Research Group

Detalle de: Bioinformatics and Functional Genomics

Title	Bioinformatics and Functional Genomics
Description	Dr. JAVIER DE LAS RIVAS (MSc, PhD) is Full Professor ("Profesor de Investigación") of the Consejo Superior de Investigaciones Científicas (CSIC, Spain), the University of Salamanca (USAL) and the Institute for Biomedical Research of Salamanca (IBSAL). Director as Principal Investigator (PI) of the Bioinformatics and Functional Genomics Research Group at the Cancer Research Center (CiC-IBMCC, CSIC/USAL) in Salamanca (Spain).
Home Page	http://bioinfow.dep.usal.es/
Contact Email	jrivas@usal.es
Collaborating Companies
Spin Off
Patents
Hpc Resources
Institution	IBMCC
Ontology	Omics, Computational Methods, Resources, Transcriptomics, RNA Sequencing (RNA-seq), Data Analysis, Artificial Intelligence, Bioinformatics Software and Tools, Analysis packages (R, Python, etc.), Applications of Computational Biology, Bioinformatics enabling techniques, Genomics, Functional genomics, Structural bioinformatics, Expression Profiling, Computational models and simulations, Gene regulatory networks, Systems Biology, Variant calling, Statistical Methods for Biology, Bioinformatics education, Proteomics, Multivariate statistics, Network Biology, Drug Discovery and design, Single-cell omics, Single-cell (scRNA-seq), Molecular Interactions/Docking, Protein-Protein Interactions, Non-parametric statistics, Deep Learning in Biology, Clinical data, Spatial transcriptomics
Tools	APID Interactomes: protein-protein interactions database
Service Units
Research Lines	Drug Discovery, Application of Machine Learning for Cancer Biomarker Discovery, Multi-omics Integration, Transcriptomics, Cancer Genomics and Transcriptomics, Protein interactions and network molecular biology, Cell type markers and single-cell data analysis, Single-cell and spatial omics
Funded Projects
Selected Publications	Novel Gene Biomarkers Specific to Human Mesenchymal Stem Cells Isolated from Bone Marrow Article · 6 Nov 2024 Stratification of Colorectal Patients Based on Survival Analysis Shows the Value of Consensus Molecular Subtypes and Reveals the CBLL1 Gene as a Biomarker of CMS2 Tumours Article · 5 Feb 2024 Cabergoline as a Novel Strategy for Post-Pregnancy Breast Cancer Prevention in Mice and Human Preprint · 5 Feb 2024 Comparative Analysis of Cell Mixtures Deconvolution and Gene Signatures Generated for Blood, Immune and Cancer Cells Article · 28 Jun 2023 Systematic Evaluation of Antigenic Stimulation in Chronic Lymphocytic Leukemia: Humoral Immunity as Biomarkers for Disease Evolution Article · 31 Jan 2023 View all (130 more) Identification of a gene expression signature associated with breast cancer survival and risk that improves clinical genomic platforms Article · 1 Jan 2023 A single-cell clusters similarity measure for different batches, datasets, and samples Preprint · 16 Mar 2022 A Gene Signature Derived from the Loss of CDKN1A (p21) Is Associated with CMS4 Colorectal Cancer Article · 28 Dec 2021 Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model Article · 26 Nov 2021 Resistance to Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia—From Molecular Mechanisms to Clinical Relevance Article · 26 Sep 2021 40 Years of RAS—A Historic Overview Article · 1 May 2021 Stroma-Mediated Resistance to S63845 and Venetoclax through MCL-1 and BCL-2 Expression Changes Induced by miR-193b-3p and miR-21-5p Dysregulation in Multiple Myeloma Article · 4 Mar 2021 Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations Article · 30 Apr 2020 Mining Drug-Target Associations in Cancer: Analysis of Gene Expression and Drug Activity Correlations Article · 25 Apr 2020 Deciphering Master Gene Regulators and Associated Networks of Human Mesenchymal Stromal Cells Article · 5 Apr 2020 Proteomic and Transcriptomic Profiling Identifies Early Developmentally Regulated Proteins in Dictyostelium Discoideum Article · 1 Oct 2019 DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling Article · 1 Mar 2019 APID database: redefining protein–protein interaction experimental evidences and binary interactomes Software · 1 Jan 2019 Searching the overlap between network modules with specific betweeness (S2B) and its application to cross-disease analysis Article · 1 Aug 2018 Lmo2 expression defines tumor cell identity during T-cell leukemogenesis Article · 7 Jun 2018 JAMI: A Java library for molecular interactions and data interoperability Article · 11 Apr 2018 Encompassing new use cases - Level 3.0 of the HUPO-PSI format for molecular interactions Article · 11 Apr 2018 Human Interactomics: Comparative Analysis of Different Protein Interaction Resources and Construction of a Cancer Protein-Drug Bipartite Network Book / chapter · 2018 Corrigendum: Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures [Briefings in Bioinformatics, (2017)] doi: 10.1093/bib/bbx064 Article · 2 Sep 2017 Infection exposure promotes ETV6-RUNX1 precursor B-cell leukemia via impaired H3K4 demethylases Article · 14 Aug 2017 Mesenchymal stromal cells (MSC) from JAK2+myeloproliferative neoplasms differ from normal MSC and contribute to the maintenance of neoplastic hematopoiesis Article · 10 Aug 2017 Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies Article · 17 Apr 2017 Epidermal Growth Factor Signaling towards Proliferation: Modeling and Logic Inference Using Forward and Backward Search Article · 2017 Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling Article · 21 Nov 2016 Identification of expression patterns in the progression of disease stages by integration of transcriptomic data Article · Nov 2016 Path2enet: Generation of human pathway-derived networks in an expression specific context Article · Oct 2016 Evolutionary hallmarks of the human proteome: Chasing the age and coregulation of protein-coding genes Article · Oct 2016 Role of nerve growth factor signaling in cancer cell proliferation and survival using a reachability analysis approach Book / chapter · 2016 Infection exposure is a causal factor in B-cell precursor acute lymphoblastic leukemia as a result of Pax5-inherited susceptibility Article · 1 Dec 2015 Cystatin D locates in the nucleus at sites of active transcription and modulates gene and protein expression Article · Oct 2015 Analyse multiple disease subtypes and build associated gene networks using genome-wide expression profiles Article · 26 May 2015 ColoLipidGene: Signature of lipid metabolism-related genes to predict prognosis in stage-II colon cancer patients Article · 6 Feb 2015 Analysis of cellular proliferation and survival signaling by using two ligand/receptor systems modeled by pathway logic Book / chapter · 2015 Transcriptomic profile induced in bone marrow mesenchymal stromal cells after interaction with multiple myeloma cells: Implications in myeloma progression and myeloma bone disease Article · 4 Jun 2014 Identification of a characteristic copy number alteration profile by high-resolution single nucleotide polymorphism arrays associated with metastatic sporadic colorectal cancer Article · 25 Mar 2014 MiRNA cargo within exosome-like vesicle transfer influences metastatic bone colonization Article · 6 Feb 2014 TET2 overexpression in chronic lymphocytic leukemia is unrelated to the presence of TET2 variations Article · 2014 Gene Expression Analysis and Profiling of Microarrays Data and RNA-Sequencing Data Book / chapter · 2014 Transcriptome analysis in prenatal IGF1-deficient mice identifies molecular pathways and target genes involved in distal lung differentiation Article · 31 Dec 2013 RHOB influences lung adenocarcinoma metastasis and resistance in a host-sensitive manner Article · 12 Nov 2013 A gene signature of bone metastatic colonization sensitizes for tumor-induced osteolysis and predicts survival in lung cancer Article · 28 Oct 2013 Best practices in bioinformatics training for life scientists Article · 25 Jun 2013 IAnn: An event sharing platform for the life sciences Article · 5 Jun 2013 Molecular Characterization of Chronic Lymphocytic Leukemia Patients with a High Number of Losses in 13q14 Article · 13 Nov 2012 Genome-wide profiling of methylation identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes Article · 31 Aug 2012 Protein-protein interaction networks: Unraveling the wiring of molecular machines within the cel Article · 20 Aug 2012 Prognostic impact of del(17p) and del(22q) as assessed by interphase FISH in sporadic colorectal carcinomas Article · 17 Aug 2012 A novel molecular mechanism involved in multiple myeloma development revealed by targeting MafB to haematopoietic progenitors Article · 17 Aug 2012 Identification of a novel recurrent gain on 20q13 in chronic lymphocytic leukemia by array CGH and gene expression profiling Article · Aug 2012 Receptor of activated protein C promotes metastasis and correlates with clinical outcome in lung adenocarcinoma Article · 1 Jul 2012 Integrating literature-constrained and data-driven inference of signalling networks Article · 25 Jun 2012 Unique genetic profile of sporadic colorectal cancer liver metastasis versus primary tumors as defined by high-density single-nucleotide polymorphism arrays Article · Apr 2012 Impaired expression of DICER, DROSHA, SBDS and some microRNAs in mesenchymal stromal cells from myelodysplastic syndrome patients Article · 27 Feb 2012 Cortactin (CTTN) overexpression in osteosarcoma correlates with advanced stage and reduced survival Article · 21 Jan 2012 Protein interactions: Mapping interactome networks to support drug target discovery and selection Book / chapter · 2012 Bioinformatics training network (BTN): A community resource for bioinformatics trainers Article · 22 Nov 2011 Ten simple rules for developing a short bioinformatics training course Article · 27 Oct 2011 Functional analysis beyond enrichment: Non-redundant reciprocal linkage of genes and biological terms Article · 16 Sep 2011 Transcriptional repression of the tumor suppressor DRO1 by AIB1 Article · 24 Aug 2011 Functional integrative levels in the human interactome recapitulate organ organization Article · 20 Jul 2011 PSICQUIC and PSISCORE: Accessing and scoring molecular interactions Article · 29 Jun 2011 Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number aberrations and gene-loci expression Article · Feb 2011 Mapping of genetic abnormalities of primary tumours from metastatic CRC by high-resolution SNP arrays Article · 29 Oct 2010 Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. Article · 24 Jun 2010 Bioinformatics training: A review of challenges, actions and support requirements Article · 18 Jun 2010 GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs Article · 29 Apr 2010 Deregulation of microRNA expression in the different genetic subtypes of multiple myeloma and correlation with gene expression profiling Article · 7 Jan 2010 Structural domain-domain interactions: Assessment and comparison with protein-protein interaction data to improve the interactome Article · 27 Nov 2009 Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle Article · 6 Nov 2009 Profiling of chemonaive osteosarcoma and paired-normal cells identifies EBF2 as a mediator of osteoprotegerin inhibition to tumor necrosis factor-related apoptosis-inducing ligand-induced apoptosis Article · 12 Aug 2009 RasGRF1 disruption causes retinal photoreception defects and associated transcriptomic alterations Article · 25 Jun 2009 Improving k-NN for human cancer classification using the gene expression profiles Book / chapter · 2009 Human gene coexpression landscape: Confident network derived from tissue transcriptomic profiles Article · 15 Dec 2008 Role of electrostatics on membrane binding, aggregation and destabilization induced by NAD(P)H dehydrogenases. Implication in membrane fusion Article · Oct 2008 Dynamic flexibility in the structure and function of photosystem II in higher plant thylakoid membranes: The grana enigma Article · Oct 2008 Classification of multiple cancer types in a hyper reproducing kernel hilbert space Conference paper · Oct 2008 A novel lung cancer signature mediates metastatic bone colonization by a dual mechanism Article · 1 Apr 2008 Interleukin-12 inhibits liver-specific drug-inducible systems in vivo Article · 22 Nov 2007 Combining dissimilarity based classifiers for cancer prediction using gene expression profiles Article · Nov 2007 Ensemble of kernel based classifiers to improve the human cancer prediction using DNA microarrays Conference paper · Oct 2007 The 90S preribosome is a multimodular structure that is assembled through a hierarchical mechanism Article · 1 Aug 2007 Methylseleninic acid enhances the effect of etoposide to inhibit prostate cancer growth in vivo Article · 23 Jul 2007 APID2NET: Unified interactome graphic analyzer Article · 21 Jul 2007 Oxygen-evolving extrinsic proteins (PsbO,P,Q,R): Bioinformatic and functional analysis Article · Jun 2007 Laser microdissection and microarray analysis of the hippocampus of Ras-GRF1 knockout mice reveals gene expression changes affecting signal transduction pathways related to memory and learning Article · Apr 2007 Linear array of conserved sequence motifs to discriminate protein subfamilies: Study on pyridine nucleotide-disulfide reductases Article · 16 Mar 2007 Gene expression profiling of B lymphocytes and plasma cells from Waldenström's macroglobulinemia: Comparison with expression patterns of the same cell counterparts from chronic lymphocytic leukemia, multiple myeloma and normal individuals Article · 25 Jan 2007 Ensemble of support vector machines to improve the cancer class prediction based on the gene expression profiles Book / chapter · 2007 Proteomic profiles of thylakoid membranes and changes in response to iron deficiency Article · Sep 2006 Transcriptional networks of knockout cell lines identify functional specificities of H-Ras and N-Ras: Significant involvement of N-Ras in biotic and defense responses Article · 7 Aug 2006 APID: Agile protein interaction DataAnalyzer Article · 1 Jul 2006 Algorithm to find gene expression profiles of deregulation and identify families of disease-altered genes Article · 24 Feb 2006 Structure and evolution of the extrinsic proteins that stabilize the oxygen-evolving engine Article · Dec 2005 The 1.49 Å resolution crystal structure of PsbQ from photosystem II of Spinacia oleracea reveals a PPII structure in the N-terminal region Article · Jul 2005 Mobilisation with