• Echinocandin-induced microevolution of Candida parapsilosis influences virulence and abiotic stress tolerance

  Papp, Csaba; Kocsis, Katica; Tóth, Renáta; Bodai, László; Willis, Jesse R.; Ksiezopolska, Ewa; Lozoya-Pérez, Nancy E.; Vágvölgyi, Csaba; Mora Montes, Hector; Gabaldón Estevan, Juan Antonio, 1973-; Nosanchuk, Joshua D.; Gácser, Attila (American Society for Microbiology, 2018)

  Candida species are a major cause of life-threatening bloodstream infections worldwide. Although Candida albicans is responsible for the vast majority of infections, the clinical relevance of other Candida species has also ...
• Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication

  Legras, Jean-Luc; Galeote, Virginie; Bigey, Frédéric; Camarasa, Carole; Marsit, Souhir; Nidelet, Thibault; Sanchez, Isabelle; Couloux, Arnaud; Guy, Julie; Franco-Duarte, Ricardo; Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973-; Schuller, Dorit; Sampaio, José Paulo; Dequin, Sylvie (Oxford University Press, 2018)

  The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how ...
• Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition

  Willis, Jesse R.; González-Torres, Pedro; Pittis, Alexandros, 1982-; Bejarano, Luis A.; Cozzuto, Luca; Andreu Somavilla, Núria; Alloza-Trabado, Miriam; Valentín, Antònia; Ksiezopolska, Ewa; Company, Carlos; Onywera, Harris; Montfort, Magda; Hermoso Pulido, Antonio; Iraola Guzman, Susana; Saus Martínez, Ester; Labeeuw, Annick; Carolis, Carlo; Hecht, Jochen; Ponomarenko, Julia; Gabaldón Estevan, Juan Antonio, 1973- (BioMed Central, 2018)

  Background: The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the ...
• Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM

  Mayer, Jürgen, 1977-; Robert Moreno, Alexandre; Sharpe, James; Swoger, Jim (Nature Research, 2018)

  Light sheet fluorescence microscopy (LSFM) is rapidly becoming an essential technology for mesoscopic imaging of samples such as embryos and adult mouse organs. However, LSFM can suffer from optical artifacts for which ...
• Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis

  Gabaldón Estevan, Juan Antonio, 1973- (Wiley, 2018)

  The origin of eukaryotes stands as a major open question in biology. Central to this question is the nature and timing of the origin of the mitochondrion, an ubiquitous eukaryotic organelle originated by the endosymbiosis ...
• Pergola: boosting visualization and analysis of longitudinal data by unlocking genomic analysis tools

  Espinosa-Carrasco, José; Erb, Ionas; Hermoso Pulido, Antonio; Ponomarenko, Julia; Dierssen, Mara; Notredame, Cedric (Elsevier, 2018)

  The growing appetite of behavioral neuroscience for automated data production is prompting the need for new computational standards allowing improved interoperability, reproducibility, and shareability. We show here how ...
• Signaling by steroid hormones in the 3D nuclear space

  Le Dily, François; Beato, Miguel (MDPI, 2018)

  Initial studies showed that ligand-activated hormone receptors act by binding to the proximal promoters of individual target genes. Genome-wide studies have now revealed that regulation of transcription by steroid hormones ...
• Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome

  Zapata Ortiz, Luis, 1985-; Pich, Oriol; Serrano Pubull, Luis, 1982-; Kondrashov, Fyodor A., 1979-; Ossowski, Stephan; Schaefer, Martin H. (BioMed Central, 2018)

  Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic ...
• Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture

  Grau Bové, Xavier; Ruiz Trillo, Iñaki; Irimia, Manuel (BioMed Central, 2018)

  Background: Alternative splicing, particularly through intron retention and exon skipping, is a major layer of pre-translational regulation in eukaryotes. While intron retention is believed to be the most prevalent mode ...
• Evolutionary emergence of drug resistance in Candida opportunistic pathogens

  Ksiezopolska, Ewa; Gabaldón Estevan, Juan Antonio, 1973- (MDPI, 2018)

  Fungal infections, such as candidiasis caused by Candida, pose a problem of growing medical concern. In developed countries, the incidence of Candida infections is increasing due to the higher survival of susceptible ...
• A method for RNA structure prediction shows evidence for structure in lncRNAs

  Delli Ponti, Riccardo, 1987-; Armaos, Alexandros; Marti, Stefanie; Tartaglia, Gian Gaetano (Frontiers, 2018)

