Javier De Las Rivas

Summary

Affiliation: Universidad de Salamanca
Country: Spain

Publications

  1. doi request reprint Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell
    Javier De Las Rivas
    Bioinformatics and Functional Genomics Research Group, Cancer Research Center IBMCC, CSIC USAL, Salamanca, Spain
    Brief Funct Genomics 11:489-96. 2012
  2. pmc Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancer
    Celia Fontanillo
    Cancer Research Center, Consejo Superior de Investigaciones Cientificas, Campus Miguel de Unamuno, Salamanca, Spain
    BMC Genomics 13:S5. 2012
  3. doi request reprint Protein interactions: mapping interactome networks to support drug target discovery and selection
    Javier De Las Rivas
    Bioinformatics and Functional Genomics Group, Cancer Research Center IBMCC, CSIC USAL, Salamanca, Spain
    Methods Mol Biol 910:279-96. 2012
  4. ncbi request reprint Oxygen-evolving extrinsic proteins (PsbO,P,Q,R): bioinformatic and functional analysis
    Javier De Las Rivas
    Bioinformatics and Functional Genomics Research Group, Instituto de Biología Molecular y Celular del Cáncer IBMCC, CSIC USAL Salamanca, Spain
    Biochim Biophys Acta 1767:575-82. 2007
  5. ncbi request reprint Structure and evolution of the extrinsic proteins that stabilize the oxygen-evolving engine
    Javier De Las Rivas
    Bioinformatics and Functional Genomics Research Group, Instituto de Biología Molecular y Celular del Cáncer IBMCC, CSIC USAL, Salamanca, Spain
    Photochem Photobiol Sci 4:1003-10. 2005
  6. pmc Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle
    Esther Castellano
    Centro de Investigacion del Cancer, IBMCC CSIC USAL, University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain
    Genome Biol 10:R123. 2009
  7. pmc Interactome data and databases: different types of protein interaction
    Javier De Las Rivas
    Cancer Research Center CIC, USAL CSIC, University of Salamanca and CSIC, Campus Miguel de Unamuno, Salamanca E37007, Spain
    Comp Funct Genomics 5:173-8. 2004
  8. pmc Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases
    César L Avila
    Departamento Bioquímica de la Nutrición, Instituto Superior de Investigaciones Biológicas CONICET UNT, San Miguel de Tucuman, Tucuman, Argentina
    BMC Bioinformatics 8:96. 2007
  9. doi request reprint Unique genetic profile of sporadic colorectal cancer liver metastasis versus primary tumors as defined by high-density single-nucleotide polymorphism arrays
    Luís Muñoz-Bellvis
    Unidad de Cirugía Hepatobiliopancreática, Departamento de Cirugia, Hospital Universitario de Salamanca, Salamanca, Spain
    Mod Pathol 25:590-601. 2012
  10. ncbi request reprint The single tryptophan of the PsbQ protein of photosystem II is at the end of a 4-alpha-helical bundle domain
    Monica Balsera
    Instituto de Recursos Naturales y Agrobiología CSIC, Cordel de Merinas, Salamanca, Spain
    Eur J Biochem 270:3916-27. 2003

