A5077024139- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- Viral Infectious Diseases and Gene Expression in Insects
- Cancer-related molecular mechanisms research
- Genomics and Rare Diseases
- Genetics, Bioinformatics, and Biomedical Research
- GDF15 and Related Biomarkers
- Macrophage Migration Inhibitory Factor
- Semantic Web and Ontologies
- Molecular Biology Techniques and Applications
- Scientific Computing and Data Management
- Topic Modeling
- Nuclear Receptors and Signaling
- Natural Language Processing Techniques
- Machine Learning in Bioinformatics
- Enzyme Catalysis and Immobilization
- Inflammatory mediators and NSAID effects
- Lysosomal Storage Disorders Research
University of Lausanne
2012-2024
SIB Swiss Institute of Bioinformatics
2013-2024
University College London
2015
University of Maryland, Baltimore
2015
European Bioinformatics Institute
2014
Abstract Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating data types (RNA-Seq, Affymetrix, situ hybridization, EST data). It based exclusively on curated healthy wild-type (e.g., no knock-out, treatment, disease), provide comparable reference of normal expression. Curation includes very large datasets such as GTEx (re-annotation samples ‘healthy’ or not) well many small ones. Data are integrated made between species...
Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species (msAOs; vertebrate skeletal, homologous, teleost, amphibian AOs) developed 'natural' phenotypic across species. Our aim has integrate ssAOs msAOs for various purposes, including establishing links between candidate genes.Previously, contained a mixture of unique overlapping...
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.
We identify biomarkers for disease progression in three type 2 diabetes cohorts encompassing 2,973 individuals across molecular classes, metabolites, lipids and proteins. Homocitrulline, isoleucine 2-aminoadipic acid, eight triacylglycerol species, lowered sphingomyelin 42:2;2 levels are predictive of faster towards insulin requirement. Of ~1,300 proteins examined two cohorts, GDF15/MIC-1, IL-18Ra, CRELD1, NogoR, FAS, ENPP7 associated with progression, whilst SMAC/DIABLO, SPOCK1 HEMK2...
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...
Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations considerably grown recent years. However, reliability these varies; it thus necessary be able assess confidence annotations. Although several resources already provide information about that they produce, standard way providing such yet defined. This lack standardization undermines propagation knowledge across resources, as well credibility results from high-throughput analyses. Seeded...
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...
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...
Abstract Background Prior knowledge networks (PKNs) provide a framework for the development of computational biological models, including Boolean models regulatory which are focus this work. PKNs created by painstaking process literature curation, and generally describe all relevant interactions identified using variety experimental conditions systems, such as specific cell types or tissues. Certain these may not occur in contexts interest, their presence dramatically change dynamical...
Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integrated made comparable between species thanks consistent annotation processing. In the past years, we have single-cell RNA-sequencing into through careful curation of public datasets We fully this new technology along with wealth other existing Bgee. As result, can now provide one definitive answer all way cell resolution about gene's pattern,...
In a previous paper we introduced novel model-based approach (OLAV) to the problem of identifying peptides via tandem mass spectrometry, for which early implementations showed promising performance. We recently further improved this performance remarkable level (1-2% false positive rate at 95% true rate) and characterized key properties OLAV like robustness training set size. present these results in synthetic coherent way along with detailed comparisons, new scoring component making use...
We present an integrated proteomics platform designed for performing differential analyses. Since reproducible results are essential comparative studies, we explain how improved reproducibility at every step of our laboratory processes, e.g. by taking advantage the powerful information management system developed. The capacity is validated detecting known markers in a real sample and spiking experiment. introduce innovative two-dimensional (2-D) plot displaying identification combined with...
Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. We investigated cohort 15 individuals with clinical suspicion SMS who showed neither deletion in the critical region nor damaging variants RAI1 using whole exome sequencing. A combination network analysis (co-expression biomedical text mining),...
A large variety of molecular interactions occurs between biomolecular components in cells. When a interaction results regulatory effect, exerted by one component onto downstream component, so-called 'causal interaction' takes place. Causal constitute the building blocks our understanding larger networks These causal and biological processes they enable (e.g. gene regulation) need to be described with careful appreciation underlying reactions. proper description this information enables...
Most anatomical ontologies are species-specific, whereas a framework for comparative studies is needed. We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species.vHOG multispecies ontology lineage. It based on HOGs in Bgee database of gene evolution. vHOG version 1.4 includes 1184 terms, follows OBO principles and Common Anatomy Reference Ontology (CARO). only describes structures with historical homology relations model species....
Obesity is considered by many as a lifestyle choice rather than chronic progressive disease. The Innovative Medicines Initiative (IMI) SOPHIA (Stratification of Phenotypes to Optimize Future Therapy) project part momentum shift aiming provide better tools for the stratification people with obesity according disease risk and treatment response. One challenges achieving these goals that clinical cohorts are siloed, limiting potential combined data biomarker discovery. In SOPHIA, we have...
As part of the development database Bgee (a dataBase for Gene Expression Evolution), we annotate and analyse expression data from different types sources, notably Affymetrix GEO ArrayExpress, RNA-Seq SRA. During our quality control procedure, have identified duplicated content in affecting ∼14% data: fully or partially experiments independent submissions, chips reused several experiments, within an experiment. We present here procedure that established to filter such duplicates data,...
There is growing interest to use mass spectrometry data search genome sequences directly. Previous work by other authors demonstrated that this approach able correct and complement available annotations. We discuss the practical difficulty of searching large eukaryotic genomes with peptide ion trap tandem spectra small proteins (<40 kDa). The challenging problem automatically identifying peptides span across exon/intron boundaries explored for first time using experimental data. In a human...
Cytokinesis in fission yeast is controlled by the Septation Initiation Network (SIN), a protein kinase signaling network using spindle pole body as scaffold. In order to describe qualitative behavior of system and predict unknown mutant behaviors we decided adopt Boolean modeling approach. this paper, report construction an extended, model SIN, comprising most SIN components regulators individual, experimentally testable nodes. The uses CDK activity levels control nodes for simulation...
A large variety of molecular interactions occurs between biomolecular components in cells. When one or a cascade results regulatory effect, by component onto downstream component, so-called &lsquo;causal interaction&rsquo; takes place. Causal constitute the building blocks our understanding larger networks These causal and biological processes they enable (e.g., gene regulation) need to be described with careful appreciation that occur entities. proper description this information...
Knowledgebases play an increasingly important role in scientific research, where the expert curation of biological knowledge forms that are amenable to computational analysis (using ontologies for example)–provides a significant added value and enables new types analyses high throughput datasets. In this work, we demonstrate how can also more direct by supporting use network-based dynamical models study specific process. This effort is focused on regulatory interactions between entities,...
ABSTRACT Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating data types (RNA-Seq, Affymetrix, situ hybridization, EST data). It based exclusively on curated healthy wild-type (e.g., no knock-out, treatment, disease), provide comparable reference of normal expression. Curation includes very large datasets such as GTEx (re-annotation samples “healthy” or not) well many small ones. Data are integrated made between species...
ABSTRACT We have deployed a multi-omics approach in large cohorts of patients with existing type 2 diabetes to identify biomarkers for disease progression across three molecular classes, metabolites, lipids and proteins. A Cox regression analysis association time insulin requirement 2,973 the DCS, ANDIS GoDARTS identified homocitrulline, isoleucine 2-aminoadipic acid, as well bile acids glycocholic taurocholic acids, predictive more rapid deterioration. Increased levels eight triacylglycerol...