{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T07:44:25Z","timestamp":1769067865503,"version":"3.49.0"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T00:00:00Z","timestamp":1678060800000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Japan Society for the Promotion of Science (JSPS) Invitational Fellowship","award":["L21503"],"award-info":[{"award-number":["L21503"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["HARS-22-03-G3"],"award-info":[{"award-number":["HARS-22-03-G3"]}],"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":["62202388"],"award-info":[{"award-number":["62202388"]}],"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":["32101797"],"award-info":[{"award-number":["32101797"]}],"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":["32170677"],"award-info":[{"award-number":["32170677"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Lysine 2-hydroxyisobutylation (Khib), which was first reported in 2014, has been shown to play vital roles in a myriad of biological processes including gene transcription, regulation of chromatin functions, purine metabolism, pentose phosphate pathway and glycolysis\/gluconeogenesis. Identification of Khib sites in protein substrates represents an initial but crucial step in elucidating the molecular mechanisms underlying protein 2-hydroxyisobutylation. Experimental identification of Khib sites mainly depends on the combination of liquid chromatography and mass spectrometry. However, experimental approaches for identifying Khib sites are often time-consuming and expensive compared with computational approaches. Previous studies have shown that Khib sites may have distinct characteristics for different cell types of the same species. Several tools have been developed to identify Khib sites, which exhibit high diversity in their algorithms, encoding schemes and feature selection techniques. However, to date, there are no tools designed for predicting cell type-specific Khib sites. Therefore, it is highly desirable to develop an effective predictor for cell type-specific Khib site prediction. Inspired by the residual connection of ResNet, we develop a deep learning-based approach, termed ResNetKhib, which leverages both the one-dimensional convolution and transfer learning to enable and improve the prediction of cell type-specific 2-hydroxyisobutylation sites. ResNetKhib is capable of predicting Khib sites for four human cell types, mouse liver cell and three rice cell types. Its performance is benchmarked against the commonly used random forest (RF) predictor on both 10-fold cross-validation and independent tests. The results show that ResNetKhib achieves the area under the receiver operating characteristic curve values ranging from 0.807 to 0.901, depending on the cell type and species, which performs better than RF-based predictors and other currently available Khib site prediction tools. We also implement an online web server of the proposed ResNetKhib algorithm together with all the curated datasets and trained model for the wider research community to use, which is publicly accessible at https:\/\/resnetkhib.erc.monash.edu\/.<\/jats:p>","DOI":"10.1093\/bib\/bbad063","type":"journal-article","created":{"date-parts":[[2023,3,7]],"date-time":"2023-03-07T13:28:34Z","timestamp":1678195714000},"source":"Crossref","is-referenced-by-count":8,"title":["ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning"],"prefix":"10.1093","volume":"24","author":[{"given":"Xiaoti","family":"Jia","sequence":"first","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops, and Key Laboratory of Rice Biology in Henan Province, College of Agronomy, Henan Agricultural University , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pei","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences , Anyang 455 000, Henan , China"},{"name":"Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University , Zhengzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuyi","family":"Li","sequence":"additional","affiliation":[{"name":"Monash University, Australia. He is currently a professor at the College of Information Engineering, Northwest A&F University , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhaohui","family":"Qin","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops, and Key Laboratory of Rice Biology in Henan Province, College of Agronomy, Henan Agricultural University , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haoran","family":"Ren","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops, and Key Laboratory of Rice Biology in Henan Province, College of Agronomy, Henan Agricultural University , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junzhou","family":"Li","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops, and Key Laboratory of Rice Biology in Henan Province, College of Agronomy, Henan Agricultural University , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunbo","family":"Miao","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops, and Key Laboratory of Rice Biology in Henan Province, College of Agronomy, Henan Agricultural University , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Quanzhi","family":"Zhao","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, and Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatsuya","family":"Akutsu","sequence":"additional","affiliation":[{"name":"DEng degree in information engineering in 1989 from the University of Tokyo, Japan. Since 2001, he has been a professor in the Bioinformatics Center, Institute for Chemical Research, Kyoto University , Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gensheng","family":"Dou","sequence":"additional","affiliation":[{"name":"College of Agronomy, Henan Agricultural University"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Chen","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Rice Biology in Henan Province and Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8031-9086","authenticated-orcid":false,"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"Monash Biomedicine Discovery Institute, Monash 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