{"id":"https://openalex.org/W4402000442","doi":"https://doi.org/10.1101/2024.08.28.610120","title":"PICASO: Profiling Integrative Communities of Aggregated Single-cell Omics data","display_name":"PICASO: Profiling Integrative Communities of Aggregated Single-cell Omics data","publication_year":2024,"publication_date":"2024-08-29","ids":{"openalex":"https://openalex.org/W4402000442","doi":"https://doi.org/10.1101/2024.08.28.610120"},"language":"en","primary_location":{"id":"doi:10.1101/2024.08.28.610120","doi":"https://doi.org/10.1101/2024.08.28.610120","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1101/2024.08.28.610120","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://dx.doi.org/10.1101/2024.08.28.610120","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054104640","display_name":"Markus Joppich","orcid":"https://orcid.org/0000-0002-6665-8951","observed_orcids":["https://orcid.org/0000-0002-6665-8951"]},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Markus Joppich","raw_affiliation_strings":["Institute for Informatics, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","LMU Munich;","LMU Munich"],"raw_orcid":"https://orcid.org/0000-0002-6665-8951","affiliations":[{"raw_affiliation_string":"Institute for Informatics, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","institution_ids":["https://openalex.org/I8204097"]},{"raw_affiliation_string":"LMU Munich;","institution_ids":["https://openalex.org/I8204097"]},{"raw_affiliation_string":"LMU Munich","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028674815","display_name":"Rafael Kramann","orcid":"https://orcid.org/0000-0003-4048-6351","observed_orcids":["https://orcid.org/0000-0003-4048-6351"]},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rafael Kramann","raw_affiliation_strings":["Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center","Department of Medicine 2 (Nephrology, Rheumatology, Clinical Immunology and Hypertension), RWTH Aachen University, Medical Faculty","RWTH Aachen University"],"raw_orcid":"https://orcid.org/0000-0003-4048-6351","affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center","institution_ids":[]},{"raw_affiliation_string":"Department of Medicine 2 (Nephrology, Rheumatology, Clinical Immunology and Hypertension), RWTH Aachen University, Medical Faculty","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"RWTH Aachen University","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041018040","display_name":"Sikander Hayat","orcid":"https://orcid.org/0000-0001-5919-8371","observed_orcids":["https://orcid.org/0000-0001-5919-8371","https://orcid.org/0000-0003-1353-4346"]},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Sikander Hayat","raw_affiliation_strings":["Department of Medicine 2 (Nephrology, Rheumatology, Clinical Immunology and Hypertension), RWTH Aachen University, Medical Faculty","RWTH Aachen University"],"raw_orcid":"https://orcid.org/0000-0001-5919-8371","affiliations":[{"raw_affiliation_string":"Department of Medicine 2 (Nephrology, Rheumatology, Clinical Immunology and Hypertension), RWTH Aachen University, Medical Faculty","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"RWTH Aachen University","institution_ids":["https://openalex.org/I887968799"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041018040"],"corresponding_institution_ids":["https://openalex.org/I887968799"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9990000128746033,"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":0.9990000128746033,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0006000000284984708,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":9.999999747378752e-05,"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/picaso","display_name":"PICASO","score":0.859000027179718},{"id":"https://openalex.org/keywords/single-cell-gene-expression","display_name":"single-cell gene expression","score":0.8339999914169312},{"id":"https://openalex.org/keywords/community-detection","display_name":"community detection","score":0.6029999852180481},{"id":"https://openalex.org/keywords/druggable-targets","display_name":"druggable targets","score":0.8019999861717224},{"id":"https://openalex.org/keywords/drug-gene-interactions","display_name":"drug-gene interactions","score":0.4729999899864197},{"id":"https://openalex.org/keywords/disease-phenotype","display_name":"disease phenotypes","score":0.5540000200271606}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5918211340904236},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5672971606254578},{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.567035436630249},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.5482209920883179},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5290704369544983},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5153088569641113},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.5047363042831421},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45645803213119507},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.44456902146339417},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34448954463005066},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.25924503803253174},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16999360918998718},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1207430362701416},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2024.08.28.610120","doi":"https://doi.org/10.1101/2024.08.28.610120","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