Livia Perfetto
A5050128493- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Acute Myeloid Leukemia Research
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Protein Degradation and Inhibitors
- Genomics and Rare Diseases
- Genomics and Chromatin Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Cell Image Analysis Techniques
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Ubiquitin and proteasome pathways
- Fungal and yeast genetics research
- Chronic Myeloid Leukemia Treatments
- Topic Modeling
- Protein Tyrosine Phosphatases
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Autism Spectrum Disorder Research
- Research Data Management Practices
- Semantic Web and Ontologies
Sapienza University of Rome
2022-2025
University of Rome Tor Vergata
2013-2024
Human Technopole
2021-2024
European Bioinformatics Institute
2018-2023
Wellcome Trust
2020
Fondazione Santa Lucia
2009-2011
Istituti di Ricovero e Cura a Carattere Scientifico
2009-2011
Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding functions of genes and gene products. Here, we report advances consortium over past two years. new GO-CAM annotation framework was notably improved, formalized model with a computational schema to check validate rapidly increasing repository 2838 GO-CAMs. In addition, describe impacts several collaborations refine GO 10% increase in number annotations,...
IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by either curated from the literature or direct depositions. has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool now utilized multiple additional teams, all whom annotate directly into database. Members team supply appropriate levels training, perform quality control on entries take...
The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein–protein interactions (PPI) reported in peer-reviewed journals. database grows steadily over the years and at September 2011 contains approximately 235 000 binary captured from 4750 publications. web interface allows users to search, visualize download data. MINT one of members International Exchange consortium (IMEx) adopts Interaction Ontology Proteomics Standard Initiative...
MINT (http://mint.bio.uniroma2.it/mint) is a public repository for molecular interactions reported in peer-reviewed journals. Since its last report, has grown considerably size and evolved scope to meet the requirements of users. The main changes include more precise definition curation policy development an enhanced user-friendly interface facilitate analysis ever-growing interaction dataset. adopted PSI-MI standards annotation representation member IMEx consortium.
Assembly of large biochemical networks can be achieved by confronting new cell-specific experimental data with an interaction subspace constrained prior literature evidence. The SIGnaling Network Open Resource, SIGNOR (available on line at http://signor.uniroma2.it), was developed to support such a strategy providing scaffold evidence causal relationships between biological entities. core is collection approximately 12 000 manually-annotated over 2800 human proteins participating in signal...
Abstract The current wealth of genomic variation data identified at nucleotide level presents the challenge understanding by which mechanisms amino acid affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in development disease. Physical interactions molecules are linking steps underlying most, if not all, Understanding that sequence has on a molecule’s is key step towards connecting mechanistic characterization...
The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of interactions, derived from the scientific literature and direct data depositions. As August 2021, provides more than one million binary by twelve global partners International Molecular Exchange consortium, for which shared curation dissemination platform. IMEx policy has always emphasised fine-grained model, aiming to capture relevant experimental detail essential interpretation provided data....
The SIGnaling Network Open Resource 2.0 (SIGNOR 2.0) is a public repository that stores signaling information as binary causal relationships between biological entities. captured represented graphically signed directed graph. Each relationship associated to an effect (up/down-regulation) and the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing up/down-regulation of target entity. Since its first release, SIGNOR has undergone significant content increase...
Abstract The SIGnaling Network Open Resource (SIGNOR 3.0, https://signor.uniroma2.it) is a public repository that captures causal information and represents it according to an ‘activity-flow’ model. SIGNOR provides freely-accessible static maps of interactions can be tailored, pruned refined build dynamic predictive models. Each signaling relationship annotated with effect (up/down-regulation) the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing regulation...
Abstract Background Metabolic syndrome represents a pancreatic ductal adenocarcinoma (PDAC) risk factor. alterations favor PDAC onset, which occurs early upon dysmetabolism. Pancreatic neoplastic lesions evolve within dense desmoplastic stroma, consisting in abundant extracellular matrix settled by cancer associated fibroblasts (CAFs). Hereby, dysmetabolism and association was analyzed focusing on CAF functions. Methods development dysmetabolic conditions investigated in: 1) high fat diet...
Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address including how the end user would oversee generated output, for instance providing ranked results, textual evidence human interpretation or time savings using...
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database that collates and summarizes information on stable, macromolecular complexes of known function. It captures complex composition, topology function links out to large range domain-specific resources hold more detailed data, such as PDB or Reactome. We have made several significant improvements since our last update, including improving compliance the FAIR data principles by providing...
About 40% of relapsed or non-responder tumors exhibit therapeutic resistance in the absence a clear genetic cause, suggesting pivotal role intracellular communication. A deeper understanding signaling pathways rewiring occurring resistant cells is crucial to propose alternative effective strategies for cancer patients. To achieve this goal, we developed novel multi-step strategy, which integrates high sensitive mass spectrometry-based phosphoproteomics with network-based analysis. This...
The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. biocurator community, as an active user of biomedical literature, provides diverse engaged end group tools. Earlier challenges involved many teams in developing basic capabilities relevant curation, but they did not address issues system usage, insertion into workflow adoption by curators. Thus III (BC-III), InterActive Task (IAT) was...
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from range model organisms. It summarizes complex composition, topology and along links to large domain-specific resources (i.e. wwPDB, EMDB Reactome). Since the last update in 2019, we have produced first draft complexome for Escherichia coli, maintained updated that Saccharomyces cerevisiae, added over 40 coronavirus increased human 1100 include...
Phosphatases and kinases contribute to the regulation of protein phosphorylation homeostasis in cell. Phosphorylation is a key post-translational modification underlying many cellular processes. Thus, comprehensive picture phosphatase function identification their target substrates would aid systematic approach mechanistic description cell signalling. Here we present website designed facilitate retrieval information about human phosphatases. To this end developed search engine recover...
Abstract The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome (SARS-CoV)-2, has spurred a wave research nearly unprecedented scale. Among different strategies that are being used to understand and develop effective treatments, study physical molecular interactions can provide fine-grained resolution mechanisms behind virus biology human organism response. We present curated dataset focused on proteins from SARS-CoV-2, SARS-CoV-1 other...
The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification drug repurposing.
DISNOR is a new resource that aims at exploiting the explosion of data on identification disease-associated genes to assemble inferred disease pathways. This may help dissecting signaling events whose disruption causes pathological phenotypes and contribute build platform for precision medicine. To this end we combine gene-disease association (GDA) annotated in DisGeNET with curation effort aimed populating SIGNOR database causal interactions related highest possible coverage. can be freely...