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Bioinformatics and Functional Genomics Research Group
Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL)
Salamanca (SPAIN)

Dr. Javier DE LAS RIVAS
Dr. Jose Manuel SÁNCHEZ SANTOS - Dr. Manuel MARTÍN MERINO
Sara AIBAR - Santiago BUENO - Francisco CAMPOS - Conrad DROSTE - Beatriz ROSÓN
Former Members
(Celia FONTANILLO - Alberto RISUEÑO - Carlos PRIETO - Juan HERNÁNDEZ TORO)

SCIENTIFIC AREAS:  Bioinformatics -  Functional Genomics -  Cancer Genomics -  Protein Interactomics -  Cancer Systems Biology

RESEARCH TOPICS:  Integrative analyses of genomic and proteomic data derived from patient-oriented studies in cancer. Bioinformatics applied to find new cancer biomarkers and cancer drivers. Using cancer genomic data to improve patient stratification, disease subtype profiling and prognosis analysis. Computational Biology and Bioinformatics applied to studies in oncohematology. Human proteome and protein interatome networks: construction, validation and analyses.




Main Bioinformatics Research Centers (USA & EUROPE):

NCBI The National Center for Biotechnology Information at NIH, USA
EBI The European Bioinformatics Institute in Cambridge, UK

Web Links related to Bioinformatics, Computational Biology and Functional Genomics:


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GENOMES

Human Genome
ENSEMBL EBI, Hinxton, UK
The Sanger Centre The Sanger Centre, Hinxton, UK
BROAD Institute BROAD Institute, MIT and Harvard, Cambridge, MA, USA

Non-Human Genomes
Mouse MGI Mouse Genome Informatics
C. elegans Wormbase
Drosophila  Flybase
Saccharomyces SGD Saccharomyces Genome Database
Human GenomeTop

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PROTEINS & GENES

 Sequence search / alignments

PROTEINS primary DB UniProt, SWISS-PROT and TrEMBL (ExPASy, CH)
GENES primary DB Gene Entrez (NCBI, USA)

Blast_NCBI Basic/Advanced BLAST  (blastall)  search at NCBI

Clustal_EBI Clustal Server at EBI

Protein analysisTop

Primary structure
 
InterPro Integrated resource of protein domains and functional sites (EBI, UK)
Pfam Protein domains and motifs  (EMBL)

ExPASy Tools ExPASy Proteomics tools
Protein analysisTop

Secondary structure
 
PredictProtein The PredictProtein server  (Columbia, USA)
Protein analysisTop

Tertiary structure
 
Swiss-Model SWISS-MODEL. An Automated Comparative Protein Modelling Server (ExPASy, CH)

PDB - RCSB Protein Data Bank (RCSB)
PDBsum Summaries and structural analyses of PDB data files (UCL, UK)

SCOP Structural Classification of Proteins (MRC-LMB, UK)
CATH CATH Protein Structure Classification (UCL-BSM, UK)
FSSP Fold classification based on Structure-Structure alignment of Proteins (FSSP) (EBI)
Protein analysisTop

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PATWAYS

KEGG KEGG:Kyoto Encyclopedia of Genes and Genomes (ICR, JP)
REACTOME Reactome is a database of biological pathways
 

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BIBLIOGRAPHY & SCIENTIFIC JOURNALS

PubMed PubMed is the National Library of Medicine's search service 
   
Science The EMBO Journal Bioinformatics
Nature Journal of Biological Chemistry PLoS Computational Biology
Nature Biotecnology Current Opinions Online BMC Bioinformatics
Nature Cell Biol. Journal of Molecular Biology BMC Genomics
Nature Genetics Molecular Cell  Protein Science
Nature Struct. Biol. Molecular and Cellular Biology  Protein Engineering
Cell Nucleic Acid Research Proteins: Struc. Func. and Bioinformatics
Proc. Natl. Acad. Sci. USA FEBS Letters BBA
   

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Copyright
Javier De Las Rivas
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Last update: February, 2015.