publications

a recent list of publications by categories in reversed chronological order.

2025

  1. BioRxiv
    scape.jpg
    ScAPE: A lightweight multitask learning baseline method to predict transcriptomic responses to perturbations
    Sergio Romero-Tapiador, Pablo Rodriguez-Mier, Martin Garrido-Rodriguez, Ruben Tolosana, and 2 more authors
    bioRxiv, 2025
  2. Nat. Mach. Intell.
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    Unifying multi-sample network inference from prior knowledge and omics data with CORNETO
    Pablo Rodriguez-Mier, Martin Garrido-Rodriguez, Attila Gabor, and Julio Saez-Rodriguez
    Nature Machine Intelligence, 2025
    DOI
    N/A Google Scholar citations
  3. Bioinformatics
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    NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks
    Victor Paton, Denes Türei, Olga Ivanova, Sophia Müller-Dott, and 5 more authors
    Bioinformatics, 2025
    DOI
    N/A Google Scholar citations

2024

  1. Nat. Cell Biol.
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    LIANA+ provides an all-in-one framework for cell–cell communication inference
    Daniel Dimitrov, Philipp Sven Lars Schäfer, Elias Farr, Pablo Rodriguez-Mier, and 6 more authors
    Nature Cell Biology, 2024
    DOI
    N/A Google Scholar citations
  2. Mol. Syst. Biol.
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    Molecular causality in the advent of foundation models
    Sebastian Lobentanzer, Pablo Rodriguez-Mier, Stefan Bauer, and Julio Saez-Rodriguez
    Molecular Systems Biology, 2024
    DOI
    N/A Google Scholar citations
  3. signaling.jpg
    Evaluating signaling pathway inference from kinase-substrate interactions and phosphoproteomics data
    Martin Garrido-Rodriguez, Clement Potel, Mira Lea Burtscher, Isabelle Becher, and 4 more authors
    bioRxiv, 2024
    DOI
    N/A Google Scholar citations
  4. PLoS Comput. Biol.
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    Genome scale metabolic network modelling for metabolic profile predictions
    Juliette Cooke, Maxime Delmas, Cecilia Wieder, Pablo Rodriguez-Mier, and 5 more authors
    PLoS Computational Biology, 2024
    DOI
    N/A Google Scholar citations

2023

  1. GigaScience
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    Suggesting disease associations for overlooked metabolites using literature from metabolic neighbors
    Maxime Delmas, Olivier Filangi, Christophe Duperier, Nils Paulhe, and 5 more authors
    GigaScience, 2023
    DOI
    N/A Google Scholar citations

2022

  1. metabo-environ.jpg
    Avoiding the Misuse of Pathway Analysis Tools in Environmental Metabolomics
    Cecilia Wieder, Jacob G Bundy, Clement Frainay, Nathalie Poupin, and 6 more authors
    Environmental Science & Technology, 2022

2021

  1. PLoS Comput. Biol.
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    DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks
    Pablo Rodriguez-Mier, Nathalie Poupin, Carlo Blasio, Laurent Le Cam, and 1 more author
    PLoS Computational Biology, 2021
    DOI
    N/A Google Scholar citations
  2. PLoS Comput. Biol.
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    Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis
    Cecilia Wieder, Clement Frainay, Nathalie Poupin, Pablo Rodriguez-Mier, and 6 more authors
    PLoS computational biology, 2021
    DOI
    N/A Google Scholar citations
  3. Comput. Biomed.
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    COVID-19: Estimation of the transmission dynamics in Spain using a stochastic simulator and black-box optimization techniques
    Marcos Matabuena, Pablo Rodriguez-Mier, Carlos Garcia-Meixide, and Victor Leboran
    Computer Methods and Programs in Biomedicine, 2021
    DOI
    N/A Google Scholar citations