{"id":"https://openalex.org/W2199280985","doi":null,"title":"Development of an approach for ab initio estimation of compound-induced liver injury based on global gene transcriptional profiles.","display_name":"Development of an approach for ab initio estimation of compound-induced liver injury based on global gene transcriptional profiles.","publication_year":2006,"publication_date":"2006-01-01","ids":{"openalex":"https://openalex.org/W2199280985","mag":"2199280985","pmid":"https://pubmed.ncbi.nlm.nih.gov/17503381"},"language":"en","primary_location":{"id":"pmid:17503381","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17503381","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,"listed_in":[],"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":"Genome informatics. International Conference on Genome Informatics","raw_type":"Journal Article"},"volume":null,"type":"conference-paper","is_traditional":true,"indexed_in":["pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001041573","display_name":"Xudong Dai","orcid":"https://orcid.org/0009-0008-9987-7916","observed_orcids":["https://orcid.org/0009-0008-9987-7916"]},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xudong Dai","raw_affiliation_strings":["Rosetta Inpharmatics LLC, Merck & Co., Inc., Seattle, WA 98109, USA. xudong_dai@merck.com","Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rosetta Inpharmatics LLC, Merck & Co., Inc., Seattle, WA 98109, USA. xudong_dai@merck.com","institution_ids":["https://openalex.org/I1285764155"]},{"raw_affiliation_string":"Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101440725","display_name":"Yudong D. He","orcid":"https://orcid.org/0000-0003-0818-605X","observed_orcids":["https://orcid.org/0000-0003-0818-605X"]},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yudong D He","raw_affiliation_strings":["Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101790056","display_name":"Hongyue A. Dai","orcid":"https://orcid.org/0000-0002-6609-9141","observed_orcids":["https://orcid.org/0000-0002-6609-9141"]},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongyue Dai","raw_affiliation_strings":["Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091462073","display_name":"Pek Yee Lum","orcid":"https://orcid.org/0000-0002-7496-1934","observed_orcids":["https://orcid.org/0000-0002-7496-1934"]},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pek Y Lum","raw_affiliation_strings":["Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054523246","display_name":"Christopher J. Roberts","orcid":"https://orcid.org/0000-0001-9978-2767","observed_orcids":["https://orcid.org/0000-0001-9978-2767"]},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher J Roberts","raw_affiliation_strings":["Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091020033","display_name":"Jeffrey F. Waring","orcid":"https://orcid.org/0000-0002-7769-0367","observed_orcids":["https://orcid.org/0000-0002-7769-0367"]},"institutions":[{"id":"https://openalex.org/I4210088555","display_name":"Abbott (United States)","ror":"https://ror.org/0052svj16","country_code":"US","type":"company","lineage":["https://openalex.org/I4210088555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey F Waring","raw_affiliation_strings":["Abbott Laboratories"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Abbott Laboratories","institution_ids":["https://openalex.org/I4210088555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111568617","display_name":"Roger G. Ulrich","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roger G Ulrich","raw_affiliation_strings":["Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rosetta Inpharmatics LLC\u2014A Wholly Owned Subsidiary of Merck & Co., Inc","institution_ids":["https://openalex.org/I1285764155"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":23.6471,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":1.0,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":87,"max":97},"biblio":{"volume":"17","issue":"2","first_page":"77","last_page":"88"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11465","display_name":"Drug-Induced Hepatotoxicity and Protection","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11465","display_name":"Drug-Induced Hepatotoxicity and Protection","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.005100000184029341,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.000699999975040555,"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/hepatotoxicity-prediction","display_name":"hepatotoxicity prediction","score":0.921999990940094},{"id":"https://openalex.org/keywords/toxicogenomics","display_name":"toxicogenomics","score":0.9139999747276306},{"id":"https://openalex.org/keywords/gene-expression-profiles","display_name":"gene expression profiles","score":0.7960000038146973},{"id":"https://openalex.org/keywords/drug-toxicity","display_name":"drug toxicity","score":0.6060000061988831},{"id":"https://openalex.org/keywords/machine-learning-prediction-models","display_name":"machine learning prediction models","score":0.753000020980835}],"concepts":[{"id":"https://openalex.org/C29730261","wikidata":"https://www.wikidata.org/wiki/Q274160","display_name":"Toxicity","level":2,"score":0.7804615497589111},{"id":"https://openalex.org/C2776637226","wikidata":"https://www.wikidata.org/wiki/Q6658207","display_name":"Liver injury","level":2,"score":0.7146056890487671},{"id":"https://openalex.org/C2993709057","wikidata":"https://www.wikidata.org/wiki/Q1349821","display_name":"Liver