{"id":"https://openalex.org/W2141090745","doi":"https://doi.org/10.1093/bioinformatics/btv315","title":"Trans-species learning of cellular signaling systems with bimodal deep belief networks","display_name":"Trans-species learning of cellular signaling systems with bimodal deep belief networks","publication_year":2015,"publication_date":"2015-05-20","ids":{"openalex":"https://openalex.org/W2141090745","doi":"https://doi.org/10.1093/bioinformatics/btv315","mag":"2141090745","pmid":"https://pubmed.ncbi.nlm.nih.gov/25995230"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv315","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3008/49034687/bioinformatics_31_18_3008.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3008/49034687/bioinformatics_31_18_3008.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101855033","display_name":"Lujia Chen","orcid":"https://orcid.org/0000-0003-4157-0440"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lujia Chen","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15237, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15237, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103133075","display_name":"Chunhui Cai","orcid":"https://orcid.org/0000-0002-1742-4999"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chunhui Cai","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15237, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15237, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103190540","display_name":"Vicky Chen","orcid":"https://orcid.org/0000-0003-4595-154X"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vicky Chen","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15237, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15237, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046515259","display_name":"Xinghua Lu","orcid":"https://orcid.org/0000-0002-8599-2269"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xinghua Lu","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15237, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15237, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5046515259"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.4803,"has_fulltext":true,"cited_by_count":34,"citation_normalized_percentile":{"value":0.89688472,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"31","issue":"18","first_page":"3008","last_page":"3015"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.659600019454956,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.659600019454956,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.08060000091791153,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.06069999933242798,"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/deep-learning","display_name":"Deep learning","score":0.7664800882339478},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.686774730682373},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.6669608354568481},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5909278988838196},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5404011607170105},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.5373067259788513},{"id":"https://openalex.org/keywords/deep-belief-network","display_name":"Deep belief network","score":0.4692402184009552},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.461725652217865},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4251038432121277},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4159248173236847},{"id":"https://openalex.org/keywords/model-system","display_name":"Model system","score":0.4153209626674652},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3024403750896454},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26975542306900024},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23550722002983093}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7664800882339478},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.686774730682373},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.6669608354568481},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5909278988838196},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5404011607170105},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.5373067259788513},{"id":"https://openalex.org/C97385483","wikidata":"https://www.wikidata.org/wiki/Q16954980","display_name":"Deep belief network","level":3,"score":0.4692402184009552},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.461725652217865},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4251038432121277},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4159248173236847},{"id":"https://openalex.org/C2988540567","wikidata":"https://www.wikidata.org/wiki/Q12070446","display_name":"Model system","level":2,"score":0.4153209626674652},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3024403750896454},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26975542306900024},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23550722002983093},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":"D001980","descriptor_name":"Bronchi","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btv315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv315","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3008/49034687/bioinformatics_31_18_3008.