G-CSF in healthy donors promotes a high but temporal deregulation of genes [7] Article · 14 Apr 2005 Single mutations of residues outside the active center of the xylanase Xys1Δ from Streptomyces halstedii JM8 affect its activity Article · Nov 2004 Structural stability of the PsbQ protein of higher plant photosystem II Article · 13 Oct 2004 Analysis of the structure of the PsbO protein and its implications Article · Sep 2004 Interactome data and databases: Different types of protein interaction Article · Mar 2004 Evolution of oxygenic photosynthesis: Genome-wide analysis of the OEC extrinsic proteins Article · Jan 2004 Calcium-dependent conformational change and thermal stability of the isolated PsbO protein detected by FTIR spectroscopy Article · 20 Sep 2003 The single tryptophan of the PsbQ protein of photosystem II is at the end of a 4-α-helical bundle domain Article · 9 Sep 2003 Structural analysis of the PsbQ protein of photosystem II by fourier transform infrared and circular dichroic spectroscopy and by bioinformatic methods Article · 1 Jan 2003 Fluorescence induction of Photosystem II membranes shows the steps till reduction and protonation of the quinone pool Article · 2003 Water oxidation chemistry of photosystem II Article · 29 Oct 2002 Evidence for Cu(I)-thiolate ligation and prediction of a putative copper-binding site in the Escherichia coli NADH dehydrogenase-2 Article · Sep 2002 Comparative analysis of chloroplast genomes: Functional annotation, genome-based phylogeny, and deduced evolutionary patterns Article · 1 Apr 2002 Three-dimensional electron cryo-microscopy study of the extrinsic domains of the oxygen-evolving complex of spinach. Assignment of the PsbO protein Article · Apr 2002 Structural and functional properties of Escherichia coli-derived nucleoplasmin: A comparative study of recombinant and natural proteins Article · 15 Mar 2001 Expression of cysteine proteinase mRNA in chickpea (Cicer arietinum L.) is localized to provascular cells in the developing root Article · 2001 Structural predictions on the 33 kDa extrinsic protein associated to the oxygen evolving complex of photosynthetic organisms Article · Jul 1999 Structure and thermal stability of photosystem II reaction centers studied by infrared spectroscopy Article · 1 Jul 1997 Comparison of primary charge separation in the photosystem II reaction center complex isolated from wild-type and D1-130 mutants of the cyanobacterium Synechocystis PCC 6803 Article · Jan 1996 pH sensitivity of the redox state of cytochrome b559 may regulate its function as a protectant against donor and acceptor side photoinhibition Article · Nov 1995 Indirect reduction of cytochrome b559 in isolated reaction centres of photosystem II by exogenous flavins Article · Aug 1995 Effect of Photosystem II inhibitor K-15 on photochemical reactions of the isolated D1/D2 cytochrome b559 complex Article · May 1995 A comparison of the photochemical activity of two forms of Photosystem II reaction centre isolated from sugar beet Article · Mar 1994 A functional model for the role of cytochrome b559 in the protection against donor and acceptor side photoinhibition Article · Dec 1993 Acceptor Side Mechanism of Photoinduced Proteolysis of the D1 Protein in Photosystem II Reaction Centers Article · 1 Jul 1993 Two coupled β-carotene molecules protect P680 from photodamage in isolated Photosystem II reaction centres Article · Apr 1993 Long-lived primary radical pair state detected by time-resolved fluorescence and absorption spectroscopy in an isolated Photosystem two core Article · Dec 1992 Two sites of primary degradation of the D1-protein induced by acceptor or donor side photo-inhibition in photosystem II core complexes Article · 27 Apr 1992 Determination of carotenoid pigments in several tree leaves by reversed-phase high-performance liquid chromatography Article · Oct 1991 β-Carotene within the isolated Photosystem II reaction centre: photooxidation and irreversible bleaching of this chromophore by oxidised P680 Article · Sep 1991 Reversed-phase high-performance liquid chromatographic separation of lutein and lutein fatty acid esters from marigold flower petal powder Article · Jun 1991 Phycomyces blakesleeanus car B mutants: Their use in assays of phytoene desaturase Article · Jan 1991 Isolation of a yellow carotenoprotein from carrot Article · Jan 1991 Photosynthetic pigments and mineral composition of iron deficient pear leaves Article · Jul 1989 Further studies on the blue carotenoprotein from Astacus leptodactylus Article · Jan 1988 Characterization of a blue astaxanthin protein from the carapace of the crayfish Astacus leptodactylus Article · Jan 1986
Researchers	Javier De Las Rivas, Alberto Berral González, Enrique De La Rosa Morón

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