{"id":"https://openalex.org/W3115897200","doi":"https://doi.org/10.1007/s40484-020-0227-0","title":"Identifying patient\u2010specific flow of signal transduction perturbed by multiple single\u2010nucleotide alterations","display_name":"Identifying patient\u2010specific flow of signal transduction perturbed by multiple single\u2010nucleotide alterations","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3115897200","doi":"https://doi.org/10.1007/s40484-020-0227-0","mag":"3115897200"},"language":"en","primary_location":{"id":"doi:10.1007/s40484-020-0227-0","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-020-0227-0","pdf_url":null,"source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.1007/s40484-020-0227-0","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052141799","display_name":"Olha Kholod","orcid":"https://orcid.org/0000-0001-6257-4948"},"institutions":[{"id":"https://openalex.org/I2800649613","display_name":"University of Missouri Health System","ror":"https://ror.org/03yp8z857","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800649613"]},{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Olha Kholod","raw_affiliation_strings":["<!--1--> MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","<!--2--> Department Pathology and Anatomical Sciences School of Medicine University of Missouri Columbia MO 65212 USA","Department Pathology and Anatomical Sciences School of Medicine University of Missouri Columbia MO 65212 USA","MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"<!--1--> MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"<!--2--> Department Pathology and Anatomical Sciences School of Medicine University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department Pathology and Anatomical Sciences School of Medicine University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","institution_ids":["https://openalex.org/I2800649613","https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013031415","display_name":"Chi\u2010Ren Shyu","orcid":"https://orcid.org/0000-0001-9197-9522"},"institutions":[{"id":"https://openalex.org/I2800649613","display_name":"University of Missouri Health System","ror":"https://ror.org/03yp8z857","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800649613"]},{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chi\u2010Ren Shyu","raw_affiliation_strings":["<!--1--> MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","<!--5--> Department of Electrical Engineering &amp; Computer Science University of Missouri Columbia MO 65212 USA","MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","Department of Electrical Engineering &amp; Computer Science University of Missouri Columbia MO 65212 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"<!--1--> MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"<!--5--> Department of Electrical Engineering &amp; Computer Science University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","institution_ids":["https://openalex.org/I2800649613","https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Electrical Engineering &amp; Computer Science University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018574284","display_name":"Jonathan B. Mitchem","orcid":"https://orcid.org/0000-0002-5385-7038"},"institutions":[{"id":"https://openalex.org/I2800649613","display_name":"University of Missouri Health System","ror":"https://ror.org/03yp8z857","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800649613"]},{"id":"https://openalex.org/I4210107726","display_name":"Harry S. Truman Memorial Veterans' Hospital","ror":"https://ror.org/01a4gqp27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210107726","https://openalex.org/I4210165236"]},{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Mitchem","raw_affiliation_strings":["<!--1--> MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","<!--3--> Department of Surgery School of Medicine University of Missouri Columbia MO 65212 USA","<!--4--> Harry S. Truman Memorial Veterans\u2019 Hospital Columbia MO 65201 USA","MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","Department of Surgery School of Medicine University of Missouri Columbia MO 65212 USA","Harry S. Truman Memorial Veterans\u2019 Hospital Columbia MO 65201 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"<!--1--> MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"<!--3--> Department of Surgery School of Medicine University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"<!--4--> Harry S. Truman Memorial Veterans\u2019 Hospital Columbia MO 65201 USA","institution_ids":["https://openalex.org/I4210107726"]},{"raw_affiliation_string":"MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","institution_ids":["https://openalex.org/I2800649613","https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Surgery School of Medicine University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Harry S. Truman Memorial Veterans\u2019 Hospital Columbia MO 65201 USA","institution_ids":["https://openalex.org/I4210107726"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065897181","display_name":"Jussuf T. Kaifi","orcid":"https://orcid.org/0000-0003-3425-2356"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jussuf Kaifi","raw_affiliation_strings":["<!--3--> Department of Surgery School of Medicine University of Missouri Columbia MO 65212 USA","Department of Surgery School of Medicine University of Missouri Columbia MO 65212 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"<!--3--> Department of Surgery School of Medicine University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Surgery School of Medicine University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034457600","display_name":"Dmitriy Shin","orcid":"https://orcid.org/0000-0002-5571-9384"},"institutions":[{"id":"https://openalex.org/I2800649613","display_name":"University of Missouri Health System","ror":"https://ror.org/03yp8z857","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800649613"]},{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmitriy Shin","raw_affiliation_strings":["<!--1--> MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","<!--2--> Department Pathology and Anatomical Sciences School of Medicine University of Missouri Columbia MO 65212 USA","Department Pathology and Anatomical Sciences School of Medicine University of Missouri Columbia MO 65212 USA","MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"<!--1--> MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"<!