Javier De Las Rivas
Affiliation: Universidad de Salamanca
- A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samplesAlberto Risueño
Bioinformatics and Functional Genomics Research Group, Cancer Research Center CIC IBMCC, CSIC USAL IBSAL, Salamanca 37007, Spain
BMC Genomics 15:879. 2014..One of the omic technologies widely used in many studies on human samples are the exon-specific expression microarray platforms...
- Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placentaBeatriz Roson-Burgo
Bioinformatics and Functional Genomics Group, Cancer Research Center IBMCC, CSIC USAL IBSAL, Consejo Superior de Investigaciones Cientificas CSIC, Salamanca, Spain
BMC Genomics 15:910. 2014..The potential utility of MSCs is nowadays strongly investigated in the field of regenerative medicine and cell therapy, although many questions about their molecular identity remain uncertain...
- APID: Agile Protein Interaction DataAnalyzerCarlos 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/...
- Protein-protein interaction networks: unraveling the wiring of molecular machines within the cellJavier De Las Rivas
Bioinformatics and Functional Genomics Research Group, Cancer Research Center IBMCC, CSIC USAL, Salamanca, Spain
Brief Funct Genomics 11:489-96. 2012....
- Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancerCelia 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...
- Protein interactions: mapping interactome networks to support drug target discovery and selectionJavier 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...
- Oxygen-evolving extrinsic proteins (PsbO,P,Q,R): bioinformatic and functional analysisJavier 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...
- Structure and evolution of the extrinsic proteins that stabilize the oxygen-evolving engineJavier 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...
- Interactome data and databases: different types of protein interactionJavier 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....
- Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductasesCésar 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...
- Unique genetic profile of sporadic colorectal cancer liver metastasis versus primary tumors as defined by high-density single-nucleotide polymorphism arraysLuís 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...
- APID2NET: unified interactome graphic analyzerJuan 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...
- Identification of a characteristic copy number alteration profile by high-resolution single nucleotide polymorphism arrays associated with metastatic sporadic colorectal cancerMaría González-González
General Cytometry Service Nucleus, Department of Medicine and Cancer Research Center, Institute of Molecular Biology and Cellular Oncology of the University of Salamanca and Salamanca Institute of Biomedical Research, University of Salamanca, Salamanca, Spain
Cancer 120:1948-59. 2014....
- TET2 overexpression in chronic lymphocytic leukemia is unrelated to the presence of TET2 variationsMaría Hernández-Sánchez
IBSAL, IBMCC, Centro de Investigacion del Cancer, Universidad de Salamanca CSIC, 37007 Salamanca, Spain
Biomed Res Int 2014:814294. 2014..002). However, no novel mutations were observed. Therefore, overexpression of TET2 in CLL seems to be unrelated to the presence of genomic TET2 variations. ..
- The single tryptophan of the PsbQ protein of photosystem II is at the end of a 4-alpha-helical bundle domainMonica 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...
- Prognostic Impact of del(17p) and del(22q) as assessed by interphase FISH in sporadic colorectal carcinomasMaría 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...
- Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteinsJavier 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...
- Structural analysis of the PsbQ protein of photosystem II by Fourier transform infrared and circular dichroic spectroscopy and by bioinformatic methodsMonica 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...
- GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAsAlberto 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...
- Microvesicles from Mesenchymal Stromal Cells Are Involved in HPC-Microenvironment Crosstalk in Myelodysplastic PatientsSandra Muntion
Servicio de Hematologia, Hospital Universitario de Salamanca, Salamanca, Spain
PLoS ONE 11:e0146722. 2016..037) were observed when MVs from MDS patients were incorporated. In summary, we show that BM-MSC release MVs with a different cargo in MDS patients compared with HD. These structures are incorporated into HPC and modify their properties. ..
- Human gene coexpression landscape: confident network derived from tissue transcriptomic profilesCarlos 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...
- Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological termsCelia 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...
- Molecular characterization of chronic lymphocytic leukemia patients with a high number of losses in 13q14Ana 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...
- Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patternsJavier 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...
- Single mutations of residues outside the active center of the xylanase Xys1 Delta from Streptomyces halstedii JM8 affect its activityMargarita 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...
- Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clusteringSara Aibar
Bioinformatics and Functional Genomics Research Group, Cancer Research Center Consejo Superior de Investigaciones Científicas, Universidad de Salamanca and Instituto de Investigación Biomédica de Salamanca, CSIC USAL IBSAL, Salamanca, Spain
Bioinformatics 31:1686-8. 2015..The application includes an interface to directly perform FEA queries using different external tools: DAVID, GeneTerm Linker, TopGO or GAGE; and a graphical interface to facilitate the use...
- Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycleEsther 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...
- Deregulation of genes related to iron and mitochondrial metabolism in refractory anemia with ring sideroblastsMónica del Rey
IBMCC, Centro de Investigación del Cáncer CIC, Universidad de Salamanca CSIC, Salamanca, Spain IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
PLoS ONE 10:e0126555. 2015..The deregulation of genes involved in iron and mitochondrial metabolism provides new insights in our knowledge of MDS-RS. New variants that could be involved in the pathogenesis of these diseases have been identified. ..
- Transcriptomic profile induced in bone marrow mesenchymal stromal cells after interaction with multiple myeloma cells: implications in myeloma progression and myeloma bone diseaseAntonio Garcia-Gomez
Centro de Investigacion del Cancer, IBMCC Universidad de Salamanca CSIC, Salamanca, Spain Hospital Universitario de Salamanca IBSAL, Salamanca, Spain Centro en Red de Medicina Regenerativa y Terapia Celular de Castilla y León, Salamanca, Spain
Oncotarget 5:8284-305. 2014....
- Impaired expression of DICER, DROSHA, SBDS and some microRNAs in mesenchymal stromal cells from myelodysplastic syndrome patientsCarlos Santamaria
Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
Haematologica 97:1218-24. 2012....
- Mapping of genetic abnormalities of primary tumours from metastatic CRC by high-resolution SNP arraysJose 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....