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Phosphorylation plays fundamental roles in many signalling pathways and biological processes, such as protein degradation and protein-protein interactions. Experimental studies have revealed that signalling defects caused by aberrant phosphorylation are highly associated with a variety of human diseases, especially cancers. In light of this, a number of computational methods aiming to accurately predict protein kinase family-specific or kinase-specific phosphorylation sites have been established, thereby facilitating phosphoproteomic data analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this work, we present Quokka, a novel bioinformatics tool that allows users to rapidly and accurately identify human kinase family-regulated phosphorylation sites. Quokka was developed by using a variety of sequence scoring functions combined with an optimized logistic regression algorithm. We evaluated Quokka based on well-prepared up-to-date benchmark and independent test datasets, curated from the Phospho.ELM and UniProt databases, respectively. The independent test demonstrates that Quokka improves the prediction performance compared with state-of-the-art computational tools for phosphorylation prediction. In summary, our tool provides users with high-quality predicted human phosphorylation sites for hypothesis generation and biological validation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The Quokka webserver and datasets are freely available at http:\/\/quokka.erc.monash.edu\/.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty522","type":"journal-article","created":{"date-parts":[[2018,6,26]],"date-time":"2018-06-26T11:16:11Z","timestamp":1530011771000},"page":"4223-4231","source":"Crossref","is-referenced-by-count":157,"title":["<i>Quokka<\/i>: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome"],"prefix":"10.1093","volume":"34","author":[{"given":"Fuyi","family":"Li","sequence":"first","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Li","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia"},{"name":"Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatiana T","family":"Marquez-Lago","sequence":"additional","affiliation":[{"name":"Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andr\u00e9","family":"Leier","sequence":"additional","affiliation":[{"name":"Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatsuya","family":"Akutsu","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony W","family":"Purcell","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A","family":"Ian Smith","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia"},{"name":"ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Trevor","family":"Lithgow","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roger J","family":"Daly","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8031-9086","authenticated-orcid":false,"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia"},{"name":"Monash Centre for Data Science, Monash University, Clayton, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kuo-Chen","family":"Chou","sequence":"additional","affiliation":[{"name":"Gordon Life Science Institute, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,6,27]]},"reference":[{"key":"2023012712242636900_bty522-B1","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1080\/00031305.1992.10475879","article-title":"An introduction to kernel and nearest-neighbor nonparametric regression","volume":"46","author":"Altman","year":"1992","journal-title":"Am. 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