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View article: Alterations in peroxisome-mitochondria interplay in skeletal muscle accelerate muscle dysfunction
Alterations in peroxisome-mitochondria interplay in skeletal muscle accelerate muscle dysfunction Open
Skeletal muscles, which constitute 40-50% of body mass, regulate whole-body energy expenditure and glucose and lipid metabolism. Peroxisomes are dynamic organelles that play a crucial role in lipid metabolism and clearance of reactive oxyg…
View article: ADSL deficiency is a secondary mitochondrial disease affecting organelle homeostasis and ERK2/AKT signaling in a linear genotype-phenotype relation
ADSL deficiency is a secondary mitochondrial disease affecting organelle homeostasis and ERK2/AKT signaling in a linear genotype-phenotype relation Open
Adenylosuccinate lyase deficiency (ADSLd) is a rare autosomal recessive purine metabolism disorder with several clinical manifestations. While toxic substrate accumulation is a known hallmark, no additional molecular mechanisms have been e…
View article: Differentially expressed transcripts associated with depressive symptoms during pregnancy and postpartum
Differentially expressed transcripts associated with depressive symptoms during pregnancy and postpartum Open
View article: Author response: Ezrin defines TSC complex activation at endosomal compartments through EGFR–AKT signaling
Author response: Ezrin defines TSC complex activation at endosomal compartments through EGFR–AKT signaling Open
View article: Ezrin defines TSC complex activation at endosomal compartments through EGFR–AKT signaling
Ezrin defines TSC complex activation at endosomal compartments through EGFR–AKT signaling Open
Endosomes have emerged as major signaling hubs where different internalized ligand–receptor complexes are integrated and the outcome of signaling pathways are organized to regulate the strength and specificity of signal transduction events…
View article: Prion protein promotes copper toxicity in Wilson disease
Prion protein promotes copper toxicity in Wilson disease Open
Copper (Cu) is a vitally important micronutrient, whose balance between essential and toxic levels requires a tightly regulated network of proteins. Dysfunction in key components of this network leads to the disruption of Cu homeostasis, r…
View article: Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling
Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling Open
Endosomes have emerged as major signaling hubs where different internalized ligand-receptor complexes are integrated and the outcome of signaling pathways are organized to regulate the strength and specificity of signal transduction events…
View article: Author response: Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling
Author response: Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling Open
View article: Ezrin defines TSC complex activation at endosomal compartments through EGFR–AKT signaling
Ezrin defines TSC complex activation at endosomal compartments through EGFR–AKT signaling Open
Endosomes have emerged as major signaling hubs where different internalized ligand–receptor complexes are integrated and the outcome of signaling pathways are organized to regulate the strength and specificity of signal transduction events…
View article: Ezrin defines TSC1 activation at endosomal compartments through EGFR-AKT signaling
Ezrin defines TSC1 activation at endosomal compartments through EGFR-AKT signaling Open
Endosomes have emerged as major signaling hubs where different internalized ligand-receptor complexes are integrated and the outcome of signaling pathways are organized to regulate the strength and specificity of signal transduction events…
View article: Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling
Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling Open
Endosomes have emerged as major signaling hubs where different internalized ligand-receptor complexes are integrated and the outcome of signaling pathways are organized to regulate the strength and specificity of signal transduction events…
View article: ALTERATIONS IN PEROXISOMAL-MITOCHONDRIAL INTERPLAY IN SKELETAL MUSCLE ACCELERATES MUSCLE DYSFUNCTION
ALTERATIONS IN PEROXISOMAL-MITOCHONDRIAL INTERPLAY IN SKELETAL MUSCLE ACCELERATES MUSCLE DYSFUNCTION Open
Whole-body energy expenditure, as well as glucose and lipid metabolism, are regulated by skeletal muscles, which account for 40-50% of human body mass. Peroxisomes are dynamic organelles that play a crucial role in lipid metabolism and cle…
View article: Transcriptomic signatures of peripartum depression trajectories
Transcriptomic signatures of peripartum depression trajectories Open
View article: Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data Open
Background Inherited retinal diseases (IRD) are genetically heterogeneous disorders that cause the dysfunction or loss of photoreceptor cells and ultimately lead to blindness. To date, next-generation sequencing procedures fail to detect p…
View article: Additional file 1 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
Additional file 1 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data Open
Additional file 1: Supplementary Dataset File 1. List of the IRD genes analyzed in this study.