toxicity","level":3,"score":0.5364485383033752},{"id":"https://openalex.org/C93231420","wikidata":"https://www.wikidata.org/wiki/Q841450","display_name":"Toxicogenomics","level":4,"score":0.5151116251945496},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4972057640552521},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.4464513659477234},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.44418567419052124},{"id":"https://openalex.org/C64903051","wikidata":"https://www.wikidata.org/wiki/Q2198549","display_name":"Drug development","level":3,"score":0.41756346821784973},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34837427735328674},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3353074789047241},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32467979192733765},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3226247727870941},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.31833964586257935},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.30616307258605957},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15889644622802734},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.11374574899673462}],"mesh":[{"descriptor_ui":"D000410","descriptor_name":"Alanine Transaminase","qualifier_ui":"Q000097","qualifier_name":"blood","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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001219","descriptor_name":"Aspartate Aminotransferases","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D001663","descriptor_name":"Bilirubin","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D002624","descriptor_name":"Chemistry, Clinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002784","descriptor_name":"Cholesterol","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D004305","descriptor_name":"Dose-Response Relationship, Drug","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017207","descriptor_name":"Rats, Sprague-Dawley","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D043922","descriptor_name":"Toxicogenetics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":"Q000139","qualifier_name":"chemically induced","is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":2,"locations":[{"id":"pmid:17503381","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17503381","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,"listed_in":[],"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":"Genome informatics. International Conference on Genome Informatics","raw_type":"Journal Article"},{"id":"mag:2199280985","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17503381","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,"listed_in":[],"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":null,"is_accepted":false,"is_published":false,"raw_source_name":"PubMed","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.9537000060081482}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1513444097","https://openalex.org/W1540861017","https://openalex.org/W1544324307","https://openalex.org/W1727290854","https://openalex.org/W1895993106","https://openalex.org/W2011678217","https://openalex.org/W2024390537","https://openalex.org/W2031838201","https://openalex.org/W2073173883","https://openalex.org/W2078072721","https://openalex.org/W2087826013","https://openalex.org/W2094147349","https://openalex.org/W2095018624","https://openalex.org/W2128985829","https://openalex.org/W2141341794","https://openalex.org/W2145413925","https://openalex.org/W2146264532","https://openalex.org/W2150948905","https://openalex.org/W2160450758"],"related_works":["https://openalex.org/W7100302087","https://openalex.org/W7098004646","https://openalex.org/W2054035259","https://openalex.org/W2045058545","https://openalex.org/W1968774774","https://openalex.org/W2609161598","https://openalex.org/W2138646011","https://openalex.org/W4301120077","https://openalex.org/W7098768824","https://openalex.org/W2318981334"],"abstract_inverted_index":{"Toxicity":[0],"is":[1],"a":[2,15,45,57,81,85,108,115],"major":[3],"cause":[4],"of":[5,24,56,60,93,100,107,134,156,160],"failure":[6],"in":[7,129],"drug":[8,25],"development.":[9],"A":[10],"toxicogenomic":[11],"approach":[12,47],"may":[13],"provide":[14],"powerful":[16],"tool":[17],"for":[18,32,48,89],"better":[19],"assessing":[20,49,90],"the":[21,91,98,101,105,138,154],"potential":[22],"toxicity":[23,41,162],"candidates.":[26],"Several":[27],"approaches":[28],"have":[29],"been":[30],"reported":[31],"predicting":[33],"hepatotoxicity":[34,82,102],"based":[35,122,163],"on":[36,123,164],"reference":[37],"compounds":[38,74],"with":[39,67,145],"well-studied":[40],"mechanisms.":[42],"We":[43],"developed":[44],"new":[46],"compound-induced":[50,119,142],"liver":[51,70,77,95,120,143,161],"injury":[52,121],"without":[53,75],"prior":[54],"knowledge":[55],"compound's":[58],"mechanism":[59],"toxicity.":[61],"Using":[62],"samples":[63],"from":[64],"rodents":[65],"treated":[66],"49":[68],"known":[69,76],"toxins":[71],"and":[72,104,148],"10":[73],"toxicity,":[78],"we":[79,112],"derived":[80],"score":[83,103],"as":[84],"single":[86],"quantitative":[87],"measurement":[88],"degree":[92],"induced":[94],"damage.":[96],"Combining":[97],"sensitivity":[99,147],"power":[106],"machine":[109],"learning":[110],"algorithm,":[111],"then":[113],"built":[114,139],"model":[116,140],"to":[117],"predict":[118],"212":[124],"expression":[125,136],"profiles.":[126,166],"As":[127],"estimated":[128],"an":[130],"independent":[131],"data":[132],"set":[133],"54":[135],"profiles,":[137],"predicted":[141],"damage":[144],"90.9%":[146],"88.4%":[149],"specificity.":[150],"Our":[151],"findings":[152],"illustrate":[153],"feasibility":[155],"ab":[157],"initio":[158],"estimation":[159],"transcriptional":[165]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}