--2--> Department Pathology and Anatomical Sciences School of Medicine University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department Pathology and Anatomical Sciences School of Medicine University of Missouri Columbia MO 65212 USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"MU Institute for Data Science and Informatics University of Missouri Columbia MO 65201 USA","institution_ids":["https://openalex.org/I2800649613","https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5052141799"],"corresponding_institution_ids":["https://openalex.org/I2800649613","https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12690552,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"8","issue":"4","first_page":"336","last_page":"346"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9876000285148621,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9767000079154968,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5667853355407715},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4827274978160858},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.4699174463748932},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4555065631866455},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41505327820777893},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.41203033924102783},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3655741214752197},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19917139410972595}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5667853355407715},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4827274978160858},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.4699174463748932},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4555065631866455},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41505327820777893},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.41203033924102783},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3655741214752197},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19917139410972595},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s40484-020-0227-0","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-020-0227-0","pdf_url":null,"source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s40484-020-0227-0","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-020-0227-0","pdf_url":null,"source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.6299999952316284,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W258733445","https://openalex.org/W1940319397","https://openalex.org/W1971727526","https://openalex.org/W1988222759","https://openalex.org/W1997074238","https://openalex.org/W2001939488","https://openalex.org/W2021653518","https://openalex.org/W2030899725","https://openalex.org/W2056196348","https://openalex.org/W2056924558","https://openalex.org/W2073711680","https://openalex.org/W2074549773","https://openalex.org/W2096192437","https://openalex.org/W2100980426","https://openalex.org/W2108215899","https://openalex.org/W2114843025","https://openalex.org/W2132151898","https://openalex.org/W2135782451","https://openalex.org/W2156651988","https://openalex.org/W2156788906","https://openalex.org/W2269777088","https://openalex.org/W2325767305","https://openalex.org/W2559588208","https://openalex.org/W2795190507","https://openalex.org/W2807869290","https://openalex.org/W2889965505","https://openalex.org/W2914170009","https://openalex.org/W2948505931","https://openalex.org/W2949129392","https://openalex.org/W2950595506","https://openalex.org/W2957335523","https://openalex.org/W2967870286","https://openalex.org/W2978056557","https://openalex.org/W2979585789","https://openalex.org/W2982321167","https://openalex.org/W3004517324","https://openalex.org/W3136918052"],"related_works":["https://openalex.org/W2943623134","https://openalex.org/W2494523064","https://openalex.org/W2215759665","https://openalex.org/W2960358116","https://openalex.org/W2030292806","https://openalex.org/W3041172967","https://openalex.org/W2749065928","https://openalex.org/W2147155098","https://openalex.org/W4287727129","https://openalex.org/W2938171715"],"abstract_inverted_index":{"Background":[0],"Identifying":[1],"patient\u2010specific":[2,78,218],"flow":[3,79,219],"of":[4,24,70,80,112,126,139,152,164,178,217,240],"signal":[5,81],"transduction":[6,82],"perturbed":[7],"by":[8,196,220],"multiple":[9,61,85,224],"single\u2010nucleotide":[10,62,86,153,225],"alterations":[11,154,226],"is":[12],"critical":[13],"for":[14,31,56,148],"improving":[15],"patient":[16],"outcomes":[17],"in":[18,155,175,182],"cancer":[19],"cases.":[20],"However,":[21],"accurate":[22],"estimation":[23],"mutational":[25,72,122,166],"effects":[26,59],"at":[27],"the":[28,47,50,71,77,110,113,136,156,162,165,176,197,200,207,229,237],"pathway":[29,40],"level":[30],"such":[32],"patients":[33],"remains":[34],"an":[35,68,215],"open":[36],"problem.":[37],"While":[38],"probabilistic":[39],"topology":[41],"methods":[42],"are":[43,233],"gaining":[44],"interest":[45],"among":[46],"scientific":[48],"community,":[49],"overwhelming":[51],"majority":[52],"do":[53],"not":[54],"account":[55],"network":[57],"perturbation":[58],"from":[60,101,130,199,223],"alterations.":[63],"Methods":[64],"Here":[65],"we":[66],"present":[67],"improvement":[69],"forks":[73,167],"formalism":[74,168,208],"to":[75,108,132,169,213,227],"infer":[76],"based":[83,235],"on":[84,135,236],"alterations,":[87],"including":[88],"non\u2010synonymous":[89],"and":[90,96,185],"synonymous":[91],"mutations.":[92],"The":[93,124,158,190],"lung":[94,183],"adenocarcinoma":[95,184],"skin":[97,186],"cutaneous":[98,187],"melanoma":[99,188],"datasets":[100],"TCGA":[102],"Pan\u2010Cancer":[103],"Atlas":[104],"have":[105,118,145,192],"been":[106,146,193],"employed":[107],"show":[109],"utility":[111],"proposed":[114],"method.":[115],"Results":[116],"We":[117,204],"comprehensively":[119],"characterized":[120],"six":[121],"forks.":[123],"number":[125],"mutated":[127],"nodes":[128],"ranged":[129],"one":[131],"four":[133],"depending":[134],"topological":[137],"characteristics":[138],"a":[140,171,210,241],"fork.":[141,157],"Transitional":[142],"confidences":[143],"(TCs)":[144],"computed":[147],"every":[149],"possible":[150],"combination":[151],"performed":[159],"analysis":[160],"demonstrated":[161],"capacity":[163],"follow":[170],"biologically":[172],"explainable":[173],"logic":[174],"identification":[177],"high\u2010likelihood":[179],"signaling":[180],"routes":[181],"patients.":[189],"findings":[191],"largely":[194],"supported":[195],"evidence":[198],"biomedical":[201],"literature.":[202],"Conclusion":[203],"conclude":[205],"that":[206,232],"has":[209],"great":[211],"chance":[212],"enable":[214],"assessment":[216],"leveraging":[221],"information":[222],"adjust":[228],"transitional":[230],"likelihoods":[231],"solely":[234],"canonical":[238],"view":[239],"disease.":[242]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}