Sébastien Moretti
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View article: StereoMapper: Clarifying Metabolite Identity Through Stereochemically Aware Relationship Assignment
StereoMapper: Clarifying Metabolite Identity Through Stereochemically Aware Relationship Assignment Open
Inaccuracies in metabolite cross-mapping frequently introduce errors into genome-scale metabolic models (GEMs). A key challenge lies in distinguishing truly identical metabolites from closely related structural variants, such as stereoisom…
View article: MetaNetX: a bridge between metabolic resources for enhanced curation and multi-omics data harmonization
MetaNetX: a bridge between metabolic resources for enhanced curation and multi-omics data harmonization Open
MetaNetX (https://www.metanetx.org/) is a comprehensive resource for the reconciliation and integration of metabolic information across diverse biochemical databases. The 2025 update significantly enhances chemical and reaction coverage, i…
View article: Software Quality Indicators: extraction, categorisation and recommendations from canonical sources
Software Quality Indicators: extraction, categorisation and recommendations from canonical sources Open
Research software plays a central role in modern science, and its quality is increasingly recognized as essential for reproducibility, sustainability, and trust. Numerous initiatives have proposed indicators to guide quality assessment, ye…
View article: Inverse hourglass pattern of conservation in rodent molar development
Inverse hourglass pattern of conservation in rodent molar development Open
Although it is well established that certain stages of development are more conserved than others, the reasons for this phenomenon remain largely unknown. We study molecular conservation in the development of an organ, the molar, by compar…
View article: A large collection of bioinformatics question–query pairs over federated knowledge graphs: methodology and applications
A large collection of bioinformatics question–query pairs over federated knowledge graphs: methodology and applications Open
Background In recent decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoptio…
View article: Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools Open
Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integrated and made comparable between species thanks to consistent data annotation and processing.…
View article: Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs
Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs Open
Phenotypic variation among individuals plays a key role in evolution, since variation provides the material on which natural selection can act. One important link between genetic and phenotypic variation is gene expression. As for other ph…
View article: A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications
A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications Open
Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adop…
View article: Systems Biology in ELIXIR: modelling in the spotlight
Systems Biology in ELIXIR: modelling in the spotlight Open
In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Com…
View article: BioHackEU23: FAIR Workflow Execution with WfExS and Workflow Run Crate
BioHackEU23: FAIR Workflow Execution with WfExS and Workflow Run Crate Open
FAIR Computational Workflows argues that workflows should be FAIR scholarly community research objects in their own right as a kind of FAIR Research Software. In this project we go one step further, and argue that workflow executions shoul…
View article: A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery
A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery Open
The ENPKG framework organizes large heterogeneous metabolomics data sets as a knowledge graph, offering exciting opportunities for drug discovery and chemodiversity characterization.
View article: Bioschemas Resource Index for Chem and Plants
Bioschemas Resource Index for Chem and Plants Open
As part of the BioHackathon Europe 2023, we here report on the progress of the hacking team preparing a resource index and knowledge graph based on the JSON-LD Bioschemas markup from several resources in the life- and natural sciences, pre…
View article: A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery
A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery Open
Modern natural products (NPs) research relies on untargeted liquid chromatography coupled with mass spectrometry metabolomics. Together with cutting-edge processing and computational annotation strategies, such approaches can yield extensi…
View article: Application of the RDF framework to integrate heterogenous experimental data of a large chemo- and biodiverse collection from a research collaborative project
Application of the RDF framework to integrate heterogenous experimental data of a large chemo- and biodiverse collection from a research collaborative project Open
Plants have a complex chemo-diversity and represent a reservoir of potential new therapeutic agents. Within a Swiss research project, six scientific research groups from different disciplines are collaborating to investigate a collection o…
View article: EPDnew: FTP directory, Nov 2023
EPDnew: FTP directory, Nov 2023 Open
Snapshot of the EPDnew FTP directory of November 2023. The acronym EPDnew refers to the newer versions of the Eukaryotic Promoter Database published in the format introduced in 2013. The directory contains all database versions for 15 mode…
View article: EPDnew: FTP directory, Nov 2023
EPDnew: FTP directory, Nov 2023 Open
Snapshot of the EPDnew FTP directory of November 2023. The acronym EPDnew refers to the newer versions of the Eukaryotic Promoter Database published in the format introduced in 2013. The directory contains all database versions for 15 mode…
View article: The SIB Swiss Institute of Bioinformatics Semantic Web of data
The SIB Swiss Institute of Bioinformatics Semantic Web of data Open
The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/) is a federation of bioinformatics research and service groups. The international life science community in academia and industry has been accessing the freely available dat…
View article: A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery
A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery Open
Modern natural products (NPs) research relies on untargeted liquid chromatography coupled with mass spectrometry metabolomics. Together with cutting-edge processing and computational annotation strategies, such approaches can yield extensi…
View article: BioHackEU22 Report for Project 16: Make your own or favourite software available on your cluster with EasyBuild/EESSI
BioHackEU22 Report for Project 16: Make your own or favourite software available on your cluster with EasyBuild/EESSI Open
EasyBuild is a community effort to develop a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. As its name suggests, EasyBuild makes s…
View article: Corrigendum: Ni2+-assisted hydrolysis may affect the human proteome; filaggrin degradation ex vivo as an example of possible consequences
Corrigendum: Ni2+-assisted hydrolysis may affect the human proteome; filaggrin degradation ex vivo as an example of possible consequences Open
[This corrects the article DOI: 10.3389/fmolb.2022.828674.].
View article: Systems Biology in ELIXIR: modelling in the spotlight
Systems Biology in ELIXIR: modelling in the spotlight Open
In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Com…
View article: Bioschemas data harvesting project report
Bioschemas data harvesting project report Open
The promise of Bioschemas is that it makes consuming data from multiple resources more straightforward. However, this hypothesis has not been tested by conducting a large scale harvest of deployed markup and making this available for other…
View article: Ni2+-Assisted Hydrolysis May Affect the Human Proteome; Filaggrin Degradation Ex Vivo as an Example of Possible Consequences
Ni2+-Assisted Hydrolysis May Affect the Human Proteome; Filaggrin Degradation Ex Vivo as an Example of Possible Consequences Open
Deficiency in a principal epidermal barrier protein, filaggrin (FLG), is associated with multiple allergic manifestations, including atopic dermatitis and contact allergy to nickel. Toxicity caused by dermal and respiratory exposures of th…
View article: MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models Open
MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with resp…
View article: MetaNetX/MNXref - unified namespace for metabolites and biochemical reactions in the context of metabolic models
MetaNetX/MNXref - unified namespace for metabolites and biochemical reactions in the context of metabolic models Open
MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with resp…
View article: The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals Open
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated heal…
View article: The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals Open
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated heal…
View article: Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis Open
Motivation Genome-scale metabolic networks and transcriptomic data represent complementary sources of knowledge about an organism’s metabolism, yet their integration to achieve biological insight remains challenging. Results We investigate…
View article: Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis Open
Motivation Genome-scale metabolic networks and transcriptomic data represent complementary sources of knowledge about an organism’s metabolism, yet their integration to achieve biological insight remains challenging. Results We investigate…
View article: Gearing up to handle the mosaic nature of life in the quest for orthologs
Gearing up to handle the mosaic nature of life in the quest for orthologs Open
Summary: The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here rep…