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Software testing in microbial bioinformatics: a call to action.
van der Putten BCL, Mendes CI, Talbot BM, de Korne-Elenbaas J, Mamede R, Vila-Cerqueira P, Coelho LP, Gulvik CA, Katz LS, The Asm Ngs Hackathon Participants. van der Putten BCL, et al. Among authors: coelho lp. Microb Genom. 2022 Mar;8(3):000790. doi: 10.1099/mgen.0.000790. Microb Genom. 2022. PMID: 35259087 Free PMC article.
Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.
Belda E, Voland L, Tremaroli V, Falony G, Adriouch S, Assmann KE, Prifti E, Aron-Wisnewsky J, Debédat J, Le Roy T, Nielsen T, Amouyal C, André S, Andreelli F, Blüher M, Chakaroun R, Chilloux J, Coelho LP, Dao MC, Das P, Fellahi S, Forslund S, Galleron N, Hansen TH, Holmes B, Ji B, Krogh Pedersen H, Le P, Le Chatelier E, Lewinter C, Mannerås-Holm L, Marquet F, Myridakis A, Pelloux V, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Sokolovska N, Søndertoft NB, Touch S, Vieira-Silva S; MetaCardis Consortium; Galan P, Holst J, Gøtze JP, Køber L, Vestergaard H, Hansen T, Hercberg S, Oppert JM, Nielsen J, Letunic I, Dumas ME, Stumvoll M, Pedersen OB, Bork P, Ehrlich SD, Zucker JD, Bäckhed F, Raes J, Clément K. Belda E, et al. Among authors: coelho lp. Gut. 2022 Dec;71(12):2463-2480. doi: 10.1136/gutjnl-2021-325753. Epub 2022 Jan 11. Gut. 2022. PMID: 35017197 Free PMC article.
A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community; Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. Costello JC, et al. Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1. Nat Biotechnol. 2014. PMID: 24880487 Free PMC article.
Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection.
Liehl P, Zuzarte-Luís V, Chan J, Zillinger T, Baptista F, Carapau D, Konert M, Hanson KK, Carret C, Lassnig C, Müller M, Kalinke U, Saeed M, Chora AF, Golenbock DT, Strobl B, Prudêncio M, Coelho LP, Kappe SH, Superti-Furga G, Pichlmair A, Vigário AM, Rice CM, Fitzgerald KA, Barchet W, Mota MM. Liehl P, et al. Among authors: coelho lp. Nat Med. 2014 Jan;20(1):47-53. doi: 10.1038/nm.3424. Epub 2013 Dec 22. Nat Med. 2014. PMID: 24362933 Free PMC article.
For long-term sustainable software in bioinformatics.
Coelho LP. Coelho LP. PLoS Comput Biol. 2024 Mar 15;20(3):e1011920. doi: 10.1371/journal.pcbi.1011920. eCollection 2024 Mar. PLoS Comput Biol. 2024. PMID: 38489255 Free PMC article. No abstract available.
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