Browsing Center for Genomic Regulation (CRG) by Title

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  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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.
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...

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