{"id":"https://openalex.org/W2165391797","doi":"https://doi.org/10.1145/2382936.2382979","title":"Signed network propagation for detecting differential gene expressions and DNA copy number variations","display_name":"Signed network propagation for detecting differential gene expressions and DNA copy number variations","publication_year":2012,"publication_date":"2012-10-07","ids":{"openalex":"https://openalex.org/W2165391797","doi":"https://doi.org/10.1145/2382936.2382979","mag":"2165391797"},"language":"en","primary_location":{"id":"doi:10.1145/2382936.2382979","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2382979","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","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/A5100441789","display_name":"Wei Zhang","orcid":"https://orcid.org/0000-0003-3605-9373"},"institutions":[{"id":"https://openalex.org/I4210101327","display_name":"Twin Cities Orthopedics","ror":"https://ror.org/01en4s460","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210101327"]},{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Zhang","raw_affiliation_strings":["University of Minnesota Twin Cities, Minneapolis, Minnesota"],"affiliations":[{"raw_affiliation_string":"University of Minnesota Twin Cities, Minneapolis, Minnesota","institution_ids":["https://openalex.org/I4210101327","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034956786","display_name":"Nicholas D. Johnson","orcid":"https://orcid.org/0000-0003-3229-6849"},"institutions":[{"id":"https://openalex.org/I4210101327","display_name":"Twin Cities Orthopedics","ror":"https://ror.org/01en4s460","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210101327"]},{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Johnson","raw_affiliation_strings":["University of Minnesota Twin Cities, Minneapolis, Minnesota"],"affiliations":[{"raw_affiliation_string":"University of Minnesota Twin Cities, Minneapolis, Minnesota","institution_ids":["https://openalex.org/I4210101327","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029703168","display_name":"Baolin Wu","orcid":"https://orcid.org/0000-0001-6676-0422"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I4210101327","display_name":"Twin Cities Orthopedics","ror":"https://ror.org/01en4s460","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210101327"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Baolin Wu","raw_affiliation_strings":["University of Minnesota Twin Cities, Minneapolis, Minnesota"],"affiliations":[{"raw_affiliation_string":"University of Minnesota Twin Cities, Minneapolis, Minnesota","institution_ids":["https://openalex.org/I4210101327","https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066338313","display_name":"Rui Kuang","orcid":"https://orcid.org/0000-0002-4916-903X"},"institutions":[{"id":"https://openalex.org/I4210101327","display_name":"Twin Cities Orthopedics","ror":"https://ror.org/01en4s460","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210101327"]},{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rui Kuang","raw_affiliation_strings":["University of Minnesota Twin Cities, Minneapolis, Minnesota"],"affiliations":[{"raw_affiliation_string":"University of Minnesota Twin Cities, Minneapolis, Minnesota","institution_ids":["https://openalex.org/I4210101327","https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100441789"],"corresponding_institution_ids":["https://openalex.org/I130238516","https://openalex.org/I4210101327"],"apc_list":null,"apc_paid":null,"fwci":0.5378,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.66735856,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"337","last_page":"344"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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/T10885","display_name":"Gene expression and cancer classification","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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9929999709129333,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9922000169754028,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.5881087183952332},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4960871636867523},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.46467453241348267},{"id":"https://openalex.org/keywords/smoothing","display_name":"Smoothing","score":0.4592582583427429},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4589792788028717},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.42343637347221375},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4159674346446991},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3673788905143738},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3620840907096863},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.346510648727417},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2902078628540039},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2234642505645752},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.18740180134773254}],"concepts":[{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.5881087183952332},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4960871636867523},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.46467453241348