Computational Biology of RNA Processing

BIOINFORMATICS AND GENOMICS

GROUP LEADER: Roderic Guigó (Coordinator of the Bionformatics and Genomics Programme)

STAFF SCIENTIST: Silvia Pérez-Lluch

POSTDOCTORAL FELLOWS: Ferran Reverter, Cecilia Klein, Marina Ruiz, Ramil Nurtdinov, Bruna Correa, Valentin Wucher, Estel Aparicio (until March), Didac Santesmasses (until June), Gireesh Kumar (until July), Alessandra Breschi (until August)

PHD STUDENTS: Sebastian Ullrich, Reza Sodaei, Diego Garrido, Andrés Arturo Lanzos, Manuel Muñoz, Beatrice Borsari

BIOINFORMATICIANS: Julien Lagarde, Francisco Câmara, Emilio Palumbo, Anna Vlasova, Joao Curado

TECHNICIANS: Carmen Arnán, Amaya Abad

STUDENTS: Raziel Tomás, Aida Ripoll, David Mas

VISITING SCIENTISTS: Lourdes Pena, Denis Tagu

Summary

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 it is involved in a number of international projects: ENCODE, GTEx, BluePrint and the International Cancer Genome Consortium, among others.

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Research Projects

  • Gene Prediction/Genome Annotation
  • Genome-Wide Search for Selenoproteins
  • Relationship between tissue transcriptomes and phenotypes
  • Epigenetic regulation of RNA production and processing
  • Identification and characterization of long non-coding RNAs
  • Development of computational methods for functional annotation of genomes

Selected Publications

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, 18(1):7 (2017).

Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso T, Palumbo E, Ponomarenko J, Guigo R, Johnson R.
“Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.”
PLoS Comput Biol, 13(3):e1005341 (2017).

Breschi A, Gingeras TR, Guigó R.
“Comparative transcriptomics in human and mouse.”
Nat Rev Genet, 18(7):425-440 (2017).

Santesmasses D, Mariotti M, Guigó R.
“Computational identification of the selenocysteine tRNA (tRNASec) in genomes.”
PLoS Comput Biol, 13(2):e1005383 (2017).

Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R.
“High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.”
Nat Genet, 49(12):1731-1740 (2017).