{"id":"https://openalex.org/W2744616328","doi":"https://doi.org/10.1021/acs.jcim.7b00281","title":"Molecular Structure-Based Large-Scale Prediction of Chemical-Induced Gene Expression Changes","display_name":"Molecular Structure-Based Large-Scale Prediction of Chemical-Induced Gene Expression Changes","publication_year":2017,"publication_date":"2017-08-10","ids":{"openalex":"https://openalex.org/W2744616328","doi":"https://doi.org/10.1021/acs.jcim.7b00281","mag":"2744616328","pmid":"https://pubmed.ncbi.nlm.nih.gov/28796500"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.7b00281","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00281","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5100738736","display_name":"Ruifeng Liu","orcid":"https://orcid.org/0000-0001-7582-9217"},"institutions":[{"id":"https://openalex.org/I2800986571","display_name":"Telemedicine & Advanced Technology Research Center","ror":"https://ror.org/014pvr265","country_code":"US","type":"other","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2800986571","https://openalex.org/I2802581893"]},{"id":"https://openalex.org/I2802581893","display_name":"United States Army Medical Research and Development Command","ror":"https://ror.org/03cd02q50","country_code":"US","type":"facility","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ruifeng Liu","raw_affiliation_strings":["Department of Defense Biotechnology High\rPerformance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, United States"],"raw_orcid":"https://orcid.org/0000-0001-7582-9217","affiliations":[{"raw_affiliation_string":"Department of Defense Biotechnology High\rPerformance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, United States","institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051906581","display_name":"Mohamed Diwan M. AbdulHameed","orcid":"https://orcid.org/0000-0003-1483-4084"},"institutions":[{"id":"https://openalex.org/I2800986571","display_name":"Telemedicine & Advanced Technology Research Center","ror":"https://ror.org/014pvr265","country_code":"US","type":"other","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2800986571","https://openalex.org/I2802581893"]},{"id":"https://openalex.org/I2802581893","display_name":"United States Army Medical Research and Development Command","ror":"https://ror.org/03cd02q50","country_code":"US","type":"facility","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohamed Diwan M. AbdulHameed","raw_affiliation_strings":["Department of Defense Biotechnology High\rPerformance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Defense Biotechnology High\rPerformance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, United States","institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030271505","display_name":"Anders Wallqvist","orcid":"https://orcid.org/0000-0002-9775-7469"},"institutions":[{"id":"https://openalex.org/I2800986571","display_name":"Telemedicine & Advanced Technology Research Center","ror":"https://ror.org/014pvr265","country_code":"US","type":"other","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2800986571","https://openalex.org/I2802581893"]},{"id":"https://openalex.org/I2802581893","display_name":"United States Army Medical Research and Development Command","ror":"https://ror.org/03cd02q50","country_code":"US","type":"facility","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Anders Wallqvist","raw_affiliation_strings":["Department of Defense Biotechnology High\rPerformance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Defense Biotechnology High\rPerformance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, United States","institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5030271505","https://openalex.org/A5100738736"],"corresponding_institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"],"apc_list":null,"apc_paid":null,"fwci":0.4251,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.65485423,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"57","issue":"9","first_page":"2194","last_page":"2202"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9807000160217285,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.980400025844574,"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/computational-biology","display_name":"Computational biology","score":0.5669822692871094},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5542857646942139},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.541163980960846},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4310585856437683},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41968047618865967},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3089514374732971},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.27123284339904785},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2547151446342468},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1006636917591095}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5669822692871094},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5542857646942139},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.541163980960846},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4310585856437683},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41968047618865967},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3089514374732971},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.27123284339904785},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2547151446342468},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1006636917591095},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000187","qualifier_name":"drug