A5070887609- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Circular RNAs in diseases
- RNA modifications and cancer
- Ovarian cancer diagnosis and treatment
- RNA Research and Splicing
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Mitochondrial Function and Pathology
- Physiological and biochemical adaptations
- Aquaculture Nutrition and Growth
- Autophagy in Disease and Therapy
- Gene Regulatory Network Analysis
- Neurobiology and Insect Physiology Research
- Histone Deacetylase Inhibitors Research
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Marine Bivalve and Aquaculture Studies
- Aquaculture disease management and microbiota
- Genomics and Chromatin Dynamics
- Spaceflight effects on biology
- CRISPR and Genetic Engineering
- Medicinal Plant Pharmacodynamics Research
- Plant Genetic and Mutation Studies
- ATP Synthase and ATPases Research
University of Padua
2016-2025
University of Turin
2010-2025
Azienda Ospedaliera Citta' della Salute e della Scienza di Torino
2022
University of California, Berkeley
2021
Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione
2018
Mario Negri Institute for Pharmacological Research
2013
University of Milano-Bicocca
2013
University of Oxford
2012
University of Bologna
2010
Pontifícia Universidade Católica de Minas Gerais
2005
Mitochondrial fatty acid oxidation (FAO) is essential for hematopoietic stem cell (HSC) self-renewal; however, the mechanism by which mitochondrial metabolism controls HSC fate remains unknown. Here, we show that within lineage, HSCs have largest NADPH pools, are required proper and homeostasis. Bioinformatic analysis of transcriptome, biochemical assays, genetic inactivation FAO all indicate FAO-generated fuels cholesterol synthesis in HSCs. Interference with disturbs segregation toward...
Gene set analysis is moving towards considering pathway topology as a crucial feature. Pathway elements are complex entities such protein complexes, gene family members and chemical compounds. The conversion of to gene/protein networks (where nodes simple element like gene/protein) critical challenging task that enables topology-based analyses.Unfortunately, currently available R/Bioconductor packages provide only from single databases. They do not propagate signals through compounds...
MAGIA (miRNA and genes integrated analysis) is a novel web tool for the integrative analysis of target predictions, miRNA gene expression data. divided into two parts: query section allows user to retrieve browse updated predictions computed with number different algorithms (PITA, miRanda Target Scan) Boolean combinations thereof. The comprises multistep procedure (i) direct integration through functional measures (parametric non-parametric correlation indexes, variational Bayesian model,...
MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It dedicated to integrated analysis in silico target prediction, microRNA (miRNA) gene expression data for reconstruction post-transcriptional regulatory networks. miRNAs are fundamental regulators several key biological pathological processes. As act prevalently through degradation, their profiles expected be inversely correlated those genes. Low specificity prediction algorithms makes...
Gene set analysis using biological pathways has become a widely used statistical approach for gene expression analysis. A pathway can be represented through graph where genes and their interactions are, respectively, nodes edges of the graph. From point view only some portions are expected to altered; however, few methods topology have been proposed none them tries identify signal paths, within pathway, mostly involved in problem. Here, we present novel algorithm clipper, that fill this gap....
Abstract Cisplatin (CDDP) is commonly used to treat a multitude of tumors including sarcomas, ovarian and cervical cancers. Despite recent investigations allowed improve chemotherapy effectiveness, the molecular mechanisms underlying development CDDP resistance remain major goal in cancer research. Here, we show that mitochondrial morphology autophagy are altered different resistant cell lines. In osteosarcoma carcinoma, mitochondria fragmented closely juxtaposed endoplasmic reticulum; rates...
Ionizing radiation (IR) can be extremely harmful for human cells since an improper DNA-damage response (DDR) to IR contribute carcinogenesis initiation. Perturbations in DDR pathway originate from alteration the functionality of microRNA-mediated gene regulation, being microRNAs (miRNAs) small noncoding RNA that act as post-transcriptional regulators expression. In this study we gained insight into role miRNAs regulation under microgravity, a condition weightlessness experienced by...
Abstract Motivation: Inferring large transcriptional networks using mutual information has been shown to be effective in several experimental setup. Unfortunately, this approach two main drawbacks: (i) estimators are prone biases and (ii) available software still computational costs when processing thousand of genes. Results: Here, we present parmigene (PARallel Mutual Information estimation for GEne NEtwork reconstruction), an R package that tries fill the above gaps. It implements a...
