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Despite the availability of the Plasmodium falciparum genome since 2002, 74% of the genes remain uncharacterized. To remedy this paucity of functional information, we used transcriptomic data to build gene co-expression networks for two Plasmodium species (P. falciparum and P. berghei), and included genomic data of four other Plasmodium species, P. yoelii, P. knowlesi, P. vivax and P. cynomolgi, as well as two non-Plasmodium species from the Apicomplexa, Toxoplasma gondii and Theileria parva. The genomic and transcriptomic data were incorporated into the resulting database, malaria.tools, which is preloaded with tools that allow the identification and cross-species comparison of co-expressed gene neighbourhoods, clusters and life stage-specific expression, thus providing sophisticated tools to predict gene function. Moreover, we exemplify how the tools can be used to easily identify genes relevant for pathogenicity and various life stages of the malaria parasite. The database is freely available at www.malaria.tools.<\/jats:p>","DOI":"10.1093\/nar\/gkz662","type":"journal-article","created":{"date-parts":[[2019,7,24]],"date-time":"2019-07-24T11:26:52Z","timestamp":1563967612000},"page":"D768-D775","source":"Crossref","is-referenced-by-count":18,"title":["Malaria.tools\u2014comparative genomic and transcriptomic database for Plasmodium species"],"prefix":"10.1093","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5690-7478","authenticated-orcid":false,"given":"Qiao Wen","family":"Tan","sequence":"first","affiliation":[{"name":"School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7848-0126","authenticated-orcid":false,"given":"Marek","family":"Mutwil","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,8,2]]},"reference":[{"key":"2020010521381865200_B1","doi-asserted-by":"crossref","DOI":"10.30875\/f309483f-en","volume-title":"World Malaria Report 2018","author":"World Health Organisation","year":"2018"},{"key":"2020010521381865200_B2","doi-asserted-by":"crossref","first-page":"2569","DOI":"10.1111\/febs.14127","article-title":"Combating multidrug-resistant Plasmodium falciparum malaria","volume":"284","author":"Thu","year":"2017","journal-title":"FEBS J."},{"key":"2020010521381865200_B3","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1051\/parasite\/2010174273","article-title":"Bioinformatic strategies to provide functional clues to the unknown genes in Plasmodium falciparum genome","volume":"17","author":"Florent","year":"2010","journal-title":"Parasite"},{"key":"2020010521381865200_B4","doi-asserted-by":"crossref","first-page":"12783","DOI":"10.1073\/pnas.192159399","article-title":"Transitive functional annotation by shortest-path analysis of gene expression data","volume":"99","author":"Zhou","year":"2002","journal-title":"Proc. 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