SCIENTIFIC PRODUCTION

Artificial intelligence: the human response to approach the complexity of big data in biology

GigaScience, 14 (2025) by Giovanni Melandri, Georges R-Radohery, Pierre Pétriacq, Chloé Beaumont, Sara M de Cripan, Coralie Muller, Sophie Colombié, Sylvain Prigent (University of Bordeaux), Luca Piras, Xavier Domingo-Almenara, Biotza Gutierrez Arechederra, Nuria Canela Canela (Eurecat), Maria Alcina Pereira, Andreia Ferreira Salvador (University of Minho) & Marie Bolger (Institute of Bio- and Geosciences, IBG-4) Abstract…

The recipient metabolome explains the asymmetric ovarian impact on fetal sex development after embryo transfer in cattle

Journal of Animal Science, 102 (2024) by Isabel Gimeno; Susana Carrocera; Enrique Gómez (Servicio Regional de Investigación y Desarrollo Agroalimentario); Pascal Salvetti; Julie Gatien & Daniel Le Bourhis (ELIANCE) Abstract In cattle, lateral asymmetry affects ovarian function and embryonic sex, but the underlying molecular mechanisms remain unknown. The plasma metabolome of recipients serves to predict…

Computational Expansion of High-Resolution-MSn Spectral Libraries

Analytical Chemistry, 0 (2023) by Brandon Y. Lieng; Andrew T. Quaile; Hannes L. Rös (Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto); Xavier Domingo-Almenara (Centre for Omics Sciences, Eurecat – Technology Centre of Catalonia & Rovira i Virgili University Joint Unit) Abstract Commonly, in MS-based untargeted metabolomics, some metabolites cannot be confidently…

Enzyme-based kinetic modelling of ASC–GSH cycle during tomato fruit development reveals the importance of reducing power and ROS availability

New Phytologist, Volume 240, Issue 1 (2023) by Guillaume Decros; Thomas Dussarrat; Pierre Baldet; Martine Dieuaide-Noubhani; Alice Destailleur; Sylvain Prigent; Kentaro Mori; Joana Jorly; Sophie Colombié; Bertrand Beauvoit (INRAE, University of Bordeaux); Yves Gibon; Cédric Cassan; Amélie Flandin; Cécile Cabasson; Pierre Pétriacq (Bordeaux Metabolome, MetaboHUB) Abstract The ascorbate–glutathione (ASC–GSH) cycle is at the heart of…

Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth-defence trade-off

The Plant Journal (2023) by Sophie Colombie, Sylvain Prigent, Cedric Cassan, Annick Moing, Chloe Beaumont, Bertrand Beauvoit, Yves Gibon, Ghislaine Hilbert-Masson, Christel Renaud (Univ. Bordeaux), Emilia Dell’Aversana, Petronia Carillo (University of Campania “Luigi Vanvitelli”), Tim McCubbin, and Lars Keld Nielsen (The University of Queensland). Abstract Although primary metabolism is well conserved across species, it is…

Biomarker metabolite mating of viable frozen-thawed IVP bovine embryos with pregnancy-competent recipients leads to improved birth rates

Journal of Dairy Sciente (May 2023) by Isabel Gimeno; Susana Carrocera; Enrique Gómez (Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal); Pascal Salvetti; Julie Gatien (ELIANCE, Experimental facilities); Pablo García-Manrique; Cristina López-Hidalgo; Luis Valledor (Univerisy of Oviedo) Abstract Selection of competent recipients before embryo transfer (ET) is indispensable for improving pregnancy…

Fitness of calves born from in vitro-produced fresh and cryopreserved embryos

Frontiers in Veterinary Science (November 2022) by Enrique Gómez; Antonio Murillo; Susana Carrocera; David Martín-González; Isabel Gimeno (Servicio Regional de Investigación y Desarrollo Agroalimentario – SERIDA); Juan José Pérez-Jánez (Cooperativa de Agricultores y Usuarios de Gijón); Jose Luis Benedito (University of Santiago de Compostela) Abstract In cattle, vitrified/warmed (V/W) and frozen/thawed (F/T), in vitro-produced (IVP)…

UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets

Computational and Structural Biotechnology Journal (April 2022) by João C. Sequeira; Miguel Rocha; M. Madalena Alves; Andreia F. Salvador (CEB – Centre of Biological Engineering, University of Minho; LABBELS – Associate Laboratory) Abstract Omics and meta-omics technologies are powerful approaches to explore microorganisms’ functions, but the sheer size and complexity of omics datasets often turn…

Machine Learning-Based Retention Time Prediction of Trimethylsilyl Derivatives of Metabolites

Biomedicines Journal (MDPI), Special Issue: Omics Data Analysis and Integration in Complex Diseases (April 2022) by Sara M. de Cripan (Computational Metabolomics for Systems Biology Lab, Omics Sciences Unit, Eurecat—Technology Centre of Catalonia; Centre for Omics Sciences (COS), Eurecat—Technology Centre of Catalonia & Rovira i Virgili University Joint Unit; Department of Electrical, Electronic and Control…

Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience

New Phytologist Journal (March 2022) by Thomas Dussarrat (Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, FONDAP Center for Genome Regulation and Millenium Institute for Integrative Biology (iBio); Univ. Bordeaux, INRAE); Sylvain Prigent; Stéphane Bernillon; Amélie Flandin; Cédric Cassan; Daniel Jacob; Yves Gibon; Dominique Rolin (Univ. Bordeaux, INRAE; Bordeaux Metabolome, MetaboHUB,PHENOME-EMPHASIS); Claudio…

The Metabolic Signature of In Vitro Produced Bovine Embryos Helps Predict Pregnancy and Birth after Embryo Transfer

Metabolites Journal (MDPI), Section “Endocrinology and Clinical Metabolic Research” (July 2021) by Isabel Gimeno; Susana Carrocera; David Martín-González; Enrique Gomez (Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal); Pablo García-Manrique (Molecular Mass Spectrometry Unit, Scientific and Technical Services, University of Oviedo); Cristina López-Hidalgo; Luis Valledor (Department of Organisms and Systems Biology,…

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