A5032127010- Constraint Satisfaction and Optimization
- Data Management and Algorithms
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Semantic Web and Ontologies
- Biomedical Text Mining and Ontologies
- Gene Regulatory Network Analysis
- Rough Sets and Fuzzy Logic
- Advanced Proteomics Techniques and Applications
- Machine Learning in Bioinformatics
- Microbial Metabolic Engineering and Bioproduction
- AI-based Problem Solving and Planning
- Redox biology and oxidative stress
- Gene expression and cancer classification
- Logic, Reasoning, and Knowledge
- RNA and protein synthesis mechanisms
- Microbial Natural Products and Biosynthesis
- Molecular Biology Techniques and Applications
- Sports Performance and Training
- Microbial Community Ecology and Physiology
- Exercise and Physiological Responses
- Algorithms and Data Compression
- Mass Spectrometry Techniques and Applications
- Plant responses to water stress
- Vehicle Routing Optimization Methods
University of Padua
2012-2025
Fondazione Edmund Mach
2014
Veneto Institute of Molecular Medicine
2014
Centro di Ricerca in Matematica Pura ed Applicata
2007
Engineering (Italy)
2006
Automated annotation of protein function is challenging. As the number sequenced genomes rapidly grows, overwhelming majority products can only be annotated computationally. If computational predictions are to relied upon, it crucial that accuracy these methods high. Here we report results from first large-scale community-based critical assessment (CAFA) experiment. Fifty-four representing state art for prediction were evaluated on a target set 866 proteins 11 organisms. Two findings stand...
A major bottleneck in our understanding of the molecular underpinnings life is assignment function to proteins. While experiments provide most reliable annotation proteins, their relatively low throughput and restricted purview have led an increasing role for computational prediction. However, assessing methods protein prediction tracking progress field remain challenging.We conducted second critical assessment functional (CAFA), a timed challenge assess that automatically assign function....
Predicting protein function has become increasingly demanding in the era of next generation sequencing technology. The task to assign a curator-reviewed every single sequence is impracticable. Bioinformatics tools, easy use and able provide automatic reliable annotations at genomic scale, are necessary urgent. In this scenario, Gene Ontology provided means standardize annotation classification with structured vocabulary which can be easily exploited by computational methods. Argot2 web-based...
Targeted amplicon sequencing of the 16S ribosomal RNA gene is one key tools for studying microbial diversity. The accuracy this approach strongly depends on choice primer pairs and, in particular, balance between efficiency, specificity and sensitivity amplification different bacterial sequences contained a sample. There thus need computational methods to design optimal primers able take into account knowledge provided by new technologies.We propose here method optimizing sets, based...
Amyotrophic lateral sclerosis (ALS) is characterized by the degeneration of both upper and lower motor neurons (UMNs LMNs). Recognizing involvement UMNs challenging because absence reliable biomarkers beyond clinical evaluation. To identify a marker UMN damage in cohort patients with ALS referring to Motor Neuron Disease Clinic University Hospital Padova. We retrospectively evaluated records 79 compared results various investigations, including motor-evoked potentials (MEPs), positron...
Clear evidence has highlighted a role for hormones in the plant stress response, including salt stress. Interplay and cross-talk among different hormonal pathways are of vital importance abiotic tolerance. A genome-wide transcriptional analysis was performed on leaves roots three-day treated untreated plants two Italian rice varieties, Baldo Vialone Nano, which differ sensitivity. Genes correlated with were identified analyzed. The contents abscisic acid, indoleacetic cytokinins,...
Abstract Background Next generation sequencing (NGS) is being increasingly used for the detection and characterization of pathogens during outbreaks. This technology allows rapid pathogen full genomes, useful not only accurate genotyping molecular epidemiology, but also identification drug resistance virulence traits. Methods In this study, an approach based on whole genome by NGS, comparative genomics, gene function prediction was set up retrospectively applied investigation two N....
Abstract Summary: The search for short words that are absent in the genome of one or more organisms (neverwords, also known as nullomers) is attracting growing interest because impact they may have recent molecular biology applications. keeSeek able to find sequences with primer-like features, which can be used unique labels exogenously inserted DNA fragments recover their exact position into using PCR techniques. main differences respect previously developed tools neverwords generation (i)...
Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for analysis: the identification differentially expressed genes and a topology-based analysis enriched pathways. equipped with ad hoc interactive graphical interfaces simplifying discovery modulated pathways integration corresponding pathway topology.Pathway available at website http://admiral.fmach.it/PI has been...
Studying biological networks at topological level is a major issue in computational biology studies and simulation often used this context, either to assess reverse engineering algorithms or investigate how properties depend on network parameters. In both contexts, it desirable for topology simulator reproduce the current knowledge networks, be able generate number of with same flexible respect possibility mimic different organisms. We propose simulator, SimBioNeT, which module structures...
The marathon is the most classic Olympic running event. In several cities worldwide it has become very popular with participation increasing during last 20 years, particularly by Master Athletes. There are evidences that long-distance could provide considerable health benefits for older runners, specifically risk reduction of cardiovascular diseases, cancer, diabetes, depression, and falls. Several studies have focused on distribution participants their performance famous marathons such as...
In this paper we study the problem of representing different forms imperfect temporal knowledge. Imperfection in knowledge can be present coarse about events or even form incomplete, imprecise, vague uncertain information. The two orthogonal notions coarseness and fuzziness seem to quite adequate manage these kinds ignorance they combined develop a more general model. first part is dedicated definition new Neighborhood Temporal Qualitative Algebra nQA starting from Freksa's work Allen's...
The advances of omics technologies have triggered the production an enormous volume data coming from thousands species. Meanwhile, joint international efforts like Gene Ontology (GO) consortium worked to provide functional information for a vast amount proteins. With these available, we developed FunTaxIS, tool that is first attempt infer taxonomy (i.e. how functions are distributed over taxa) combining and taxonomic information. FunTaxIS able define taxon specific space by exploiting...
Several challenges prevent extracting knowledge from biomedical resources, including data heterogeneity and the difficulty to obtain collaborate on annotations by medical doctors. Therefore, flexibility in their representation interconnection is required; it also essential be able interact easily with such data. In recent years, semantic tools have been developed: wikis are collections of wiki pages that can annotated properties so combine expressiveness, two desirable aspects when modeling...