Recent Submissions

  • Strategies to enhance logic modeling-based cell line-specific drug synergy prediction 

    Niederdorfer, Barbara; Touré, Vasundra; Vazquez, Miguel; Thommesen, Liv; Kuiper, Martin; Lægreid, Astrid; Flobak, Åsmund (Frontiers Media, 2020-07)
    Article
    Open Access
    Discrete dynamical modeling shows promise in prioritizing drug combinations for screening efforts by reducing the experimental workload inherent to the vast numbers of possible drug combinations. We have investigated ...
  • Pan-cancer analysis of whole genomes 

    The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium; Royo, Romina; Vazquez, Miguel; Bosio, Mattia; Valencia, Alfonso; Torrents, David; Gelpi, Josep; Milovanovic, Ana; Puiggròs, Montserrat; Bartolome, Javier; Vicente, David; Fink, J. Lynn; Dueso Barroso, Ana; Villasante, Izar; Bartolomé Rodriguez, Javier (Nature Research, 2020)
    Article
    Open Access
    Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 ...
  • Integrative data analytic framework to enhance cancer precision medicine 

    Gaudelet, Thomas; Malod Dognin, Noël; Przulj, Natasa (Mary Ann Liebert, Inc., publishers, 2021-03)
    Article
    Open Access
    With the advancement of high-throughput biotechnologies, we increasingly accumulate biomedical data about diseases, especially cancer. There is a need for computational models and methods to sift through, integrate, and ...
  • NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II 

    Amengual Rigo, Pep; Guallar, Victor (Nature Research, 2021)
    Article
    Open Access
    Antigens presented on the cell surface have been subjected to multiple biological processes. Among them, C-terminal antigen processing constitutes one of the main bottlenecks of the peptide presentation pathways, as it ...
  • Ten years of collaborative progress in the quest for orthologs 

    Linard, Benjamin; Ebersberger, Ingo; McGlynn, Shawn E; Glover, Natasha; Mochizuki, Tomohiro; Gabaldón, Toni (Oxford University Press, 2021-08)
    Article
    Open Access
    Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology—evolutionary relatedness—is in many cases readily determined based on sequence similarity analysis. ...
  • Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations 

    Mixão, Verónica; Hegedűsová, Eva; Saus, Ester; Pryszcz, Leszek P; Cillingová, Andrea; Nosek, Jozef; Gabaldón, Toni (Oxford University Press, 2021-06)
    Article
    Open Access
    Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, ...
  • Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins 

    Gabriel Torres, Adrian; Rodríguez-Escribà, Marta; Marcet Houben, Marina; Santos Vieira, Helaine Graziele; Camacho, Noelia; Gabaldón, Toni (Oxford University Press, 2021-07)
    Article
    Open Access
    The modification of adenosine to inosine at the wobble position (I34) of tRNA anticodons is an abundant and essential feature of eukaryotic tRNAs. The expansion of inosine-containing tRNAs in eukaryotes followed the ...
  • Elucidation of ligand binding and dimerization of NADPH: protochlorophyllide (Pchlide) oxidoreductase from pea (Pisum sativum L.) by structural analysis and simulations 

    Hassan, Sameer; Guallar, Victor; Solymosi, Katalin; Aronsson, Henrik (Wiley, 2021-05)
    Article
    Open Access
    NADPH:protochlorophyllide (Pchlide) oxidoreductase (POR) is a key enzyme of chlorophyll biosynthesis in angiosperms. It is one of few known photoenzymes, which catalyzes the light-activated trans-reduction of the C17-C18 ...
  • Transcriptomic and genetic associations between Alzheimer’s disease, Parkinson’s disease, and cancer 

    Forés Martos, Jaume; Boullosa, Cesar; Rodrigo Domínguez, David; Sánchez, Jon; Suay García, Beatriz; Valencia, Alfonso (MDPI, 2021)
    Article
    Open Access
    Alzheimer’s (AD) and Parkinson’s diseases (PD) are the two most prevalent neurodegenerative disorders in human populations. Epidemiological studies have shown that patients suffering from either condition present a reduced ...
  • Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units 

    Chorostecki, Uciel; Saus, Ester; Gabaldón, Toni (Elsevier, 2021)
    Article
    Open Access
    Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the functions of lncRNAS are largely mediated by their structures. ...
  • FAIRification of genomic track metadata [version 1; peer review: 2 approved] 

    Gundersen, Sveinung; Boddu, Sanjay; Capella Gutiérrez, Salvador; Drabløs, Finn; Fernández González, Jose María; Kompova, Radmila; Taylor, Kieron; Titov, Dmytro; Zerbino, Daniel; Hovig, Eivind (F1000 Research, 2021)
    Article
    Open Access
    Background: Many types of data from genomic analyses can be represented as genomic tracks, i.e. features linked to the genomic coordinates of a reference genome. Examples of such data are epigenetic DNA methylation data, ...
  • Impact of transcriptome and gut microbiome on the response of HIV-1 infected individuals to a dendritic cell-based HIV therapeutic vaccine 

    Pastor Ibáñez, Roque; Díez Fuertes, Francisco; Sánchez Palomino, Sonsoles; Alcamí, Jose; Plana, Montserrat; Torrents, David; Leal, Lorna; García, Felipe (MDPI, 2021)
    Article
    Open Access
    Therapeutic vaccines based on dendritic cells offer a good approach to HIV-specific T-cell responses and partial control of the viral load after antiretroviral therapy interruption. The aim of the present study was to ...

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