{"id":"https://openalex.org/W2135883001","doi":"https://doi.org/10.1093/bioinformatics/btu569","title":"Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets","display_name":"Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets","publication_year":2014,"publication_date":"2014-08-24","ids":{"openalex":"https://openalex.org/W2135883001","doi":"https://doi.org/10.1093/bioinformatics/btu569","mag":"2135883001","pmid":"https://pubmed.ncbi.nlm.nih.gov/25152231"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu569","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu569","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/492/49011724/bioinformatics_31_4_492.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":"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/492/49011724/bioinformatics_31_4_492.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047847184","display_name":"Sahand Hormoz","orcid":"https://orcid.org/0000-0002-4384-4428"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":true,"raw_author_name":"Sahand Hormoz","raw_affiliation_strings":["1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I154570441","https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018308750","display_name":"Gyan Bhanot","orcid":"https://orcid.org/0000-0001-7822-5259"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Gyan Bhanot","raw_affiliation_strings":["1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I154570441","https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083548477","display_name":"Michael Biehl","orcid":"https://orcid.org/0000-0001-5148-4568"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Michael Biehl","raw_affiliation_strings":["1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I154570441","https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026742254","display_name":"Erhan Bilal","orcid":"https://orcid.org/0009-0002-0778-6635"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Erhan Bilal","raw_affiliation_strings":["1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I154570441","https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046474433","display_name":"Pablo Meyer","orcid":"https://orcid.org/0000-0001-5281-4661"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Pablo Meyer","raw_affiliation_strings":["1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I154570441","https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073775720","display_name":"Raquel Norel","orcid":"https://orcid.org/0000-0001-7737-4172"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Raquel Norel","raw_affiliation_strings":["1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I154570441","https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003192265","display_name":"Kahn Rhrissorrakrai","orcid":"https://orcid.org/0000-0002-1567-9090"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Kahn Rhrissorrakrai","raw_affiliation_strings":["1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I154570441","https://openalex.org/I169381384"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044793261","display_name":"Adel Dayarian","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Adel Dayarian","raw_affiliation_strings":["1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 \u00a01Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, 2Department of Physics, 3Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, 4Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and 5IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I154570441","https://openalex.org/I169381384"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5047847184"],"corresponding_institution_ids":["https://openalex.org/I102322142","https://openalex.org/I154570441","https://openalex.org/I169381384"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2603,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.57484463,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"31","issue":"4","first_page":"492","last_page":"500"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.5266000032424927,"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":0.5266000032424927,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0843999981880188,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0835999995470047,"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/transcriptome","display_name":"Transcriptome","score":0.7286533117294312},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6585851907730103},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6125847101211548},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5787904262542725},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5698608160018921},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.532394528388977},{"id":"https://openalex.org/keywords/drug-development","display_name":"Drug