• 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, ...
• 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 ...
• RD-Connect, NeurOmics and EURenOmics: collaborative European initiative for rare diseases

  Lochmüller, Hanns; Badowska, Dorota M.; Thompson, Rachel; Knoers, Nine V.; Aartsma-Rus, Annemieke; Gut, Ivo Glynne; Wood, Libby; Harmuth, Tina; Durudas, Andre; Graessner, Holm; Schaefer, Franz; Riess, Olaf; RD-Connect consortium; NeurOmics consortium; EURenOmics consortium (Nature Research, 2018)

  Although individually uncommon, rare diseases (RDs) collectively affect 6-8% of the population. The unmet need of the rare disease community was recognized by the European Commission which in 2012 funded three flagship ...
• The genetic landscape of a physical interaction

  Diss, Guillaume; Lehner, Ben, 1978- (eLife, 2018)

  A key question in human genetics and evolutionary biology is how mutations in different genes combine to alter phenotypes. Efforts to systematically map genetic interactions have mostly made use of gene deletions. However, ...
• Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis

  Martínez Abadías, Neus; Mateu-Estivill, Roger; Sastre-Tomas, Jaume; Motch Perrine, Susan; Yoon, Melissa; Robert Moreno, Alexandre; Swoger, Jim; Russo, Lucia; Kawasaki, Kazuhiko (eLife, 2018)

  The earliest developmental origins of dysmorphologies are poorly understood in many congenital diseases. They often remain elusive because the first signs of genetic misregulation may initiate as subtle changes in gene ...
• Prevalence of dementia diagnoses not otherwise specified in eight European countries: a cross-sectional cohort study

  Lethin, Connie; Rahm Hallberg, Ingalill; Renom-Guiteras, Anna; Verbeek, Hilde; Saks, Kai; Stolt, Minna; Zabalegui, Adelaida; Soto-Martin, Maria; Nilsson, Christer (BioMed Central, 2019)

  BACKGROUND: Dementia is a syndrome, with a wide range of symptoms. It is important to have a timely diagnosis during the disease course to reduce the risk of medication errors, enable future care planning for the patient ...
• GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI

  Couto Alves, Alexessander; Estivill, Xavier, 1955-; Sunyer Deu, Jordi; Early Growth Genetics (EGG) Consortium (American Association for the Advancement of Science (AAAS), 2019)

  Early childhood growth patterns are associated with adult health, yet the genetic factors and the developmental stages involved are not fully understood. Here, we combine genome-wide association studies with modeling of ...
• Association of maternal iodine status with child IQ: a meta-analysis of individual participant data

  Levie, Deborah; Korevaar, Tim I. M.; Bath, Sarah C.; Murcia, Mario; Dineva, Mariana; Llop, Sabrina; Espada, Mercedes; van Herwaarden, Antonius E.; de Rijke, Yolanda B.; Ibarluzea, Jesús; Sunyer Deu, Jordi; Tiemeier, Henning; Rayman, Margaret P.; Guxens Junyent, Mònica; Peeters, Robin P. (Oxford University Press, 2019)

  Context: Although the consequences of severe iodine deficiency are beyond doubt, the effects of mild to moderate iodine deficiency in pregnancy on child neurodevelopment are less well established. Objective: To study the ...
• Maternal circulating Vitamin D3 levels during pregnancy and behaviour across childhood

  López Vicente, Mònica, 1988-; Sunyer Deu, Jordi; Lertxundi, Nerea; González, Llúcia; Rodríguez Dehli, Cristina; Espada Sáenz-Torre, Mercedes; Vrijheid, Martine; Tardón, Adonina; Llop, Sabrina; Torrent Quetglas, Maties; Ibarluzea, Jesús; Guxens Junyent, Mònica (Nature Research, 2019)

  Vitamin D deficiency during critical periods of development could lead to persistent brain alterations. We aimed to assess the association between maternal vitamin D3, the major circulatory form of vitamin D, at pregnancy ...
• Da-TACOS: A dataset for cover song identification and understanding

  Yesiler, Furkan; Tralie, Chris; Correya, Albin Andrew; Silva, Diego F.; Tovstogan, Philip; Gómez Gutiérrez, Emilia, 1975-; Serra, Xavier (International Society for Music Information Retrieval (ISMIR), 2019)

  This paper focuses on Cover Song Identification (CSI), an important research challenge in content-based Music Information Retrieval (MIR). Although the task itself is interesting and challenging for both academia and ...

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