Bioinformatics and Genomics

roderic-guigo
Computational Biology of RNA Processing

Group Structure

GROUP LEADER:
Roderic Guigó
STAFF SCIENTIST:
Rory Johnson
POSTDOCTORAL FELLOWS:
Sarah Djebali, Dmitry Pervouchine, Marta Melé, Silvia Pérez-Lluch, Ferran Reverter, Ivan Junier, Darek Kedra, Barbara Uszczynska, PhD Students
TECHNICIANS:
Julien Lagarde, Francisco Câmara, Carmen Arnán, Emilio Palumbo, Maria Sanz, Anna Vlasova, Amaya Abad, Judith Escarré
STUDENTS:
Jakob Goldmann, Joana Carlevaro, Núria Bosch, Iago Maceda, Maria Velasco, Bernardo Rodríguez, Roderic Guigó-Corominas
VISITING SCIENTISTS:
Nikki Gentle

Summary

Research in our group (http://big.crg.cat/bioinformatics_and_genomics) focuses on the investigation of the signals involved in gene specification in genomic sequences (promoter elements, splice sites, translation initiation sites, etc.). We are interested both in the mechanism of their recognition and processing, and in their evolution. In addition, but related to this basic component of our research, our group is also involved in the development of software for gene prediction and 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. We are the Genomics node of the Spanish Instituto Nacional de Bioinformatica.


Research Projects

  • Gene prediction/Genome Annotation
  • Selenoprotein identification and evolution
  • Computational Methods for Transcriptome analysis
  • Epigenetic Regulation of RNA processing
  • Identification and characterization of long non coding RNAs

Selected Publications

  1. Pervouchine DD, Knowles DG, Guigó R.
    “Intron-centric estimation of alternative splicing from RNA-seq data”.
    Bioinformatics, 29(2):273-4 (2013).
  2. Knowles DG, Röder M, Merkel A, Guigó R.
    “Grape RNA-Seq analysis pipeline environment”.
    Bioinformatics, 29(5):614-21 (2013).
  3. Geuvadis Consortium (including Guigo R).
    “Transcriptome and genome sequencing uncovers functional variation in humans”.
    Nature, 501(7468):506-11 (2013).
  4. Engström PG, Steijger T, Sipos B, Grant GR, Kahles A; RGASP Consortium, Alioto T, Behr J, Bertone P, Bohnert R, Campagna D, Davis CA, Dobin A, Engström PG, Gingeras TR, Goldman N, Grant GR, Guigó R, Harrow J, Hubbard TJ, Jean G, Kahles A, Kosarev P, Li S, Liu J, Mason CE, Molodtsov V, Ning Z, Ponstingl H, Prins JF, Rätsch G, Ribeca P, Seledtsov I, Sipos B, Solovyev V, Steijger T, Valle G, Vitulo N, Wang K, Wu TD, Zeller G, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P.
    “Systematic evaluation of spliced alignment programs for RNA-seq data”.
    Nat Methods, 10(12):1185-91 (2013).
  5. Ferreira PG, Jares P, Rico D, Gómez-López G, Martínez-Trillos A, Villamor N, Ecker S, González-Pérez A, Knowles DG, Monlong J, Johnson R, Quesada V, Gouin A, Djebali S, López-Guerra M, Colomer D, Royo C, Cazorla M, Pinyol M, Clot G, Aymerich M, Rozman M, Kulis M, Tamborero D, Papasaikas P, Blanc J, Gut M, Gut I, Puente XS, Pisano DG, Martin-Subero JI, López-Bigas N, López-Guillermo A, Valencia A, López-Otín C, Campo E, Guigo R.
    “Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia”.
    Genome Res, 2013 Nov 21. [Epub ahead of print]