Lucila Aimo
A5067959898- Trace Elements in Health
- Metabolomics and Mass Spectrometry Studies
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Advanced Proteomics Techniques and Applications
- Aluminum toxicity and tolerance in plants and animals
- Heavy Metal Exposure and Toxicity
- Genomics and Phylogenetic Studies
- Scientific Computing and Data Management
- RNA Research and Splicing
- Computational Drug Discovery Methods
- Cancer Cells and Metastasis
- Machine Learning in Bioinformatics
- Research Data Management Practices
- Fatty Acid Research and Health
- RNA regulation and disease
- Genetics, Bioinformatics, and Biomedical Research
- Adipose Tissue and Metabolism
- Lipid metabolism and biosynthesis
- Data Analysis with R
- Biofuel production and bioconversion
- Mass Spectrometry Techniques and Applications
- Biochemical Acid Research Studies
- Estrogen and related hormone effects
SIB Swiss Institute of Bioinformatics
2014-2024
European Bioinformatics Institute
2024
University of Padua
2023
University College London
2023
Stanford University
2023
Phoenix Bioinformatics
2023
University at Buffalo, State University of New York
2023
University of Southern California
2023
University of California, Davis
2005-2017
University of California System
2006
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this article, we describe significant updates that have made over last two years resource. number in UniProtKB has risen approximately 190 million, despite continued work reduce sequence redundancy at proteome level. We adopted new methods assessing completeness quality. continue extract detailed annotations from...
Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication we describe enhancements made our data processing pipeline website adapt an ever-increasing information content. number in UniProtKB has risen over 227 million are working towards including reference proteome for each taxonomic group. We continue extract detailed annotations from literature...
Abstract Motivation To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities Biological Interest), to better support efforts study and predict functionally interactions between protein sequences structures small molecule ligands. Results We structured data model cognate ligand site annotations performed a complete reannotation all stable unique identifiers from...
Abstract Rhea (https://www.rhea-db.org) is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI (Chemical Entities Biological Interest) (https://www.ebi.ac.uk/chebi). In this paper, we describe a number key developments in since our last report database issue Nucleic Acids Research 2019. These include improved reaction coverage Rhea, adoption as reference vocabulary for enzyme annotation UniProt UniProtKB (https://www.uniprot.org), development new...
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication, we describe ongoing changes our production pipeline limit available in UniProtKB high-quality, non-redundant reference proteomes. We continue manually curate scientific literature add latest data use machine learning techniques. also encourage community curation...
Motivation: Lipids are a large and diverse group of biological molecules with roles in membrane formation, energy storage signaling. Cellular lipidomes may contain tens thousands structures, staggering degree complexity whose significance is not yet fully understood. High-throughput mass spectrometry-based platforms provide means to study this complexity, but the interpretation lipidomic data its integration prior knowledge lipid biology suffers from lack appropriate tools manage extract it.
Although a requirement of zinc (Zn) for normal brain development is well documented, the extent to which Zn can modulate neuronal proliferation and apoptosis not clear. Thus, we investigated role in regulation these two critical events. A low availability leads decreased cell viability human neuroblastoma IMR-32 cells primary cultures rat cortical neurons. This occurs part as consequence increased apoptotic death. In cells, deficiency led inhibition through arrest cycle at G0/G1 phase....
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of over 11 000 expert-curated biochemical reactions that uses chemical entities from the ChEBI ontology to represent reaction participants. Originally designed as an annotation vocabulary for UniProt Knowledgebase (UniProtKB), also provides data range other core knowledgebases repositories including MetaboLights. Here we describe recent developments in Rhea, focusing on new description framework representation SPARQL...
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation enzymes description metabolic networks. describes enzyme-catalyzed covering IUBMB Enzyme Nomenclature list as well additional reactions, including spontaneously occurring using entities from ChEBI (Chemical Entities Biological Interest) ontology small molecules. Here we describe developments in since our last report database issue Nucleic...
Abstract Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result genome sequencing and prediction protein-coding genes. Providing functional annotation for these proteins presents significant continuing challenge. Results In response this challenge, has developed method annotation, known UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) by members...
Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities Biological Interest) ontology small molecules. has been designed for functional annotation enzymes description genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed (covering IUBMB Enzyme Nomenclature list additional reactions), transport spontaneously occurring reactions. are...
Zinc deficiency affects the development of central nervous system (CNS) through mechanisms only partially understood. We previously showed that zinc causes CNS oxidative stress, damaging microtubules and impairing protein nuclear shuttling. STAT1 STAT3 transcription factors, which require import for their functions, play major roles in development. Thus, we investigated whether disrupts signaling pathways developing fetal CNS, characterizing involvement stress cytoskeleton adverse effects....
This work investigated the capacity of alpha-lipoic acid (LA) and N-acetyl-L-cysteine (NAC) to reduce zinc deficiency-induced oxidative stress, prevent activation nuclear factor-kappaB (NF-kappaB) activator protein-1 (AP-1), cross-talk between both activated cascades through beta-Transducin Repeat-containing Protein (beta-TrCP). IMR-32 cells were incubated in control media or containing variable concentrations zinc, without with 0.5 mM LA 1 NAC. Relative supplemented (15 microM Zn) groups,...
Lead (Pb2+) is a major environmental pollutant that has severe adverse effects on the nervous system. Similar human populations are at risk of suffering both Pb2+ toxicity and zinc (Zn) deficiency. Thus, in present study we investigated whether Zn deficiency can increase susceptibility neuroblastoma IMR-32 cells to Pb2+-induced oxidative stress which could trigger activation mitogen-activated protein kinases (MAPKs) c-Jun-N-terminal kinase (JNK) p38 subsequently activate transcription factor...
Lifetime breast cancer risk reflects an unresolved combination of early life factors including diet, body mass index, metabolic syndrome, obesity, and age at first menses. In parallel, the onset allometric growth by mammary glands around puberty is widely held to be estrogen (E)-dependent. Here we report that several physiological changes associated with syndrome in response a diet supplemented trans -10, cis -12 isomer conjugated linoleic acid lead ovary-independent ducts. The...