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While many computational methods for predicting human microbe-disease associations (MDAs) have been developed, few systematic reviews on these methods have been reported. In this study, we provide a comprehensive overview of the existing methods. Firstly, we introduce the data used in existing MDA prediction methods. Secondly, we classify those methods into different categories by their nature and describe their algorithms and strategies in detail. Next, experimental evaluations are conducted on representative methods using different similarity data and calculation methods to compare their prediction performances. Based on the principles of computational methods and experimental results, we discuss the advantages and disadvantages of those methods and propose suggestions for the improvement of prediction performances. Considering the problems of the MDA prediction at present stage, we discuss future work from three perspectives including data, methods and formulations at the end.<\/jats:p>","DOI":"10.1093\/bib\/bbaa157","type":"journal-article","created":{"date-parts":[[2020,6,22]],"date-time":"2020-06-22T19:40:54Z","timestamp":1592854854000},"source":"Crossref","is-referenced-by-count":29,"title":["A survey on predicting microbe-disease associations: biological data and computational methods"],"prefix":"10.1093","volume":"22","author":[{"given":"Zhongqi","family":"Wen","sequence":"first","affiliation":[{"name":"Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering at Central South University, Hunan, China"}]},{"given":"Cheng","family":"Yan","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, Changsha, Hunan, China"}]},{"given":"Guihua","family":"Duan","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University"}]},{"given":"Suning","family":"Li","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4593-9332","authenticated-orcid":false,"given":"Fang-Xiang","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Engineering and the Department of Computer Sciences, University of Saskatchewan, Saskatoon, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1516-0480","authenticated-orcid":false,"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering at Central South University, Hunan, 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