":["https://openalex.org/I1284308235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051406638","display_name":"Jessica M. Rusert","orcid":"https://orcid.org/0000-0003-0751-2693"},"institutions":[{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jessica Rusert","raw_affiliation_strings":["Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I188891513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066651467","display_name":"Robert J. Wechsler\u2010Reya","orcid":"https://orcid.org/0000-0002-7463-8352"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Wechsler-Reya","raw_affiliation_strings":["Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I188891513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079679478","display_name":"Patrick Pirrotte","orcid":"https://orcid.org/0000-0003-1360-6039"},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick Pirrotte","raw_affiliation_strings":["Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA"],"affiliations":[{"raw_affiliation_string":"Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA","institution_ids":["https://openalex.org/I1284308235"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5077840174"],"corresponding_institution_ids":["https://openalex.org/I1284308235"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12510692,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"32","issue":null,"first_page":"752","last_page":"758"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12009","display_name":"Hedgehog Signaling Pathway Studies","score":0.9994999766349792,"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/T12009","display_name":"Hedgehog Signaling Pathway Studies","score":0.9994999766349792,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9957000017166138,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.991599977016449,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/kinase","display_name":"Kinase","score":0.6114997863769531},{"id":"https://openalex.org/keywords/phosphoproteomics","display_name":"Phosphoproteomics","score":0.5751343369483948},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5301191210746765},{"id":"https://openalex.org/keywords/medulloblastoma","display_name":"Medulloblastoma","score":0.5224924683570862},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5135262608528137},{"id":"https://openalex.org/keywords/phosphorylation","display_name":"Phosphorylation","score":0.497287780046463},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.4016442894935608},{"id":"https://openalex.org/keywords/protein-phosphorylation","display_name":"Protein phosphorylation","score":0.2830435037612915},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.25947970151901245},{"id":"https://openalex.org/keywords/protein-kinase-a","display_name":"Protein kinase A","score":0.25638917088508606},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23823228478431702}],"concepts":[{"id":"https://openalex.org/C184235292","wikidata":"https://www.wikidata.org/wiki/Q421851","display_name":"Kinase","level":2,"score":0.6114997863769531},{"id":"https://openalex.org/C6675166","wikidata":"https://www.wikidata.org/wiki/Q7187538","display_name":"Phosphoproteomics","level":5,"score":0.5751343369483948},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5301191210746765},{"id":"https://openalex.org/C2780789225","wikidata":"https://www.wikidata.org/wiki/Q1333608","display_name":"Medulloblastoma","level":2,"score":0.5224924683570862},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5135262608528137},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.497287780046463},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4016442894935608},{"id":"https://openalex.org/C87325107","wikidata":"https://www.wikidata.org/wiki/Q7251493","display_name":"Protein phosphorylation","level":4,"score":0.2830435037612915},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.25947970151901245},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.25638917088508606},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23823228478431702}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe50027.2020.00128","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe50027.2020.00128","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.4099999964237213,"id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W61851215","https://openalex.org/W2016680278","https://openalex.org/W2092926517","https://openalex.org/W2147054306","https://openalex.org/W2157658519","https://openalex.org/W2266222342","https://openalex.org/W2606710299","https://openalex.org/W2620760558","https://openalex.org/W2626440326","https://openalex.org/W2788651753","https://openalex.org/W2889956622","https://openalex.org/W2891014905","https://openalex.org/W2892282588","