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Searching for virus phylotypes.
Chevenet F, Jung M, Peeters M, de Oliveira T, Gascuel O. Chevenet F, et al. Among authors: de oliveira t. Bioinformatics. 2013 Mar 1;29(5):561-70. doi: 10.1093/bioinformatics/btt010. Epub 2013 Jan 17. Bioinformatics. 2013. PMID: 23329414 Free PMC article.
RegaDB: community-driven data management and analysis for infectious diseases.
Libin P, Beheydt G, Deforche K, Imbrechts S, Ferreira F, Van Laethem K, Theys K, Carvalho AP, Cavaco-Silva J, Lapadula G, Torti C, Assel M, Wesner S, Snoeck J, Ruelle J, De Bel A, Lacor P, De Munter P, Van Wijngaerden E, Zazzi M, Kaiser R, Ayouba A, Peeters M, de Oliveira T, Alcantara LC, Grossman Z, Sloot P, Otelea D, Paraschiv S, Boucher C, Camacho RJ, Vandamme AM. Libin P, et al. Among authors: de bel a, de oliveira t, de munter p. Bioinformatics. 2013 Jun 1;29(11):1477-80. doi: 10.1093/bioinformatics/btt162. Epub 2013 May 2. Bioinformatics. 2013. PMID: 23645815 Free PMC article.
Renewing Felsenstein's phylogenetic bootstrap in the era of big data.
Lemoine F, Domelevo Entfellner JB, Wilkinson E, Correia D, Dávila Felipe M, De Oliveira T, Gascuel O. Lemoine F, et al. Among authors: de oliveira t. Nature. 2018 Apr;556(7702):452-456. doi: 10.1038/s41586-018-0043-0. Epub 2018 Apr 18. Nature. 2018. PMID: 29670290 Free PMC article.
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. Mavian C, et al. Among authors: de oliveira t. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. Proc Natl Acad Sci U S A. 2020. PMID: 32381734 Free PMC article. No abstract available.
Sustained human outbreak of a new MPXV clade I lineage in eastern Democratic Republic of the Congo.
Vakaniaki EH, Kacita C, Kinganda-Lusamaki E, O'Toole Á, Wawina-Bokalanga T, Mukadi-Bamuleka D, Amuri-Aziza A, Malyamungu-Bubala N, Mweshi-Kumbana F, Mutimbwa-Mambo L, Belesi-Siangoli F, Mujula Y, Parker E, Muswamba-Kayembe PC, Nundu SS, Lushima RS, Makangara-Cigolo JC, Mulopo-Mukanya N, Pukuta-Simbu E, Akil-Bandali P, Kavunga H, Abdramane O, Brosius I, Bangwen E, Vercauteren K, Sam-Agudu NA, Mills EJ, Tshiani-Mbaya O, Hoff NA, Rimoin AW, Hensley LE, Kindrachuk J, Baxter C, de Oliveira T, Ayouba A, Peeters M, Delaporte E, Ahuka-Mundeke S, Mohr EL, Sullivan NJ, Muyembe-Tamfum JJ, Nachega JB, Rambaut A, Liesenborghs L, Mbala-Kingebeni P. Vakaniaki EH, et al. Among authors: de oliveira t. Nat Med. 2024 Oct;30(10):2791-2795. doi: 10.1038/s41591-024-03130-3. Epub 2024 Jun 13. Nat Med. 2024. PMID: 38871006 Free PMC article.
Phylogenetic evidence of extensive spatial mixing of diverse HIV-1 group M lineages within Cameroon but not between its neighbours.
Godwe C, Goni OH, San JE, Sonela N, Tchakoute M, Nanfack A, Koro FK, Butel C, Vidal N, Duerr R, Martin DP, de Oliveira T, Peeters M, Altfeld M, Ayouba A, Ndung'u T, Tongo M. Godwe C, et al. Among authors: de oliveira t. Virus Evol. 2024 Sep 2;10(1):veae070. doi: 10.1093/ve/veae070. eCollection 2024. Virus Evol. 2024. PMID: 39386075 Free PMC article.
An automated genotyping system for analysis of HIV-1 and other microbial sequences.
de Oliveira T, Deforche K, Cassol S, Salminen M, Paraskevis D, Seebregts C, Snoeck J, van Rensburg EJ, Wensing AM, van de Vijver DA, Boucher CA, Camacho R, Vandamme AM. de Oliveira T, et al. Bioinformatics. 2005 Oct 1;21(19):3797-800. doi: 10.1093/bioinformatics/bti607. Epub 2005 Aug 2. Bioinformatics. 2005. PMID: 16076886
1,061 results