List of works by Javier De Las Rivas

A New Reversed Phase-HPLC Method Resolving All Major Higher Plant Photosynthetic Pigments

article

A comparison of the photochemical activity of two forms of Photosystem II reaction centre isolated from sugar beet

article by Guillermo Montoya et al published March 1994 in BBA - Bioenergetics

A functional model for the role of cytochrome b559 in the protection against donor and acceptor side photoinhibition

scientific article published on December 1993

A gene signature of bone metastatic colonization sensitizes for tumor-induced osteolysis and predicts survival in lung cancer.

scientific article published on 28 October 2013

A global perspective on bioinformatics training needs

A high number of losses in 13q14 chromosome band is associated with a worse outcome and biological differences in patients with B-cell chronic lymphoid leukemia.

scientific article published on March 2009

A novel lung cancer signature mediates metastatic bone colonization by a dual mechanism

scientific article

A novel molecular mechanism involved in multiple myeloma development revealed by targeting MafB to haematopoietic progenitors

scientific article

A proteome-scale map of the human interactome network

scientific article

A reference map of the human binary protein interactome

scientific article published on 08 April 2020

A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples.

scientific article

APID database: redefining protein-protein interaction experimental evidences and binary interactomes

scientific article published on 01 January 2019

APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.

scientific article

APID2NET: unified interactome graphic analyzer

scientific article published on 21 July 2007

APID: Agile Protein Interaction DataAnalyzer

scientific article

Acceptor side mechanism of photoinduced proteolysis of the D1 protein in photosystem II reaction centers

scientific article published on 01 July 1993

Algorithm to find gene expression profiles of deregulation and identify families of disease-altered genes

scientific article published on 24 February 2006

Analyse multiple disease subtypes and build associated gene networks using genome-wide expression profiles

scientific article

Analysis of Cellular Proliferation and Survival Signaling by Using Two Ligand/Receptor Systems Modeled by Pathway Logic

article published in 2015

Analysis of the Structure of the PsbO Protein and its Implications

article

Best practices in bioinformatics training for life scientists

scientific article published on 25 June 2013

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.

scientific article

Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures.

scientific article published in November 2017

Bioinformatics training: a review of challenges, actions and support requirements.

scientific article published on 18 June 2010

Calcium-dependent conformational change and thermal stability of the isolated PsbO protein detected by FTIR spectroscopy.

scientific article published in October 2003

Characterization of a blue astaxanthin protein from the carapace of the crayfish Astacus leptodactylus

scientific article published in 1986

Classification of multiple cancer types in a Hyper Reproducing Kernel Hilbert Space

ColoLipidGene: signature of lipid metabolism-related genes to predict prognosis in stage-II colon cancer patients.

scientific article published on March 2015

Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancer.

scientific article

Combining Dissimilarities in a Hyper Reproducing Kernel Hilbert Space for Complex Human Cancer Prediction

Combining dissimilarities in a Hyper Reproducing Kernel Hilbert Space for complex human cancer prediction

scientific article

Combining dissimilarity based classifiers for cancer prediction using gene expression profiles.

scientific article

Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns.

scientific article published on April 2002

Comparison of Primary Charge Separation in the Photosystem II Reaction Center Complex Isolated from Wild-type and D1-130 Mutants of the CyanobacteriumSynechocystisPCC 6803

scientific article published in Journal of Biological Chemistry

Computational approaches in cancer multidrug resistance research: Identification of potential biomarkers, drug targets and drug-target interactions

scientific article published on 18 October 2019

Cortactin (CTTN) overexpression in osteosarcoma correlates with advanced stage and reduced survival.

scientific article published in January 2011

Crebbp loss cooperates with Bcl2 overexpression to promote lymphoma in mice.

scientific article

Cystatin D locates in the nucleus at sites of active transcription and modulates gene and protein expression.

scientific article published on 13 September 2015

DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling

scientific article published on 01 October 2019

Deregulation of genes related to iron and mitochondrial metabolism in refractory anemia with ring sideroblasts

scientific article published on 8 May 2015

Deregulation of microRNA expression in the different genetic subtypes of multiple myeloma and correlation with gene expression profiling.

scientific article

Determination of carotenoid pigments in several tree leaves by reversed-phase high-performance liquid chromatography

Dynamic flexibility in the structure and function of photosystem II in higher plant thylakoid membranes: the grana enigma

scientific article published on October 2008

Effect of Photosystem II inhibitor K-15 on photochemical reactions of the isolated D1/D2 cytochrome b559 complex.

scientific article published in May 1995

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

scientific article published on 11 April 2018

Ensemble of Kernel Based Classifiers to Improve the Human Cancer Prediction using DNA Microarrays

Ensemble of Support Vector Machines to Improve the Cancer Class Prediction Based on the Gene Expression Profiles

article

Epidermal Growth Factor Signaling towards Proliferation: Modeling and Logic Inference Using Forward and Backward Search

scientific article published on 16 January 2017

Evidence for Cu(I)-thiolate ligation and prediction of a putative copper-binding site in the Escherichia coli NADH dehydrogenase-2.