View article: Additional file 4 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
Additional file 4 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data Open
Additional file 4: Supplementary Dataset File 4. Overall contribution to gene expression of annotated and novel transcripts with more than 1 median TPM for each IRD gene.
View article: Additional file 2 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
Additional file 2 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data Open
Additional file 2: Supplementary Dataset File 2. List of all IRD transcripts with more than 1 median TPM.
View article: Additional file 5 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
Additional file 5 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data Open
Additional file 5: Supplementary Dataset File 5. Annotated transcripts with a) more than 1 median TPM and b) relative contribution to gene expression greater than 5%.
View article: Additional file 6 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
Additional file 6 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data Open
Additional file 6:Supplementary Dataset File 6. Putative novel IRD transcripts with a) more than 1 median TPM and b) relative contribution to overall expression of the corresponding gene greater than 5%.
View article: Additional file 3 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
Additional file 3 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data Open
Additional file 3: Supplementary Dataset File 3. Summary of transcripts identified for each IRD gene.
View article: ADViSELipidomics: a workflow for analyzing lipidomics data
ADViSELipidomics: a workflow for analyzing lipidomics data Open
Summary ADViSELipidomics is a novel Shiny app for preprocessing, analyzing and visualizing lipidomics data. It handles the outputs from LipidSearch and LIQUID for lipid identification and quantification and the data from the Metabolomics W…
View article: Performance of Web tools for predicting changes in protein stability caused by mutations
Performance of Web tools for predicting changes in protein stability caused by mutations Open
Background Despite decades on developing dedicated Web tools, it is still difficult to predict correctly the changes of the thermodynamic stability of proteins caused by mutations. Here, we assessed the reliability of five recently develop…
View article: GeenaR: A Web Tool for Reproducible MALDI-TOF Analysis
GeenaR: A Web Tool for Reproducible MALDI-TOF Analysis Open
Mass spectrometry is a widely applied technology with a strong impact in the proteomics field. MALDI-TOF is a combined technology in mass spectrometry with many applications in characterizing biological samples from different sources, such…
View article: Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue
Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue Open
Non-coding RNA transcripts originating from Ultraconserved Regions (UCRs) have tissue specific expression and play relevant roles in the pathophysiology of multiple cancer types. Among them, we recently identified and characterized the ult…
View article: Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue
Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue Open
Non-coding RNA transcripts originating from Ultraconserved Regions (UCRs) have tissue-specific expression and play relevant roles in the pathophysiology of multiple cancer types. Among them, we recently identified and characterized the ult…
View article: Additional file 13 of Performance of Web tools for predicting changes in protein stability caused by mutations
Additional file 13 of Performance of Web tools for predicting changes in protein stability caused by mutations Open
Additional file 13: File S1. Reference monomeric and multimeric datasets. Data sheets report the original PON-tstab dataset, the selection of proteins for the full dataset, the full datasets (monomeric and multimeric proteins) with predict…
View article: "Integration of Bioinformatics Approaches and Experimental Multi-Omics Studies to Support Personalized Medicine"
"Integration of Bioinformatics Approaches and Experimental Multi-Omics Studies to Support Personalized Medicine" Open
View article: Reusing microarray clinical data from a complex disease with bioinformatics tool
Reusing microarray clinical data from a complex disease with bioinformatics tool Open
Clinical bioinformatics, translational bioinformatics and personalised medicine are connected by the common task of analysing and integrating clinical data and results, in order to find important biomarkers related to pathologies and facil…
View article: Reusing microarray clinical data from a complex disease with bioinformatics tool
Reusing microarray clinical data from a complex disease with bioinformatics tool Open
Clinical bioinformatics, translational bioinformatics and personalised medicine are connected by the common task of analysing and integrating clinical data and results, in order to find important biomarkers related to pathologies and facil…
View article: A Gene Set Enrichment Analysis of multiomic celiac disease data
A Gene Set Enrichment Analysis of multiomic celiac disease data Open
Celiac disease is a chronic condition, which can be described as inflammatory and autoimmune. The well-known treatment is a lifelong gluten-free diet, but it can be not totally effective for a high percentage of the patients. The aim of th…