https://openalex.org/W2912820434","https://openalex.org/W2918408501","https://openalex.org/W2999309192"],"related_works":["https://openalex.org/W4221100616","https://openalex.org/W2165221919","https://openalex.org/W3176104354","https://openalex.org/W1415423297","https://openalex.org/W2002813156","https://openalex.org/W1586348561","https://openalex.org/W1973530967","https://openalex.org/W2051108283","https://openalex.org/W2762736481","https://openalex.org/W838395694"],"abstract_inverted_index":{"Medulloblastoma":[0],"(MB),":[1],"the":[2,34,60,108,121,132,148,178,193,196,202,220,235,238,255,259,269,278,296,319,335,347],"most":[3,122],"common":[4],"malignant":[5],"pediatric":[6],"brain":[7],"cancer,":[8],"has":[9],"four":[10],"subtypes":[11],"based":[12,288],"on":[13,80,192,289],"genomics":[14,55],"profiling:":[15],"Wingless":[16],"(WNT),":[17],"Sonic":[18],"Hedgehog":[19],"(SHH),":[20],"Group":[21,24,309,320],"3,":[22],"and":[23,29,219,266,311,338],"4.":[25],"However,":[26],"subtype":[27],"heterogeneity":[28],"low":[30],"mutation":[31],"rates":[32],"hinder":[33],"identification":[35],"of":[36,49,53,97,157,206,281,298,308,313,325,369],"actionable":[37],"molecular":[38],"targets":[39],"within":[40],"each":[41,164],"group.":[42],"Studies":[43],"thus":[44],"suggest":[45],"a":[46,54,130,154,166,182],"phosphoproteomics":[47,355],"(study":[48],"protein":[50,70,73],"phosphorylation),":[51],"instead":[52],"approach,":[56],"to":[57,88,106,119,127,138,146,177,226,234,301,343,364],"better":[58],"distinguish":[59],"MB":[61,111,239,260,351],"subgroups.":[62],"Thus,":[63],"this":[64,144,360],"research":[65],"will":[66,160],"measure":[67],"MB's":[68],"irregular":[69],"activity":[71,263,291],"via":[72],"phosphorylation":[74,341],"patterns.":[75],"Protein":[76],"kinases":[77,109,124,257],"phosphorylate":[78,114],"proteins":[79],"specific":[81],"amino":[82],"acids,":[83],"also":[84,358],"known":[85],"as":[86],"substrates,":[87,158],"regulate":[89],"their":[90,115],"functions.":[91],"Given":[92],"that":[93],"less":[94],"than":[95],"5%":[96],"substrates":[98,116,194],"have":[99],"annotated":[100,151],"kinase":[101,262],"associations,":[102],"it":[103],"is":[104],"difficult":[105],"identify":[107,181],"in":[110,117,143,195,211,242,334,373],"which":[112],"irregularly":[113],"order":[118],"determine":[120],"effective":[123],"for":[125,185,237,273],"drugs":[126],"target.":[128],"As":[129],"result,":[131],"publicly-available":[133],"tool":[134,279,363],"NetworKIN":[135,159,189],"was":[136,190,224,232],"employed":[137],"predict":[139],"novel":[140,244,340],"kinase-substrate":[141,162,209,247,371],"interactions":[142,210,253,300,372],"study":[145],"expand":[147],"currently":[149],"limited":[150],"interactions.":[152,248],"For":[153],"given":[155],"dataset":[156],"output":[161],"predictions,":[163,188],"receiving":[165],"confidence":[167,187,246,333],"score":[168,170,183,223],"(higher":[169],"=":[171],"higher":[172],"confidence)":[173],"ranging":[174],"from":[175,284],"zero":[176],"hundreds.":[179],"To":[180,249],"threshold":[184,231],"high":[186,245],"run":[191],"Human":[197],"PhosphoSite":[198],"Plus":[199],"Database":[200],"(PSP),":[201],"largest":[203],"curated":[204],"database":[205],"experimentally":[207],"verified":[208],"humans.":[212],"Three":[213],"statistical":[214],"thresholding":[215],"methods":[216],"were":[217,271],"tested":[218],"optimal":[221],"cutoff":[222],"determined":[225],"lie":[227],"at":[228],"5.88.":[229],"This":[230],"applied":[233],"predictions":[236,270],"dataset,":[240],"resulting":[241],"774":[243],"understand":[250],"how":[251],"these":[252,290,326],"altered":[254],"enriched":[256],"across":[258],"subgroups,":[261],"scores":[264,292],"before":[265],"after":[267],"adding":[268],"calculated":[272],"all":[274],"20":[275],"samples":[276],"using":[277],"Inference":[280],"Kinase":[282],"Activities":[283],"Phosphoproteomics.":[285],"Subgroup":[286],"classification":[287],"revealed":[293],"that,":[294],"with":[295,328],"addition":[297],"high-confidence":[299],"PSP,":[302],"there":[303],"are":[304],"two":[305],"smaller":[306],"subgroups":[307,315],"3":[310],"one":[312],"those":[314],"more":[316,344],"closely":[317],"resembled":[318],"4":[321],"samples.":[322],"The":[323],"alignment":[324],"findings":[327],"current":[329],"literature":[330],"increases":[331],"our":[332,367],"prediction":[336,362],"algorithm":[337],"elucidates":[339],"patterns":[342],"accurately":[345],"portray":[346],"phosphosignaling":[348],"pathways":[349],"driving":[350],"tumorigenesis.":[352],"Future":[353],"cancer":[354],"studies":[356],"can":[357],"employ":[359],"robust":[361],"continue":[365],"expanding":[366],"understanding":[368],"aberrant":[370],"human":[374],"diseases.":[375]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}