Recent Submissions

  • Hybridization and the origin of new yeast lineages 

    Gabaldón, Toni (Oxford University Press (OUP), 2020-08)
    Article
    Open Access
    Hybrids originate from the mating of two diverged organisms, resulting in novel lineages that have chimeric genomes. Hybrids may exhibit unique phenotypic traits that are not necessarily intermediate between those present ...
  • Fungal evolution: cellular, genomic and metabolic complexity 

    Naranjo‐Ortiz, Miguel A.; Gabaldón, Toni (Wiley, 2020-10)
    Article
    Open Access
    The question of how phenotypic and genomic complexity are inter‐related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and ...
  • Predicción de mortalidad en recién nacidos prematuros. Revisión sistemática actualizada 

    Río, Ruth del; Thió, Marta; Bosio, Mattia; Figueras, Josep; Iriondo, Martín (Elsevier, 2020-07)
    Article
    Open Access
    Introducción La prematuridad extrema se asocia a altas tasas de mortalidad. Para profesionales y familias, es prioritario establecer de forma individualizada las probabilidades de muerte en diferentes momentos. El objetivo ...
  • The quiet and underappreciated rise of drug-resistant invasive fungal pathogens 

    Arastehfar, Amir; Lass-Flörl, Cornelia; Garcia-Rubio, Rocio; Daneshnia, Farnaz; Ilkit, Macit; Boekhout, Teun; Gabaldon, Toni; Perlin, David S. (MDPI, 2020-08)
    Article
    Open Access
    Human fungal pathogens are attributable to a significant economic burden and mortality worldwide. Antifungal treatments, although limited in number, play a pivotal role in decreasing mortality and morbidities posed by ...
  • Tracking of antibiotic resistance transfer and rapid plasmid evolution in a hospital setting by Nanopore sequencing 

    Peter, Silke; Bosio, Mattia; Gross, Caspar; Bezdan, Daniela; Gutierrez, Javier; Oberhettinger, Philipp; Liese, Jan; Vogel, Wichard; Dörfel, Daniela; Berger, Lennard; Marschal, Matthias; Willmann, Matthias; Gut, Ivo; Gut, Marta; Autenrieth, Ingo; Ossowski, Stephan (American Society for Microbiology, 2020)
    Article
    Open Access
    Infections with multidrug-resistant bacteria often leave limited or no treatment options. The transfer of antimicrobial resistance genes (ARG) carrying plasmids between bacterial species by horizontal gene transfer represents ...
  • Predicting Gastric Cancer Molecular Subtypes from Gene Expression Data 

    Moreno, Marta; Sousa, Abel; Melé, Marta; Oliveira, Rui; Ferreira, Pedro G. (MDPI, 2020)
    Article
    Open Access
    Stomach cancer is a complex disease and one of the leading causes of cancer mortality in the world. With the view to improve patient diagnosis and prognosis, it has been stratified into four molecular subtypes. In this ...
  • Patterns and impacts of nonvertical evolution in eukaryotes: a paradigm shift 

    Gabaldon, Toni (Wiley, 2020)
    Article
    Open Access
    Abstract Evolution of eukaryotic species and their genomes has been traditionally understood as a vertical process in which genetic material is transmitted from parents to offspring along a lineage, and in which genetic ...
  • Cis and trans effects differentially contribute to the evolution of promoters and enhancers 

    Mattioli, Kaia; Oliveros, Winona; Gerhardinger, Chiara; Andergassen, Daniel; Maass, Philipp G.; Rinn, John L.; Melé, Marta (Springer Nature, 2020-08-20)
    Article
    Open Access
    Background Gene expression differences between species are driven by both cis and trans effects. Whereas cis effects are caused by genetic variants located on the same DNA molecule as the target gene, trans effects are ...
  • Modeling of protein complexes and molecular assemblies with pyDock 

    Rosell, Mireia; Rodríguez-Lumbreras, Luis Angel; Fernández-Recio, Juan (Springer Link, 2020)
    Part of book or chapter of book
    Restricted access - publisher's policy
    The study of the 3D structural details of protein interactions is essential to understand biomolecular functions at the molecular level. In this context, the limited availability of experimental structures of protein–protein ...
  • IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms 

    Nadeu, Ferran; Mas-de-les-Valls, Rut; Navarro, Alba; Royo, Romina; Martín, Silvia; Villamor, Neus; Suárez-Cisneros, Helena; Mares, Rosó; Lu, Junyan; Enjuanes, Anna; Rivas-Delgado, Alfredo; Aymerich, Marta; Baumann, Tycho; Colomer, Dolors; Delgado, Julio; Morin, Ryan D.; Zenz, Thorsten; Puente, Xose S.; Campbell, Peter J.; Beà, Sílvia; Maura, Francesco; Campo, Elías (Springer Nature, 2020-07)
    Article
    Open Access
    Immunoglobulin (Ig) gene rearrangements and oncogenic translocations are routinely assessed during the characterization of B cell neoplasms and stratification of patients with distinct clinical and biological features, ...
  • Phylogenomics identifies an ancestral burst of gene duplications predating the diversification of aphidomorpha 

    Julca, Irene; Marcet-Houben, Marina; Cruz, Fernando; Vargas-Chavez, Carlos; Johnston, John Spencer; Gómez-Garrido, Jèssica; Frias, Leonor; Corvelo, André; Loska, Damian; Cámara, Francisco; Gut, Marta; Alioto, Tyler; Latorre, Amparo; Gabaldon, Toni (Oxford University Press (OUP), 2020-03)
    Article
    Open Access
    Large-scale gene duplication, including whole-genome duplication (WGD), is a very common phenomenon in eukaryotic genomes. Bursts of gene duplications are considered a major source of evolutionary innovation and have been ...
  • A user guide for the online exploration and visualization of PCAWG data 

    Goldman, Mary J.; Zhang, Junjun; Fonseca, Nuno A.; Cortés-Ciriano, Isidro; Xiang, Qian; Craft, Brian; Piñeiro-Yáñez, Elena; O'connor, Brian D.; Bazant, Wojciech; Barrera, Elisabet; Muñoz-Pomer, Alfonso; Petryszak, Robert; Füllgrabe, Anja; Al-Shahrour, Fatima; Keays, Maria; Haussler, David; Weinstein, John N; Huber, Wolfgang; Park, Peter J.; Papatheodorou, Elena; Valencia, Alfonso; Zhu, Jingchun; Ferretti, Vincent; Vazquez, Miguel (Springer Nature, 2020)
    Article
    Open Access
    The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which ...

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