Browsing Center for Genomic Regulation (CRG) by Title

Sort by: Order: Results:

  • Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
    Hansen, Peter; Hecht, Jochen; Ibn-Salem, Jonas; Menkuec, Benjamin S.; Roskosch, Sebastian; Truss, Matthias; Robinson, Peter N. (BioMed Central, 2016)
    Background: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal ...
  • QCloud2: an improved cloud-based quality-control system for mass-spectrometry-based proteomics laboratories
    Olivella, Roger; Chiva, Cristina; Serret, Marc; Mancera, Daniel; Cozzuto, Luca; Hermoso Pulido, Antonio; Borràs, Eva; Espadas, Guadalupe; Morales Sanfrutos, Julia; Pastor, Olga; Solé, Amanda; Ponomarenko, Julia; Sabidó Aguadé, Eduard, 1981- (American Chemical Society (ACS), 2021)
    QCloud is a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, and automated data processing. Since its release, QCloud has facilitated automated ...
  • QCloud: a cloud-based quality control system for mass spectrometry-based proteomics laboratories
    Chiva, Cristina; Olivella, Roger; Borràs, Eva; Espadas, Guadalupe; Pastor, Olga; Solé, Amanda; Sabidó Aguadé, Eduard, 1981- (Public Library of Science (PLoS), 2018)
    The increasing number of biomedical and translational applications in mass spectrometry-based proteomics poses new analytical challenges and raises the need for automated quality control systems. Despite previous efforts ...
  • Quality control of protein complex assembly by a transmembrane recognition factor
    Natarajan, Nivedita; Foresti, Ombretta; Wendrich, Kim; Stein, Alexander; Carvalho, Pedro C. (Elsevier, 2020)
    The inner nuclear membrane (INM) is continuous with the endoplasmic reticulum (ER) but harbors a distinctive proteome essential for nuclear functions. In yeast, the Asi1/Asi2/Asi3 ubiquitin ligase complex safeguards the ...
  • Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users
    Chiva, Cristina; Mendes Maja, Teresa; Panse, Christian; Stejskal, Karel; Douché, Thibaut; Matondo, Mariette; Loew, Darmarys; Helm, Dominic; Rettel, Mandy; Mechtler, Karl; Impens, Francis; Nanni, Paolo; Shevchenko, Anna; Sabidó Aguadé, Eduard, 1981- (EMBO Press, 2021)
    Proteomics research infrastructures and core facilities within the Core for Life alliance advocate for community policies for quality control to ensure high standards in proteomics services.
  • 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 ...
  • Quantification of rare somatic single nucleotide variants by droplet digital PCR using SuperSelective primers
    Pablo Fontecha, Verónica; Hernández-Illán, Eva; Reparaz, Andrea; Asensio Juan, Elena; Morata, Jordi; Tonda, Raúl; Lahoz, Sara; Parra, Carolina; Lozano, Juan José; García-Heredia, Anabel; Martínez-Roca, Alejandro; Beltran, Sergi; Balaguer, Francesc; Jover, Rodrigo; Castells, Antoni; Trullàs, Ramón; Podlesniy, Petar; Camps-Puchadas, Jordi (Nature Research, 2023)
    Somatic single-nucleotide variants (SNVs) occur every time a cell divides, appearing even in healthy tissues at low frequencies. These mutations may accumulate as neutral variants during aging, or eventually, promote the ...
  • Quantifying the monomer-dimer equilibrium of tubulin with mass photometry
    Fineberg, Adam; Surrey, Thomas; Kukura, Philipp (Elsevier, 2020)
    The αβ-tubulin heterodimer is the fundamental building block of microtubules, making it central to several cellular processes. Despite the apparent simplicity of heterodimerisation, the associated energetics and kinetics ...
  • Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing
    Lucas, Morghan C.; Pryszcz, Leszek Piotr, 1985-; Medina, Rebeca; Milenkovic, Ivan; Camacho, Noelia; Marchand, Virginie; Motorin, Yuri; Ribas de Pouplana, Lluís; Novoa, Eva Maria (Nature Research, 2024)
    Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we ...
  • A quantitative atlas of Even-skipped and Hunchback expression in Clogmia albipunctata (Diptera: Psychodidae) blastoderm embryos
    Janssens, Hilde; Siggens, Ken; Cicin Sain, Damjan; Jiménez Guri, Eva; Musy, Marco; Akam, Michael; Jaeger, Johannes, 1973- (BioMed Central, 2014)
    Background: Comparative studies of developmental processes are one of the main approaches to evolutionary developmental biology (evo-devo). Over recent years, there has been a shift of focus from the comparative study of ...
  • Quantitative measurements in 3-dimensional datasets of mouse lymph nodes resolve organ-wide functional dependencies