Collaborators

  • Monica Balsera
  • Juan B Arellano
  • Jesús M Hernández-Rivas
  • Juan Luis Garcia
  • Angel R Ortiz
  • Juan Jose Lozano
  • Ramón I Santamaría
  • Marcel E Dinger
  • Florencio Pazos
  • Alfonso Valencia
  • Alberto Pascual-Montano
  • Celia Fontanillo
  • María González-González
  • Luís Muñoz-Bellvis
  • Carlos Prieto
  • Alberto Risueño
  • Alberto Orfao
  • Oscar Bengoechea
  • Jose Maria Sayagues
  • Carlos Santamaria
  • Marcos Gonzalez
  • Ana Eugenia Rodríguez
  • Eva Garcia
  • Emilio Fonseca
  • Esther Castellano
  • Juan Hernandez-Toro
  • César L Avila
  • Margarita Diaz
  • Norma C Gutierrez
  • M L Gutierrez
  • Soraya Carrancio
  • Alfonso García de Coca
  • Manuel Fuentes
  • Jose Manuel Sanchez-Santos
  • María Hernández-Sánchez
  • Isabel Recio
  • M M Abad
  • Maria Diez-Campelo
  • Manuel Iglesias
  • Maria Consuelo del Cañizo
  • Cristina Teodosio
  • Jose Angel Hernandez
  • Encarna Fermiñán
  • M Eugenia Sarasquete
  • J M Sayagues
  • Fermin M Sanchez-Guijo
  • Rocio Benito
  • Sara Aibar
  • M Mar Abad
  • Natalia de las Heras
  • Carlos Mackintosh
  • Oliver Gutierrez
  • Belen Blanco
  • Jesus F San Miguel
  • Maria E Sarasquete
  • Stela Alvarez-Fernández
  • Beatriz Roson
  • Guillermo Martín-Nuñez
  • M Laura Gutiérrez
  • Sandra Muntion
  • Olga Lopez-Villar
  • Carmen Esteban
  • Rosa Fisac
  • Ruben Nogales-Cadenas
  • María Del Mar Abad
  • Maria del Carmen Chillon
  • Maria Eugenia Sarasquete
  • Marcos Gonzalez-Diaz
  • Eugenio Santos
  • Alejandro Nunez
  • Carmen Guerrero
  • Ricardo N Farias
  • Viviana A Rapisarda
  • Rosana Chehín
  • Sonia Rodriguez
  • Valery L Shnyrov
  • Alberto Ruiz-Arribas
  • Jose Manuel Fernández-Abalos

