Recent Submissions

  • Functional geometry of protein interactomes 

    Malod Dognin, Noël; Pržulj, Nataša (Oxford University Press (OUP), 2019-10-01)
    Article
    Open Access
    Motivation Protein–protein interactions (PPIs) are usually modeled as networks. These networks have extensively been studied using graphlets, small induced subgraphs capturing the local wiring patterns around nodes in ...
  • Unveiling new disease, pathway, and gene associations via multi-scale neural network 

    Gaudelet, Thomas; Malod Dognin, Noël; Sánchez, Jon; Pancaldi, Vera; Valencia, Alfonso; Pržulj, Nataša (PLOS, 2020-04-06)
    Article
    Open Access
    Diseases involve complex modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, new biological knowledge about a disease can ...
  • Towards a data-integrated cell 

    Malod Dognin, Noël; Petschnigg, Julia; Windels, Sam F. L.; Povh, Janez; Hemingway, Harry; Ketteler, Robin; Pržulj, Nataša (Springer Nature, 2019-02-18)
    Article
    Open Access
    We are increasingly accumulating molecular data about a cell. The challenge is how to integrate them within a unified conceptual and computational framework enabling new discoveries. Hence, we propose a novel, data-driven ...
  • Patient dossier: healthcare queries over distributed resources 

    Vazquez, Miguel; Valencia, Alfonso (PLOS, 2019-10-17)
    Article
    Open Access
    As with many other aspects of the modern world, in healthcare, the explosion of data and resources opens new opportunities for the development of added-value services. Still, a number of specific conditions on this domain ...
  • The quest for orthologs benchmark service and consensus calls in 2020 

    Altenhoff, Adrian M; Garrayo Ventas, Javier; Consentino, Salvatore; Emms, David; Glover, Natasha M; Hernández Plaza, Ana; Nevers, Yannis; Szklarczyk, Damian; Fernández González, Jose María; Codó, Laia; Gelpi, Josep; Huertas Cepas, Jaime; Iwasaki, Wataru; Kelly, Steven; Lecompte, Odile; Muffato, Matthieu; Martín, María Jesús; Capella Gutiérrez, Salvador; Thomas, Paul D.; Sonnhammer, Erik; Dessimoz, Christophe; the Quest for Orthologs Consortium (Oxford University Press (OUP), 2020-05-06)
    Article
    Open Access
    The identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous ...
  • FragPELE: dynamic ligand growing within a binding site. A novel tool for hit-to-lead drug design 

    Pérez, Carles; Soler, Daniel; Soliva, Robert; Guallar, Víctor (American Chemical Society (ACS), 2020)
    Article
    Restricted access - publisher's policy
    The early stages of drug discovery rely on hit-to-lead programs, where initial hits undergo partial optimization to improve binding affinities for their biological target. This is an expensive and time-consuming process, ...
  • BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows 

    Andrio, Pau; Hospital, Adam; Conejero Bañón, Javier; Jordá, Luis; del Pino, Marc; Codo, Laia; Soiland Reyes, Stian; Goble, Carole; Lezzi, Daniele; Badia Sala, Rosa Maria; Orozco López, Modesto; Gelpi Buchaca, Josep Lluís (Nature, 2019-09-10)
    Article
    Open Access
    In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed ...
  • MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life 

    Chorostecki, Uciel; Molina, Manuel; Pryszcz, Leszek P.; Gabaldon, Toni (Oxford University Press (OUP), 2020-04-28)
    Article
    Open Access
    Inferring homology relationships across genes in different species is a central task in comparative genomics. Therefore, a large number of resources and methods have been developed over the years. Some public databases ...
  • Random forest as a tumour genetic marker extractor 

    Pérez Arnal, Raquel; Garcia Gasulla, Dario; Torrents Rodas, David; Pares, Ferran; Cortés García, Claudio Ulises; Labarta Mancho, Jesús José; Ayguadé Parra, Eduard (IOS Press, 2019)
    Conference report
    Open Access
    Finding tumour genetic markers is essential to biomedicine due to their relevance for cancer detection and therapy development. In this paper, we explore a recently released dataset of chromosome rearrangements in 2,586 ...
  • Co-occurrence patterns in diagnostic data 

    Piceno Cabrera, Marie Ely; Rodríguez Navas, Laura; Balcázar Navarro, José Luis (Wiley (John Wiley & Sons), 2020-04-12)
    Article
    Open Access
    We demonstrate how graph decomposition techniques can be employed for the visualization of hierarchical co-occurrence patterns between medical data items. Our research is based on Gaifman graphs (a mathematical concept ...
  • Monte Carlo simulations using PELE to identify a protein–protein inhibitor binding site and pose 

    Díaz, Lucía; Soler, Daniel; Tresadern, Gary; Buyck, Christophe; Perez-Benito, Laura; Saen-Oon, Suwipa; Guallar, Victor; Soliva, Robert (Royal Society of Chemistry (RSC), 2020-02-17)
    Article
    Open Access
    In silico binding site location and pose prediction for a molecule targeted at a large protein surface is a challenging task. We report a blind test with two peptidomimetic molecules that bind the flu virus hemagglutinin ...
  • Modulating Fatty Acid Epoxidation vs Hydroxylation in a Fungal Peroxygenase 

    Carro, Juan; González-Benjumea, Alejandro; Fernández-Fueyo, Elena; Aranda, Carmen; Guallar, Victor; Gutiérrez, Ana; Martínez, Angel T. (American Chemical Society, 2019-06-14)
    Article
    Open Access
    Unspecific peroxygenases (UPOs) are fungal secreted counterparts of the cytochrome P450 monooxygenases present in most living cells. Both enzyme types share the ability to perform selective oxygenation reactions. Moreover, ...

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