A5041332204- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- RNA Research and Splicing
- Amyloidosis: Diagnosis, Treatment, Outcomes
- DNA Repair Mechanisms
- RNA and protein synthesis mechanisms
- Gene Regulatory Network Analysis
- Glioma Diagnosis and Treatment
- Autism Spectrum Disorder Research
- Systemic Lupus Erythematosus Research
- Genetic and Kidney Cyst Diseases
- Testicular diseases and treatments
- Alzheimer's disease research and treatments
- Gut microbiota and health
- Prion Diseases and Protein Misfolding
- Rheumatoid Arthritis Research and Therapies
- Cancer-related molecular mechanisms research
- Urologic and reproductive health conditions
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Cancer-related Molecular Pathways
- Myeloproliferative Neoplasms: Diagnosis and Treatment
Novartis (Switzerland)
2021-2024
Institute of Biomedical Technologies
2017-2023
National Research Council
2018-2023
Novartis Institutes for BioMedical Research
2023
University of Pavia
2017-2020
National Academies of Sciences, Engineering, and Medicine
2018-2019
Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of flux along open reading frames (ORFs) are not fully understood. Combining measurements rate footprinting data, we here inferred translation initiation elongation rates for over a 1,000 ORFs in exponentially growing wild-type yeast cells. We found that amino acid composition synthesized proteins is as important determinant parameters related to codon...
Recurrently mutated genes and chromosomal abnormalities have been identified in myelodysplastic syndromes (MDS). We aim to integrate these genomic features into disease classification prognostication.We retrospectively enrolled 2,043 patients. Using Bayesian networks Dirichlet processes, we combined mutations 47 with cytogenetic identify genetic associations subgroups. Random-effects Cox proportional hazards multistate modeling was used for developing prognostic models. An independent...
Abstract The Werner syndrome RecQ helicase WRN was identified as a synthetic lethal target in cancer cells with microsatellite instability (MSI) by several genetic screens 1–6 . Despite advances treatment immune checkpoint inhibitors 7–10 , there is an unmet need the of MSI cancers 11–14 Here we report structural, biochemical, cellular and pharmacological characterization clinical-stage inhibitor HRO761, which through innovative hit-finding lead-optimization strategy. HRO761 potent,...
Intestinal microorganisms impact health by maintaining gut homeostasis and shaping the host immunity, while dysbiosis associates with many conditions, including autism, a complex neurodevelopmental disorder multifactorial aetiology. In correlates symptom severity is characterised reduced bacterial variability diminished beneficial commensal relationship. Microbiota can influence expression of microRNAs that, in turn, regulate growth intestinal bacteria means bidirectional host-gut microbiota...
Abstract The complex web of macromolecular interactions occurring within cells—the interactome—is the backbone an increasing number studies, but a clear consensus on exact structure this network is still lacking. Different genome-scale maps human interactome have been obtained through several experimental techniques and functional analyses. Moreover, these can be enriched literature-mining approaches, different combinations various ‘source’ databases used in literature. It therefore unclear...
Abstract The RecQ DNA helicase WRN was identified as a synthetic lethal target in tumors with microsatellite instability (MSI) by several genetic screens. Despite recent advances the treatment of MSI immune checkpoint inhibitors, significant proportion patients still fails to respond or relapses after single agent anti-PD1 combination plus anti-CTLA4 treatments. We present biochemical, cellular and pharmacological characterization first potent selective inhibitor, HRO761. show that HRO761 is...
Recent comparative studies have brought to our attention how somatic mutation detection from next-generation sequencing data is still an open issue in bioinformatics, because different pipelines result a low consensus. In this context, it suggested integrate results multiple calling tools, but operation not trivial and the burden of merging, comparing, filtering explaining demands appropriate software. We developed isma (integrative analysis), R package for integrative analysis mutations...
Current studies suggest that autism spectrum disorders (ASDs) may be caused by many genetic factors. In fact, collectively considering multiple aimed at characterizing the basic pathophysiology of ASDs, a large number genes has been proposed. Addressing problem molecular data interpretation using gene networks helps to explain heterogeneity in terms shared pathways. Besides, integrative analysis omics emerged as an approach provide more comprehensive view disease. this work, we carry out...
Multi-omics approaches offer the opportunity to reconstruct a more complete picture of molecular events associated with human diseases, but pose challenges in data analysis. Network-based methods for analysis multi-omics leverage complex web macromolecular interactions occurring within cells extract significant patterns alterations. Existing network-based typically address specific combinations omics and are limited terms number layers that can be jointly analysed. In this study, we...
Abstract Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of flux along open reading frames (ORFs) are not fully understood. Combining measurements rate footprinting data, we here inferred translation initiation elongation rates for over a thousand ORFs in exponentially-growing wildtype yeast cells. We found that amino acid composition synthesized proteins is as important determinant parameters related to...
Abstract The amyloidoses constitute a group of diseases occurring in humans and animals that are characterized by abnormal deposits aggregated proteins organs, affecting their structure function. In the Abyssinian cat breed, familial form renal amyloidosis has been described. this study, multi-omics analyses were applied integrated to explore some aspects unknown pathogenetic processes cats. Whole-genome sequences two affected Abyssinians 195 controls other breeds (part 99 Lives initiative)...
ABSTRACT Copy number variations (CNVs) are genomic events where the of copies a particular gene varies from cell to cell. Cancer cells associated with somatic CNV changes resulting in amplifications and deletions. However, short single-cell whole-genome sequencing, it is difficult detect quantify single cells. In contrast, rapid development RNA sequencing (scRNA-seq) technologies has enabled easy acquisition expression data. this work, we employ three methods infer scRNA-seq data provide...
Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which one main obstacles for development effective cancer treatments. Such tumors typically contain a mixture cells with aberrant genomic and transcriptomic profiles affecting specific sub-populations that might have pivotal role in progression, whose identification eludes bulk RNA-sequencing approaches. We present scMuffin, an R package enables characterization cell identity...
Network Diffusion has been proposed in several applications, thanks to its ability of amplifying biological signals and prioritizing genes that may be associated with a disease. Not surprising, the success on “single layer” led first approaches for joint analysis multi-omics data. Here, we review integrative methods based have aims (e.g. patient stratification, module detection, function prediction). We used analyse, context physical functional protein-protein interactions, genetic...
Network Diffusion has been proposed in several applications, thanks to its ability of amplifying biological signals and prioritizing genes that may be associated with a disease. Not surprising, the success on “single layer” led first approaches for joint analysis multi-omics data. Here, we review integrative methods based have aims (e.g. patient stratification, module detection, function prediction). We used analyse, context physical functional protein-protein interactions, genetic...
Abstract INTRODUCTION Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which one main obstacles for development effective cancer treatments. Such tumors typically contain a mixture cells with aberrant genomic and transcriptomic profiles affecting specific sub-populations that might have pivotal role in progression, whose identification eludes bulk RNA-sequencing approaches. We presentscMuffin, an R package enables...
Abstract Alternative splicing is critical for human gene expression regulation and plays an important role in multiple diseases. In this context, RNA sequencing has emerged as powerful approach to detect alternative events. parallel, fast alignment-free methods have a viable quantify transcript level abundance from RNAseq data. However, the ability differential events dependent on annotation of reference provided by user. Here, we introduce new transcriptome aware events, TRAWLING, which...