{"id":"https://openalex.org/W2144858257","doi":"https://doi.org/10.1093/bioinformatics/btr002","title":"Recovering key biological constituents through sparse representation of gene expression","display_name":"Recovering key biological constituents through sparse representation of gene expression","publication_year":2011,"publication_date":"2011-01-21","ids":{"openalex":"https://openalex.org/W2144858257","doi":"https://doi.org/10.1093/bioinformatics/btr002","mag":"2144858257","pmid":"https://pubmed.ncbi.nlm.nih.gov/21258061"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr002","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr002","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/655/48864899/bioinformatics_27_5_655.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/27/5/655/48864899/bioinformatics_27_5_655.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080012505","display_name":"Yosef Prat","orcid":"https://orcid.org/0000-0002-2939-9858"},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Yosef Prat","raw_affiliation_strings":["1 School of Computer Science and Engineering, 2Sudarsky Center for Computational Biology and 3Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computer Science and Engineering, 2Sudarsky Center for Computational Biology and 3Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel","institution_ids":["https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051946088","display_name":"Menachem Fromer","orcid":"https://orcid.org/0000-0003-3749-4342"},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Menachem Fromer","raw_affiliation_strings":["1 School of Computer Science and Engineering, 2Sudarsky Center for Computational Biology and 3Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computer Science and Engineering, 2Sudarsky Center for Computational Biology and 3Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel","institution_ids":["https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113686886","display_name":"Nathan Linial","orcid":null},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Nathan Linial","raw_affiliation_strings":["1 School of Computer Science and Engineering, 2Sudarsky Center for Computational Biology and 3Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computer Science and Engineering, 2Sudarsky Center for Computational Biology and 3Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel","institution_ids":["https://openalex.org/I197251160"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085924022","display_name":"Michal Linial","orcid":"https://orcid.org/0000-0002-9357-4526"},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Michal Linial","raw_affiliation_strings":["1 School of Computer Science and Engineering, 2Sudarsky Center for Computational Biology and 3Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computer Science and Engineering, 2Sudarsky Center for Computational Biology and 3Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel","institution_ids":["https://openalex.org/I197251160"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5085924022","https://openalex.org/A5113686886"],"corresponding_institution_ids":["https://openalex.org/I197251160"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6653,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.69565289,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"27","issue":"5","first_page":"655","last_page":"661"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9940000176429749,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.993399977684021,"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/key","display_name":"Key (lock)","score":0.732483983039856},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6648610234260559},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5647162795066833},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5634905695915222},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5265182256698608},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4258365333080292},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3967609405517578},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27057886123657227},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1975034475326538},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09186485409736633},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.0814957320690155}],"concepts":[{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.732483983039856},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6648610234260559},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5647162795066833},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5634905695915222},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5265182256698608},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4258365333080292},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3967609405517578},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27057886123657227},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1975034475326538},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09186485409736633},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0814957320690155},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012331","descriptor_name":"RNA, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012331","descriptor_name":"RNA, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012331","descriptor_name":"RNA, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016053","descriptor_name":"RNA, Protozoan","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016053","descriptor_name":"RNA, Protozoan","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016053","descriptor_name":"RNA, Protozoan","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btr002","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr002","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/655/48864899/bioinformatics_27_5_655.