Now showing items 1-13 of 13

    • CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies 

      Hovhannisyan, Hrant; Hafez, Ahmed; Llorens, Carlos; Gabaldon, Toni (Oxford University Press, 2020)
      Article
      Open Access
      Motivation Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing ...
    • Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans 

      Mixão, Verónica; Saus, Ester; Boekhout, Teun; Gabaldon, Toni (Oxford University Press, 2021-02)
      Article
      Open Access
      Candida albicans is the most commonly reported species causing candidiasis. The taxonomic classification of C. albicans and related lineages is controversial, with Candida africana (syn. C. albicans var. africana) and ...
    • Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans 

      Priest, Shelby J.; Coelho, Marco A.; Mixão, Verónica; Applen Clancey, Shelly; Xu, Yitong; Sun, Sheng; Gabaldon, Toni; Heitman, Joseph (PLOS, 2021)
      Article
      Open Access
      Hybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that ...
    • Fungal evolution: diversity, taxonomy and phylogeny of the Fungi 

      Naranjo Ortíz, Miguel A.; Gabaldon, Toni (Wiley, 2019)
      Article
      Open Access
      The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely ...
    • Genome Assemblies of Two Rare Opportunistic Yeast Pathogens: Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii) 

      Mixão, Verónica; Saus, Ester; Perez Hansen, Antonio; Lass Florl, Cornelia; Gabaldon, Toni (Genetics Society of America (GSA), 2019)
      Article
      Open Access
      Infections caused by opportunistic yeast pathogens have increased over the last years. These infections can be originated by a large number of diverse yeast species of varying incidence, and with distinct clinically relevant ...
    • Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.) 

      Julca, Irene; Marcet-Houben, Marina; Cruz, Fernando; Gómez-Garrido, Jèssica; Gaut, Brandon S.; Díez, Concepción M.; Gut, Ivo G.; Alioto, Tyler S.; Vargas, Pablo; Gabaldon, Toni (Springer Nature, 2020)
      Article
      Open Access
      Background Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties ...
    • Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel 

      Gerdol, Marco; Moreira, Rebeca; Cruz, Fernando; Gómez-Garrido, Jessica; Vlasova, Anna; Rosani, Umberto; Venier, Paola; Naranjo-Ortiz, Miguel A.; Murgarella, Maria; Greco, Samuele; Balseiro, Pablo; Corvelo, André; Frias, Leonor; Gut, Marta; Gabaldon, Toni; Pallavicini, Alberto; Canchaya, Carlos; Novoa, Beatriz; Alioto, Tyler S.; Posada, David; Figueras, Antonio (Springer Nature, 2020)
      Article
      Open Access
      Background The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive ...
    • 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 ...
    • Oral microbiome in down syndrome and its implications on oral health 

      Willis, Jesse R; Iraola-Guzmán, Susana; Saus, Ester; Ksiezopolska, Ewa; Cozzuto, Luca; Bejarano, Luis A; Alloza-Trabado, Miriam; Puig-Sola, Anna; Blanco, Andrea; Broglio, Elisabetta; Carolis, Carlo; Hecht, Jochen; Ponomarenko, Julia; Gabaldon, Toni (Taylor and Francis, 2020)
      Article
      Open Access
      Introduction: The oral cavity harbors an abundant and diverse microbial community (i.e. the microbiome), whose composition and roles in health and disease have been the focus of intense research. Down syndrome (DS) is ...
    • 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 ...
    • 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 ...
    • Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum 

      Fernández, Rosa; Marcet Houben, Marina; Legeai, Fabrice; Richard, Gautier; Robin, Stéfanie; Wucher, Valentin; Pegueroles, Cinta; Gabaldon, Toni; Tagu, Denis (Oxford University Press (OUP), 2020-05-02)
      Article
      Open Access
      Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including ...
    • 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 ...