{"id":"https://openalex.org/W4400140847","doi":"https://doi.org/10.1093/bioinformatics/btae241","title":"Integrating patients in time series clinical transcriptomics data","display_name":"Integrating patients in time series clinical transcriptomics data","publication_year":2024,"publication_date":"2024-06-28","ids":{"openalex":"https://openalex.org/W4400140847","doi":"https://doi.org/10.1093/bioinformatics/btae241","pmid":"https://pubmed.ncbi.nlm.nih.gov/38940139"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae241","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae241","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae241","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046070068","display_name":"Euxhen Hasanaj","orcid":"https://orcid.org/0000-0002-6940-8683"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Euxhen Hasanaj","raw_affiliation_strings":["Machine Learning Department, Carnegie Mellon University , Pittsburgh, PA 15213, United States"],"affiliations":[{"raw_affiliation_string":"Machine Learning Department, Carnegie Mellon University , Pittsburgh, PA 15213, United States","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042102236","display_name":"Sachin Mathur","orcid":"https://orcid.org/0009-0008-9899-0458"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sachin Mathur","raw_affiliation_strings":["R&D Data and Computational Sciences, Sanofi , Cambridge, MA 02141, United States"],"affiliations":[{"raw_affiliation_string":"R&D Data and Computational Sciences, Sanofi , Cambridge, MA 02141, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065673127","display_name":"Ziv Bar\u2010Joseph","orcid":"https://orcid.org/0000-0003-3430-6051"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ziv Bar-Joseph","raw_affiliation_strings":["Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, United States","Machine Learning Department, Carnegie Mellon University , Pittsburgh, PA 15213, United States","R&D Data and Computational Sciences, Sanofi , Cambridge, MA 02141, United States"],"affiliations":[{"raw_affiliation_string":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, United States","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Machine Learning Department, Carnegie Mellon University , Pittsburgh, PA 15213, United States","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"R&D Data and Computational Sciences, Sanofi , Cambridge, MA 02141, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5046070068"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6869,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.68905977,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"40","issue":"Supplement_1","first_page":"i151","last_page":"i159"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9980000257492065,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9980000257492065,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9966999888420105,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9961000084877014,"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/series","display_name":"Series (stratigraphy)","score":0.6421359777450562},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5705997943878174},{"id":"https://openalex.org/keywords/time-series","display_name":"Time series","score":0.5637155175209045},{"id":"https://openalex.org/keywords/clinical-trial","display_name":"Clinical trial","score":0.4808717370033264},{"id":"https://openalex.org/keywords/cohort","display_name":"Cohort","score":0.43149295449256897},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4176042973995209},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3209264874458313},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.28666257858276367},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24989157915115356},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15771153569221497},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13688495755195618},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.13289904594421387}],"concepts":[{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.6421359777450562},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5705997943878174},{"id":"https://openalex.org/C151406439","wikidata":"https://www.wikidata.org/wiki/Q186588","display_name":"Time series","level":2,"score":0.5637155175209045},{"id":"https://openalex.org/C535046627","wikidata":"https://www.wikidata.org/wiki/Q30612","display_name":"Clinical trial","level":2,"score":0.4808717370033264},{"id":"https://openalex.org/C72563966","wikidata":"https://www.wikidata.org/wiki/Q1303415","display_name":"Cohort","level":2,"score":0.43149295449256897},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4176042973995209},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3209264874458313},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.28666257858276367},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24989157915115356},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15771153569221497},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13688495755195618},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.13289904594421387},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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},{"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},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae241","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae241","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38940139","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38940139","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},{"id":"pmh:oai:pubmedcentral.nih.gov:11256926","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11256926","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11256926/pdf/btae241.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae241","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae241","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1963126400","display_name":null,"funder_award_id":"AG075931","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3782027633","display_name":null,"funder_award_id":"1U54AG075931","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5827920988","display_name":null,"funder_award_id":"2134999","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6755165505","display_name":null,"funder_award_id":"award","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7075047960","display_name":null,"funder_award_id":"13499","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7528676281","display_name":null,"funder_award_id":"1U24CA268108","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7825199617","display_name":null,"funder_award_id":"U24CA268108","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8577951192","display_name":null,"funder_award_id":"U54AG075931","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320307781","display_name":"Sanofi","ror":"https://ror.org/027vj4x92"},{"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":43,"referenced_works":["https://openalex.org/W1515641485","https://openalex.org/W1969289662","https://openalex.org/W1969766619","https://openalex.org/W2040072657","https://openalex.org/W2067324660","https://openalex.org/W2085526700","https://openalex.org/W2093457571","https://openalex.org/W2098156682","https://openalex.org/W2101142880","https://openalex.org/W2103017472","https://openalex.org/W2107018762","https://openalex.org/W2107665951","https://openalex.org/W2130410032","https://openalex.org/W2144738674","https://openalex.org/W2155357014","https://openalex.org/W2162262128","https://openalex.org/W2181999119","https://openalex.org/W2503361011","https://openalex.org/W2803660147","https://openalex.org/W2889326414","https://openalex.org/W2897249806","https://openalex.org/W2907756900","https://openalex.org/W2927507212","https://openalex.org/W2954675852","https://openalex.org/W2991077754","https://openalex.org/W3015272799","https://openalex.org/W3023451851","https://openalex.org/W3036569631","https://openalex.org/W3084428275","https://openalex.org/W3106188259","https://openalex.org/W3210112288","https://openalex.org/W4205496949","https://openalex.org/W4210403261","https://openalex.org/W4226278788","https://openalex.org/W4226478228","https://openalex.org/W4242767541","https://openalex.org/W4255375128","https://openalex.org/W4297216152","https://openalex.org/W4309944312","https://openalex.org/W4378212544","https://openalex.org/W4380368096","https://openalex.org/W6683073260","https://openalex.org/W6685884626"],"related_works":["https://openalex.org/W1919101720","https://openalex.org/W4390822878","https://openalex.org/W96888382","https://openalex.org/W2041308758","https://openalex.org/W4386126592","https://openalex.org/W4392529072","https://openalex.org/W4394131749","https://openalex.org/W2622688551","https://openalex.org/W1550175370","https://openalex.org/W1990205660"],"abstract_inverted_index":{"The":[0],"source":[1],"code":[2],"and":[3],"instructions":[4],"to":[5],"download":[6],"the":[7],"data":[8],"have":[9],"been":[10],"deposited":[11],"on":[12],"GitHub":[13],"at":[14],"https://github.com/euxhenh/Truffle.":[15]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
