Bioinformatics and Genomics

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Computational Biology of RNA Processing



GROUP LEADER:
Roderic Guigó
STAFF SCIENTIST:
Rory Johnson
POSTDOCTORAL FELLOWS:
Sarah Djebali, Dmitry Pervouchine, Marta Melé (until March), Silvia Pérez-Lluch, Ferran Reverter, Barbara Uszczynska, Alexandre Esteban (from March), Marco Mariotti (from November)
PhD STUDENTS:
Joao Curado, Didac Santesmases, Alessandra Breschi, Amadis Pagés, Sebastian Ullrich, Reza Sodaei, Juna Carlevaro
TECHNICIANS:
Julien Lagarde, Francisco Câmara, Carmen Arnán, Emilio Palumbo, Maria Sanz (until July), Anna Vlasova, Amaya Abad
STUDENTS:
Annalaura Vacca, Iago Maceda, Bernardo Rodríguez, Andrés Arturo Lanzos

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 Annotatoin
  • Selenoprotein identification and evolution
  • Compuational Methods for Transcriptome analysis
  • Epigenetic Regulation of RNA processing
  • Identification and characterization of long non coding RNAs

Selected Publications

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,24(2):212-26. doi: 10.1101/gr.152132.112 (2014).

Letourneau A, Santoni FA, Bonilla X, Sailani MR, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Garieri M, Popadin K, Falconnet E, Gagnebin M, Gehrig C, Vannier A, Guipponi M, Farinelli L, Robyr D, Migliavacca E, Borel C, Deutsch S, Feki A, Stamatoyannopoulos JA, Herault Y, van Steensel B, Guigo R, Antonarakis SE.
“Domains of genome-wide gene expression dysregulation in Down’s syndrome”.
Nature, 508(7496):345-50 (2014).

Johnson R, Guigó R.
“The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs”.
RNA, 20(7):959-76 (2014).

Monlong J, Calvo M, Ferreira PG, Guigó R.
“Identification of genetic variants associated with alternative splicing using sQTLseekeR”.
Nat Commun, 5:4698 (2014).

Yue F et al; Mouse ENCODE Consortium (including Guigo R, Notredame C, Pervouchine DD, Djebali S, Breschi A, Prieto P, Lagarde J, Bussotti G, Tanzer A.).
“A comparative encyclopedia of DNA elements in the mouse genome”.
Nature, 515(7527):355-64 (2014).