  To compare the secondary structure profiles of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict ...
• Discovering putative prion-like proteins in plasmodium falciparum: a computational and experimental analysis

  Pallarès, Irantzu; de Groot, Natalia S.; Iglesias, Valentin; Sant'Anna, Ricardo; Biosca, Arnau; Fernàndez Busquets, Xavier; Ventura, Salvador (Frontiers, 2018)

  Prions are a singular subset of proteins able to switch between a soluble conformation and a self-perpetuating amyloid state. Traditionally associated with neurodegenerative diseases, increasing evidence indicates that ...
• Genome variation in the model halophilic bacterium Salinibacter ruber

  González-Torres, Pedro; Gabaldón Estevan, Juan Antonio, 1973- (Frontiers, 2018)

  The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered ...
• Sexually transmitted infections in young people and factors associated with HIV coinfection: an observational study in a large city

  Sentís, Alexis; Martin-Sánchez, Mario; Arando, Maider; Vall, Martí; Barbera, María Jesús; Ocaña, Inma; González Cordón, Ana; Alsina, Mercè; Martin-Ezquerra, Gemma; Knobel Freud, Hernando; Gurguí, Mercè; Vives, Alvaro; Coll, Josep; Caylà i Busqueras, Joan A.; Garcia de Olalla, Patricia; STI-HIV groupo Barcelona (BMJ Publishing Group, 2019)

  OBJECTIVES: Young people are a critical target group for sexually transmitted infections (STI) surveillance due to their particular behavioural and social related vulnerability. The aim of this study was to describe the ...
• Impact of antibiotic resistance on outcomes of neutropenic cancer patients with Pseudomonas aeruginosa bacteraemia (IRONIC study): study protocol of a retrospective multicentre international study

  Albasanz-Puig, Adaia; Montero, Maria Milagro; Carratalà, Jordi; IRONIC study group (BMJ Publishing Group, 2019)

  INTRODUCTION: Pseudomonas aeruginosa (PA) has historically been one of the major causes of severe sepsis and death among neutropenic cancer patients. There has been a recent increase of multidrug-resistant PA (MDRPA) ...
• Incisional hernia recurrence after open elective repair: expertise in abdominal wall surgery matters

  Pereira Rodríguez, José Antonio; Bravo-Salva, Alejandro; Montcusí Ventura, Blanca; Pérez-Farre, Silvia; Fresno de Prado, L.; López-Cano, Manuel (BioMed Central, 2019)

  BACKGROUND: Recurrence after incisional hernia repair is one of the major problems related with this operation. Our objective is to analyze the influence of abdominal wall surgery expertise in the results of the open ...
• LRBA deficiency in a patient with a novel homozygous mutation due to chromosome 4 segmental uniparental isodisomy

  Soler-Palacín, Pere; Garcia-Prat, Marina; Martín-Nalda, Andrea; Franco-Jarava, Clara; Rivière, Jacques G.; Plaja, Alberto; Bezdan, Daniela; Bosio, Mattia; Martínez-Gallo, Mónica; Ossowski, Stephan; Colobran, Roger (Frontiers, 2018)

  LRBA deficiency was first described in 2012 as an autosomal recessive disorder caused by biallelic mutations in the LRBA gene (OMIM #614700). It was initially characterized as producing early-onset hypogammaglobulinemia, ...
• Ten steps to get started in Genome Assembly and Annotation

  Dominguez Del Angel, Victoria; Hjerde, Erik; Sterck, Lieven; Capella Gutiérrez, Salvador Jesús, 1985-; Notredame, Cedric; Vinnere Pettersson, Olga; Amselem, Joëlle; Bouri, Laurent; Bocs, Stephanie; Klopp, Christophe; Gibrat, Jean-François; Vlasova, Anna; Leskosek, Brane L.; Soler, Lucile; Binzer-Panchai, Mahesh; Lantz, Henrik (F1000Research, 2018)

  As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, ...
• Registered access: authorizing data access

  Dyke, Stephanie O. M.; De Argila, Jordi Rambla; Flicek, Paul (Nature Research, 2018)

  The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of ...
• Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species

  Anastasiadi, Dafni, 1986-; Esteve-Codina, Anna; Piferrer, Francesc (BioMed Central, 2018)

  Background: DNA methylation is one of the main epigenetic mechanisms for the regulation of gene expression in eukaryotes. In the standard model, methylation in gene promoters has received the most attention since it is ...

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