1101/2024.08.28.610120","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2024.08.28.610120","doi":"https://doi.org/10.1101/2024.08.28.610120","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1101/2024.08.28.610120","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.504800021648407}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":64,"referenced_works":["https://openalex.org/W1966680971","https://openalex.org/W1998819524","https://openalex.org/W2002436590","https://openalex.org/W2002850151","https://openalex.org/W2010457001","https://openalex.org/W2026364268","https://openalex.org/W2042831991","https://openalex.org/W2046592449","https://openalex.org/W2046805092","https://openalex.org/W2056496907","https://openalex.org/W2063819332","https://openalex.org/W2076984671","https://openalex.org/W2098264959","https://openalex.org/W2110620844","https://openalex.org/W2132022337","https://openalex.org/W2156588647","https://openalex.org/W2214074259","https://openalex.org/W2255109474","https://openalex.org/W2489254161","https://openalex.org/W2497192058","https://openalex.org/W2557833574","https://openalex.org/W2559588208","https://openalex.org/W2604808360","https://openalex.org/W2611326266","https://openalex.org/W2768720550","https://openalex.org/W2782454362","https://openalex.org/W2800392236","https://openalex.org/W2808845633","https://openalex.org/W2898440040","https://openalex.org/W2979835214","https://openalex.org/W2983166786","https://openalex.org/W3003257820","https://openalex.org/W3005127469","https://openalex.org/W3040496092","https://openalex.org/W3092387592","https://openalex.org/W3096674342","https://openalex.org/W3104014715","https://openalex.org/W3123290933","https://openalex.org/W3136918052","https://openalex.org/W3138055079","https://openalex.org/W3211402536","https://openalex.org/W3217284213","https://openalex.org/W4223520048","https://openalex.org/W4288060600","https://openalex.org/W4290989128","https://openalex.org/W4295198017","https://openalex.org/W4308834893","https://openalex.org/W4309306035","https://openalex.org/W4318983406","https://openalex.org/W4323076268","https://openalex.org/W4367312557","https://openalex.org/W4379879135","https://openalex.org/W4384198561","https://openalex.org/W4384664738","https://openalex.org/W4384816663","https://openalex.org/W4385840369","https://openalex.org/W4391940656","https://openalex.org/W4398142212","https://openalex.org/W4398171339","https://openalex.org/W4400948944","https://openalex.org/W4400956442","https://openalex.org/W4401047215","https://openalex.org/W4402902773","https://openalex.org/W6931283491"],"related_works":["https://openalex.org/W2556855892","https://openalex.org/W24553703","https://openalex.org/W4214810602","https://openalex.org/W4211000692","https://openalex.org/W4212920271","https://openalex.org/W2523769397","https://openalex.org/W2887882375","https://openalex.org/W4285502407","https://openalex.org/W2030404924","https://openalex.org/W4229599664"],"abstract_inverted_index":{"Abstract":[0],"Various":[1],"single-cell":[2,26,34,100],"modalities":[3],"covering":[4],"transcriptomics,":[5],"epigenetic":[6],"and":[7,12,117,134,146,164,183,196,203],"spatio-temporal":[8],"changes":[9],"in":[10,17,60],"health":[11],"disease":[13,114,155],"phenotypes":[14],"are":[15],"used":[16,48],"an":[18,105],"exploratory":[19],"way":[20],"to":[21,40,49,108],"understand":[22],"biological":[23],"systems":[24],"at":[25,81],"resolution.":[27],"However,":[28],"the":[29,75,95,142,166,177,190,198],"vast":[30],"amount":[31],"of":[32,57,77,87,141,179,192,200],"such":[33,127],"data":[35,59,103],"is":[36],"not":[37],"systematically":[38],"linked":[39],"existing":[41],"biomedical":[42,52,58,125],"data.":[43,53,91],"Networks":[44],"have":[45],"previously":[46],"been":[47],"represent":[50,109],"harmonized":[51],"Integrating":[54],"various":[55],"resources":[56],"networks":[61,69,174],"has":[62],"recently":[63],"received":[64],"increasing":[65],"attention.":[66],"These":[67],"aggregated":[68],"can":[70,157],"provide":[71],"additional":[72,106],"insight":[73],"into":[74],"biology":[76],"complex":[78],"human":[79],"diseases":[80],"cell-type":[82],"level,":[83],"however,":[84],"lack":[85],"inclusion":[86],"single":[88],"cell":[89,112,138],"expression":[90,102,151,167],"Here,":[92],"we":[93],"present":[94],"PICASO":[96,120],"framework,":[97,143],"which":[98],"incorporates":[99],"gene":[101],"as":[104,128,187,189],"layer":[107],"associations":[110],"between":[111,154,169],"types,":[113],"phenotypes,":[115],"drugs":[116],"genes.":[118],"The":[119],"network":[121],"includes":[122],"several":[123],"standardized":[124],"databases":[126],"STRING,":[129],"Uniprot,":[130],"GeneOntology,":[131],"Reactome,":[132],"OmniPath":[133],"OpenTargets.":[135],"Using":[136],"multiple":[137],"type-specific":[139],"instances":[140],"each":[144],"annotated":[145],"scored":[147],"with":[148],"their":[149],"respective":[150,162],"data,":[152],"comparisons":[153],"states":[156],"be":[158],"made":[159],"by":[160],"computing":[161],"sub-networks":[163],"comparing":[165],"scores":[168],"conditions.":[170],"Ultimately,":[171],"these":[172],"group-specific":[173,201],"will":[175],"allow":[176],"identification":[178,199],"relevant":[180],"genes,":[181],"processes":[182],"potentially":[184],"druggable":[185],"targets,":[186],"well":[188],"comparison":[191],"different":[193],"measured":[194],"groups":[195],"thus":[197],"communities":[202],"interactions.":[204]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2025-10-10T00:00:00"}