scientific article published in September 2002

Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteins

scientific article published on January 2004

Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes

scientific article

Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations

scientific article published on 30 April 2020

Expression of cysteine proteinase mRNA in chickpea (Cicer arietinum L.) is localized to provascular cells in the developing root

Fluorescence induction of Photosystem II membranes shows the steps till reduction and protonation of the quinone pool

scientific article

Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering

scientific article published on 18 January 2015

Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms.

scientific article

GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

scientific article

Gene Expression Analysis and Profiling of Microarrays Data and RNA-Sequencing Data

article

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

scientific article

Genome-wide profiling of methylation identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes.

scientific article published on 31 August 2012

Human Interactomics: Comparative Analysis of Different Protein Interaction Resources and Construction of a Cancer Protein-Drug Bipartite Network

scientific article published on 6 November 2017

Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles

scientific article

Identification of a characteristic copy number alteration profile by high-resolution single nucleotide polymorphism arrays associated with metastatic sporadic colorectal cancer

scientific article published on 25 March 2014

Identification of a novel recurrent gain on 20q13 in chronic lymphocytic leukemia by array CGH and gene expression profiling

article

Identification of expression patterns in the progression of disease stages by integration of transcriptomic data

scientific article

Impaired expression of DICER, DROSHA, SBDS and some microRNAs in mesenchymal stromal cells from myelodysplastic syndrome patients

scientific article

Improving k-NN for Human Cancer Classification Using the Gene Expression Profiles

article

In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins.

scientific article published on 9 July 2015

Infection Exposure Promotes ETV6-RUNX1 Precursor B-cell Leukemia via Impaired H3K4 Demethylases.

scientific article

Infectious stimuli promote malignant B-cell acute lymphoblastic leukemia in the absence of AID

scientific article published on 05 December 2019

Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling

scientific article

Integrating literature-constrained and data-driven inference of signalling networks

scientific article

Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project

scientific article

Interactome data and databases: different types of protein interaction

scientific article

Interleukin-12 inhibits liver-specific drug-inducible systems in vivo

scientific article published on 22 November 2007

JAMI: a Java library for molecular interactions and data interoperability.

scientific article published on 11 April 2018

Kernel Alignment k-NN for Human Cancer Classification Using the Gene Expression Profiles

article

Las metástasis óseas del cáncer

scientific article published on 01 May 2006

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

scientific article

Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases

scientific article

Linking amyotrophic lateral sclerosis and spinal muscular atrophy through RNA-transcriptome homeostasis: a genomics perspective

scientific article published on 5 January 2017

Lmo2 expression defines tumor cell identity during T-cell leukemogenesis

scientific article published on 07 June 2018

Long-lived primary radical pair state detected by time-resolved fluorescence and absorption spectroscopy in an isolated Photosystem two core

scientific article published in December 1992

Mapping of genetic abnormalities of primary tumours from metastatic CRC by high-resolution SNP arrays

scientific article

Matrix-Gla protein promotes osteosarcoma lung metastasis and associates with poor prognosis

scientific article published on 12 May 2016

Maximizing binary interactome mapping with a minimal number of assays

scientific article published on 29 August 2019

Mesenchymal stromal cells (MSC) from JAK2+ myeloproliferative neoplasms differ from normal MSC and contribute to the maintenance of neoplastic hematopoiesis.

scientific article published on 10 August 2017

Methylseleninic acid enhances the effect of etoposide to inhibit prostate cancer growth in vivo

scientific article published on September 2007

MicroRNA (miR)-203 and miR-205 expression patterns identify subgroups of prognosis in cutaneous squamous cell carcinoma

scientific article

Microvesicles from Mesenchymal Stromal Cells Are Involved in HPC-Microenvironment Crosstalk in Myelodysplastic Patients.

scientific article published on 2 February 2016

Mobilisation with G-CSF in healthy donors promotes a high but temporal deregulation of genes

article

Molecular characterization of chronic lymphocytic leukemia patients with a high number of losses in 13q14.

scientific article

Oxygen-evolving extrinsic proteins (PsbO,P,Q,R): bioinformatic and functional analysis.

scientific article

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

scientific article (publication date: 29 June 2011)

Path2enet: generation of human pathway-derived networks in an expression specific context

scientific article

Photosynthetic pigments and mineral composition of iron deficient pear leaves

article

Phycomyces blakesleeanus car B mutants: Their use in assays of phytoene desaturase

article by Paul D. Fraser et al published January 1991 in Phytochemistry

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

scientific article published on 11 August 2009

Prognostic Impact of del(17p) and del(22q) as assessed by interphase FISH in sporadic colorectal carcinomas.

scientific article

Protein interactions: mapping interactome networks to support drug target discovery and selection

scientific article published on January 2012

Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell.

