{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T08:50:16Z","timestamp":1770540616075,"version":"3.49.0"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,11,5]],"date-time":"2018-11-05T00:00:00Z","timestamp":1541376000000},"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\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61622213"],"award-info":[{"award-number":["61622213"]}],"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":["61732009"],"award-info":[{"award-number":["61732009"]}],"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":["61420106009"],"award-info":[{"award-number":["61420106009"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013314","name":"111 Project","doi-asserted-by":"crossref","award":["B18059"],"award-info":[{"award-number":["B18059"]}],"id":[{"id":"10.13039\/501100013314","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Fundamental Research Funds for the Central Universities of Central South University","award":["2018zzts028"],"award-info":[{"award-number":["2018zzts028"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Reconstructing gene regulatory networks (GRNs) based on gene expression profiles is still an enormous challenge in systems biology. Random forest-based methods have been proved a kind of efficient methods to evaluate the importance of gene regulations. Nevertheless, the accuracy of traditional methods can be further improved. With time-series gene expression data, exploiting inherent time information and high order time lag are promising strategies to improve the power and accuracy of GRNs inference.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we propose a scalable, flexible approach called BiXGBoost to reconstruct GRNs. BiXGBoost is a bidirectional-based method by considering both candidate regulatory genes and target genes for a specific gene. Moreover, BiXGBoost utilizes time information efficiently and integrates XGBoost to evaluate the feature importance. Randomization and regularization are also applied in BiXGBoost to address the over-fitting problem. The results on DREAM4 and Escherichia coli datasets show the good performance of BiXGBoost on different scale of networks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Our Python implementation of BiXGBoost is available at https:\/\/github.com\/zrq0123\/BiXGBoost.<\/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\/bty908","type":"journal-article","created":{"date-parts":[[2018,11,4]],"date-time":"2018-11-04T20:06:56Z","timestamp":1541362016000},"page":"1893-1900","source":"Crossref","is-referenced-by-count":75,"title":["BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks"],"prefix":"10.1093","volume":"35","author":[{"given":"Ruiqing","family":"Zheng","sequence":"first","affiliation":[{"name":"School of Information Science and Engineering, Central South University, Changsha, China"}]},{"given":"Min","family":"Li","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Central South University, Changsha, China"}]},{"given":"Xiang","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Central South University, Changsha, China"}]},{"given":"Fang-Xiang","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Central South University, Changsha, China"},{"name":"Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, Canada"}]},{"given":"Yi","family":"Pan","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Central South University, Changsha, China"},{"name":"Department of Computer Science, Georgia State University, Atlanta, GA, USA"}]},{"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Central South University, Changsha, China"}]}],"member":"286","published-online":{"date-parts":[[2018,11,5]]},"reference":[{"key":"2023012713155005400_bty908-B1","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1093\/nar\/gkg210","article-title":"Evolution of transcription factors and the gene regulatory network in Escherichia coli","volume":"31","author":"Babu","year":"2003","journal-title":"Nucl. 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