A5078591821- Genomics and Rare Diseases
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Protein Structure and Dynamics
- Genetic Associations and Epidemiology
- Genomic variations and chromosomal abnormalities
- Bioinformatics and Genomic Networks
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Genetics and Neurodevelopmental Disorders
- Enzyme Structure and Function
- Advanced biosensing and bioanalysis techniques
- Ion channel regulation and function
- Photoreceptor and optogenetics research
- RNA Interference and Gene Delivery
- MicroRNA in disease regulation
- Glycosylation and Glycoproteins Research
- Retinal Development and Disorders
- Cancer Genomics and Diagnostics
- Ubiquitin and proteasome pathways
- Insect and Pesticide Research
- Genetics, Bioinformatics, and Biomedical Research
- Receptor Mechanisms and Signaling
- Gene Regulatory Network Analysis
The University of Texas Health Science Center at Houston
2023-2025
Cleveland Clinic Lerner College of Medicine
2022-2024
University of Houston
2024
Cleveland Clinic
2023
University of Padua
2018-2021
Institut de Biologia Evolutiva
2011-2018
Universitat Pompeu Fabra
2010-2018
Consejo Superior de Investigaciones Científicas
2012
University of Bologna
2006-2009
Polytechnic University of Bari
2009
Predicting the effect of single point variations on protein stability constitutes a crucial step toward understanding relationship between structure and function. To this end, several methods have been developed to predict changes in Gibbs free energy unfolding (∆∆G) wild type variant proteins, using sequence information. Most available however do not exhibit anti-symmetric prediction property, which guarantees that predicted ∆∆G value for variation is exact opposite reverse variation, i.e.,...
Abstract Estimating the functional effect of single amino acid variants in proteins is fundamental for predicting change thermodynamic stability, measured as difference Gibbs free energy unfolding, between wild-type and variant protein (ΔΔG). Here, we present web-server DDGun method, which was previously developed ΔΔG prediction upon variants. an untrained method based on basic features derived from evolutionary information. It antisymmetric, it predicts opposite values direct (A → B)...
Copy number variants (CNV) are established risk factors for neurodevelopmental disorders with seizures or epilepsy. With the hypothesis that seizure share genetic factors, we pooled CNV data from 10,590 individuals disorders, 16,109 clinically validated epilepsy, and 492,324 population controls identified 25 genome-wide significant loci, 22 of which novel such as deletions at 1p36.33, 1q44, 2p21-p16.3, 3q29, 8p23.3-p23.2, 9p24.3, 10q26.3, 15q11.2, 15q12-q13.1, 16p12.2, 17q21.31, duplications...
In this work the feasibility of near infrared spectroscopy was evaluated combined with chemometric approaches, as a tool for botanical origin prediction 119 honey samples. Four varieties related to polyfloral, acacia, chestnut, and linden were first characterized by their physical–chemical parameters then analyzed in triplicate using spectrophotometer equipped an optical path gold reflector. Three different classifiers built on distinct multivariate machine learning approaches...
SCN1A variants cause a range of epilepsy syndromes, including Dravet syndrome, leading to early cognitive and functional impairment. Despite advances in medical management, drug-resistant remains common. Vagal nerve stimulation (VNS) has been suggested reducing seizure frequency these patients but there is lack long-term follow-up, quantitative analysis that corrected for confounding factors such as antiseizure medications (ASMs) the impact VNS settings on response. This two-center,...
Introduction Pasteurella multocida is a key bacterial agent involved in most respiratory disorders rabbits. The objective of this study was to evaluate the risk selecting strains resistant enrofloxacin (ENRO) food producing rabbits treated with ENRO via drinking water, according standard husbandry practices. Indeed, despite EU community guidelines recommend prudent use antibiotics and promote new strategies prevent diseases, antimicrobial therapy remains primary approach for pasteurellosis...
Background/Objectives: Mast cell tumors (MCTs) are the second most common malignant neoplasms in dogs. Histopathological grading and clinical staging main tools for estimating biological behavior disease extent; thus, both essential therapeutic decision-making prognostication. However, of MCTs dogs is variable, it sometimes deviates from expectations. In a previous study, we identified 12 transcripts whose expression profile allowed clear distinction between Kiupel low-grade high-grade...
Abstract Motivation Accurate prediction of protein stability changes upon single-site variations (ΔΔG) is important for design, as well our understanding the mechanisms genetic diseases. The performance high-throughput computational methods to this end evaluated mostly based on Pearson correlation coefficient between predicted and observed data, assuming that upper bound would be 1 (perfect correlation). However, these predictors can limited by distribution noise experimental data. Here we...
Clinically identified genetic variants in ion channels can be benign or cause disease by increasing decreasing the protein function. As a consequence, therapeutic decision-making is challenging without molecular testing of each variant. Our biophysical knowledge ion-channel structures and function just emerging, it currently not well understood which amino acid residues when mutated. We sought to systematically identify biological properties associated with variant pathogenicity across all...