    Mayer, Jürgen, 1977-; Swoger, Jim; Ozga, Aleksandra J.; Stein, Jens V.; Sharpe, James (Hindawi, 2012)
    Deep tissue imaging has become state of the art in biology, but now the problem is to quantify spatial information in a global, organ-wide context. Although access to the raw data is no longer a limitation, the computational ...
  • Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing
    Begik, Oguzhan; Lucas, Morghan C.; Pryszcz, Leszek Piotr, 1985-; Ramirez, Jose Miguel; Medina, Rebeca; Milenkovic, Ivan; Cruciani, Sonia; Liu, Huanle; Santos Vieira, Helaine Graziele; Sas Chen, Aldema; Mattick, John S.; Schwartz, Schraga; Novoa, Eva Maria (Nature Research, 2021)
    Nanopore RNA sequencing shows promise as a method for discriminating and identifying different RNA modifications in native RNA. Expanding on the ability of nanopore sequencing to detect N6-methyladenosine, we show that ...
  • Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita
    Karl R., Wotton; Jiménez Guri, Eva; Crombach, Anton; Janssens, Hilde; Alcaine Colet, Anna, 1992-; Lemke, Steffen; Schmidt Ott, Urs; Jaeger, Johannes, 1973- (eLife, 2015)
    The segmentation gene network in insects can produce equivalent phenotypic outputs despite differences in upstream regulatory inputs between species. We investigate the mechanistic basis of this phenomenon through a ...
  • Quantitative videomicroscopy reveals latent control of cell-pair rotations in vivo
    Kozak, Eva L.; Miranda-Rodríguez, Jerónimo R.; Borges, Augusto; Dierkes, Kai; Mineo, Alessandro; Pinto-Teixeira, Filipo; Viader Llargués, Oriol; Solon, Jérôme; Chara, Osvaldo; López-Schier, Hernán (Company of Biologists, 2023)
    Collective cell rotations are widely used during animal organogenesis. Theoretical and in vitro studies have conceptualized rotating cells as identical rigid-point objects that stochastically break symmetry to move ...
  • Quest for orthologs entails quest for tree of life: in search of the gene stream
    Boeckmann, Brigitte; Marcet Houben, Marina; Rees, Jonathan A.; Forslund, Kristoffer; Huerta Cepas, Jaime; Muffato, Matthieu; Yilmaz, Pelin; Xenarios, Ioannis; Bork, Peer; Lewis, Suzanna E.; Gabaldón Estevan, Juan Antonio, 1973-; Quest for Orthologs Species Tree Working Group (Oxford University Press, 2015)
    Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between ...
  • RANKL/RANK control Brca1 mutation-driven mammary tumors
    Sigl, Verena; Vidal Ocabo, Enrique; Penninger, Josef M. (Nature Publishing Group, 2016)
    Breast cancer is the most common female cancer, affecting approximately one in eight women during their life-time. Besides environmental triggers and hormones, inherited mutations in the breast cancer 1 (BRCA1) or BRCA2 ...
  • Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock
    Amat, Ramon; Böttcher, René; Le Dily, François; Vidal Ocabo, Enrique; Quilez Oliete, Javier; Cuartero, Yasmina; Beato, Miguel; Nadal Clanchet, Eulàlia de; Posas Garriga, Francesc (Cold Spring Harbor Laboratory Press (CSHL Press), 2019)
    Nuclear architecture is decisive for the assembly of transcriptional responses. However, how chromosome organization is dynamically modulated to permit rapid and transient transcriptional changes in response to environmental ...
  • Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
    Mathers, Thomas C.; Gabaldón Estevan, Juan Antonio, 1973-; Julca, Irene; Loska, Damian; Hogenhout, Saskia A. (BioMed Central, 2017)
    BACKGROUND: The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a ...
  • Rare functional genetic variants in COL7A1, COL6A5, COL1A2 and COL5A2 frequently occur in Chiari Malformation Type 1
    Urbizu, Aintzane; Garrett, Melanie E.; Soldano, Karen; Drechsel, Oliver; Loth, Dorothy; Marcé-Grau, Anna; Mestres Soler, Olga; Poca, María A.; Ossowski, Stephan; Macaya, Alfons; Loth, Francis; Labuda, Rick; Ashley-Koch, Allison (Public Library of Science (PLoS), 2021)
    Chiari Malformation Type 1 (CM-1) is characterized by herniation of the cerebellar tonsils below the foramen magnum and the presence of headaches and other neurologic symptoms. Cranial bone constriction is suspected to be ...
  • Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19
    Matuozzo, Daniela; Gut, Marta; Cobat, Aurélie (BioMed Central, 2023)
    Background: We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases ...

Search DSpace


Advanced Search

Browse

My Account

In collaboration with Compliant to Partaking