• 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 ...
• Language reconfiguration in bilinguals: a study with Huntington’s disease patients

  Calabria, Marco; Pérez Pérez, Jesús; Martínez Horta, Saúl; Horta Barba, Andrea; Carceller, Mar; Kulisevsky, Jaime; Costa, Albert, 1970- (John Benjamins Publishing, 2018)

  The present study investigated language inhibition and cross-language interference as two possible mechanisms of bilingual language control (BLC) that can be affected by Huntington’s disease (HD), a neurodegenerative disease ...
• Neural basis of bilingual language control

  Calabria, Marco; Costa, Albert, 1970-; Green, David W.; Abutalebi, Jubin (Wiley, 2018)

  Acquiring and speaking a second language increases demand on the processes of language control for bilingual as compared to monolingual speakers. Language control for bilingual speakers involves the ability to keep the two ...
• DYRK1A overexpression alters cognition and neural-related proteomic pathways in the hippocampus that are rescued by green tea extract and/or environmental enrichment

  De Toma, Ilario; Ortega Crespo, Mireia, 1988-; Aloy, Patrick, 1972-; Sabidó Aguadé, Eduard, 1981-; Dierssen, Mara (Frontiers, 2019)

  Down syndrome (DS), caused by trisomy of chromosome 21, is the most common genetic cause of intellectual disability. We recently discovered that green tea extracts containing epigallocatechin-3-gallate (EGCG) improve ...
• Impact of chromosome fusions on 3D genome organization and gene expression in budding yeast

  Di Stefano, Marco; Di Giovanni, Francesca, 1985-; Pozharskaia, Vasilia; Gomar-Alba, Mercè; Baù, Davide; Carey, Lucas, 1980-; Marti-Renom, Marc A.; Mendoza, Manuel (Mendoza Palomares) (Genetics Society of America, 2020)

  The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription ...
• Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual

  Kuderna, Lukas F.K.; Solís Moruno, Manuel; Batlle Masó, Laura; Julià, Eva; Lizano, Esther; Anglada Busquets, Roger; Ramírez Bautista, Eva; Bote, Alex; Tormo, Marc; Marquès i Bonet, Tomàs, 1975-; Fornas Carreño, Oscar; Casals López, Ferran (Frontiers Media, 2020)

  Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome. We have recently developed a ...
• Color matching images with unknown non-linear encodings

  Gil Rodríguez, Raquel; Vazquez Corral, Javier; Bertalmío, Marcelo (Institute of Electrical and Electronics Engineers (IEEE), 2020)

  We present a color matching method that, given two different views of the same scene taken by two cameras with unknown settings and unknown internal parameter values, and encoded with unknown non-linear curves, is able to ...

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