• 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 ...
• Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution

  Schaerli, Yolanda; Jiménez, Alba; Duarte, José M.; Mihajlovic, Ljiljana; Renggli, Julien; Isalan, Mark; Sharpe, James; Wagner, Andreas (Wiley-Blackwell, 2018)

  Phenotypic variation is the raw material of adaptive Darwinian evolution. The phenotypic variation found in organismal development is biased towards certain phenotypes, but the molecular mechanisms behind such biases are ...
• Exon junction complex shapes the transcriptome by repressing recursive splicing

  Blazquez, Lorea; Emmett, Warren; Faraway, Rupert; Pineda, Jose Mario Bello; Bajew, Simon; Gohr, André; Haberman, Nejc; Sibley, Christopher R.; Bradley, Robert K.; Irimia, Manuel; Ule, Jernej (Elsevier, 2018)

  Recursive splicing (RS) starts by defining an "RS-exon," which is then spliced to the preceding exon, thus creating a recursive 5' splice site (RS-5ss). Previous studies focused on cryptic RS-exons, and now we find that ...
• 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 ...
• Regulation of lipid droplets by metabolically controlled Ldo isoforms

  Teixeira, Vítor; Martínez-Montañés, Fernando; Grippa, Alexandra, 1980-; Buxó, Laura; Idrissi, Fatima-Zahra; Ejsing, Christer S.; Carvalho, Pedro C. (Rockefeller University Press, 2018)

  Storage and consumption of neutral lipids in lipid droplets (LDs) are essential for energy homeostasis and tightly coupled to cellular metabolism. However, how metabolic cues are integrated in the life cycle of LDs is ...
• 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 ...
• Maternal and fetal genetic contribution to gestational weight gain

  Warrington, Nicole M.; Espinosa Díaz, Ana; Guxens Junyent, Mònica; Kogevinas, Manolis; Bustamante Pineda, Mariona; Lawlor, Debbie A. (Nature Research, 2018)

  Background: Clinical recommendations to limit gestational weight gain (GWG) imply high GWG is causally related to adverse outcomes in mother or offspring, but GWG is the sum of several inter-related complex phenotypes ...
• 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 ...
• Recommendations for improving the quality of rare disease registries

  Kodra, Yllka; Lochmüller, Hanns; Taruscio, Domenica (MDPI, 2018)

  Rare diseases (RD) patient registries are powerful instruments that help develop clinical research, facilitate the planning of appropriate clinical trials, improve patient care, and support healthcare management. They ...
• Mutations in glycyl-tRNA synthetase impair mitochondrial metabolism in neurons

  Boczonadi, Veronika; Meyer, Kathrin; Gonczarowska-Jorge, Humberto; Griffin, Helen; Roos, Andreas; Bartsakoulia, Marina; Bansagi, Boglarka; Ricci, Giulia; Palinkas, Fanni; Zahedi, René P.; Bruni, Francesco; Kaspar, Brian; Lochmüller, Hanns; Boycott, Kym M.; Müller, Juliane; Horvath, Rita (Oxford University Press, 2018)

  The nuclear-encoded glycyl-tRNA synthetase gene (GARS) is essential for protein translation in both cytoplasm and mitochondria. In contrast, different genes encode the mitochondrial and cytosolic forms of most other tRNA ...
• GFPT1 deficiency in muscle leads to myasthenia and myopathy in mice

  Issop, Yasmin; Hathazi, Denisa; Khan, Muzamil Majid; Rudolf, Rüdiger; Weis, Joachim; Spendiff, Sally; Slater, Clarke R.; Roos, Andreas; Lochmüller, Hanns (Oxford University Press, 2018)

  Glutamine-fructose-6-phosphate transaminase 1 (GFPT1) is the rate-limiting enzyme in the hexosamine biosynthetic pathway which yields precursors required for protein and lipid glycosylation. Mutations in GFPT1 and other ...
• 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 ...
• 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 ...
• VarQ: a tool for the structural and functional analysis of human protein variants

  Radusky, Leandro; Modenutti, Carlos; Delgado, Javier; Bustamante, Juan P.; Vishnopolska, Sebastian; Kiel, Christina; Serrano Pubull, Luis, 1982-; Marti, Marcelo; Turjanski, Adrián (Frontiers, 2018)

  Understanding the functional effect of Single Amino acid Substitutions (SAS), derived from the occurrence of single nucleotide variants (SNVs), and their relation to disease development is a major issue in clinical genomics. ...
• 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, ...

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