Browsing Center for Genomic Regulation (CRG) by Title

Sort by: Order: Results:

  • FA-nf: a functional annotation pipeline for proteins from non-model organisms implemented in nextflow
    Vlasova, Anna; Hermoso Pulido, Antonio; Camara, Francisco; Ponomarenko, Julia; Guigó Serra, Roderic (MDPI, 2021)
    Functional annotation allows adding biologically relevant information to predicted features in genomic sequences, and it is, therefore, an important procedure of any de novo genome sequencing project. It is also useful for ...
  • Factor structure of the spanish version of the Edinburgh postnatal depression scale
    Gutierrez-Zotes, Alfonso; Gallardo-Pujol, David; Labad, Javier; Martín Santos, Rocío; García-Esteve, Luisa; Gelabert, Estel; Jover, Manuel; Guillamat, Roser; Mayoral Cleries, Fermín; Gornemann, Isolde; Canellas, Francesca; Gratacós Mayora, Mònica; Guitart, Miriam; Roca, Miquel; Costas, Javier; Ivorra, Jose Luis; Navinés, Ricard; Diego, Yolanda de; Vilella, Elisabet; Sanjuan, Julio (Fundación López Ibor, 2018)
    INTRODUCTION: The Edinburgh Postnatal Depression Scale (EPDS) is considered the gold standard in screening for postpartum depression. Although the Spanish version has been widely used, its factorial structure has not yet ...
  • Fast and inexpensive whole-genome sequencing library preparation from intact yeast cells
    Vonesch, Sibylle C.; Li, Shengdi; Szu-Tu, Chelsea; Henning, Bianca P.; Dobrev, Nikolay; Steinmetz, Lars M. (Oxford University Press, 2021)
    Through the increase in the capacity of sequencing machines massively parallel sequencing of thousands of samples in a single run is now possible. With the improved throughput and resulting drop in the price of sequencing, ...
  • Fast computation and applications of genome mappability
    Derrien, Thomas; Estellé, Jordi; Marco Sola, Santiago; Knowles, David G.; Raineri, Emanuele; Guigó Serra, Roderic; Ribeca, Paolo (Public Library of Science (PLoS), 2012)
    We present a fast mapping-based algorithm to compute the mappability of each region of a reference genome up to a specified number of mismatches. Knowing the mappability of a genome is crucial for the interpretation of ...
  • Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis
    Al-Refaie, Nada; Padovani, Francesco; Hornung, Johanna; Pudelko, Lorenz; Binando, Francesca; Carmen Fabregat, Andrea del; Zhao, Qiuxia; Towbin, Benjamin D.; Sarinay Cenik, Elif; Stroustrup, Nicholas; Padeken, Jan; Schmoller, Kurt M.; Cabianca, Daphne S. (Nature Research, 2024)
    Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom, yet how it impacts three-dimensional (3D) genome organization is unknown. Here we show ...
  • FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies
    Miravet Verde, Samuel, 1992-; Burgos, Raul; Delgado Blanco, Javier; Lluch-Senar, Maria 1982-; Serrano Pubull, Luis, 1982- (Oxford University Press, 2020)
    Transposon sequencing is commonly applied for identifying the minimal set of genes required for cellular life; a major challenge in fields such as evolutionary or synthetic biology. However, the scientific community has ...
  • FBXW7 tumor suppressor regulation by dualspecificity tyrosine-regulated kinase 2
    Jiménez-Izquierdo, Rafael; Morrugares, Rosario; Suanes-Cobos, Lucía; Correa-Sáez, Alejandro; Garrido-Rodríguez, Martín; Cerero-Tejero, Laura; Khan, Omar M.; Luna, Susana de la; Sancho, Rocío; Calzado, Marco A. (Springer, 2023)
    FBXW7 is a member of the F-box protein family, which functions as the substrate recognition component of the SCF E3 ubiquitin ligase. FBXW7 is a main tumor suppressor due to its ability to control proteasome-mediated ...
  • Federated discovery and sharing of genomic data using Beacons
    Fiume, Marc; Rambla de Argila, Jordi; Torre, Sabela de la; Scollen, Serena (Nature Research, 2019)
  • Fiber-like action of d-fagomine on the gut microbiota and body weight of healthy rats
    Ramos-Romero, Sara; Ponomarenko, Julia; Amézqueta, Susana; Hereu, Mercè; Miralles-Pérez, Bernat; Romeu, Marta; Méndez, Lucía; Medina, Isabel; Torres, Josep Lluís (MDPI, 2022)
    The goal of this work is to explore if the changes induced by d-fagomine in the gut microbiota are compatible with its effect on body weight and inflammation markers in rats. Methods: Sprague Dawley rats were fed a standard ...
  • Fibril-induced glutamine-/asparagine-rich prions recruit stress granule proteins in mammalian cells
