{"id":"https://openalex.org/W2198221950","doi":"https://doi.org/10.1109/bibm.2015.7359843","title":"Patho-finder \u2014 A fast and accurate program for pathogen identification through RNA-seq","display_name":"Patho-finder \u2014 A fast and accurate program for pathogen identification through RNA-seq","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2198221950","doi":"https://doi.org/10.1109/bibm.2015.7359843","mag":"2198221950"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359843","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359843","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5100987247","display_name":"Chin-Ting Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Chin-Ting Wu","raw_affiliation_strings":["Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan"],"affiliations":[{"raw_affiliation_string":"Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102940992","display_name":"Tzu\u2010Hung Hsiao","orcid":"https://orcid.org/0000-0003-0365-9970"},"institutions":[{"id":"https://openalex.org/I4210091773","display_name":"Taichung Veterans General Hospital","ror":"https://ror.org/00e87hq62","country_code":"TW","type":"healthcare","lineage":["https://openalex.org/I4210091773"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Tzu-Hung Hsiao","raw_affiliation_strings":["Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan","institution_ids":["https://openalex.org/I4210091773"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028190064","display_name":"Yu\u2010Chiao Chiu","orcid":"https://orcid.org/0000-0003-1647-8634"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas Health Science Center at San Antonio","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966"]},{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW","US"],"is_corresponding":false,"raw_author_name":"Yu-Chiao Chiu","raw_affiliation_strings":["Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan","Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas"],"affiliations":[{"raw_affiliation_string":"Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100995413","display_name":"Yu-Ching Hsu","orcid":null},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yu-Ching Hsu","raw_affiliation_strings":["Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan"],"affiliations":[{"raw_affiliation_string":"Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062893898","display_name":"Eric Y. Chuang","orcid":"https://orcid.org/0000-0003-2530-0096"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Eric Y. Chuang","raw_affiliation_strings":["Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100689057","display_name":"Yidong Chen","orcid":"https://orcid.org/0000-0001-6806-2185"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas Health Science Center at San Antonio","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yidong Chen","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, Texas"],"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, Texas","institution_ids":["https://openalex.org/I165951966"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100987247"],"corresponding_institution_ids":["https://openalex.org/I16733864"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06866017,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"140","issue":null,"first_page":"1148","last_page":"1151"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9980000257492065,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.9070388674736023},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7570616006851196},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6435301303863525},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5357118844985962},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42652010917663574},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.42251208424568176},{"id":"https://openalex.org/keywords/real-time-computing","display_name":"Real-time computing","score":0.3617979884147644},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33804529905319214},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32120442390441895},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1858278214931488},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10143572092056274},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.0959155261516571},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.0879666805267334}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.9070388674736023},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7570616006851196},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6435301303863525},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5357118844985962},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42652010917663574},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.42251208424568176},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.3617979884147644},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33804529905319214},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32120442390441895},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1858278214931488},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10143572092056274},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0959155261516571},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0879666805267334},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2015.7359843","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359843","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1987350137","https://openalex.org/W1988460088","https://openalex.org/W2000336618","https://openalex.org/W2053057991","https://openalex.org/W2055043387","https://openalex.org/W2070791418","https://openalex.org/W2098521327","https://openalex.org/W2107097628","https://openalex.org/W2126419817","https://openalex.org/W2140729960","https://openalex.org/W2170551349","https://openalex.org/W2944088418","https://openalex.org/W4236236547","https://openalex.org/W6639884556"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W188202134","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2010229520"],"abstract_inverted_index":{"Technology":[0],"of":[1,8,37,40,82,126],"next":[2,30],"generation":[3,31],"sequencing":[4,32,76],"to":[5,26,54,96],"detect":[6,27,55],"pathogens":[7,16,28],"sample":[9,59],"can":[10],"impact":[11],"human":[12],"health":[13],"by":[14,84,91],"revealing":[15],"which":[17],"cause":[18],"disease.":[19],"Several":[20],"workflow":[21,52,69],"has":[22],"developed":[23],"in":[24,29,74,142],"purposed":[25],"data.":[33,77],"However,":[34],"the":[35,44,51,93,108,124,140],"requirement":[36],"computation":[38],"power":[39],"these":[41],"workflows":[42],"limited":[43],"application.":[45],"The":[46,132],"time":[47,109],"consuming":[48,110],"problem":[49],"make":[50],"difficult":[53],"datasets":[56],"with":[57,129],"large":[58],"size.":[60],"Here":[61],"we":[62,88,106,120],"presented":[63],"Patho-finder,":[64],"a":[65],"fast":[66],"and":[67,111,115],"accurate":[68],"designed":[70],"for":[71],"detecting":[72],"pathogen":[73],"RNA":[75],"We":[78],"have":[79],"evaluated":[80],"performance":[81,90],"Patho-finder":[83,99,114,122],"three":[85],"aspects.":[86],"First,":[87],"evaluate":[89],"alter":[92],"data":[94],"features,":[95],"see":[97],"how":[98],"work":[100],"under":[101],"different":[102],"simulation":[103],"conditions.":[104],"Next,":[105],"compare":[107],"accuracy":[112],"between":[113],"existing":[116],"workflow.":[117],"At":[118],"last,":[119],"used":[121],"on":[123],"RNA-seq":[125],"cell":[127],"lines":[128],"known":[130],"virus-infected.":[131],"validation":[133],"result":[134],"demonstrated":[135],"our":[136],"approach":[137],"could":[138],"finish":[139],"task":[141],"real":[143],"datasets.":[144]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