scientific article published on 20 August 2012

Protein-protein interactions essentials: key concepts to building and analyzing interactome networks

scientific article

Proteomic profiles of thylakoid membranes and changes in response to iron deficiency

scientific article published on 13 September 2006

RHOB influences lung adenocarcinoma metastasis and resistance in a host-sensitive manner

scientific article published on 12 November 2013

RasGRF1 disruption causes retinal photoreception defects and associated transcriptomic alterations.

scientific article

Receptor of activated protein C promotes metastasis and correlates with clinical outcome in lung adenocarcinoma

scientific article

Responses of Sugar Beet Roots to Iron Deficiency. Changes in Carbon Assimilation and Oxygen Use

article

Role of Nerve Growth Factor Signaling in Cancer Cell Proliferation and Survival Using a Reachability Analysis Approach

Role of electrostatics on membrane binding, aggregation and destabilization induced by NAD(P)H dehydrogenases. Implication in membrane fusion

scientific article

Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies.

scientific article published on 5 April 2017

Searching the overlap between network modules with specific betweeness (S2B) and its application to cross-disease analysis

scientific article published in Scientific Reports

Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number aberrations and gene-loci expression

scientific article

Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle

scientific article

Single mutations of residues outside the active center of the xylanase Xys1Î fromStreptomyces halstediiJM8 affect its activity

scientific article published on 01 November 2004

Structural analysis of the PsbQ protein of photosystem II by Fourier transform infrared and circular dichroic spectroscopy and by bioinformatic methods.

scientific article

Structural and functional properties of Escherichia coli -derived nucleoplasmin

scholarly article by Aitor Hierro et al published 15 March 2001 in FEBS Journal

Structural and functional properties of Escherichia coli-derived nucleoplasmin. A comparative study of recombinant and natural proteins

scientific article published in March 2001

Structural domain-domain interactions: assessment and comparison with protein-protein interaction data to improve the interactome

scientific article

Structural predictions on the 33 kDa extrinsic protein associated to the oxygen evolving complex of photosynthetic organisms

Structural stability of the PsbQ protein of higher plant photosystem II.

scientific article published on November 2004

Structure and Thermal Stability of Photosystem II Reaction Centers Studied by Infrared Spectroscopy†

scientific article published in 1997

Structure and evolution of the extrinsic proteins that stabilize the oxygen-evolving engine

scientific article published on 4 November 2005

TET2 overexpression in chronic lymphocytic leukemia is unrelated to the presence of TET2 variations.

scientific article published on 18 February 2014

Ten simple rules for developing a short bioinformatics training course

scientific article

Ten simple rules for forming a scientific professional society

scientific article published on 23 March 2017

The 1.49 A resolution crystal structure of PsbQ from photosystem II of Spinacia oleracea reveals a PPII structure in the N-terminal region

scientific article published in July 2005

The 90S preribosome is a multimodular structure that is assembled through a hierarchical mechanism.

scientific article

The minimum information required for reporting a molecular interaction experiment (MIMIx).

scientific article published on August 2007

The single tryptophan of the PsbQ protein of photosystem II is at the end of a 4-alpha-helical bundle domain

scientific article published on October 2003

Threading structural model of the manganese-stabilizing protein PsbO reveals presence of two possible beta-sandwich domains

scientific article published in December 2001

Three-dimensional electron cryo-microscopy study of the extrinsic domains of the oxygen-evolving complex of spinach: assignment of the PsbO protein

scientific article published on 28 January 2002

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

scientific article published on 7 August 2006

Transcriptional repression of the tumor suppressor DRO1 by AIB1.

scientific article

Transcriptome analysis in prenatal IGF1-deficient mice identifies molecular pathways and target genes involved in distal lung differentiation

scientific article

Transcriptomic effects of Tet-on and mifepristone-inducible systems in mouse liver

scientific article

Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta

scientific article

Transcriptomic profile induced in bone marrow mesenchymal stromal cells after interaction with multiple myeloma cells: implications in myeloma progression and myeloma bone disease

scientific article published on September 2014

Two coupled β-carotene molecules protect P680 from photodamage in isolated Photosystem II reaction centres

Two sites of primary degradation of the D1-protein induced by acceptor or donor side photo-inhibition in photosystem II core complexes

article

Unique genetic profile of sporadic colorectal cancer liver metastasis versus primary tumors as defined by high-density single-nucleotide polymorphism arrays

Unraveling heterogeneous susceptibility and the evolution of breast cancer using a systems biology approach

scientific article

iAnn: an event sharing platform for the life sciences

scientific article published on 05 June 2013

miRNA cargo within exosome-like vesicle transfer influences metastatic bone colonization.

scientific article published on 6 February 2014

pH sensitivity of the redox state of cytochrome b559 may regulate its function as a protectant against donor and acceptor side photoinhibition

scientific article published on 01 November 1995

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