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RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons.
Bioinformatics. 2019 Dec 15;35(24):5357-5358. doi: 10.1093/bioinformatics/btz534.
Bioinformatics. 2019.
PMID: 31250887
Free PMC article.
Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons.
Trefflich S, Dalmolin RJS, Ortega JM, Castro MAA.
Trefflich S, et al.
Biochim Biophys Acta Gene Regul Mech. 2020 Jun;1863(6):194472. doi: 10.1016/j.bbagrm.2019.194472. Epub 2019 Dec 9.
Biochim Biophys Acta Gene Regul Mech. 2020.
PMID: 31825805
Review.
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TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves.
Cardoso MA, Rizzardi LEA, Kume LW, Groeneveld CS, Trefflich S, Morais DAA, Dalmolin RJS, Ponder BAJ, Meyer KB, Castro MAA.
Cardoso MA, et al. Among authors: trefflich s.
Bioinformatics. 2022 Feb 7;38(5):1463-1464. doi: 10.1093/bioinformatics/btab819.
Bioinformatics. 2022.
PMID: 34864914
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Novel lncRNAs Co-Expression Networks Identifies LINC00504 with Oncogenic Role in Luminal A Breast Cancer Cells.
Mathias C, Groeneveld CS, Trefflich S, Zambalde EP, Lima RS, Urban CA, Prado KB, Ribeiro EMSF, Castro MAA, Gradia DF, de Oliveira JC.
Mathias C, et al. Among authors: trefflich s.
Int J Mol Sci. 2021 Feb 28;22(5):2420. doi: 10.3390/ijms22052420.
Int J Mol Sci. 2021.
PMID: 33670895
Free PMC article.
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The chromatin accessibility landscape of primary human cancers.
Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network; Greenleaf WJ, Chang HY.
Corces MR, et al.
Science. 2018 Oct 26;362(6413):eaav1898. doi: 10.1126/science.aav1898.
Science. 2018.
PMID: 30361341
Free PMC article.
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Protein Function Prediction.
Cruz LM, Trefflich S, Weiss VA, Castro MAA.
Cruz LM, et al. Among authors: trefflich s.
Methods Mol Biol. 2017;1654:55-75. doi: 10.1007/978-1-4939-7231-9_5.
Methods Mol Biol. 2017.
PMID: 28986783
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Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses.
Campos LRS, Trefflich S, Morais DAA, Imparato DO, Chagas VS, Albanus RD, Dalmolin RJS, Castro MAA.
Campos LRS, et al. Among authors: trefflich s.
Mol Biol Evol. 2024 Feb 1;41(2):msae019. doi: 10.1093/molbev/msae019.
Mol Biol Evol. 2024.
PMID: 38306290
Free PMC article.
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