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21258061","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21258061","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr002","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr002","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/655/48864899/bioinformatics_27_5_655.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.4699999988079071,"display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144858257.pdf","grobid_xml":"https://content.openalex.org/works/W2144858257.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1978455510","https://openalex.org/W1987231101","https://openalex.org/W1988491013","https://openalex.org/W1988790447","https://openalex.org/W1989034333","https://openalex.org/W1995027235","https://openalex.org/W2015418199","https://openalex.org/W2028781966","https://openalex.org/W2050834445","https://openalex.org/W2055064119","https://openalex.org/W2080182143","https://openalex.org/W2087684630","https://openalex.org/W2096721473","https://openalex.org/W2096939566","https://openalex.org/W2106391842","https://openalex.org/W2107598685","https://openalex.org/W2125310307","https://openalex.org/W2129131372","https://openalex.org/W2146179241","https://openalex.org/W2146997276","https://openalex.org/W2148541040","https://openalex.org/W2150926065","https://openalex.org/W2154437541","https://openalex.org/W2155974384","https://openalex.org/W2159203162","https://openalex.org/W2160875291","https://openalex.org/W2162491638","https://openalex.org/W2163485494","https://openalex.org/W2611370172","https://openalex.org/W4240689716","https://openalex.org/W6684281289"],"related_works":["https://openalex.org/W2140798747","https://openalex.org/W2948169060","https://openalex.org/W2062195135","https://openalex.org/W2392243736","https://openalex.org/W2730112582","https://openalex.org/W86652014","https://openalex.org/W2358580169","https://openalex.org/W2111347279","https://openalex.org/W2110696645","https://openalex.org/W2487211728"],"abstract_inverted_index":{"MOTIVATION:":[0],"Large-scale":[1],"RNA":[2],"expression":[3,55,75,125,153],"measurements":[4],"are":[5,40,62],"generating":[6],"enormous":[7],"quantities":[8],"of":[9,57,77,87,89,104,116,151,182,218],"data.":[10,30,221],"During":[11],"the":[12,24,74,102,108,114,124,137,148,152,167,172,183,201,207],"last":[13],"two":[14],"decades,":[15],"many":[16],"methods":[17,39],"were":[18,162],"developed":[19],"for":[20,73,214],"extracting":[21,120],"insights":[22],"regarding":[23],"interrelationships":[25],"between":[26,169],"genes":[27,58,170],"from":[28,123,147,200],"such":[29],"The":[31,144],"mathematical":[32],"and":[33,139,176,194],"computational":[34],"perspectives":[35],"that":[36,206],"underlie":[37],"these":[38],"usually":[41],"algebraic":[42],"or":[43],"probabilistic.":[44],"RESULTS:":[45],"Here,":[46],"we":[47,71,127],"introduce":[48],"an":[49],"unexplored":[50],"geometric":[51],"view":[52],"point":[53],"where":[54],"levels":[56],"in":[59,66,101,107,119,189,195],"multiple":[60],"experiments":[61,133],"interpreted":[63],"as":[64,83],"vectors":[65],"a":[67,84,90,158,215],"high-dimensional":[68,219],"space.":[69],"Specifically,":[70],"find,":[72],"profile":[76],"each":[78],"particular":[79],"gene,":[80],"its":[81],"approximation":[82],"linear":[85],"combination":[86],"profiles":[88],"few":[91],"other":[92],"genes.":[93],"This":[94],"method":[95],"is":[96,212],"inspired":[97],"by":[98],"recent":[99],"developments":[100],"realm":[103],"compressed":[105],"sensing":[106],"machine":[109],"learning":[110,160],"domain.":[111],"To":[112],"demonstrate":[113],"power":[115],"our":[117],"approach":[118,209],"valuable":[121],"information":[122],"data,":[126],"independently":[128],"applied":[129],"it":[130],"to":[131,157,164],"large-scale":[132],"carried":[134],"out":[135],"on":[136],"yeast":[138],"malaria":[140],"parasite":[141],"whole":[142],"transcriptomes.":[143],"parameters":[145],"extracted":[146],"sparse":[149],"reconstruction":[150],"profiles,":[154],"when":[155],"fed":[156],"supervised":[159],"platform,":[161],"used":[163],"successfully":[165],"predict":[166],"relationships":[168],"throughout":[171],"Gene":[173],"Ontology":[174],"hierarchy":[175],"protein-protein":[177],"interaction":[178],"map.":[179],"Extensive":[180],"assessment":[181],"biological":[184],"results":[185],"shows":[186],"high":[187],"accuracy":[188],"both":[190],"recovering":[191],"known":[192],"predictions":[193,198],"yielding":[196],"accurate":[197],"missing":[199],"current":[202],"databases.":[203],"We":[204],"suggest":[205],"geometrical":[208],"presented":[210],"here":[211],"suitable":[213],"broad":[216],"range":[217],"experimental":[220]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}