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Article
Mutational landscape of risk variants in comorbid depression and obesity: a next-generation sequencing approach
Major depression (MD) and obesity are complex genetic disorders that are frequently comorbid. However, the study of both diseases concurrently remains poorly addressed and therefore the underlying genetic mech...
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Article
Open AccessReal-world evidence with a retrospective cohort of 15,968 COVID-19 hospitalized patients suggests 21 new effective treatments
Despite the extensive vaccination campaigns in many countries, COVID-19 is still a major worldwide health problem because of its associated morbidity and mortality. Therefore, finding efficient treatments as f...
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Article
Open AccessRapid degeneration of iPSC-derived motor neurons lacking Gdap1 engages a mitochondrial-sustained innate immune response
Charcot-Marie-Tooth disease is a chronic hereditary motor and sensory polyneuropathy targeting Schwann cells and/or motor neurons. Its multifactorial and polygenic origin portrays a complex clinical phenotype ...
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Article
Open AccessMetabolic reprogramming by Acly inhibition using SB-204990 alters glucoregulation and modulates molecular mechanisms associated with aging
ATP-citrate lyase is a central integrator of cellular metabolism in the interface of protein, carbohydrate, and lipid metabolism. The physiological consequences as well as the molecular mechanisms orchestratin...
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Article
Open AccessProtein and functional isoform levels and genetic variants of the BAFF and APRIL pathway components in systemic lupus erythematosus
Systemic lupus erythematosus (SLE) is the prototype of an autoimmune disease. Belimumab, a monoclonal antibody targets BAFF, is the only biologic approved for SLE and active lupus nephritis. BAFF is a cytokine...
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Article
Open AccessA comprehensive database for integrated analysis of omics data in autoimmune diseases
Autoimmune diseases are heterogeneous pathologies with difficult diagnosis and few therapeutic options. In the last decade, several omics studies have provided significant insights into the molecular mechanism...
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Article
Open AccessGenome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development
Hirschsprung disease (HSCR, OMIM 142623) is a rare congenital disorder that results from a failure to fully colonize the gut by enteric precursor cells (EPCs) derived from the neural crest. Such incomplete gut...
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Article
Open AccessMechanistic modeling of the SARS-CoV-2 disease map
Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map. In this framework, the detailed activity of the human signaling circuits related to the viral in...
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Article
Open AccessDrug repurposing for COVID-19 using machine learning and mechanistic models of signal transduction circuits related to SARS-CoV-2 infection
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Article
Open AccessUsing mechanistic models for the clinical interpretation of complex genomic variation
The sustained generation of genomic data in the last decade has increased the knowledge on the causal mutations of a large number of diseases, especially for highly penetrant Mendelian diseases, typically caus...
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Article
Open AccessExploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models
In spite of the abundance of genomic data, predictive models that describe phenotypes as a function of gene expression or mutations are difficult to obtain because they are affected by the curse of dimensional...
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Article
Open AccessDifferential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models
In spite of the increasing availability of genomic and transcriptomic data, there is still a gap between the detection of perturbations in gene expression and the understanding of their contribution to the mol...
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Article
Open AccessModels of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome
Despite the progress in neuroblastoma therapies the mortality of high-risk patients is still high (40–50%) and the molecular basis of the disease remains poorly known. Recently, a mathematical model was used t...
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Article
Open AccessVISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy
The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the u...
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Article
Open AccessA new parallel pipeline for DNA methylation analysis of long reads datasets
DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of t...
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Article
Open AccessATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data
In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a use...
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Article
Open AccessThe pan-cancer pathological regulatory landscape
Dysregulation of the normal gene expression program is the cause of a broad range of diseases, including cancer. Detecting the specific perturbed regulators that have an effect on the generation and the develo...
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Article
Open AccessThe transcriptomics of an experimentally evolved plant-virus interaction
Models of plant-virus interaction assume that the ability of a virus to infect a host genotype depends on the matching between virulence and resistance genes. Recently, we evolved tobacco etch potyvirus (TEV) ...
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Article
Open AccessImproving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel
Next-generation sequencing (NGS) has overcome important limitations to the molecular diagnosis of Inherited Retinal Dystrophies (IRD) such as the high clinical and genetic heterogeneity and the overlap** phe...
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Article
Open AccessExome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease
Hirschsprung disease (HSCR; OMIM 142623) is a developmental disorder characterized by aganglionosis along variable lengths of the distal gastrointestinal tract, which results in intestinal obstruction. Interac...
