• Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals

  López Escardó, David, 1988-; Grau Bové, Xavier; Guillaumet-Adkins, Amy; Gut, Marta; Sieracki, Michael E.; Ruiz Trillo, Iñaki (Royal Society, 2019)

  Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data have unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there ...
• Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo

  Otterstrom, Jason; Castells García, Àlvaro, 1991-; Vicario, Chiara; Gómez García, Pablo; Cosma, Maria Pia, 1970-; Lakadamyali, Melike (Oxford University Press, 2019)

  Chromatin organization is crucial for regulating gene expression. Previously, we showed that nucleosomes form groups, termed clutches. Clutch size correlated with the pluripotency grade of mouse embryonic stem cells and ...
• Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning

  Buitrago, Diana; Codó, Laia; Illa, Ricard; Jorge, Pau de; Battistini, Federica; Flores, Oscar; Bayarri, Genis; Royo, Romina; Pino, Marc del; Heath, Simon; Hospital, Adam; Gelpí, Josep Lluís; Brun-Heath, Isabelle; Orozco, Modesto (Oxford University Press, 2019)

  We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the ...
• GNE genotype explains 20% of phenotypic variability in GNE myopathy

  Pogoryelova, Oksana; Wilson, Ian J.; Mansbach, Hank; Argov, Zohar; Nishino, Ichizo; Lochmüller, Hanns (Wolters Kluwer (LWW), 2019)

  Objective: To test the hypothesis that common GNE mutations influence disease severity; using statistical analysis of patient cohorts from different countries. Methods: Systematic literature review identified 11 articles ...
• The mutational landscape of a prion-like domain

  Bolognesi, Benedetta; Faure, Andre J.; Seuma, Mireia; Schmiedel, Jörn M.; Tartaglia, Gian Gaetano; Lehner, Ben, 1978- (Nature Research, 2019)

  Insoluble protein aggregates are the hallmarks of many neurodegenerative diseases. For example, aggregates of TDP-43 occur in nearly all cases of amyotrophic lateral sclerosis (ALS). However, whether aggregates cause ...
• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration

  Lucic, Bojana; Chen, Heng-Chang; Kuzman, Maja; Zorita, Eduard; Wegner, Julia; Minneker, Vera; Wang, Wei; Fronza, Raffaele; Laufs, Stefanie; Schmidt, Manfred; Stadhouders, Ralph; Roukos, Vassilis; Vlahovicek, Kristian; Filion, Guillaume; Lusic, Marina (Nature Research, 2019)

  HIV-1 recurrently targets active genes and integrates in the proximity of the nuclear pore compartment in CD4+ T cells. However, the genomic features of these genes and the relevance of their transcriptional activity for ...
• In-cell identification and measurement of RNA-protein interactions

  Graindorge, Antoine; Pinheiro, Inês; Nawrocka, Anna; Mallory, Allison C.; Tsvetkov, Peter; Gil, Noa; Carolis, Carlo; Buchholz, Frank; Ulitsky, Igor; Heard, Edith; Taipale, Mikko; Shkumatava, Alena (Nature Research, 2019)

  Regulatory RNAs exert their cellular functions through RNA-binding proteins (RBPs). Identifying RNA-protein interactions is therefore key for a molecular understanding of regulatory RNAs. To date, RNA-bound proteins have ...
• A practical guide for mutational signature analysis in hematological malignancies

  Maura, Francesco; Degasperi, Andrea; Nadeu, Ferran; Leongamornlert, Daniel; Davies, Helen; Moore, Luiza; Royo, Romina; Ziccheddu, Bachisio; Puente, Xosé S.; Avet-Loiseau, Herve; Campbell, Peter J.; Nik Zainal, Serena; Campo, Elias; Munshi, Nikhil; Bolli, Niccolò (Nature Research, 2019)

  Analysis of mutational signatures is becoming routine in cancer genomics, with implications for pathogenesis, classification, prognosis, and even treatment decisions. However, the field lacks a consensus on analysis and ...
• Performance assessment technologies for the support of musical instrument learning

  Eremenko, Vsevolod; Morsi, Alia; Narang, Jyoti; Serra, Xavier (2020)

  Recent technological developments are having a significant impact on musical instruments and singing voice learning. A proof is the number of successful software applications that are being used by aspiring musicians in ...
• Advances and applications in the quest for orthologs

  Glover, Natasha; Dessimoz, Christophe; Ebersberger, Ingo; Forslund, Sofia K.; Gabaldón Estevan, Juan Antonio, 1973-; Huerta Cepas, Jaime; Martin, Maria-Jesus; Muffato, Matthieu; Patricio, Mateus; Pereira, Cecile; Sousa da Silva, Alan; Wang, Yan-Dong; Sonnhammer, Erik; Thomas, Paul D. (Oxford University Press, 2019)

  Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play ...
• Microbiome and colorectal cancer: Roles in carcinogenesis and clinical potential

  Saus Martínez, Ester; Iraola Guzman, Susana; Willis, Jesse R.; Brunet-Vega, Anna; Gabaldón Estevan, Juan Antonio, 1973- (Elsevier, 2019)

  The gastrointestinal tract harbors most of the microbiota associated with humans. In recent years, there has been a surge of interest in assessing the relationships between the gut microbiota and several gut alterations, ...
• Genome sequence of the yeast Saprochaete ingens CBS 517.90

