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Biomedicine
The
main
interest
The
background
?
Clinical
informatics
Bioinformatics
The tools
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Outline
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Outline
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Working on Network
Data Analysis
HH RR
Infrastructure
Training
Biological data
BIOCOMPUTATION &
STRUCTURAL BIOLOGY PROGRAM
BIOINFORMATICS UNIT
Molecular Biology of
Childhood Tumors
FB
CHUVI
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CNIO
Molecular Oncology (Dr. Maria Blasco)
Structural Biology & Biocomputation (Dr. Alfonso Valencia)
Molecular Pathology (Dr. M. A. Piris)
Human Cancer Genetics (Dr. Javier Benítez)
Experimental Therapies (Dr. James R. Bischoff)
Biotechnology (Dr. Ignacio Casal)
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Outline
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CNIO Bioinformatics Unit & PDG Group.
David Gonzalez. Pisano (Head)
Eduardo Andrés (CNIO)
Angel Carro (CNIO)
Andrés Cañada (INB)
Jose Maria Fdez.(UBio)
Jaime Fdez. Vera (PDG)
Gonzalo Gómez (CHUVI-INB)
Osvaldo Graña (UBio)
Jose Manuel Rodríguez. (INB)
PDG Group
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Bioinformatics Group. (FICHUVI - Universidade de Vigo)
Enrique Caso (Head)
Florentino Fdez. Riverola (Head)
Gonzalo Gómez (Postdoc)
Daniel Gonzalez (PhD Student)
Pablo Vicente Carrera (Student)
Alberto Molares (PhD Student)
Carmen M. Redondo (Postdoc)
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Outline
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Research lines
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Research lines.
B-cell lymphomas functional analysis.
Almost 200 B-cell lymphomas
8 clinical subtypes
Clustering analysis
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Research lines.
B-cell lymphomas functional analysis.
Gene Set Enrichment Analysis of NFKB pathway genes in Follicular and Burkitt Lymphomas
using Biocarta annotations.
Figure 1. Applying Kolmogorov-Smirnof test to find assymmetries in expression levels of functional related blocks
of genes, NFKB pathway genes was found enriched in Follicular lymphomas in comparison to Burkitt lymphomas.
Figure 2. Heatmap for expression values of those genes involved in NFKB pathway. Figure 3. Map of interactions
for NFKB pathway related genes.
Figure 3
Figure
1
Figure
2
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Research lines.
B-cell lymphomas transcriptome.
Clustering the behaviour of
whole pathways in B-cell
lymphomas.
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Research lines.
Genetic Instability in Ewing Sarcomas.
-Gene Set Enrichment Analysis of Cytobands and Pathways in
Ewing Sarcomas. .
Confirmed gains in chromosomes 5, 8,13,14,18 by enrichment
analysis.
Based on CNA and expression profiling we found G2 pathway,
TNFR2, ATBRCA and other pathways enriched in stable vs unstable
(3 or more aberrations) phenotypes.
- Statistical multivariate analysis support the statistically significant
relationship between genetic stability and survival of patients.
SUBMITTED TO ONCOGENE.
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Research lines.
Role of DAX1 in Ewing´s sarcoma.
GE Whole genome arrays:
GFP shRNA
EWS/FL1 shRNA
DAX shRNA
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Research Lines.
Lung Adeocarcinoma Healthy/Tumoral/Peritumoral markers.
Healthy distant tissue (H)
Healthy periphery
tumour tissue (P)
2 cm
Tumour tissue (T)
Analyzed tissues
Bioinformatics analysis
RNA isolation
sscDNA
dscDNA
cRNA
Affymetrix HG
FocusArray
cRNA fragments
quality control
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Research Lines.
Lung Adeocarcinoma Healthy/Tumoral/Peritumoral markers.
Functional analysis for differentially expressed
genes in lung adenocarcinoma. 24 genes were found
capable to discriminate among surgical classes (healthy,
peritumoral and tumoral).
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Research Lines.
CpGs in EBV.
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Research lines
CARGO: Cancer And Related Genes On Line
•CARGO: a web portal to integrate customized biological information.
Cases I, Pisano DG, Andres E, Carro A, Fernandez JM, Gomez-Lopez G, Rodriguez JM,
Vera JF, Valencia A, Rojas AM.
Nucleic Acids Res. 2007 May 5.
http://cargo.bioinfo.cnio.es
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Research Lines
CARGO: Cancer And Related Genes On Line
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Industry Collaborations.
Pharmamar.
Effects of Yondelis treatment on sensitive and resistant cell lines.
Functional analysis of microarrays points to effects on G2 pathway..
Experimental data support this analysis.
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Academic Activities.
-1st Course on Functional Analysis (CNIO).
-Summer School in Bioinformatics (UCM).
-PhD Course in Bioinformatics (UAM).
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Outline
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Software tools
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Outline
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Target journals & conferences
B-Cell Lymphomas transcriptome:
Transcriptome classification of B-cell non-Hodgkins lymphoma
Mohit Aggarwal, Miguel A. Piris, Raquel Villuendas, Abel Sánchez-Aguilera, Nerea Martínez, Alberto Pérez, Paloma de la Cueva, María Jesús Artiga,
Fatima Al-Sharour, Joaquín Dopazo, Gonzalo Gomez, Elena Ruiz-Ballesteros, Francisca I.Camacho, José A.García-Marco
CNIO Cancer Conferences “Molecular Mechanisms in Lymphoid Neoplasm”
Madrid, February 19-21 2007. Poster.
Pending to be submitted to Nature Genetics.
Genetic Instability in Ewing Sarcomas:
Ewing’s sarcomas integrated expression and arrayCGH profiling reveals distinct genomic instability patterns associated with DNA repair and
cell cycle checkpoint pathways
Bibiana I. Ferreira (1), Javier Alonso (2) (*), Jaime Carrillo (2), Francesco Acquadro (1), Cristina Largo (1), Javier Suela (1), Manuel R. Teixeira (3);
Nuno Ceveira (3), Alberto Molares (4), Gonzalo Goméz-López (4) (5), Ángel Pestaña (2), Ana Sastre (6), Purificacion Garcia-Miguel (6),
and Juan C. Cigudosa (1) (*).
Oncogene. On revision.
Lung Adenocarcinomas Healthy/Tumoral/Peritumoral markers:
cRNA Microarrays and Bioinformatics application in lung carcinoma samples.
A.Molares, E.Carrillo, G.Gómez, G. Muñoz Molina, I. Muguruza, I.Sanchez, R.Moreno, V.Leiro, F.Carrillo, E.Caso.
5th European Conference on Computational Biology, Eliat, Israel.
21-24, Enero. 2007. Poster.
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Outline
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Main Interests
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Outline
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Collaboration offered
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Acknowledgements.
UBio staff & PDG group
Lymphoma´s group
Miguel Angel Piris
Raquel Villuendas
Mohit Aggarwal
Cytogenetics group
Juan C. Cigudosa
Bibiana Ferreira.
Childhood tumors group
Javier Alonso
CHUVI Bioinformatics group
Enrique Caso
Carmen M. Redondo
Alberto Molares
F. Fdez-Riverola
Epigenetics group.
Agustín Fernández.
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