    Riemschoss, Katrin; Arndt, Verena; Bolognesi, Benedetta; von Eisenhart-Rothe, Philipp; Liu, Shu; Buravlova, Oleksandra; Duernberger, Yvonne; Paulsen, Lydia; Hornberger, Annika; Hossinger, André; Lorenzo Gotor, Maria de las Nieves; Hogl, Sebastian; Müller, Stephan A.; Tartaglia, Gian Gaetano; Lichtenthaler, Stefan F.; Vorberg, Ina M. (Life Science Alliance, 2019)
    Prions of lower eukaryotes are self-templating protein aggregates that replicate by converting homotypic proteins into stable, tightly packed beta-sheet-rich protein assemblies. Propagation is mediated by prion domains, ...
  • Finding the missing honey bee genes: lessons learned from a genome upgrade
    Elsik, Christine G; Cámara, Francisco; Honey Bee Genome Sequencing Consortium (BioMed Central, 2014)
    Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the ...
  • Fine-scale population structure in five rural populations from the Spanish Eastern Pyrenees using high-coverage whole-genome sequence data
    Maceda Porto, Iago, 1986-; Martín Álvarez, Miguel; Athanasiadis, Georgios; Tonda, Raúl; Camps-Puchadas, Jordi; Beltran, Sergi; Camps, Agustí; Fàbrega, Jordi; Felisart, Josefina; Grané, Joan; Remón, José Luis; Serra, Jordi; Moral, Pedro; Lao Grueso, Oscar, 1976- (Springer Nature, 2021)
    The area of the Spanish Pyrenees is particularly interesting for studying the demographic dynamics of European rural areas given its orography, the main traditional rural condition of its population and the reported higher ...
  • The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede strigamia maritima
    Chipman, Ariel D; Capella Gutiérrez, Salvador Jesús, 1985-; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic; Mariotti, Marco, 1984-; Richards, Stephan (Public Library of Science (PLoS), 2014)
    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda ...
  • Fitness landscape of a dynamic RNA structure
    Soo, Valerie W. C.; Swadling, Jacob B.; Faure, Andre J.; Warnecke, Tobias (Public Library of Science (PLoS), 2021)
    RNA structures are dynamic. As a consequence, mutational effects can be hard to rationalize with reference to a single static native structure. We reasoned that deep mutational scanning experiments, which couple molecular ...
  • A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
    Esnaola, Mikel; Puig, Pedro; González, David; Castelo Valdueza, Robert; González Ruiz, Juan Ramón (BioMed Central, 2013)
    Background: High-throughput RNA sequencing (RNA-seq) offers unprecedented power to capture the real dynamics of gene expression. Experimental designs with extensive biological replication present a unique opportunity to ...
  • Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual
    Kuderna, Lukas, 1989-; Solís Moruno, Manuel, 1993-; Batlle Masó, Laura, 1993-; Julià, Eva; Lizano González, Esther, 1974-; 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 ...
  • Fluorescent transgenic mouse models for whole-brain imaging in health and disease
    Arias, Adrian; Manubens-Gil, Linus, 1989-; Dierssen, Mara (Frontiers, 2022)
    A paradigm shift is occurring in neuroscience and in general in life sciences converting biomedical research from a descriptive discipline into a quantitative, predictive, actionable science. Living systems are becoming ...
  • FoldX 5.0: working with RNA, small molecules and a new graphical interface
    Delgado Blanco, Javier; Radusky, Leandro; Cianferoni, Damiano; Serrano Pubull, Luis, 1982- (Oxford University Press, 2019)
    SUMMARY: A new version of FoldX, whose main new features allows running classic FoldX commands on structures containing RNA molecules and includes a module that allows parametrization of ligands or small molecules (ParamX) ...
  • FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1)
    Delgado Blanco, Javier; Radusky, Leandro; Climente González, Héctor; Serrano Pubull, Luis, 1982- (Oxford University Press, 2018)
    The speed at which new genomes are being sequenced highlights the need for genome-wide methods capable of predicting protein-DNA interactions. Here, we present PADA1, a generic algorithm that accurately models structural ...
  • Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation
    Banse, Paul; Luiselli, Juliette; Parsons, David P.; Grohens, Théotime; Foley, Marco; Trujillo, Leonardo; Rouzaud-Cornabas, Jonathan; Knibbe, Carole; Beslon, Guillaume (Wiley, 2023)
    While chromosomal rearrangements are ubiquitous in all domains of life, very little is known about their evolutionary significance, mostly because, apart from a few specifically studied and well-documented mechanisms ...

Search DSpace


Advanced Search

Browse

My Account

In collaboration with Compliant to Partaking