Recent Submissions

  • The transposable element-rich genome of the cereal pest Sitophilus oryzae 

    Parisot, Nicolas; Vargas Chávez, Carlos; Goubert, Clément; Baa-Puyoulet, Patrice; Balmand, Séverine; Gabaldón, Toni; Marcet Houben, Marina (BMC, 2021)
    Article
    Open Access
    Background The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship ...
  • COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain 

    Ponce De Leon, Miguel; Valle, Javier del; Fernández González, Jose María; Bernardo, Marc; Cirillo, Davide; Sanchez Valle, Jon; Smith, Matthew; Capella Gutiérrez, Salvador; Gullón, Tania; Valencia, Alfonso (Nature Research, 2021)
    Article
    Open Access
    COVID-19 is an infectious disease caused by the SARS-CoV-2 virus, which has spread all over the world leading to a global pandemic. The fast progression of COVID-19 has been mainly related to the high contagion rate of the ...
  • Mutations suppressing the lack of prepilin peptidase provide insights into the maturation of the major Pilin Protein in Cyanobacteria 

    Linhartová, Markéta; Skotnicová, Petra; Hakkila, Kaisa; Tichý, Martin; Komenda, Josef; Knoppová, Jana; Gilabert, Joan F.; Guallar, Victor; Tyystjärvi, Taina; Sobotka, Roman (Frontiers Media, 2021)
    Article
    Open Access
    Type IV pili are bacterial surface-exposed filaments that are built up by small monomers called pilin proteins. Pilins are synthesized as longer precursors (prepilins), the N-terminal signal peptide of which must be removed ...
  • PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies 

    Fuentes, Diego; Molina, Manuel; Chorostecki, Uciel; Capella Gutiérrez, Salvador; Marcet Houben, Marina; Gabaldón, Toni (Oxford University Press, 2021)
    Article
    Open Access
    PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous ...
  • Human albumin enhances the pathogenic potential of Candida glabrata on vaginal epithelial cells 

    Pekmezovic, Marina; Kaune, Ann Kristin; Austermeier, Sophie; Hitzler, Sophia U. J.; Mogavero, Selene; Hovhannisyan, Hrant; Gabaldón, Toni; Gresnigt, Mark S.; Hube, Bernhard (Public Library of Science (PLoS), 2021)
    Article
    Open Access
    The opportunistic pathogen Candida glabrata is the second most frequent causative agent of vulvovaginal candidiasis (VVC), a disease that affects 70–75% of women at least once during their life. However, C. glabrata is ...
  • FA-nf: A functional annotation pipeline for proteins from non-model organisms implemented in Nextflow 

    Vlasova, Anna; Hermoso Pulido, Toni; Camara, Francisco; Ponomarenko, Julia; Guigó, Roderic (MDPI, 2021)
    Article
    Open Access
    Functional annotation allows adding biologically relevant information to predicted features in genomic sequences, and it is, therefore, an important procedure of any de novo genome sequencing project. It is also useful for ...
  • A multi-objective genetic algorithm to find active modules in multiplex biological networks 

    Novoa del Toro, Elva María; Mezura Montes, Efrén; Vignes, Matthieu; Térézol, Morgane; Magdinier, Frédérique; Tichit, Laurent; Baudot, Anais (Public Library of Science (PLoS), 2021)
    Article
    Open Access
    The identification of subnetworks of interest—or active modules—by integrating biological networks with molecular profiles is a key resource to inform on the processes perturbed in different cellular conditions. We here ...
  • Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients 

    Hérivaux, Anaïs; Willis, Jesse R; Mercier, Toine; Lagrou, Katrien; Gonçalves, Samuel M; Maertens, Johan; Carvalho, Agostinho; Gabaldon, Toni; Cunha, Cristina (BMJ Publishing Group, 2021)
    Article
    Open Access
    Abstract Rationale Recent studies have revealed that the lung microbiota of critically ill patients is altered and predicts clinical outcomes. The incidence of invasive fungal infections, namely, invasive pulmonary ...
  • Assessing the accuracy of contact and distance predictions in CASP14 

    Ruiz Serra, Victoria; Pontes, Camila; Milanetti, Edoardo; Kryshtafovych, Andriy; Lepore, Rosalba; Valencia, Alfonso (Wiley, 2021)
    Article
    Open Access
    We present the results of the assessment of the intramolecular residue–residue contact and distance predictions from groups participating in the 14th round of the CASP experiment. The performance of contact prediction ...
  • TIGER: The gene expression regulatory variation landscape of human pancreatic islets 

    Alonso, Lorena; Piron, Anthony; Morán, Ignasi; Guindo Martínez, Marta; Bonàs Guarch, Sílvia; Royo, Romina; Puiggròs, Montserrat; Amela, Ramon; Mercader, Josep M.; Torrents, David (Cell Press, 2021)
    Article
    Open Access
    Genome-wide association studies (GWASs) identified hundreds of signals associated with type 2 diabetes (T2D). To gain insight into their underlying molecular mechanisms, we have created the translational human pancreatic ...
  • STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells 

    Richart, Laia; Lapi, Eleonora; Pancaldi, Vera; Cuenca Ardura, Mirabai; Carrillo de Santa Pau, Enrique; Madrid, Miguel; Serra, François; Valencia, Alfonso (Oxford University Press, 2021-10-14)
    Article
    Open Access
    Cohesin exists in two variants containing STAG1 or STAG2. STAG2 is one of the most mutated genes in cancer and a major bladder tumor suppressor. Little is known about how its inactivation contributes to tumorigenesis. Here, ...
  • COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms 

    Ostaszewski, Marek; Niarakis, Anna; Mazein, Alexander; Kuperstein, Inna; Phair, Robert; Montagud, Arnau; Ponce De Leon, Miguel; Vazquez, Miguel; Valencia, Alfonso (Wiley Open Access, 2021-10-21)
    Article
    Open Access
    We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. ...

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