Detail Information

Publications23

  1. doi request reprint Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell
    Javier De Las Rivas
    Bioinformatics and Functional Genomics Research Group, Cancer Research Center IBMCC, CSIC USAL, Salamanca, Spain
    Brief Funct Genomics 11:489-96. 2012
    ....
  2. pmc Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancer
    Celia Fontanillo
    Cancer Research Center, Consejo Superior de Investigaciones Cientificas, Campus Miguel de Unamuno, Salamanca, Spain
    BMC Genomics 13:S5. 2012
    ..However, it has been proposed that these data can be used to identify key genomic regions, which may enclose causal genes under the assumption that disease-associated gene expression changes are caused by genomic alterations...
  3. doi request reprint Protein interactions: mapping interactome networks to support drug target discovery and selection
    Javier De Las Rivas
    Bioinformatics and Functional Genomics Group, Cancer Research Center IBMCC, CSIC USAL, Salamanca, Spain
    Methods Mol Biol 910:279-96. 2012
    ..This chapter presents our current knowledge on the human protein-protein interactome and explains how such knowledge can help us to select adequate targets for drugs...
  4. ncbi request reprint Oxygen-evolving extrinsic proteins (PsbO,P,Q,R): bioinformatic and functional analysis
    Javier De Las Rivas
    Bioinformatics and Functional Genomics Research Group, Instituto de Biología Molecular y Celular del Cáncer IBMCC, CSIC USAL Salamanca, Spain
    Biochim Biophys Acta 1767:575-82. 2007
    ..Moreover, clear differences are found for PsbQ from higher plants and green algae; and a relationship has been found between PsbR and the Mn cluster...
  5. ncbi request reprint Structure and evolution of the extrinsic proteins that stabilize the oxygen-evolving engine
    Javier De Las Rivas
    Bioinformatics and Functional Genomics Research Group, Instituto de Biología Molecular y Celular del Cáncer IBMCC, CSIC USAL, Salamanca, Spain
    Photochem Photobiol Sci 4:1003-10. 2005
    ..The results show that PsbP and PsbQ present different evolutionary profiles, and that PsbQ is more closely associated to PsbO and probably to the manganese stabilizing role assigned to this protein...
  6. pmc Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle
    Esther Castellano
    Centro de Investigacion del Cancer, IBMCC CSIC USAL, University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain
    Genome Biol 10:R123. 2009
    ..Using oligonucleotide microarrays, we compared transcriptional profiles corresponding to the initial cell cycle stages of mouse fibroblasts lacking the small GTPases H-Ras and/or N-Ras with those of matching, wild-type controls...
  7. pmc Interactome data and databases: different types of protein interaction
    Javier De Las Rivas
    Cancer Research Center CIC, USAL CSIC, University of Salamanca and CSIC, Campus Miguel de Unamuno, Salamanca E37007, Spain
    Comp Funct Genomics 5:173-8. 2004
    ....
  8. pmc Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases
    César L Avila
    Departamento Bioquímica de la Nutrición, Instituto Superior de Investigaciones Biológicas CONICET UNT, San Miguel de Tucuman, Tucuman, Argentina
    BMC Bioinformatics 8:96. 2007
    ..However, not all the PNDR members fit into these categories and this suggests the need of further studies to achieve a more comprehensive classification of this complex family...
  9. doi request reprint Unique genetic profile of sporadic colorectal cancer liver metastasis versus primary tumors as defined by high-density single-nucleotide polymorphism arrays
    Luís Muñoz-Bellvis
    Unidad de Cirugía Hepatobiliopancreática, Departamento de Cirugia, Hospital Universitario de Salamanca, Salamanca, Spain
    Mod Pathol 25:590-601. 2012
    ..Further studies in larger series of patients are necessary to dissect the specific role of each of the altered genes and chromosomal regions in the metastatic spread of colorectal tumors...
  10. ncbi request reprint The single tryptophan of the PsbQ protein of photosystem II is at the end of a 4-alpha-helical bundle domain
    Monica Balsera
    Instituto de Recursos Naturales y Agrobiología CSIC, Cordel de Merinas, Salamanca, Spain
    Eur J Biochem 270:3916-27. 2003
    ..Until then, the model can provide a starting point for further studies on the function of PsbQ...
  11. ncbi request reprint APID2NET: unified interactome graphic analyzer
    Juan Hernandez-Toro
    Bioinformatics and Functional Genomics Research Group, Cancer Research Center IBMCC CIC, CSIC USAL, Salamanca, Spain
    Bioinformatics 23:2495-7. 2007
    ..AVAILABILITY: http://bioinfow.dep.usal.es/apid/apid2net.html. SUPPLEMENTARY INFORMATION: Installation Guide and User's Guide are supplied at the Web site indicated above...
  12. pmc Prognostic Impact of del(17p) and del(22q) as assessed by interphase FISH in sporadic colorectal carcinomas
    María González-González
    Servicio General de Citometria, Departamento de Medicina and Centro de Investigación del Cáncer, IBMCC CSIC USAL, Hospital Universitario de Salamanca IBSAL, Universidad de Salamanca, Salamanca, Spain
