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Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications.
Timme RE, Karsch-Mizrachi I, Waheed Z, Arita M, MacCannell D, Maguire F, Petit Iii R, Page AJ, Mendes CI, Nasar MI, Oluniyi P, Tyler AD, Raphenya AR, Guthrie JL, Olawoye I, Rinck G, O'Cathail C, Lees J, Cochrane G, Cummins C, Brister JR, Klimke W, Feldgarden M, Griffiths E. Timme RE, et al. Among authors: mendes ci. Microb Genom. 2023 Dec;9(12):001145. doi: 10.1099/mgen.0.001145. Microb Genom. 2023. PMID: 38085797 Free PMC article.
Accelerating bioinformatics implementation in public health.
Libuit KG, Doughty EL, Otieno JR, Ambrosio F, Kapsak CJ, Smith EA, Wright SM, Scribner MR, Petit Iii RA, Mendes CI, Huergo M, Legacki G, Loreth C, Park DJ, Sevinsky JR. Libuit KG, et al. Among authors: mendes ci. Microb Genom. 2023 Jul;9(7):mgen001051. doi: 10.1099/mgen.0.001051. Microb Genom. 2023. PMID: 37428142 Free PMC article.
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: mendes ci. Microb Genom. 2022 Mar;8(3):000790. doi: 10.1099/mgen.0.000790. Microb Genom. 2022. PMID: 35259087 Free PMC article.
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. Griffiths EJ, et al. Among authors: mendes ci. Gigascience. 2022 Feb 16;11:giac003. doi: 10.1093/gigascience/giac003. Gigascience. 2022. PMID: 35169842 Free PMC article.
Streptococcus pneumoniae Serotype 3 in Mexico (1994 to 2017): Decrease of the Unusual Clonal Complex 4909 Lineage following PCV13 Introduction.
Echániz-Aviles G, Guerreiro SI, Silva-Costa C, Mendes CI, Carriço JA, Carnalla-Barajas MN, Soto-Noguerón A, Velazquez-Meza ME, Melo-Cristino J, Luévanos-Velazquez A, Martínez-Medina L, Vázquez-Larios MDR, Ramirez M. Echániz-Aviles G, et al. Among authors: mendes ci. J Clin Microbiol. 2019 Jan 2;57(1):e01354-18. doi: 10.1128/JCM.01354-18. Print 2019 Jan. J Clin Microbiol. 2019. PMID: 30404945 Free PMC article.
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