development","score":0.532335638999939},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.49374398589134216},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.4768577516078949},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46318671107292175},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4521685540676117},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.22410190105438232},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20721188187599182},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.17129796743392944},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15393304824829102},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.08411464095115662}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7286533117294312},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6585851907730103},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6125847101211548},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5787904262542725},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5698608160018921},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.532394528388977},{"id":"https://openalex.org/C64903051","wikidata":"https://www.wikidata.org/wiki/Q2198549","display_name":"Drug development","level":3,"score":0.532335638999939},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.49374398589134216},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.4768577516078949},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46318671107292175},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4521685540676117},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.22410190105438232},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20721188187599182},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.17129796743392944},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15393304824829102},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.08411464095115662},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001980","descriptor_name":"Bronchi","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001980","descriptor_name":"Bronchi","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001980","descriptor_name":"Bronchi","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001980","descriptor_name":"Bronchi","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001980","descriptor_name":"Bronchi","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001980","descriptor_name":"Bronchi","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004847","descriptor_name":"Epithelial Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D004847","descriptor_name":"Epithelial Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D004847","descriptor_name":"Epithelial Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D004847","descriptor_name":"Epithelial Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004847","descriptor_name":"Epithelial Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004847","descriptor_name":"Epithelial Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010750","descriptor_name":"Phosphoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btu569","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu569","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/492/49011724/bioinformatics_31_4_492.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":"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:25152231","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25152231","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:pure.rug.nl:openaire_cris_publications/6a871283-2e4b-476b-bd78-49515326325d","is_oa":false,"landing_page_url":"https://research.rug.nl/en/publications/6a871283-2e4b-476b-bd78-49515326325d","pdf_url":null,"source":{"id":"https://openalex.org/S4306400420","display_name":"University of Groningen research database (University of Groningen / Centre for Information Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I169381384","host_organization_name":"University of Groningen","host_organization_lineage":["https://openalex.org/I169381384"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Hormoz, S, Bhanot, G, Biehl, M, Bilal, E, Meyer, P, Norel, R, Rhrissorrakrai, K & Dayarian, A 2014, 'Inter-species Inference of Gene Set Enrichment in Lung Epithelial Cells from Proteomic and Large Transcriptomic Data Sets', Bioinformatics (Oxford, England). https://doi.org/10.1093/bioinformatics/btu569","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:alma.01RUT_INST:11665131280004646","is_oa":false,"landing_page_url":"https://scholarship.libraries.rutgers.edu/esploro/outputs/journalArticle/Inter-species-inference-of-gene-set-enrichment/991031665812704646","pdf_url":null,"source":{"id":"https://openalex.org/S4210197018","display_name":"Open Research (University of Surrey)","issn_l":"2688-268X","issn":["2688-268X","2688-3988"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:europepmc.org:3312883","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4325538","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu569","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu569","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/4/492/49011724/bioinformatics_31_4_492.