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Page 1
Computational Analysis of Transposable Elements and CircRNAs in Plants.
Oliveira LS, Patera AC, Domingues DS, Sanches DS, Lopes FM, Bugatti PH, Saito PTM, Maracaja-Coutinho V, Durham AM, Paschoal AR. Oliveira LS, et al. Methods Mol Biol. 2021;2362:147-172. doi: 10.1007/978-1-0716-1645-1_9. Methods Mol Biol. 2021. PMID: 34195962
Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi.
Gupta YK, Marcelino-Guimarães FC, Lorrain C, Farmer A, Haridas S, Ferreira EGC, Lopes-Caitar VS, Oliveira LS, Morin E, Widdison S, Cameron C, Inoue Y, Thor K, Robinson K, Drula E, Henrissat B, LaButti K, Bini AMR, Paget E, Singan V, Daum C, Dorme C, van Hoek M, Janssen A, Chandat L, Tarriotte Y, Richardson J, Melo BDVA, Wittenberg AHJ, Schneiders H, Peyrard S, Zanardo LG, Holtman VC, Coulombier-Chauvel F, Link TI, Balmer D, Müller AN, Kind S, Bohnert S, Wirtz L, Chen C, Yan M, Ng V, Gautier P, Meyer MC, Voegele RT, Liu Q, Grigoriev IV, Conrath U, Brommonschenkel SH, Loehrer M, Schaffrath U, Sirven C, Scalliet G, Duplessis S, van Esse HP. Gupta YK, et al. Among authors: oliveira ls. Nat Commun. 2023 Apr 1;14(1):1835. doi: 10.1038/s41467-023-37551-4. Nat Commun. 2023. PMID: 37005409 Free PMC article.
cirCodAn: A GHMM-based tool for accurate prediction of coding regions in circRNA.
Barbosa DF, Oliveira LS, Nachtigall PG, Valentini Junior R, de Souza N, Paschoal AR, Kashiwabara AY. Barbosa DF, et al. Among authors: oliveira ls. Adv Protein Chem Struct Biol. 2024;139:289-334. doi: 10.1016/bs.apcsb.2023.11.012. Epub 2024 Feb 17. Adv Protein Chem Struct Biol. 2024. PMID: 38448139
Small RNAs in metastatic and non-metastatic oral squamous cell carcinoma.
Severino P, Oliveira LS, Andreghetto FM, Torres N, Curioni O, Cury PM, Toporcov TN, Paschoal AR, Durham AM. Severino P, et al. Among authors: oliveira ls. BMC Med Genomics. 2015 Jun 24;8:31. doi: 10.1186/s12920-015-0102-4. BMC Med Genomics. 2015. PMID: 26104160 Free PMC article.
High-throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research.
Severino P, Oliveira LS, Torres N, Andreghetto FM, Klingbeil Mde F, Moyses R, Wünsch-Filho V, Nunes FD, Mathor MB, Paschoal AR, Durham AM. Severino P, et al. Among authors: oliveira ls. BMC Genomics. 2013 Oct 26;14:735. doi: 10.1186/1471-2164-14-735. BMC Genomics. 2013. PMID: 24160351 Free PMC article.