{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T20:57:23Z","timestamp":1779310643519,"version":"3.51.4"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2019,2,19]],"date-time":"2019-02-19T00:00:00Z","timestamp":1550534400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2016YFC1000505"],"award-info":[{"award-number":["2016YFC1000505"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2017YFC0908402"],"award-info":[{"award-number":["2017YFC0908402"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFC0116903"],"award-info":[{"award-number":["2018YFC0116903"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871325"],"award-info":[{"award-number":["31871325"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31671367"],"award-info":[{"award-number":["31671367"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31471245"],"award-info":[{"award-number":["31471245"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91631301"],"award-info":[{"award-number":["91631301"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81471484"],"award-info":[{"award-number":["81471484"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81501289"],"award-info":[{"award-number":["81501289"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai NUANWEN Information and Technology Co"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Whole-exome sequencing (WES) is now being used in clinical practice for the diagnosis of the causal genes of Mendelian diseases. In order to make the diagnosis, however, the clinical phenotypes [e.g. Human Phenotype Ontology (HPO) terms] of a patient are needed for prioritizing the variants called from the WES data of the patient. Computational tools are therefore needed to standardize and accelerate this process.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we introduce a tool named PhenoPro for prioritizing the causal gene of Mendelian disease given both the HPO terms assigned to and the variants called from the WES data of a patient. PhenoPro has been benchmarked using both simulated patients and 287 real diagnosed patients of Chinese ancestry, and shows significant improvements over five previous tools. Moreover, the addition of an internal variant data of Chinese ancestry and the variant data from the patients\u2019 parents can further improve PhenoPro\u2019s performance. To make PhenoPro a fully automated tool, we also include a natural language processing component for automated HPO term assignment from clinical reports, and demonstrate that the natural language processing is as effective as manual HPO assignment using real clinical reports. In conclusion, PhenoPro can be used as a pre-screening tool to assist in the diagnosis of Mendelian disease genes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The web server of PhenoPro is freely available at http:\/\/app.tianlab.cn.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz100","type":"journal-article","created":{"date-parts":[[2019,2,18]],"date-time":"2019-02-18T04:25:53Z","timestamp":1550463953000},"page":"3559-3566","source":"Crossref","is-referenced-by-count":32,"title":["PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease"],"prefix":"10.1093","volume":"35","author":[{"given":"Zixiu","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development , Shanghai, China"},{"name":"Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University , Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development , Shanghai, China"},{"name":"Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University , Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yukai","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University , Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Qiu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University , Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University , Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yulan","family":"Lu","sequence":"additional","affiliation":[{"name":"The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defect, Translational Medicine Research Center of Children Development and Diseases, Pediatrics Research Institute , Shanghai, China"},{"name":"Children\u2019s Hospital of Fudan University , Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lin","family":"Yang","sequence":"additional","affiliation":[{"name":"The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defect, Translational Medicine Research Center of Children Development and Diseases, Pediatrics Research Institute , Shanghai, China"},{"name":"Children\u2019s Hospital of Fudan University , Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William J","family":"Qu","sequence":"additional","affiliation":[{"name":"Centennial High School, Ellicott City , MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huijun","family":"Wang","sequence":"additional","affiliation":[{"name":"The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defect, Translational Medicine Research Center of Children Development and Diseases, Pediatrics Research Institute , Shanghai, China"},{"name":"Children\u2019s Hospital of Fudan University , Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenhao","family":"Zhou","sequence":"additional","affiliation":[{"name":"The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defect, Translational Medicine Research Center of Children Development and Diseases, Pediatrics Research Institute , Shanghai, China"},{"name":"Children\u2019s Hospital of Fudan University , Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weidong","family":"Tian","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development , Shanghai, China"},{"name":"Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University , Shanghai, China"},{"name":"Children\u2019s Hospital of Fudan University , Shanghai, 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