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Differential expression in RNA-seq: a matter of depth.
Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A. Tarazona S, et al. Among authors: conesa a. Genome Res. 2011 Dec;21(12):2213-23. doi: 10.1101/gr.124321.111. Epub 2011 Sep 8. Genome Res. 2011. PMID: 21903743 Free PMC article.
A survey of best practices for RNA-seq data analysis.
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. Conesa A, et al. Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8. Genome Biol. 2016. PMID: 26813401 Free PMC article. Review.
SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.
Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A. Tardaguila M, et al. Among authors: conesa a. Genome Res. 2018 Feb 9;28(3):396-411. doi: 10.1101/gr.222976.117. Online ahead of print. Genome Res. 2018. PMID: 29440222 Free PMC article.
tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing.
de la Fuente L, Arzalluz-Luque Á, Tardáguila M, Del Risco H, Martí C, Tarazona S, Salguero P, Scott R, Lerma A, Alastrue-Agudo A, Bonilla P, Newman JRB, Kosugi S, McIntyre LM, Moreno-Manzano V, Conesa A. de la Fuente L, et al. Among authors: conesa a. Genome Biol. 2020 May 18;21(1):119. doi: 10.1186/s13059-020-02028-w. Genome Biol. 2020. PMID: 32423416 Free PMC article.
Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes.
Balzano-Nogueira L, Ramirez R, Zamkovaya T, Dailey J, Ardissone AN, Chamala S, Serrano-Quílez J, Rubio T, Haller MJ, Concannon P, Atkinson MA, Schatz DA, Triplett EW, Conesa A. Balzano-Nogueira L, et al. Among authors: conesa a. Genome Biol. 2021 Jan 21;22(1):39. doi: 10.1186/s13059-021-02262-w. Genome Biol. 2021. PMID: 33478573 Free PMC article.
240 results