• 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 ...
• Mutations in L-type amino acid transporter-2 support SLC7A8 as a novel gene involved in age-related hearing loss

  Espino Guarch, Meritxell; Fons-Llitjós, Mariona; Murillo-Cuesta, Silvia; Errasti-Murugarren, Ekaitz; Celaya, Adelaida M.; Girotto, Giorgia; Vuckovic, Dragana; Mezzavilla, Massimo; Vilches, Clara (eLife, 2018)

  Age-related hearing loss (ARHL) is the most common sensory deficit in the elderly. The disease has a multifactorial etiology with both environmental and genetic factors involved being largely unknown. SLC7A8/SLC3A2 heterodimer ...
• High levels of histones promote whole-genome-duplications and trigger a Swe1(WEE1)-dependent phosphorylation of Cdc213(CDK1)

  Maya Miles, Douglas; Peñate, Xenia; Sanmartín Olmo, Trinidad; Jourquin, Frederic; Muñoz Centeno, Maria Cruz; Mendoza, Manuel (Mendoza Palomares); Simon, Marie-Noelle; Chávez, Sebastián; Geli, Vincent (eLife, 2018)

  Whole-genome duplications (WGDs) have played a central role in the evolution of genomes and constitute an important source of genome instability in cancer. Here, we show in Saccharomyces cerevisiae that abnormal accumulations ...
• Two consecutive microtubule-based epithelial seaming events mediate dorsal closure in the scuttle fly Megaselia abdita

  Fraire-Zamora, Juan José; Jaeger, Johannes, 1973-; Solon, Jérôme (eLife, 2018)

  Evolution of morphogenesis is generally associated with changes in genetic regulation. Here, we report evidence indicating that dorsal closure, a conserved morphogenetic process in dipterans, evolved as the consequence of ...
• Prevention and management of musculoskeletal pain in nursing staff by a multifaceted intervention in the workplace: design of a cluster randomized controlled trial with effectiveness, process and economic evaluation (INTEVAL_Spain)

  Serra, Consol; Soler-Font, Mercè; García, Ana María; Peña, Pilar; Vargas-Prada Figueroa, Sergio, 1976 -; Ramada Rodilla, José María, 1961- (BioMed Central, 2019)

  BACKGROUND: Musculoskeletal pain (MSP) is the leading cause of years lived with disability. In consequence, to reduce MSP and its associated sickness absence is a major challenge. Previous interventions have been developed ...
• Labor market situation after an episode of sickness absence due to malignant neoplasia. Evidence from a Spanish cohort

  Lear-Claveras, Ana; Ubalde López, Mònica, 1972-; Serra Saurina, Laura (BioMed Central, 2019)

  BACKGROUND: Due to the progress in screening and cancer treatments, survivor's prognosis has improved enabling a more likely return to work. However, return to work after a cancer diagnosis may be complex because of an ...
• Early outcomes of kidney transplantation from elderly donors after circulatory death (GEODAS study).

  Pérez-Saez, María José; Pascual Santos, Julio; Portolés, José; GEODAS Group (BioMed Central, 2019)

  BACKGROUND: Spain has dramatically increased the number of controlled circulatory death donors (cDCD). The initial selection criteria for considering cDCD for kidney transplantation (KT) have been expanded progressively, ...
• Determinants of international variation in the prevalence of disabling wrist and hand pain

  Coggon David; Serra, Consol; Harcombe, Helen (BioMed Central, 2019)

  BACKGROUND: Previous research has indicated that wide international variation in the prevalence of disabling low back pain among working populations is largely driven by factors predisposing to musculoskeletal pain more ...

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