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25995230","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25995230","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:d-scholarship.pitt.edu:30141","is_oa":false,"landing_page_url":"https://d-scholarship.pitt.edu/30141/7/licence.txt","pdf_url":null,"source":{"id":"https://openalex.org/S4306402372","display_name":"D-Scholarship@Pitt (University of Pittsburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I170201317","host_organization_name":"University of Pittsburgh","host_organization_lineage":["https://openalex.org/I170201317"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Conference or Workshop Item"},{"id":"pmh:oai:europepmc.org:3981551","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4668779","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"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/18/3008","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/18/3008","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv315","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3008/49034687/bioinformatics_31_18_3008.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1003797612","display_name":null,"funder_award_id":"R01LM012011","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1074945578","display_name":null,"funder_award_id":"R01LM012011","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G2613049985","display_name":null,"funder_award_id":"U54 HG008540","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3383861010","display_name":null,"funder_award_id":"R01LM 010144","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G6734885963","display_name":null,"funder_award_id":"U54 HG008540","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2141090745.pdf","grobid_xml":"https://content.openalex.org/works/W2141090745.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W32160621","https://openalex.org/W207882388","https://openalex.org/W1603152151","https://openalex.org/W1663973292","https://openalex.org/W1968524774","https://openalex.org/W1976526581","https://openalex.org/W2001502878","https://openalex.org/W2009086942","https://openalex.org/W2016799887","https://openalex.org/W2063559185","https://openalex.org/W2080504768","https://openalex.org/W2091564445","https://openalex.org/W2094201044","https://openalex.org/W2097360283","https://openalex.org/W2099866409","https://openalex.org/W2100495367","https://openalex.org/W2115096495","https://openalex.org/W2122825543","https://openalex.org/W2133033238","https://openalex.org/W2136922672","https://openalex.org/W2146241755","https://openalex.org/W2154168928","https://openalex.org/W2155653793","https://openalex.org/W2157963336","https://openalex.org/W2163922914","https://openalex.org/W2164587673","https://openalex.org/W2184188583","https://openalex.org/W2248154415","https://openalex.org/W2981638958","https://openalex.org/W4239403073","https://openalex.org/W4285719527","https://openalex.org/W4294541781","https://openalex.org/W6601360635","https://openalex.org/W6606244218","https://openalex.org/W6683994600"],"related_works":["https://openalex.org/W2906214541","https://openalex.org/W4367367217","https://openalex.org/W2133034788","https://openalex.org/W2897826427","https://openalex.org/W2792607040","https://openalex.org/W2518528680","https://openalex.org/W1257380361","https://openalex.org/W4368617646","https://openalex.org/W1970959288","https://openalex.org/W2967392952"],"abstract_inverted_index":{"MOTIVATION:":[0],"Model":[1],"organisms":[2,25],"play":[3],"critical":[4],"roles":[5],"in":[6,116,121],"biomedical":[7],"research":[8],"of":[9,48,111,143,176],"human":[10,38,62],"diseases":[11],"and":[12,61,76,84,97],"drug":[13],"development.":[14],"An":[15],"imperative":[16],"task":[17],"is":[18,158],"to":[19,26,41,73,91,148],"translate":[20],"information/knowledge":[21],"acquired":[22],"from":[23],"model":[24],"humans.":[27],"In":[28],"this":[29],"study,":[30],"we":[31,77],"address":[32],"a":[33,65,79,85,122],"trans-species":[34,99],"learning":[35],"problem:":[36],"predicting":[37],"cell":[39],"responses":[40,47],"diverse":[42],"stimuli,":[43],"based":[44],"on":[45],"the":[46,53,93,113,117,129,141,161,177,180],"rat":[49,60],"cells":[50,63],"treated":[51],"with":[52],"same":[54],"stimuli.":[55],"RESULTS:":[56],"We":[57],"hypothesized":[58],"that":[59,128],"share":[64],"common":[66,94],"signal-encoding":[67],"mechanism":[68,96],"but":[69],"employ":[70],"different":[71],"proteins":[72],"transmit":[74],"signals,":[75],"developed":[78],"bimodal":[80,87],"deep":[81,88,145],"belief":[82,89],"network":[83,90],"semi-restricted":[86],"represent":[92],"encoding":[95],"perform":[98],"learning.":[100],"These":[101],"'deep":[102],"learning'":[103],"models":[104,130,147],"include":[105],"hierarchically":[106],"organized":[107],"latent":[108],"variables":[109],"capable":[110],"capturing":[112],"statistical":[114],"structures":[115],"observed":[118],"proteomic":[119],"data":[120,166,187],"distributed":[123],"fashion.":[124],"The":[125,156,165],"results":[126],"show":[127],"significantly":[131],"outperform":[132],"two":[133],"current":[134],"state-of-the-art":[135],"classification":[136],"algorithms.":[137],"Our":[138],"study":[139],"demonstrated":[140],"potential":[142],"using":[144],"hierarchical":[146],"simulate":[149],"cellular":[150],"signaling":[151],"systems.":[152],"AVAILABILITY":[153],"AND":[154],"IMPLEMENTATION:":[155],"software":[157],"available":[159,168,189],"at":[160,190],"following":[162],"URL:":[163],"http://pubreview.dbmi.pitt.edu/TransSpeciesDeepLearning/.":[164],"are":[167,188],"through":[169],"SBV":[170],"IMPROVER":[171],"website,":[172],"https://www.sbvimprover.com/challenge-2/overview,":[173],"upon":[174],"publication":[175],"report":[178],"by":[179],"organizers.":[181],"CONTACT:":[182],"xinghua@pitt.edu":[183],"SUPPLEMENTARY":[184],"INFORMATION:":[185],"Supplementary":[186],"Bioinformatics":[191],"online.":[192]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
