Giulia Babbi
A5043369975- Genomics and Rare Diseases
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Genetic factors in colorectal cancer
- RNA and protein synthesis mechanisms
- Genetics and Neurodevelopmental Disorders
- CRISPR and Genetic Engineering
- Cancer Genomics and Diagnostics
- Microbial Metabolic Engineering and Bioproduction
- Spaceflight effects on biology
- Effects of Radiation Exposure
- Glycosylation and Glycoproteins Research
- Genetic Associations and Epidemiology
- Radiation Therapy and Dosimetry
- Genetics, Bioinformatics, and Biomedical Research
- Endoplasmic Reticulum Stress and Disease
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Metabolism and Genetic Disorders
- Lysosomal Storage Disorders Research
- Pharmaceutical and Antibiotic Environmental Impacts
- Evolution and Genetic Dynamics
- Gut microbiota and health
University of Bologna
2016-2025
Biocom
2021-2023
Abstract Critical evaluation of computational tools for predicting variant effects is important considering their increased use in disease diagnosis and driving molecular discoveries. In the sixth edition Assessment Genome Interpretation (CAGI) challenge, a dataset 28 STK11 rare variants (27 missense, 1 single amino acid deletion), identified primary non-small cell lung cancer biopsies, was experimentally assayed to characterize methods from four participating teams five publicly available...
Abstract Background Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial genes (ARGs). However, there still lack knowledge on the dispersion ARGs in production system, including external environment. Results In present study, we longitudinally followed one swine farm located Italy from weaning phase slaughterhouse comprehensively assess diversity ARGs, their diffusion, and bacteria associated...
Abstract Regular, systematic, and independent assessment of computational tools used to predict the pathogenicity missense variants is necessary evaluate their clinical research utility suggest directions for future improvement. Here, as part sixth edition Critical Assessment Genome Interpretation (CAGI) challenge, we assess variant effect predictors (or impact predictors) on an evaluation dataset rare from disease-relevant databases. Our evaluates submitted CAGI6 Annotate-All-Missense...
Genetic investigations, boosted by modern sequencing techniques, allow dissecting the genetic component of different phenotypic traits. These efforts result in compilation lists genes related to diseases and show that an increasing number is associated with multiple genes. Investigating functional relations among same disease contributes highlighting molecular mechanisms pathogenesis. We present eDGAR, a database collecting organizing data on gene/disease associations as derived from OMIM,...
Abstract Background A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing genome-wide. To aid the interpretation prioritization of vast number detected, computational methods proliferating. Knowing which tools most effective remains unclear. evaluate performance methods, to encourage innovation method development, we designed Critical...
Abstract Regular, systematic, and independent assessments of computational tools that are used to predict the pathogenicity missense variants necessary evaluate their clinical research utility guide future improvements. The Critical Assessment Genome Interpretation (CAGI) conducts ongoing Annotate-All-Missense (Missense Marathon) challenge, in which variant effect predictors (also called impact predictors) evaluated on added disease-relevant databases following prediction submission...
Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is community experiment consisting genotype-phenotype prediction challenges; participants build models, undergo assessment, share key findings. For CAGI 4, three challenges involved exome-sequencing data: Crohn's disease, bipolar disorder, warfarin dosing. Previous included prior versions the...
Familial aggregation is a significant risk factor for the development of thyroid cancer and familial non‐medullary (FNMTC) accounts 5–7% all NMTC. Whole exome sequencing analysis in family affected by FNMTC with oncocytic features where our group previously identified predisposing locus on chromosome 19p13.2, revealed novel heterozygous mutation (c.400G > A, NM_012335; p.Gly134Ser) exon 5 MYO1F , mapping to linkage locus. In FRTL‐5 cell model stably expressing mutant p.Gly134Ser protein,...
Modern genomic techniques allow to associate several Mendelian human diseases single residue variations in different proteins. Molecular mechanisms explaining the relationship among genotype and phenotype are still under debate. Change of protein stability upon variation appears assume a particular relevance annotating whether substitution can or cannot be associated given disease. Thermodynamic properties proteins their disease related variants lacking. In present work, we take advantage...
