{"id":"https://openalex.org/W2991174006","doi":"https://doi.org/10.1371/journal.pcbi.1007509","title":"Clustering-independent analysis of genomic data using spectral simplicial theory","display_name":"Clustering-independent analysis of genomic data using spectral simplicial theory","publication_year":2019,"publication_date":"2019-11-22","ids":{"openalex":"https://openalex.org/W2991174006","doi":"https://doi.org/10.1371/journal.pcbi.1007509","mag":"2991174006","pmid":"https://pubmed.ncbi.nlm.nih.gov/31756191","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/6897424"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007509","doi":"https://doi.org/10.1371/journal.pcbi.1007509","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007509","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007509&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007509&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037372907","display_name":"Kiya W. Govek","orcid":"https://orcid.org/0000-0002-2105-0715","observed_orcids":["https://orcid.org/0000-0002-2105-0715"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kiya W. Govek","raw_affiliation_strings":["Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2105-0715","affiliations":[{"raw_affiliation_string":"Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064708475","display_name":"Venkata S. Yamajala","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Venkata S. Yamajala","raw_affiliation_strings":["Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055994495","display_name":"Pablo G. C\u00e1mara","orcid":"https://orcid.org/0000-0001-6822-3604","observed_orcids":["https://orcid.org/0000-0001-6822-3604"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pablo G. Camara","raw_affiliation_strings":["Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6822-3604","affiliations":[{"raw_affiliation_string":"Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5055994495"],"corresponding_institution_ids":["https://openalex.org/I79576946"],"apc_list":{"value":2350,"currency":"USD","value_usd":2350},"apc_paid":{"value":2350,"currency":"USD","value_usd":2350},"fwci":0.9522,"has_fulltext":true,"cited_by_count":34,"citation_normalized_percentile":{"value":0.7251233,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"15","issue":"11","first_page":"e1007509","last_page":"e1007509"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6416000127792358,"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":0.6416000127792358,"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/T12536","display_name":"Topological and Geometric Data Analysis","score":0.33250001072883606,"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"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.015399999916553497,"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/abstract-simplicial-complexes","display_name":"abstract simplicial complexes","score":0.9769999980926514},{"id":"https://openalex.org/keywords/feature-selection","display_name":"feature selection","score":0.7739999890327454},{"id":"https://openalex.org/keywords/differential-expression-analysis","display_name":"differential expression analysis","score":0.6629999876022339},{"id":"https://openalex.org/keywords/single-cell-omics","display_name":"single-cell omics","score":0.8410000205039978},{"id":"https://openalex.org/keywords/spatial-gene-expression","display_name":"spatial gene expression","score":0.625},{"id":"https://openalex.org/keywords/fluorescence-in-situ-hybridization","display_name":"fluorescence in situ hybridization","score":0.9629999995231628},{"id":"https://openalex.org/keywords/topological-data-analysis","display_name":"topological data analysis","score":0.8799999952316284},{"id":"https://openalex.org/keywords/manifold-learning","display_name":"manifold learning","score":0.8349999785423279}],"concepts":[{"id":"https://openalex.org/C2776477805","wikidata":"https://www.wikidata.org/wiki/Q4460773","display_name":"Topological data analysis","level":2,"score":0.6797837018966675},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6285732984542847},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5455328226089478},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.48304158449172974},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4741603434085846},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40955838561058044},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3934929072856903},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.34718751907348633},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34639984369277954},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24693214893341064},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.23685067892074585},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21528229117393494},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2117260992527008},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.15753436088562012}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1007509","doi":"https://doi.org/10.1371/journal.pcbi.1007509","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007509","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007509&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6897424","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6897424","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmid:31756191","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31756191","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,"listed_in":[],"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":"PLoS