Description of organization

Spanish National Cancer Research Centre (Centro Nacional de Investigaciones Oncológicas, CNIO) is the leading Spanish public research centre, and one of the few integral cancer research institutes that integrates basic and applied research.

The CNIO develops activities in the areas of genomics, has a large experience in mouse models and integrates a department dedicated to medical chemistry, as well as a clinical research programme. The “Structural Biology and Biocomputing Programme” lead by Prof. Valencia includes experimental and computational groups working together in functional and structural cancer related projects.

Additionally CNIO is the central node of the Spanish Bioinformatics Institute (INB) of which Prof. Valencia is the Director. INB is a technical platform of the Spanish Health Institute (Instituto de Salud Carlos III), as such it acts as national node of the European Infrastructure for Bioinformatics ELIXIR, providing integrated bioinformatics resources and support to national and international genome projects.

Profile of staff members

PI: Alfonso Valencia, Prof. PhD 1986. Director of the Spanish Bioinformatics Institute, Director of the CNIO's Structural Biology and Biocomputing Programme. Editor of the main journal in the field (Bioinformatics OUP). Member of EMBO. Doctor Honoris causa DTU Denmark. H-Index 57 (Google-schollar 71, 55 since 2007).

Staff Scientists.
Michael Tress. UK. PhD  2001 U. Warwick. Expert in structural bioinformatics. Structure and function prediction at genomic scale. Alternative Splicing. 16 publications.

Milana Morgenstern. Israel. PhD  2006 Weizmann. 13 publications.  Expert in genome analysis. Software for Splicing and RNAseq.

PostDocs
Vera Pancaldi. Italy. Postdoc. PhD 2007 Imperial C. London. 9 publications. Modelling of biological systems.

Florian Leitner. Austria. Postdoc. PhD in 2011 Madrid. 12 Publications. Expert in information extraction from biological text. Machine learning.

Miguel Vazquez. Spain. PhD 2010 Madrid. 8 publications. Development of integrated systems for genome analysis.

Engineers Bioinformaticians

Martin Krallinger. Austria. More than 10 years of experience in Bioinformatics. 23 publications. Development of information extraction systems applied to biomedical problems. Pattern matching, Data mining.

David Juan. Spain. More than 10 years of experience in Bioinformatics. 21 publications. Development of algorithms and methods for exploration of context rich biological networks.

Recent publications relevant to the project

1.- Genome Analysis
Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics. Valencia A, Hidalgo M. Genome Med. 2012 4(7):61. PMID: 22839973

2.- Methods for the analysis of biological  networks
EnrichNet: network-based gene set enrichment analysis. Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A. Bioinformatics. 2012 28(18):i451-i457. PMID: 22962466

3.- Structure/function analysis at genomic level

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A. Genome Res. 2012 22(7):1231-42. PMID: 22588898

4-5 Methodology for information extraction in Biology
The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Leitner F, Chatr-aryamontri A, Mardis SA, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A. Nat Biotechnol. 2010 (9):897-9. PMID: 20829821

An Overview of BioCreative II.5. Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A. IEEE/ACM Trans Comput Biol Bioinform. 2010 7(3):385-99. PMID: 20704011