  Hodorová, Viktória; Lichancová, Hana; Zubenko, Stanislav; Sienkiewicz, Karolina; Penir, Sarah Mae U.; Afanasyev, Philipp; Boceck, Dominic; Bonnin, Sarah; Hakobyan, Siras; Smyczynska, Urszula; Zhivkoplias, Erik; Zlatohurska, Maryna; Tralle, Eugeniusz; Frolova, Alina; Pryszcz, Leszek Piotr, 1985-; Brejová, Broňa; Vinař, Tomáš; Nosek, Jozef (American Society for Microbiology, 2019)

  Chromosome-scale genome assembly of the yeast Saprochaete ingens CBS 517.90 was determined by a combination of technologies producing short (HiSeq X; Illumina) and long (MinION; Oxford Nanopore Technologies) reads. The ...
• Genome sequence of flavor-producing yeast saprochaete suaveolens NRRL Y-17571

  Lichancová, Hana; Hodorová, Viktória; Sienkiewicz, Karolina; Penir, Sarah Mae U.; Afanasyev, Philipp; Boceck, Dominic; Bonnin, Sarah; Hakobyan, Siras; Krawczyk, Pawel S.; Smyczynska, Urszula; Zhivkoplias, Erik; Zlatohurska, Maryna; Odrzywolski, Adrian; Tralle, Eugeniusz; Frolova, Alina; Pryszcz, Leszek Piotr, 1985-; Brejová, Broňa; Vinař, Tomáš; Nosek, Jozef (American Society for Microbiology, 2019)

  Saprochaete suaveolens is an ascomycetous yeast that produces a range of fruity flavors and fragrances. Here, we report the high-contiguity genome sequence of the ex-holotype strain, NRRL Y-17571 (CBS 152.25). The nuclear ...
• New factors for protein transport identified by a genome-wide CRISPRi screen in mammalian cells

  Bassaganyas Bars, Laia, 1985-; Popa, Stephanie J.; Horlbeck, Max; Puri, Claudia; Stewart, Sarah E.; Campelo, Felix; Ashok, Anupama, 1985-; Butnaru, Cristian M.; Brouwers, Nathalie; Heydari, Kartoosh; Ripoche, Jean; Weissman, Jonathan; Rubinsztein, David C.; Schekman, Randy; Malhotra, Vivek; Moreau, Kevin; Villeneuve, Julien (Rockefeller University Press, 2019)

  Protein and membrane trafficking pathways are critical for cell and tissue homeostasis. Traditional genetic and biochemical approaches have shed light on basic principles underlying these processes. However, the list of ...
• Predication drives verb cortical signatures

  Hernandez, Mireia; Fairhall, Scott L.; Lenci, Alessandro; Baronai, Marco; Caramazza, Alfonso (MIT Press, 2014)

  Verbs and nouns are fundamental units of language, but their neural instantiation remains poorly understood. Neuro- psychological research has shown that nouns and verbs can be damaged independently of each other, and ...
• Lying in a native and foreign language

  Duñabeitia, Jon Andoni; Costa, Albert, 1970- (Springer, 2015)

  This study explores the interaction between deceptive language and second language processing. One hundred participants were asked to produce veridical and false statements in either their first or second language. Pupil ...
• Longitudinal serum biomarker screening identifies malate dehydrogenase 2 as candidate prognostic biomarker for Duchenne muscular dystrophy

  Signorelli, Mirko; Ayoglu, Burcu; Johansson, Camilla; Lochmüller, Hanns; Straub, Volker; Muntoni, Francesco; Niks, Erik; Tsonaka, Roula; Persson, Anja; Aartsma-Rus, Annemieke; Nilsson, Peter; Al-Khalili Szigyarto, Cristina; Spitali, Pietro (Wiley-VCH Verlag, 2019)

  BACKGROUND: Duchenne muscular dystrophy (DMD) is a fatal disease for which no cure is available. Clinical trials have shown to be largely underpowered due to inter-individual variability and noisy outcome measures. The ...
• Encircling the regions of the pharmacogenomic landscape that determine drug response

  Fernández Torras, Adrià; Duran-Frigola, Miquel, 1985-; Aloy, Patrick, 1972- (BioMed Central, 2019)

  Background: The integration of large-scale drug sensitivity screens and genome-wide experiments is changing the field of pharmacogenomics, revealing molecular determinants of drug response without the need for previous ...
• Delegating sex: differential gene expression in stolonizing syllids uncovers the hormonal control of reproduction

  Álvarez Campos, Patricia; Kenny, Nathan J.; Verdes, Aida; Fernández, Rosa; Novo, Marta; Giribet, Gonzalo; Riesgo, Ana (Oxford University Press, 2019)

  Stolonization in syllid annelids is a unique mode of reproduction among animals. During the breeding season, a structure resembling the adult but containing only gametes, called stolon, is formed generally at the posterior ...
• Genome assemblies of two rare opportunistic yeast pathogens: Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii)

  Mixão, Verónica; Saus Martínez, Ester; Perez Hansen, Antonio; Lass-Florl, Cornelia; Gabaldón Estevan, Juan Antonio, 1973- (Genetics Society of America, 2019)

  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 ...

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