Purpose: Stage I epithelial ovarian cancer (EOC) represents about 10% of all EOCs and is characterized by good prognosis with fewer than 20% patients relapsing. As it occurs less frequently advanced-stage EOC, its molecular features have not been thoroughly investigated. We demonstrated that in stage EOC miR-200c-3p can predict patients' outcome. In the present study, we analyzed expression long non-coding RNAs (lncRNA) to enable potential definition a transcriptional signature prognostic...
Epithelial ovarian cancer (EOC) is one of the most lethal gynecologic diseases, with survival rate virtually unchanged for past 30 years. EOC comprises different histotypes molecular and clinical heterogeneity, but up till now present gold standard platinum-based treatment has been conducted without any patient stratification. The aim study to generate microRNA (miRNA) profiles characteristic each stage I histotype, identify subtype-specific biomarkers improve our understanding underlying...
Graphite web is a novel tool for pathway analyses and network visualization gene expression data of both microarray RNA-seq experiments. Several have been proposed either in the univariate or global multivariate context to tackle complexity interpretation results. These methods can be further divided into 'topological' 'non-topological' according their ability gain power from topology. Biological pathways are, fact, not only lists but represented through where genes connections respectively,...
Background Polar environments are characterized by extreme seasonal changes in day length, light intensity and spectrum, the extent of sea ice during winter, food availability. A key species Southern Ocean ecosystem, Antarctic krill (Euphausia superba) has evolved rhythmic physiological behavioral mechanisms to adapt daily changes. The molecular organization clockwork underlying these biological rhythms is, nevertheless, still only partially understood. Methodology/Principal Findings genome...
// Enrica Calura 1,* , Andrea Bisognin 2,* Martina Manzoni 3 Katia Todoerti 4 Elisa Taiana Gabriele Sales 1 Gareth J. Morgan 5 Giovanni Tonon 6 Nicola Amodio 7 Pierfrancesco Tassone Antonino Neri Luca Agnelli 3,** Chiara Romualdi 1,** and Stefania Bortoluzzi 2,** Department of Biology, University Padua, Italy 2 Molecular Medicine, Clinical Sciences Community Health, Milan, Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Laboratory Pre-Clinical Translational...
Antarctic krill (Euphausia superba) is a key species in Southern Ocean ecosystem where it plays central role the food web. Available information supports existence of an endogenous timing system enabling to synchronize metabolism and behavior with environment characterized by extreme seasonal changes terms day length, availability, surface ice extent. A screening our transcriptome database "KrillDB" allowed us identify putative orthologues 20 circadian clock components. Mapping conserved...
Dysregulation of miRNAs expression plays a critical role in the pathogenesis genetic, multifactorial disorders and human cancers. We exploited sequence, genomic information to investigate two main aspects post-transcriptional regulation miRNA biogenesis, namely strand selection relationships between intragenic host genes. considered profiles, measured five sizeable microarray datasets, including samples from different normal cell types tissues, as well tumours disease states. First, study...
Abstract The production rate of gene expression data is nothing less than astounding. However, with the benefit hindsight we can assert that, since completely ignored non-coding part transcriptome, spent last decade to study cell mechanisms having few in our hands. In this scenario, microRNAs, which are key post-trascriptional regulators, deserve special attention. Given state knowledge about their biogenesis, action and numerous experimentally validated target genes, miRNAs also gradually...
Abstract Motivation Metabolomics is an emerging ‘omics’ science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for visualization, exploration analysis metabolomic data within context metabolic pathways: some them became rapidly obsolete are no longer supported, others based on a single database. A systematic collection existing annotations has potential considerably boosting investigation contextualization...
Candida auris is an emerging healthcare-associated infection that can easily cause dissemination in hospitals through colonizing the skin and contaminating environmental surfaces, especially Intensive Care Units (ICU). Difficulties with identification of this organism, uncertainty about routes transmission antifungals resistance have impacted significantly outbreak detection management. Here, we describe our experience colonization/infection C. among critically ill patients, admitted to a...
DNA recovered from herbarium specimens represents a vital asset in botanical research, playing pivotal role unravelling the evolution, diversity, and ecological dynamics of plants. Despite its importance, challenges such as fragmented insufficient sequencing yields render molecular data retrieval high-risk costly endeavour involving use non-replaceable specimens. Here, we propose framework based on Artificial Intelligence (AI) to forecast success genomic extraction suitable for samples. Our...
This project develops a system for malaria classification using the Vision Transformer architecture on cellular tissue microscopy images. The implementation aims to assist in medical diagnosis by providing efficient and accurate information, with potential contribute control of endemic diseases. utilizes models from vit-pytorch library, including Transformer, Patch Merger, Small Datasets. Datasets achieved highest accuracy 98.97 an image size [150,150].