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WikiPathways: connecting communities.
Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, A Miller R, Digles D, Lopes EN, Ehrhart F, Dupuis LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, Pico AR, Kutmon M. Martens M, et al. Among authors: lopes en. Nucleic Acids Res. 2021 Jan 8;49(D1):D613-D621. doi: 10.1093/nar/gkaa1024. Nucleic Acids Res. 2021. PMID: 33211851 Free PMC article.
WikiPathways 2024: next generation pathway database.
Agrawal A, Balcı H, Hanspers K, Coort SL, Martens M, Slenter DN, Ehrhart F, Digles D, Waagmeester A, Wassink I, Abbassi-Daloii T, Lopes EN, Iyer A, Acosta JM, Willighagen LG, Nishida K, Riutta A, Basaric H, Evelo CT, Willighagen EL, Kutmon M, Pico AR. Agrawal A, et al. Among authors: lopes en. Nucleic Acids Res. 2024 Jan 5;52(D1):D679-D689. doi: 10.1093/nar/gkad960. Nucleic Acids Res. 2024. PMID: 37941138 Free PMC article.
Ten simple rules for creating reusable pathway models for computational analysis and visualization.
Hanspers K, Kutmon M, Coort SL, Digles D, Dupuis LJ, Ehrhart F, Hu F, Lopes EN, Martens M, Pham N, Shin W, Slenter DN, Waagmeester A, Willighagen EL, Winckers LA, Evelo CT, Pico AR. Hanspers K, et al. Among authors: lopes en. PLoS Comput Biol. 2021 Aug 19;17(8):e1009226. doi: 10.1371/journal.pcbi.1009226. eCollection 2021 Aug. PLoS Comput Biol. 2021. PMID: 34411100 Free PMC article. No abstract available.
In silico and in vitro arboviral MHC class I-restricted-epitope signatures reveal immunodominance and poor overlapping patterns.
Lopes-Ribeiro Á, Araujo FP, Oliveira PM, Teixeira LA, Ferreira GM, Lourenço AA, Dias LCC, Teixeira CW, Retes HM, Lopes ÉN, Versiani AF, Barbosa-Stancioli EF, da Fonseca FG, Martins-Filho OA, Tsuji M, Peruhype-Magalhães V, Coelho-Dos-Reis JGA. Lopes-Ribeiro Á, et al. Among authors: lopes en. Front Immunol. 2022 Nov 17;13:1035515. doi: 10.3389/fimmu.2022.1035515. eCollection 2022. Front Immunol. 2022. PMID: 36466864 Free PMC article.
Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses.
Giovanetti M, Alcantara LCJ, Dorea AS, Ferreira QR, Marques WA, Junior Franca de Barros J, Adelino TER, Tosta S, Fritsch H, Iani FCM, Mares-Guia MA, Salgado A, Fonseca V, Xavier J, Lopes EN, Soares GC, de Castro Amarante MF, Azevedo V, Kruger A, Correa Matta G, Paineiras-Domingos LL, Colonnello C, Bispo de Filippis AM, Montesano C, Colizzi V, Barreto FK. Giovanetti M, et al. Among authors: lopes en. Front Public Health. 2021 Jul 1;9:693743. doi: 10.3389/fpubh.2021.693743. eCollection 2021. Front Public Health. 2021. PMID: 34277552 Free PMC article. No abstract available.
Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS-CoV-2 mitigation strategies.
Lopes EN, Fonseca V, Frias D, Tosta S, Salgado Á, Assunção Vialle R, Paulo Eduardo TS, Barreto FK, Ariston de Azevedo V, Guarino M, Angeletti S, Ciccozzi M, Junior Alcantara LC, Giovanetti M. Lopes EN, et al. J Med Virol. 2021 Sep;93(9):5630-5634. doi: 10.1002/jmv.27056. Epub 2021 May 24. J Med Virol. 2021. PMID: 33934387 Free PMC article.
Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil.
Adelino TÉR, Giovanetti M, Fonseca V, Xavier J, de Abreu ÁS, do Nascimento VA, Demarchi LHF, Oliveira MAA, da Silva VL, de Mello ALES, Cunha GM, Santos RH, de Oliveira EC, Júnior JAC, de Melo Iani FC, de Filippis AMB, de Abreu AL, de Jesus R, de Albuquerque CFC, Rico JM, do Carmo Said RF, Silva JA, de Moura NFO, Leite P, Frutuoso LCV, Haddad SK, Martínez A, Barreto FK, Vazquez CC, da Cunha RV, Araújo ELL, de Oliveira Tosta SF, de Araújo Fabri A, Chalhoub FLL, da Silva Lemos P, de Bruycker-Nogueira F, de Castro Lichs GG, Zardin MCSU, Segovia FMC, Gonçalves CCM, Grillo ZDCF, Slavov SN, Pereira LA, Mendonça AF, Pereira FM, de Magalhães JJF, Dos Santos Júnior ACM, de Lima MM, Nogueira RMR, Góes-Neto A, de Carvalho Azevedo VA, Ramalho DB, Oliveira WK, Macario EM, de Medeiros AC, Pimentel V; Latin American Genomic Surveillance Arboviral Network; Holmes EC, de Oliveira T, Lourenço J, Alcantara LCJ. Adelino TÉR, et al. Nat Commun. 2021 Apr 16;12(1):2296. doi: 10.1038/s41467-021-22607-0. Nat Commun. 2021. PMID: 33863880 Free PMC article.