Computational Biology of RNA Processing


Group Leader

Roderic Guigó Serra

The overarching theme of the research in our group is the understanding of the information encoding in genomic sequences, and how this information is processed in the pathway leading from DNA to protein sequences. More specifically, we are interested in the regulation of the primary production (transcription) and post-processing (splicing) of RNA, and how this regulated production relates to cell, tissue and organism phenotypes. Our research is increasingly incorporating high throughput and experimental approaches. In addition, but related to this basic component of our research, our group is also involved in the development of software for functional annotation in genomic sequences. Our group has actively participated in the analysis of many eukaryotic genomes and is involved in a number of international projects: ENCODE, GTEx, BluePrint and the International Cancer Genome Consortium, among others.

We are the Genomics node of the Spanish Instituto Nacional de Bioinformática.

Main Publications with IMIM

• Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD, Hall IM, Battle A, Montgomery SB, GTEx Consortium (...Guigó R...). The impact of rare variation on gene expression across tissues. Nature 2017; 550(7675): 239-243. IF 40.137. D1.

• Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, Chawla A, Del Sal, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB, GTEx Consortium (...Guigó R...). Dynamic landscape and regulation of RNA editing in mammals. Nature 2017; 550(7675): 249-254. IF 40.137. D1.

• Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG, GTEx Consortium (...Guigó R...). Landscape of X chromosome inactivation across human tissues. Nature 2017; 550(7675): 244-248. IF 40.137. D1.

• Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, Engelhardt BE, Battle A, GTEx Consortium (...Guigó R...). Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res 2017; 27(11): 1843-1858. IF 11.922. D1.

• Ponomarenko J, Garrido R, Guigó R. Ten Simple Rules on How to Organize a Scientific Retreat (Editorial). PLoS Comput Biol 2017; 13(2): e1005344. IF 4.542. D1.

• Pulido-Quetglas C, Aparicio E, Arnán C, Polidori T, Hermoso T, Ponomarenko J, Guigó R, Johnson R. Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. PLoS Comput Biol 2017; 13(3): e1005341. IF 4.542. D1.

• Santesmasses D, Mariotti M, Guigó R. Computational identification of the selenocysteine tRNA (tRNASec) in genomes. PLoS Comput Biol 2017; 13(2): e1005383. IF 4.542. D1.

• Lanzós A, Carlevaro-Fita J, Mularoni L, Reverter F, Palumbo E, Guigó R, Johnson R. Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features. Sci Rep 2017; 7: 41544. IF 4.259. Q1.

• Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido, Guigó R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. RNA 2017; 23: 1080-1087. IF 4.605. Q1.

• Rodríguez-Martín B, Palumbo E, Marco-Sola S, Griebel T, Ribeca P, Alonso G, Rastrojo A, Aguado B, Guigó R, Djebali S. ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. BMC Genomics 2017; 18: 7. IF 3.729. Q1.




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