267},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.4592582583427429},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4589792788028717},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.42343637347221375},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4159674346446991},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3673788905143738},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3620840907096863},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.346510648727417},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2902078628540039},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2234642505645752},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.18740180134773254},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/2382936.2382979","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2382979","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.496.8662","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.496.8662","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www-users.cs.umn.edu/~kuang/paper/SignedNP.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.705.2034","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.705.2034","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www-users.cs.umn.edu/%7Eweizhang/papers/SignedNP.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1075044023","display_name":null,"funder_award_id":"III1117153NIH GM083345NIH CA134848","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5997059511","display_name":null,"funder_award_id":"III1117153NIH GM083345NIH CA134848","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W108936587","https://openalex.org/W1607267312","https://openalex.org/W1965302838","https://openalex.org/W1978420939","https://openalex.org/W2048296798","https://openalex.org/W2057626690","https://openalex.org/W2061151099","https://openalex.org/W2084787613","https://openalex.org/W2096079397","https://openalex.org/W2119412782","https://openalex.org/W2119803525","https://openalex.org/W2123579582","https://openalex.org/W2124975275","https://openalex.org/W2128985829","https://openalex.org/W2134672568","https://openalex.org/W2148603752","https://openalex.org/W2150533948","https://openalex.org/W2150671673","https://openalex.org/W2154455818","https://openalex.org/W2156909104","https://openalex.org/W2158217645","https://openalex.org/W2160450758","https://openalex.org/W2162632348","https://openalex.org/W2163563958","https://openalex.org/W2167769381","https://openalex.org/W2170989872","https://openalex.org/W4245024447","https://openalex.org/W6682494755","https://openalex.org/W7071374342"],"related_works":["https://openalex.org/W1978572805","https://openalex.org/W2383807498","https://openalex.org/W1997992934","https://openalex.org/W1987225439","https://openalex.org/W4238188170","https://openalex.org/W2513883126","https://openalex.org/W3118014344","https://openalex.org/W2160911017","https://openalex.org/W2125114371","https://openalex.org/W2019977573"],"abstract_inverted_index":{"Network":[0],"propagation":[1,23,36,92,107],"algorithms":[2,37,55],"have":[3],"proved":[4],"useful":[5],"for":[6,42,82],"the":[7,17],"analysis":[8],"of":[9,140,158],"high-dimensional":[10],"genomic":[11,118],"data.":[12],"One":[13],"limitation":[14],"is":[15,156],"that":[16,133,154,161],"current":[18],"formulation":[19],"only":[20],"allows":[21],"network":[22,35,148],"on":[24,93,108,123,182],"positively":[25],"weighted":[26],"graphs.":[27,96],"In":[28],"this":[29],"paper,":[30],"we":[31],"explore":[32],"two":[33],"signed":[34],"and":[38,47,59,79,84,117,129,135,143,166,171],"general":[39],"optimization":[40],"frameworks":[41],"detecting":[43],"differential":[44,80],"gene":[45,66,77,86,94,102,126,141],"expressions":[46,81],"DNA":[48],"copy":[49],"number":[50],"variations":[51],"(CNV).":[52],"The":[53,72,97,150],"proposed":[54],"consider":[56],"both":[57],"positive":[58],"negative":[60],"relations":[61],"in":[62,178],"graphs":[63,111],"to":[64,112],"model":[65],"up/down-regulation":[67],"or":[68,103],"amplification/deletion":[69],"CNV":[70,104,130,144,176],"events.":[71],"first":[73],"algorithm":[74,99],"(Signed-NP)":[75],"integrates":[76],"co-expressions":[78],"consistent":[83,167],"robust":[85],"selection":[87],"from":[88],"microarray":[89,125],"datasets":[90,128,131],"by":[91,106,180],"correlation":[95],"second":[98],"(Signed-NPBi)":[100],"identifies":[101],"markers":[105],"sample-feature":[109],"bipartite":[110],"capture":[113],"bi-clusters":[114,179],"between":[115,184],"samples":[116],"features.":[119],"Large":[120],"scale":[121],"experiments":[122,151],"several":[124],"expression":[127,142],"validate":[132],"Signed-NP":[134,155],"Signed-NPBi":[136,172],"perform":[137],"better":[138],"classification":[139],"data":[145],"than":[146],"standard":[147],"propagation.":[149],"also":[152],"demonstrate":[153],"capable":[157],"selecting":[159],"genes":[160],"are":[162],"more":[163],"biologically":[164],"interpretable":[165],"across":[168],"multiple":[169],"datasets,":[170],"can":[173],"detect":[174],"hidden":[175],"patterns":[177],"smoothing":[181],"correlations":[183],"adjacent":[185],"probes.":[186]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}