Disease resistance represents a key trait for breeding programs in aquaculture species. Here we re-analysed 2bRAD sequence data from two experimental challenges of gilthead sea bream with Photobacterium damsealae piscicida. Using high quality reference genome, carried out variant calling and imputation Beagle to obtain large set SNPs (80,744). This allowed the identification eight novel QTLs photobacteriosis across different chromosomes revealed highly polygenic genetic architecture....
Pathogenic copy-number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign part natural variation in human genomes. CNV pathogenicity classification, genotype-phenotype analyses, therapeutic target identification challenging time-consuming tasks that require the integration analysis information from multiple scattered sources by experts.Here, we introduce CNV-ClinViewer, an open-source web application for clinical evaluation visual...
Abstract Genetic variants in the SLC6A1 gene can cause a broad phenotypic disease spectrum by altering protein function. Thus, systematically curated clinically relevant genotype-phenotype associations are needed to understand mechanism and improve therapeutic decision-making. We aggregated genetic clinical data from 172 individuals with likely pathogenic/pathogenic (lp/p) functional for 184 (14.1% lp/p). Clinical were available subset of 126 individuals. explored potential variant positions...
A basic question in protein science is to which extent mutations affect thermostability. This knowledge would be particularly relevant for engineering thermostable enzymes. In several experimental approaches, this issue has been serendipitously addressed. It therefore convenient providing a computational method that predicts when given mutant more than its corresponding wild-type.We present new based on support vector machines able predict whether set of (including insertion and deletions)...
Vertebrate visual phototransduction is perhaps the most well-studied G-protein signaling pathway. A wealth of available biochemical and electrophysiological data has resulted in a rich history mathematical modeling system. However, while comprehensive models have relied upon amphibian data, modern research typically employs mammalian species, particularly mice, which exhibit significantly faster dynamics. In this work, we present an adaptation previously published, model that can produce...
N-glycosylation is one of the most important forms protein modification, serving key biological functions in multicellular organisms. N-glycans at cell surface mediate interaction between cells and surrounding matrix may act as pathogen receptors, making genes responsible for their synthesis good candidates to show signatures adaptation different environments. Here, we study forces that shaped evolution involved during divergence primates within framework functional network. We have found...
Visual perception is initiated in the photoreceptor cells of retina via phototransduction system. This system has shown marked evolution during mammalian divergence such complex attributes as activation time and recovery time. We have performed a molecular evolutionary analysis proteins involved order to unravel how action natural selection been distributed throughout evolve traits.We found selective pressures be non-randomly according both simple protein classification scheme...
Aflatoxin B1 (AFB1) induces lipid peroxidation and mortality in bovine foetal hepatocyte-derived cells (BFH12), with underlying transcriptional perturbations associated mainly cancer, cellular damage, inflammation, bioactivation, detoxification pathways. In this cell line, curcumin resveratrol have proven to be effective mitigating AFB1-induced toxicity. paper, we preliminarily assessed the potential anti-AFB1 activity of a natural polyphenol, quercetin (QUE), BFH12 cells. To end, primarily...
Pathogens have represented an important selective force during the adaptation of modern human populations to changing social and other environmental conditions. The evolution immune system has therefore been influenced by these pressures. Genomic scans revealed that is one functions enriched with genes under adaptive selection.Here, we describe how innate responded challenges, through analysis resequencing data for 132 immunity in two populations. Results are interpreted context functional...
Abstract Background Asparagine N-Glycosylation is one of the most important forms protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding proteins synthesized secretory pathway, and a downstream to give variability trans-membrane proteins, involved adaptation environment innate immunity. Here we analyze nucleotide genes this human populations, identifying which show greater...
Abstract Background Phototransduction in vertebrate photoreceptor cells represents a paradigm of signaling pathways mediated by G-protein-coupled receptors (GPCRs), which share common modules linking the initiation cascade to final response cell. In this work, we focused on recovery phase visual photoresponse, is comprised several interacting mechanisms. Results We employed current biochemical knowledge investigate mechanisms comprehensive model phototransduction pathway. particular, have...
Relationships between evolutionary rates and gene properties on a genomic, functional, pathway, or system level are being explored to unravel the principles of process. In particular, functional network have been analyzed recognize constraints they may impose fate genes. Here we took as case study core metabolic in human erythrocytes relationship its genes flux distribution throughout it. We found that correlates with ratio nonsynonymous synonymous substitution rates. Genes encoding enzymes...
Recombination varies greatly among species, as illustrated by the poor conservation of recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand evolution recombination. Here, we analyze its recent in humans. We calculated rates adjacent pairs 636,933 common single-nucleotide polymorphism loci 28 worldwide human populations analyzed them relation genetic distances populations. found a strong highly significant correlation...