Continued advances in variant effect prediction are necessary to demonstrate the ability of machine learning methods accurately determine clinical impact variants unknown significance (VUS). Towards this goal, ARSA Critical Assessment Genome Interpretation (CAGI) challenge was designed characterize progress by utilizing 219 experimentally assayed missense VUS
Body lesions in pigs are a common welfare concern, particularly during the weaning period. These can lead to pain, infection, and impaired mobility, resulting reduced growth performance increased mortality. Moreover, stress affect gut microbiota, immune response increase oxidative of piglets this transition It has been hypothesised that social body could contribute physiological piglets. The study aims evaluate impact due on microbial profile, response, status weaned Lesion score (LS) skin,...
A major obstacle faced by rare disease families is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years, and causal variants are identified in under 50%. Rare Genomes Project (RGP) direct-to-participant research study on the utility of genome sequencing (GS) for diagnosis gene discovery. Families consented sharing sequence phenotype data with researchers, allowing development Critical Assessment Genome Interpretation (CAGI) community challenge, placing...
Thermodynamic stability is a fundamental property shared by all proteins. Changes in due to mutation are widespread molecular mechanism genetic diseases. Methods for the prediction of mutation-induced change have typically been developed and evaluated on incomplete and/or biased data sets. As part Critical Assessment Genome Interpretation, we explored utility high-throughput variant profiling (VSP) assay as an alternative assessment computational methods state-of-the-art predictors against...
Poultry farms are hotspots for the development and spread of antibiotic resistance genes (ARGs), due to high stocking densities extensive use antibiotics, posing a threat contagion workers external environment. Here, we applied shotgun metagenome sequencing characterize gut microbiome resistome poultry, their households - also including microbiomes from internal farm environment – in three different Italy during complete rearing cycle. Our results highlighted relevant overlap among workers,...
Frataxin (FXN) is a highly conserved protein found in prokaryotes and eukaryotes that required for efficient regulation of cellular iron homeostasis. Experimental evidence associates amino acid substitutions the FXN to Friedreich Ataxia, neurodegenerative disorder. Recently, new thermodynamic experiments have been performed study impact somatic variations identified cancer tissues on stability. The Critical Assessment Genome Interpretation (CAGI) data provider at University Rome measured...
The NAGLU challenge of the fourth edition Critical Assessment Genome Interpretation experiment (CAGI4) in 2016, invited participants to predict impact variants unknown significance (VUS) on enzymatic activity lysosomal hydrolase α-N-acetylglucosaminidase (NAGLU). Deficiencies lead a rare, monogenic, recessive storage disorder, Sanfilippo syndrome type B (MPS IIIB). This attracted 17 submissions from 10 groups. We observed that top models were able missense mutations with Pearson's...
Testing for variation in BRCA1 and BRCA2 (commonly referred to as BRCA1/2), has emerged a standard clinical practice is helping countless women better understand manage their heritable risk of breast ovarian cancer. Yet the increased rate BRCA1/2 testing led an increasing number Variants Uncertain Significance (VUS), VUS discovery currently outpaces variant interpretation. Computational prediction key component interpretation pipeline. In CAGI5 ENIGMA Challenge, six teams submitted...
The Critical Assessment of Genome Interpretation (CAGI) is a global community experiment to objectively assess computational methods for predicting phenotypic impacts genomic variation. One the 2015–2016 competitions focused on influence mutations allosteric regulation human liver pyruvate kinase. More than 30 different researchers accessed challenge data. However, only four groups accepted challenge. Features used predictions ranged from evolutionary constraints, mutant site locations...
Modern sequencing technologies provide an unprecedented amount of data single-nucleotide variations occurring in coding regions and leading to changes the expressed protein sequences. A significant fraction these single-residue is linked disease onset collected public databases. In recent years, many scientific studies have been focusing on dissection salient features disease-related from different perspectives. this work, we complement previous analyses by updating a dataset proteins with...
Next-generation sequencing techniques provide an unprecedented characterisation of human Variants Unknown Significance (VUS). Single-residue variations are collected in public databases and associated to diseases phenotypes. However, for detailing at molecular level mechanisms involved the onset diseases, variants need structural functional annotation. Here we propose a new portal called Bioinformatic Sweeties, collecting resources ranging from protein annotation computational methods...