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":"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/G1734940047","display_name":null,"funder_award_id":"No.NSF PHY11-25915","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4433229824","display_name":null,"funder_award_id":"PHY11-25915","funder_id":"https://openalex.org/F4320332500","funder_display_name":"University of California, Santa Barbara"},{"id":"https://openalex.org/G603814699","display_name":null,"funder_award_id":"NSF PHY-11-25915","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7368600059","display_name":null,"funder_award_id":"NSF PHY11-25915","funder_id":"https://openalex.org/F4320332500","funder_display_name":"University of California, Santa Barbara"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320715","display_name":"Tata Institute of Fundamental Research","ror":"https://ror.org/03ht1xw27"},{"id":"https://openalex.org/F4320332500","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135883001.pdf","grobid_xml":"https://content.openalex.org/works/W2135883001.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W3044475","https://openalex.org/W1554944419","https://openalex.org/W1971872860","https://openalex.org/W1973614663","https://openalex.org/W1976526581","https://openalex.org/W1992242907","https://openalex.org/W1993482839","https://openalex.org/W2050034605","https://openalex.org/W2083432197","https://openalex.org/W2088169690","https://openalex.org/W2089426706","https://openalex.org/W2099671052","https://openalex.org/W2102110571","https://openalex.org/W2109963121","https://openalex.org/W2123157758","https://openalex.org/W2130410032","https://openalex.org/W2133033238","https://openalex.org/W2152652033","https://openalex.org/W2152750766","https://openalex.org/W2158698691","https://openalex.org/W2161771297","https://openalex.org/W2248154415","https://openalex.org/W2787894218","https://openalex.org/W2799061466","https://openalex.org/W4255060158"],"related_works":["https://openalex.org/W3012091774","https://openalex.org/W2009966535","https://openalex.org/W2102579905","https://openalex.org/W4247273247","https://openalex.org/W3201422854","https://openalex.org/W2734403094","https://openalex.org/W1971124177","https://openalex.org/W3089353767","https://openalex.org/W3097825150","https://openalex.org/W2135883001"],"abstract_inverted_index":{"MOTIVATION:":[0],"Translating":[1],"findings":[2],"in":[3,20,47,58,73,82,123,129,155,183,190,212,237,268],"rodent":[4],"models":[5,8],"to":[6,57,108,185,200,227,232],"human":[7,74,143],"has":[9,30],"been":[10],"a":[11,23,34,166,186,229],"cornerstone":[12],"of":[13,38,53,90,98,116,141,221,250],"modern":[14],"biology":[15,93,121],"and":[16,94,138,152,174,195,275],"drug":[17,101],"development.":[18,54,102],"However,":[19],"many":[21],"cases,":[22],"naive":[24],"'extrapolation'":[25],"between":[26],"the":[27,48,69,91,96,117,264,269],"two":[28],"species":[29],"not":[31],"succeeded.":[32],"As":[33],"result,":[35],"clinical":[36],"trials":[37],"new":[39],"drugs":[40],"sometimes":[41],"fail":[42],"even":[43],"after":[44,198,207],"considerable":[45],"success":[46],"mouse":[49],"or":[50],"rat":[51,156],"stage":[52],"In":[55,219],"addition":[56],"vitro":[59],"studies,":[60],"inter-species":[61,168],"translation":[62],"requires":[63],"analytical":[64,244],"tools":[65,85],"that":[66,162],"can":[67,86],"predict":[68,109,233],"enriched":[70],"gene":[71,111,163,202,234,273],"sets":[72,164],"cells":[75,148,214],"under":[76,149],"various":[77,150],"stimuli":[78,151],"from":[79],"corresponding":[80,153],"measurements":[81,140,154],"animals.":[83],"Such":[84],"improve":[87],"our":[88],"understanding":[89],"underlying":[92],"optimize":[95],"allocation":[97],"resources":[99],"for":[100,126,179],"RESULTS:":[103],"We":[104,160],"developed":[105],"an":[106],"algorithm":[107,231],"differential":[110],"set":[112,203,235],"enrichment":[113,204],"as":[114,255],"part":[115],"sbv":[118],"IMPROVER":[119],"(systems":[120],"verification":[122],"Industrial":[124],"Methodology":[125],"Process":[127],"Verification":[128],"Research)":[130],"Species":[131],"Translation":[132],"Challenge,":[133],"which":[134],"focused":[135],"on":[136,281],"phosphoproteomic":[137],"transcriptomic":[139],"normal":[142],"bronchial":[144],"epithelial":[145],"(NHBE)":[146],"primary":[147,158],"(NRBE)":[157],"cells.":[159,218],"find":[161],"exhibit":[165],"higher":[167],"correlation":[169],"compared":[170,215],"with":[171,216,239,263],"individual":[172],"genes,":[173],"are":[175,279],"potentially":[176],"more":[177],"suited":[178],"direct":[180],"prediction.":[181],"Furthermore,":[182],"contrast":[184],"similar":[187],"cross-species":[188],"response":[189],"protein":[191,276],"phosphorylation":[192,277],"states":[193],"5":[194],"25":[196],"min":[197],"exposure":[199,208],"stimuli,":[201],"6":[205],"h":[206],"is":[209,253],"significantly":[210],"different":[211],"NHBE":[213,238],"NRBE":[217],"spite":[220],"this":[222],"difference,":[223],"we":[224],"were":[225],"able":[226],"develop":[228],"robust":[230],"activation":[236],"high":[240],"accuracy":[241],"using":[242],"simple":[243],"methods.":[245],"AVAILABILITY":[246],"AND":[247],"IMPLEMENTATION:":[248],"Implementation":[249],"all":[251],"algorithms":[252],"available":[254,280],"source":[256],"code":[257],"(in":[258],"Matlab)":[259],"at":[260],"http://bhanot.biomaps.rutgers.edu/wiki/codes_SC3_Predicting_GeneSets.zip,":[261],"along":[262],"relevant":[265],"data":[266,278],"used":[267],"analysis.":[270],"Gene":[271],"sets,":[272],"expression":[274],"request.":[282],"CONTACT:":[283],"hormoz@kitp.ucsb.edu.":[284]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