computational biology","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:6bb8c3c33afe4193a3634bc9cfdbabed","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/6bb8c3c33afe4193a3634bc9cfdbabed","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 15, Iss 11, p e1007509 (2019)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/10820063","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/Clustering-independent_analysis_of_genomic_data_using_spectral_simplicial_theory/10820063","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007509","doi":"https://doi.org/10.1371/journal.pcbi.1007509","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007509","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007509&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2991174006.pdf","grobid_xml":"https://content.openalex.org/works/W2991174006.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1607787316","https://openalex.org/W1991566301","https://openalex.org/W2009720434","https://openalex.org/W2025796118","https://openalex.org/W2079746361","https://openalex.org/W2105381419","https://openalex.org/W2107385756","https://openalex.org/W2110065044","https://openalex.org/W2110520112","https://openalex.org/W2110734043","https://openalex.org/W2111004121","https://openalex.org/W2114104545","https://openalex.org/W2116063398","https://openalex.org/W2124954099","https://openalex.org/W2128120736","https://openalex.org/W2149620660","https://openalex.org/W2179438025","https://openalex.org/W2190545194","https://openalex.org/W2263206910","https://openalex.org/W2509957998","https://openalex.org/W2586728725","https://openalex.org/W2610774430","https://openalex.org/W2780777007","https://openalex.org/W2786672974","https://openalex.org/W2790675139","https://openalex.org/W2792647356","https://openalex.org/W2808144819","https://openalex.org/W2865352686","https://openalex.org/W2916020270","https://openalex.org/W2949177718","https://openalex.org/W2952383043","https://openalex.org/W2952650776","https://openalex.org/W2953293240","https://openalex.org/W2976681669","https://openalex.org/W3097993951","https://openalex.org/W4289236186"],"related_works":["https://openalex.org/W2900030814","https://openalex.org/W2095436466","https://openalex.org/W7133519629","https://openalex.org/W4283072384","https://openalex.org/W2354640219","https://openalex.org/W4237537084","https://openalex.org/W2980563923","https://openalex.org/W2104720650","https://openalex.org/W2169475742","https://openalex.org/W2142531048"],"abstract_inverted_index":{"The":[0],"prevailing":[1],"paradigm":[2,49],"for":[3,88,100],"the":[4,78,109,113,118,128,137,170,173,229],"analysis":[5,138,151,223,230],"of":[6,12,70,130,139,172,179,192,231],"biological":[7,233],"data":[8,114,198,222],"involves":[9],"comparing":[10],"groups":[11],"replicates":[13],"from":[14],"different":[15],"conditions":[16],"(e.g.":[17,28,176],"control":[18],"and":[19,95,115,142,162,199,206,224],"treatment)":[20],"to":[21,63,67,80,91,117,124,136,169,186,200,228],"statistically":[22],"infer":[23],"features":[24,65],"that":[25],"discriminate":[26],"them":[27],"differentially":[29,165],"expressed":[30,166],"genes).":[31],"However,":[32],"many":[33],"situations":[34,153],"in":[35,152,210],"modern":[36],"genomics":[37],"such":[38,56],"as":[39],"single-cell":[40],"omics":[41],"experiments":[42],"do":[43],"not":[44],"fit":[45],"well":[46],"into":[47,107,159],"this":[48,131,184],"because":[50],"they":[51],"lack":[52],"true":[53],"replicates.":[54],"In":[55],"instances,":[57],"spectral":[58,86],"techniques":[59],"could":[60],"be":[61,157],"used":[62],"rank":[64],"according":[66,168],"their":[68],"degree":[69],"consistency":[71],"with":[72,133,189],"an":[73],"underlying":[74],"metric":[75],"structure":[76],"without":[77],"need":[79],"cluster":[81],"samples.":[82],"Here,":[83],"we":[84,147,163],"extend":[85],"methods":[87],"feature":[89],"selection":[90],"abstract":[92],"simplicial":[93],"complexes":[94],"present":[96],"a":[97,217],"general":[98],"framework":[99,132],"clustering-independent":[101],"analysis.":[102],"Combinatorial":[103],"Laplacian":[104,120],"scores":[105],"take":[106],"account":[108],"topology":[110,171],"spanned":[111],"by":[112],"reduce":[116],"ordinary":[119],"score":[121],"when":[122],"restricted":[123],"graphs.":[125],"We":[126,181],"demonstrate":[127],"utility":[129],"several":[134],"applications":[135],"gene":[140],"expression":[141,150,174,193,208],"multi-modal":[143],"genomic":[144],"data.":[145],"Specifically,":[146],"perform":[148],"differential":[149],"where":[154],"samples":[155],"cannot":[156],"grouped":[158],"distinct":[160],"classes,":[161],"disaggregate":[164],"genes":[167,188],"space":[175],"alternative":[177],"paths":[178],"differentiation).":[180],"also":[182],"apply":[183],"formalism":[185],"identify":[187],"spatial":[190],"patterns":[191,209],"using":[194],"fluorescence":[195],"in-situ":[196],"hybridization":[197],"establish":[201],"associations":[202],"between":[203],"genetic":[204],"alterations":[205],"global":[207],"large":[211],"cross-sectional":[212],"studies.":[213],"Our":[214],"results":[215],"provide":[216],"unifying":[218],"perspective":[219],"on":[220],"topological":[221],"manifold":[225],"learning":[226],"approaches":[227],"large-scale":[232],"datasets.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2019-12-05T00:00:00"}
