Recent Submissions

  • A first update on mapping the human genetic architecture of COVID-19 

    COVID-19 Host Genetics Initiative (Nature Research, 2022-08)
    Article
    Open Access
    The COVID-19 pandemic continues to pose a major public health threat, especially in countries with low vaccination rates. To better understand the biological underpinnings of SARS-CoV-2 infection and COVID-19 severity, we ...
  • Identifying cellular cancer mechanisms through pathway-driven data integration 

    Windels, Sam F L; Malod Dognin, Noël; Przulj, Natasa (Oxford University Press, 2022-08-02)
    Article
    Open Access
    Abstract Motivation Cancer is a genetic disease in which accumulated mutations of driver genes induce a functional reorganization of the cell by reprogramming cellular pathways. Current approaches identify cancer pathways ...
  • Overlap of vitamin A and vitamin D target genes with CAKUT-related processes [version 2; peer review: 2 approved, 2 approved with reservations] 

    Ozisik, Ozan; Ehrhart, Friederike; Evelo, Chris T.; Mantovani, Alberto; Baudot, Anaı̈s (F1000Research, 2022)
    Article
    Open Access
    Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) are a group of abnormalities affecting the kidneys and their outflow tracts. CAKUT patients display a large clinical variability as well as a complex aetiology. ...
  • Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches 

    Bugnon, Leandro; Edera, Alejandro A.; Prochetto, Santiago D.; Gerard, Matias; Raad, Jonathan; Chorostecki, Uciel Pablo; Gabaldón, Toni (Oxford University Press, 2022-07)
    Article
    Restricted access - publisher's policy
    MOTIVATION: In contrast to messenger RNAs, the function of the wide range of existing long noncoding RNAs (lncRNAs) largely depends on their structure, which determines interactions with partner molecules. Thus, the ...
  • Metagenomic mining for esterases in the microbial community of Los Rueldos acid mine drainage formation 

    Vidal, Paula; Martínez Martínez, Mónica; Fernandez Lopez, Laura; Roda, Sergi; Méndez García, Celia; Golyshina, Olga V.; Guallar, Victor; Pelaez, Ana Isabel; Ferrer, Manuel (Frontiers Media, 2022-05)
    Article
    Open Access
    Acid mine drainage (AMD) systems are extremely acidic and are metal-rich formations inhabited by relatively low-complexity communities of acidophiles whose enzymes remain mostly uncharacterized. Indeed, enzymes from only ...
  • Resolving the fine structure in the energy landscapes of repeat proteins 

    Sanches, Murilo N.; Parra, Rodrigo Gonzalo; Viegas, Rafael Giordano; Oliveira Junior, Antonio Bento; Wolynes, Peter; Ferreiro, Diego U.; Leite, Vitor B.P. (Cambridge University Press, 2022)
    Article
    Open Access
    Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein–protein interactions in a diversity of biological systems. These proteins have an elongated ...
  • Universal multilayer network exploration by random walk with restart 

    Baptista, Anthony; Gonzalez, Aitor; Baudot, Anaïs (Nature Research, 2022)
    Article
    Open Access
    The amount and variety of data have been increasing drastically for several years. These data are often represented as networks and explored with approaches arising from network theory. Recent years have witnessed the ...
  • The Quest for Orthologs orthology benchmark service in 2022 

    Nevers, Yannis; Jones, Tamsin E M; Jyothi, Dushyanth; Yates, Bethan; Ferret, Meritxell; Portell Silva, Laura; Codo, Laia; Marcet Houben, Marina; Vlasova, Anna; Gabaldon, Toni; Capella Gutierrez, Salvador (Oxford University Press [, 2022)
    Article
    Open Access
    The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource ...
  • Heterogeneous infectivity and pathogenesis of SARS-CoV-2 variants Beta, Delta and Omicron in transgenic K18-hACE2 and wildtype mice 

    Tarrés Freixas, Ferran; Trinité, Benjamin; Pons Grífols, Anna; Romero Durana, Miguel; Riveira Muñoz, Eva; Guallar, Victor; Lepore, Rosalba; Valencia, Alfonso (Frontiers Media, 2022-05)
    Article
    Open Access
    The emerging SARS-CoV-2 variants of concern (VOCs) may display enhanced transmissibility, more severity and/or immune evasion; however, the pathogenesis of these new VOCs in experimental SARS-CoV-2 models or the potential ...
  • Examination of Genome-Wide Ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus 

    Crivelente Horta, Maria Augusta; Steenwyk, Jacob L.; Mead, Matthew E.; Braz dos Santos, Luciano Henrique; Zhao, Shu; Gibbons, John G.; Marcet Houben, Marina; Gabaldón, Toni; Rokas, Antonis; Goldman, Gustavo (American Society for Microbiology, 2022-06-29)
    Article
    Open Access
    Aspergillus fumigatus is a cosmopolitan species of fungus responsible for thousands of cases of invasive disease annually. Clinical and environmental isolates of A. fumigatus exhibit extensive phenotypic differences, ...
  • orsum: a Python package for filtering and comparing enrichment analyses using a simple principle 

    Ozisik, Ozan; Térézol, Morgane; Baudot, Anaïs (BioMed Central (BMC), 2022)
    Article
    Open Access
    BACKGROUND: Enrichment analyses are widely applied to investigate lists of genes of interest. However, such analyses often result in long lists of annotation terms with high redundancy, making the interpretation and ...
  • Epigenetic profiling linked to multisystem inflammatory syndrome in children (MIS-C): A multicenter, retrospective study 

    Davalos, Veronica; García Prieto, Carlos A.; Ferrer, Gerardo; Aguilera Albesa, Sergio; Valencia Ramos, Juan (Elsevier, 2022)
    Article
    Open Access
    BACKGROUND: Most children and adolescents infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain asymptomatic or develop a mild coronavirus disease 2019 (COVID-19) that usually does not ...

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