effects","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.7b00281","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00281","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:28796500","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28796500","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5799999833106995,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G5851990620","display_name":null,"funder_award_id":"CBCall14-CBS-05-2-0007","funder_id":"https://openalex.org/F4320332186","funder_display_name":"Defense Threat Reduction Agency"}],"funders":[{"id":"https://openalex.org/F4320332186","display_name":"Defense Threat Reduction Agency","ror":"https://ror.org/04tz64554"},{"id":"https://openalex.org/F4320338280","display_name":"Medical Research and Materiel Command","ror":"https://ror.org/03cd02q50"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1930021478","https://openalex.org/W1981411466","https://openalex.org/W1985258161","https://openalex.org/W1988037271","https://openalex.org/W2033757486","https://openalex.org/W2054195660","https://openalex.org/W2098967508","https://openalex.org/W2119002393","https://openalex.org/W2121066143","https://openalex.org/W2128245586","https://openalex.org/W2143364665","https://openalex.org/W2145578524","https://openalex.org/W2153863665","https://openalex.org/W2156077095","https://openalex.org/W2259983755","https://openalex.org/W2295881384","https://openalex.org/W2320620955","https://openalex.org/W2535020870","https://openalex.org/W2546032827","https://openalex.org/W2550465571"],"related_works":["https://openalex.org/W2392243736","https://openalex.org/W86652014","https://openalex.org/W3129895999","https://openalex.org/W2328518092","https://openalex.org/W3101249758","https://openalex.org/W2803323662","https://openalex.org/W3032874291","https://openalex.org/W2005057264","https://openalex.org/W2363156284","https://openalex.org/W2415025170"],"abstract_inverted_index":{"The":[0],"quantitative":[1],"structure-activity":[2],"relationship":[3],"(QSAR)":[4],"approach":[5,256],"has":[6],"been":[7,22],"used":[8],"to":[9,24,35,70,108,164,168,196,200],"model":[10,25],"a":[11,42,57,80,117,123,254],"wide":[12],"range":[13],"of":[14,38,46,56,83,87,99,113,126,138,147,212],"chemical-induced":[15,26],"biological":[16],"responses.":[17],"However,":[18,209],"it":[19],"had":[20,183],"not":[21],"utilized":[23],"genomewide":[27],"gene":[28,84,140,150,241,262],"expression":[29,85,141,151,242,263],"changes":[30],"until":[31],"very":[32,43],"recently,":[33],"owing":[34],"the":[36,54,71,96,114,129,145,148,155,177,191,204,238,248],"complexity":[37],"training":[39],"and":[40,131,157,173,179,198],"evaluating":[41],"large":[44],"number":[45],"models.":[47,208],"To":[48,143],"address":[49],"this":[50],"issue,":[51],"we":[52,105,153],"examined":[53],"performance":[55],"variable":[58],"nearest":[59],"neighbor":[60],"(v-NN)":[61],"method":[62,250],"that":[63,73,137,216,229,247],"uses":[64],"information":[65,231],"on":[66],"near":[67,221,233],"neighbors":[68,222,234],"conforming":[69],"principle":[72],"similar":[74,77,184],"structures":[75],"have":[76],"activities.":[78],"Using":[79],"data":[81],"set":[82],"signatures":[86,160,182,217],"13":[88],"150":[89],"compounds":[90,115],"derived":[91,133,159,181,225],"from":[92,194,219,226,232,240],"cell-based":[93],"measurements":[94],"in":[95,116,161],"NIH":[97],"Library":[98],"Integrated":[100],"Network-based":[101],"Cellular":[102],"Signatures":[103],"program,":[104],"were":[106],"able":[107],"make":[109],"predictions":[110],"for":[111,257],"62%":[112],"10-fold":[118],"cross":[119],"validation":[120],"test,":[121],"with":[122],"correlation":[124],"coefficient":[125],"0.61":[127],"between":[128],"predicted":[130,149,156,178,218],"experimentally":[132,158,180],"signatures-a":[134],"reproducibility":[135],"rivaling":[136],"high-throughput":[139],"measurements.":[142,243],"evaluate":[144],"utility":[146],"signatures,":[152],"compared":[154],"their":[162],"ability":[163],"identify":[165],"drugs":[166],"known":[167],"cause":[169],"specific":[170],"liver,":[171],"kidney,":[172],"heart":[174],"injuries.":[175],"Overall,":[176],"receiver":[185],"operating":[186],"characteristics,":[187],"whose":[188],"areas":[189],"under":[190],"curve":[192],"ranged":[193],"0.71":[195],"0.77":[197],"0.70":[199],"0.73,":[201],"respectively,":[202],"across":[203],"three":[205],"organ":[206],"injury":[207],"detailed":[210],"analyses":[211],"enrichment":[213],"curves":[214],"indicate":[215],"multiple":[220],"outperformed":[223],"those":[224],"experiments,":[227],"suggesting":[228],"averaging":[230],"may":[235],"help":[236],"improve":[237],"signal":[239],"Our":[244],"results":[245],"demonstrate":[246],"v-NN":[249],"can":[251],"serve":[252],"as":[253],"practical":[255],"modeling":[258],"large-scale,":[259],"genomewide,":[260],"chemical-induced,":[261],"changes.":[264]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
