{"id":"https://openalex.org/W2131659389","doi":"https://doi.org/10.1093/bioinformatics/btr634","title":"Data-driven information retrieval in heterogeneous collections of transcriptomics data links <i>SIM2s</i> to malignant pleural mesothelioma","display_name":"Data-driven information retrieval in heterogeneous collections of transcriptomics data links <i>SIM2s</i> to malignant pleural mesothelioma","publication_year":2011,"publication_date":"2011-11-20","ids":{"openalex":"https://openalex.org/W2131659389","doi":"https://doi.org/10.1093/bioinformatics/btr634","mag":"2131659389","pmid":"https://pubmed.ncbi.nlm.nih.gov/22106335"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr634","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr634","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/2/246/48868654/bioinformatics_28_2_246.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/28/2/246/48868654/bioinformatics_28_2_246.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108022392","display_name":"Jos\u00e9 Caldas","orcid":"https://orcid.org/0000-0001-7846-1884"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210096640","display_name":"Royal Brompton Hospital","ror":"https://ror.org/00cv4n034","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800036501","https://openalex.org/I4210096640"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Caldas","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066335313","display_name":"Nils Gehlenborg","orcid":"https://orcid.org/0000-0003-0327-8297"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210096640","display_name":"Royal Brompton Hospital","ror":"https://ror.org/00cv4n034","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800036501","https://openalex.org/I4210096640"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":false,"raw_author_name":"Nils Gehlenborg","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070078338","display_name":"Eeva Kettunen","orcid":"https://orcid.org/0000-0001-5769-3010"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210096640","display_name":"Royal Brompton Hospital","ror":"https://ror.org/00cv4n034","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800036501","https://openalex.org/I4210096640"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":false,"raw_author_name":"Eeva Kettunen","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046946670","display_name":"Ali Faisal","orcid":"https://orcid.org/0000-0001-9607-9371"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210096640","display_name":"Royal Brompton Hospital","ror":"https://ror.org/00cv4n034","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800036501","https://openalex.org/I4210096640"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":false,"raw_author_name":"Ali Faisal","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032201687","display_name":"Mikko R\u00f6nty","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210096640","display_name":"Royal Brompton Hospital","ror":"https://ror.org/00cv4n034","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800036501","https://openalex.org/I4210096640"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":false,"raw_author_name":"Mikko R\u00f6nty","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090076776","display_name":"Andrew G. Nicholson","orcid":"https://orcid.org/0000-0003-3257-102X"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210096640","display_name":"Royal Brompton Hospital","ror":"https://ror.org/00cv4n034","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800036501","https://openalex.org/I4210096640"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":false,"raw_author_name":"Andrew G. Nicholson","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076240896","display_name":"Sakari Knuutila","orcid":"https://orcid.org/0000-0001-5592-3839"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210096640","display_name":"Royal Brompton Hospital","ror":"https://ror.org/00cv4n034","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800036501","https://openalex.org/I4210096640"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":false,"raw_author_name":"Sakari Knuutila","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081419327","display_name":"Alvis Br\u0101zma","orcid":"https://orcid.org/0000-0001-5988-7409"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210096640","display_name":"Royal Brompton Hospital","ror":"https://ror.org/00cv4n034","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800036501","https://openalex.org/I4210096640"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":false,"raw_author_name":"Alvis Brazma","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018305257","display_name":"Samuel Kaski","orcid":"https://orcid.org/0000-0003-1925-9154"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210096640","display_name":"Royal Brompton Hospital","ror":"https://ror.org/00cv4n034","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800036501","https://openalex.org/I4210096640"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":true,"raw_author_name":"Samuel Kaski","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, Helsinki, Finland, 2Functional Genomics Group, European Bioinformatics Institute, 3Graduate School of Life Sciences, University of Cambridge, Cambridge, UK, 4Health and Work Ability, Biological Mechanisms and Prevention of Work-Related Diseases, Finnish Institute of Occupational Health, 5Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland,6Department of Histopathology, Royal Brompton Hospital, London, UK, 7Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital and 8Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5018305257"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I241749","https://openalex.org/I2801770344","https://openalex.org/I32943570","https://openalex.org/I4210096640","https://openalex.org/I9927081"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2166,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.78157402,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"2","first_page":"246","last_page":"253"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.7387999892234802,"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":0.7387999892234802,"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":0.05860000103712082,"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":0.050200000405311584,"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/mesothelioma","display_name":"Mesothelioma","score":0.7609946131706238},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6167345643043518},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.45909199118614197},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.38117051124572754},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3235090970993042},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.31263554096221924},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2942371666431427},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18264198303222656},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06479710340499878}],"concepts":[{"id":"https://openalex.org/C2777407522","wikidata":"https://www.wikidata.org/wiki/Q1077603","display_name":"Mesothelioma","level":2,"score":0.7609946131706238},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6167345643043518},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.45909199118614197},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.38117051124572754},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3235090970993042},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.31263554096221924},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2942371666431427},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18264198303222656},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06479710340499878},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"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":"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":"D008654","descriptor_name":"Mesothelioma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008654","descriptor_name":"Mesothelioma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008654","descriptor_name":"Mesothelioma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010997","descriptor_name":"Pleural Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010997","descriptor_name":"Pleural Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010997","descriptor_name":"Pleural Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btr634","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr634","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/2/246/48868654/bioinformatics_28_2_246.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22106335","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22106335","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:europepmc.org:2265832","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3259436","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr634","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr634","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/2/246/48868654/bioinformatics_28_2_246.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W411816178","https://openalex.org/W1532325895","https://openalex.org/W1982590785","https://openalex.org/W1989817005","https://openalex.org/W1997660954","https://openalex.org/W1998485305","https://openalex.org/W2001082470","https://openalex.org/W2019856979","https://openalex.org/W2020033048","https://openalex.org/W2038714085","https://openalex.org/W2040607104","https://openalex.org/W2047547533","https://openalex.org/W2061016350","https://openalex.org/W2068858902","https://openalex.org/W2069870183","https://openalex.org/W2075496125","https://openalex.org/W2084975981","https://openalex.org/W2094879937","https://openalex.org/W2099101879","https://openalex.org/W2101696428","https://openalex.org/W2103017472","https://openalex.org/W2106490775","https://openalex.org/W2107607304","https://openalex.org/W2108671185","https://openalex.org/W2111042968","https://openalex.org/W2114693731","https://openalex.org/W2121171791","https://openalex.org/W2121186913","https://openalex.org/W2121604817","https://openalex.org/W2123999617","https://openalex.org/W2125358852","https://openalex.org/W2127053639","https://openalex.org/W2127862186","https://openalex.org/W2129304235","https://openalex.org/W2130410032","https://openalex.org/W2146280873","https://openalex.org/W2147018385","https://openalex.org/W2163176957","https://openalex.org/W2168546553","https://openalex.org/W2170745030","https://openalex.org/W2912651257","https://openalex.org/W3209888570","https://openalex.org/W4213009331","https://openalex.org/W6676809733","https://openalex.org/W7033260006"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2064862277","https://openalex.org/W2399513595","https://openalex.org/W2529284065","https://openalex.org/W2025510760","https://openalex.org/W1973483231","https://openalex.org/W2045676522","https://openalex.org/W2799957336","https://openalex.org/W2105287018","https://openalex.org/W2055532379"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genome-wide":[1],"measurement":[2],"of":[3,35,67,104,148],"transcript":[4],"levels":[5],"is":[6,24],"an":[7,75,145],"ubiquitous":[8],"tool":[9],"in":[10,20,58,102,144],"biomedical":[11],"research.":[12],"As":[13],"experimental":[14,88],"data":[15,61,153],"continues":[16],"to":[17,27],"be":[18],"deposited":[19],"public":[21],"databases,":[22],"it":[23],"becoming":[25],"important":[26],"develop":[28],"search":[29,99],"engines":[30],"that":[31,52,110],"enable":[32],"the":[33,59,98],"retrieval":[34,43,77],"relevant":[36],"studies":[37,54],"given":[38],"a":[39,64,125],"query":[40],"study.":[41],"While":[42],"systems":[44],"based":[45,55,79],"on":[46,56,80],"meta-data":[47],"already":[48],"exist,":[49],"data-driven":[50],"approaches":[51],"retrieve":[53],"similarities":[57],"expression":[60,106],"itself":[62],"have":[63],"greater":[65],"potential":[66],"uncovering":[68],"novel":[69],"biological":[70,117],"insights.":[71],"RESULTS:":[72],"We":[73,108],"propose":[74],"information":[76],"method":[78,84],"differential":[81,105],"expression.":[82],"Our":[83],"deals":[85],"with":[86,93],"arbitrary":[87],"designs":[89],"and":[90,133,154],"performs":[91],"competitively":[92],"alternative":[94],"approaches,":[95],"while":[96],"making":[97],"results":[100],"interpretable":[101],"terms":[103],"patterns.":[107],"show":[109],"our":[111,137],"model":[112],"yields":[113],"meaningful":[114],"connections":[115],"between":[116,129],"conditions":[118],"from":[119,159],"different":[120],"studies.":[121],"Finally,":[122],"we":[123],"validate":[124],"previously":[126],"unknown":[127],"connection":[128],"malignant":[130],"pleural":[131],"mesothelioma":[132,149],"SIM2s":[134],"suggested":[135],"by":[136],"method,":[138],"via":[139],"real-time":[140],"polymerase":[141],"chain":[142],"reaction":[143],"independent":[146],"set":[147],"samples.":[150],"AVAILABILITY:":[151],"Supplementary":[152],"source":[155],"code":[156],"are":[157],"available":[158],"http://www.ebi.ac.uk/fg/research/rex.":[160]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-25T15:57:00.446498","created_date":"2016-06-24T00:00:00"}