    PLoS ONE 7:e42683. 2012
    ..New advances in genetic profiling of sCRC suggest that the primary tumor may contain a cell population with metastatic potential. Here we compare the cytogenetic profile of primary tumors from liver metastatic versus non-metastatic sCRC...
  13. ncbi request reprint Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteins
    Javier De Las Rivas
    Instituto de Recursos Naturales y Agrobiologia, Consejo Superior de Investigaciones Cientificas CSIC, Salamanca, Spain
    Trends Plant Sci 9:18-25. 2004
    ..This analysis traces the evolution of the extrinsic proteins from ancient cyanobacteria to higher plants and gives hints about the ancestral form of the OEC...
  14. ncbi request reprint Structural analysis of the PsbQ protein of photosystem II by Fourier transform infrared and circular dichroic spectroscopy and by bioinformatic methods
    Monica Balsera
    Instituto de Recursos Naturales y Agrobiologia, Consejo Superior de Investigaciones Cientificas, Cordel de Merinas 52, Salamanca 37008, Spain
    Biochemistry 42:1000-7. 2003
    ..The results obtained by both the spectroscopic and computational methods are in agreement, all indicating that PsbQ is mainly an alpha protein, and show the value of using both methodologies for protein structure investigation...
  15. pmc GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs
    Alberto Risueño
    Bioinformatics and Functional Genomics Research Group, Cancer Research Center CIC IBMCC, CSIC USAL, Salamanca, Spain
    BMC Bioinformatics 11:221. 2010
    ..Consequently, there is a need for new databases that combine genomic and transcriptomic information and provide updated mapping of expression probes to current genomic annotations...
  16. pmc Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms
    Celia Fontanillo
    Cancer Research Center CIC IBMCC, CSIC USAL, Campus Miguel de Unamuno, Salamanca, Spain
    PLoS ONE 6:e24289. 2011
    ..A web application to use the method here proposed is provided at http://gtlinker.cnb.csic.es...
  17. pmc Molecular characterization of chronic lymphocytic leukemia patients with a high number of losses in 13q14
    Ana Eugenia Rodríguez
    IBSAL, IBMCC, Centro de Investigacion del Cancer, Universidad de Salamanca CSIC, Salamanca, Spain
    PLoS ONE 7:e48485. 2012
    ..Thus, cases with a high number of 13q- cells (13q-H) had both shorter overall survival and time to first therapy. The goal of the study was to analyze the genetic profile of 13q-H patients...
  18. pmc Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles
    Carlos Prieto
    Bioinformatics and Functional Genomics Research Group, Cancer Research Center CIC IBMCC, CSIC USAL, Salamanca, Spain
    PLoS ONE 3:e3911. 2008
    ..Moreover, the technical noise present in genome-wide expression microarrays is another well reported problem that many times is not addressed with robust statistical methods, and the estimation of errors in the data is not provided...
  19. pmc APID: Agile Protein Interaction DataAnalyzer
    Carlos Prieto
    Bioinformatics and Functional Genomics Research Group, Cancer Research Center CIC, CSIC USAL, 37007 Salamanca, Spain
    Nucleic Acids Res 34:W298-302. 2006
    ..APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network. The application is available open access at http://bioinfow.dep.usal.es/apid/...
  20. ncbi request reprint Single mutations of residues outside the active center of the xylanase Xys1 Delta from Streptomyces halstedii JM8 affect its activity
    Margarita Diaz
    Departamento de Microbiologia y Genetica, Instituto de Microbiologia Bioquimica, Consejo Superior de Investigaciones Cientificas CSIC, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno 37007, Salamanca, Spain
    FEMS Microbiol Lett 240:237-43. 2004
    ..This study shows the usefulness of random mutagenesis to point out some key residues not directly involved in the active center, but in which mutation produces subtle structural rearrangements affecting the enzymatic function...
  21. pmc Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns
    Javier De Las Rivas
    Instituto de Recursos Naturales y Agrobiologia, Consejo Superior de Investigaciones Cientificas, 37071 Salamanca, Spain
    Genome Res 12:567-83. 2002
    ..Finally, by grouping common evolutionary patterns, we show that it is possible to determine functionally linked protein networks. This has allowed us to suggest putative associations for some unknown ORFs...
  22. pmc Impaired expression of DICER, DROSHA, SBDS and some microRNAs in mesenchymal stromal cells from myelodysplastic syndrome patients
    Carlos Santamaria
    Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
    Haematologica 97:1218-24. 2012
    ....
  23. pmc Mapping of genetic abnormalities of primary tumours from metastatic CRC by high-resolution SNP arrays
    Jose Maria Sayagues
    Servicio General de Citometria, Departamento de Medicina and Centro de Investigación del Cáncer IBMCC CSIC USAL, Universidad de Salamanca, Salamanca, Spain
    PLoS ONE 5:e13752. 2010
    ....