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Vice-Direction of Basic Research
NATIONAL
BIOINFORMATICS
INSTITUTE UNIT
Structural Biology And Biocomputing Programme | National Bioinformatics Institute Unit
Victor de la Torre Russis
( until November )
Unit Head
The INB Unit differs from the other Units in the Structural Biology
and Biocomputing Programme in the sense that its offering is
Technicians
Andrés Cañada ( TS )*, José M.
Fernández ( TS )*, José M. Rodríguez
( TS )*
not restricted to the CNIO Groups, and that its budget is funded
entirely by an external agency, the ISCIII.
Titulado Superior ( Advanced Degree )
*
RESEARCH HIGHLIGHTS
The INB service offering is distributed amongst three horizontal
Work Packages ( WP ) as well as the Training WP. These services
are integrated into six major research areas : Health, Genomics,
Functional Genomics, Structural Biology, Biological Networks
and Data mining. Besides from its coordination role, the Unit
also participates in the delivery of the services.
Data resources and Bio-computing
The storage and processing of data have become fundamental
tasks for almost all of the current research projects. Through a
collaboration model, the Unit participates in several research
projects studying the data requirements and developing solutions
to store and process the data.
An example of this is the Blueprint data-portal ( http ://blueprint-dev.
bioinfo.cnio.es/#/). BLUEPRINT is a high impact FP7 project aimed
at producing a blueprint of haemopoetic epigenomes. In the current
version, the data portal provides an epigenomic analysis obtained
from 439 samples to the scientific community. Their associated
epigenomes are characterised by : gene and transcript expression
( from RNA-Seq experiments ), hyper and hypo methylated regions
( derived from WGBS experiments ), chromatin accessibility ( DNAseSeq ), and 7 Histone marks binding activity ( ChIP-Seq ).
ɗɗ Coordinate the activities of the Institute.
ɗɗ Design ( with the support of all the nodes ) the INB scientific/
technical programme and to ensure its execution.
ɗɗ Design ( with the support of all the nodes ) the INB training
programme.
ANNUAL REPORT 2015
End users applications and services
The Unit actively contributes to the creation of an integrated
platform that connects databases, registries, biobanks and clinical
bioinformatics for research on rare diseases.
Infrastructure development
OVERVIEW
The Spanish National Bioinformatics Institute ( Instituto
Nacional de Bioinformática, INB ) is a programme of the National
Infrastructure of Biomolecular and Bioinformatics Resources
Platform ( Plataforma en Red de Recursos Biomoleculares y
Bioinformáticos, PRB2 ). The INB itself is also the Spanish Node of
the European Bioinformatics Infrastructure ELIXIR. The INB is
organised as a network composed of 10 nodes distributed across
9 centres. The INB Unit at the CNIO is the Central Node of the
network. As a Central Node, the main goals of the INB Unit are to :
Figure Diagram of the organisation and activities of the Spanish National
Bioinformatics Unit ( INB ).
Within the infrastructure development, special attention is
paid to the text-mining infrastructure for the processing of
biomedical texts. The LiMTox system ( http ://limtox.bioinfo.cnio.
es ) is the first text mining approach that extracts associations
between compounds and a particular toxicological end point at
various levels of granularity and evidence types, all inspired by
the content of toxicology reports.
“ The Unit has contributed to
the creation of a text-mining
infrastructure that identifies, for a
large number of compounds, the
associated toxicological effects
based on the evidences extracted
from several literature corpus.”
ɗɗ Coordinate the participation of Spain in ELIXIR.
ɗɗ Mediate the collaboration between the INB and third parties
including : National and International research consortia,
other infrastructures, SMEs and the Industry.
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PUBLICATIONS
Abascal F, Ezkurdia I, Rodriguez-Rivas
J, Rodriguez JM, Del Pozo A, Vázquez
J, Valencia A, Tress ML ( 2015 ). Alternatively Spliced Homologous Exons Have
∞∞
Ancient Origins and Are Highly Expressed
at the Protein Level. PLoS Comput Biol
11, e1004325.
Rodriguez JM, Carro A, Valencia A, Tress ML
( 2015 ). APPRIS WebServer and WebServices. Nucleic Acids Res 43, W455-W459.
SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO
The application allows clinicians and researchers to explore the
possible causes of the disease by combining patient’s genomic data
with phenotypic annotations. The Unit has also developed APPRIS
( http ://appris.bioinfo.cnio.es/#/), a service that automatically
annotates genes and transcripts. The GENCODE consortium uses
APPRIS to annotate the principal isoforms of several species. s
∞∞
Ezkurdia I, Rodriguez JM, Carillo-de
Santa Pau E, Vázquez J, Valencia A,
Tress ML ( 2015 ). Most highly expressed
protein-coding genes have a single
dominant isoform. J Proteome Res 14,
1880-1887.
∞∞
Lees JG et al. ( incl. Fernández JM, Krallinger M, Valencia A ) ( 2015 ). FUN-L : Gene
prioritization for RNAi screens. Bioinformatics 31, 2052-2053.
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