Browsing Center for Genomic Regulation (CRG) by Title

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  • Safe anti-programmed cell death-1 rechallenge with antibody switching after immune-related adverse events: brief communication
    Aya, Francisco; González Navarro, E. Azucena; Martínez, Clara M.; Carcelero, Esther; Arance, Ana (Future Science Group, 2021)
    Aim: To evaluate the safety of rechallenge with a different anti-PD-1 antibody after an immune-related adverse event (irAE) that has prompted the discontinuation of anti-PD-1 therapy. Patients & methods: We describe two ...
  • Salbutamol modifies the neuromuscular junction in a mouse model of ColQ myasthenic syndrome
    McMacken, Grace M.; Spendiff, Sally; Whittaker, Roger G.; O'Connor, Emily; Howarth, Rachel M.; Boczonadi, Veronika; Horvath, Rita; Slater, Clarke R.; Lochmüller, Hanns (Oxford University Press, 2019)
    The β-adrenergic agonists salbutamol and ephedrine have proven to be effective as therapies for human disorders of the neuromuscular junction, in particular many subsets of congenital myasthenic syndromes. However, the ...
  • Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts
    Dios Martínez, Toni de, 1994-; Carrión, Pablo; Olalde Marquínez, Íñigo, 1987-; Llovera Nadal, Laia; Lizano González, Esther, 1974-; Pàmies, Dídac; Marquès i Bonet, Tomàs, 1975-; Balloux, François; van Dorp, Lucy; Lalueza Fox, Carles, 1965- (Elsevier, 2021)
    Ancient pathogen genomics is an emerging field allowing reconstruction of past epidemics. The demise of post-contact American populations may, at least in part, have been caused by paratyphoid fever brought by Europeans. ...
  • Sampling time-dependent artifacts in single-cell genomics studies
    Massoni-Badosa, Ramon; Iacono, Giovanni; Moutinho, Catia; Kulis, Marta; Palau, Núria; Marchese, Domenica, 1986-; Rodríguez Ubreva, Javier; Ballestar, Esteban; Rodríguez Esteban, Gustavo; Marsal, Sara; Aymerich, Marta; Colomer Pujol, Dolors; Campo, Elias; Julià Cano, Antoni; Martín-Subero, José Ignacio; Heyn, Holger (BioMed Central, 2020)
    Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition ...
  • SARS-CoV-2 infection, vaccination, and antibody response trajectories in adults: a cohort study in Catalonia
    Karachaliou, Marianna; Moncunill, Gemma; Espinosa Díaz, Ana; Castaño Vinyals, Gemma; Rubio, Rocío; Vidal, Marta; Jiménez, Alfons; Prados, Esther; Bañuls, Marc; Melero, Natalia Rodrigo; Izquierdo, Luis; Carolis, Carlo; Goldberg, Ximena; Aguilar, Ruth; García Aymerich, Judith; Kogevinas, Manolis; Dobaño, Carlota (BioMed Central, 2022)
    Background: Heterogeneity of the population in relation to infection, COVID-19 vaccination, and host characteristics is likely reflected in the underlying SARS-CoV-2 antibody responses. Methods: We measured IgM, IgA, and ...
  • SARS-CoV-2 interaction with Siglec-1 mediates trans-infection by dendritic cells
    Perez-Zsolt, Daniel; Elosua-Bayés, Marc; Holger, Hein; Izquierdo-Useros, Nuria (Springer Nature, 2021)
  • SARS-CoV-2 sculpts the immune system to induce sustained virus-specific naïve-like and memory B-cell responses
    Campos Mata, Leire de, 1991-; Tejedor Vaquero, Sonia, 1988-; Tachó-Piñot, Roser; Piñero González, Janet, 1977-; Grasset, Emilie K.; Arrieta Aldea, Itziar; Rodrigo Melero, Natalia; Carolis, Carlo; Horcajada Gallego, Juan Pablo; Cerutti, Andrea, 1965-; Villar García, Judit; Magri, Giuliana, 1978- (Wiley Open Access, 2021)
    Objectives: SARS-CoV-2 infection induces virus-reactive memory B cells expressing unmutated antibodies, which hints at their emergence from naïve B cells. Yet, the dynamics of virus-specific naïve B cells and their impact ...
  • SARS-CoV-2 seroprevalence study in pediatric patients and health care workers using multiplex antibody immunoassays
    Prados de la Torre, Esther; Obando, Ignacio; Vidal, Marta; Felipe, Beatriz de; Aguilar, Ruth; Izquierdo, Luis; Carolis, Carlo; Olbrich, Peter; Capilla-Miranda, Ana; Serra, Pau; Santamaria, Pere; Blanco-Lobo, Pilar; Moncunill, Gemma; Rodríguez-Ortega, Manuel J.; Dobaño, Carlota (MDPI, 2022)
    SARS-CoV-2 infection has become a global health problem specially exacerbated with the continuous appearance of new variants. Healthcare workers (HCW) have been one of the most affected sectors. Children have also been ...
  • SARS-CoV-2-related MIS-C: A key to the viral and genetic causes of Kawasaki disease?
    Sancho-Shimizu, Vanessa; Brodin, Petter; Cobat, Aurélie; Biggs, Catherine M.; Toubiana, Julie; Lucas, Carrie L.; Henrickson, Sarah E.; Belot, Alexandre; MIS-C@CHGE; Tangye, Stuart G.; Milner, Joshua D.; Levin, Michael; Abel, Laurent; Bogunovic, Dusan; Casanova, Jean-Laurent; Zhang, Shen-Ying; Gut, Marta (Rockefeller University Press, 2021)
    Multisystem inflammatory syndrome in children (MIS-C) emerged in April 2020 in communities with high COVID-19 rates. This new condition is heterogenous but resembles Kawasaki disease (KD), a well-known but poorly understood ...
  • Saturation of recognition elements blocks evolution of new tRNA identities
    Saint-Léger, Adélaïde; Bello, Carla, 1990-; Dans, Pablo D.; Gabriel Torres, Adrian; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A., 1979-; Ribas de Pouplana, Lluís (American Association for the Advancement of Science (AAAS), 2016)
    Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific ...
  • Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion
    Pulido-Quetglas, Carlos; Aparicio i Prat, Estel, 1986-; Arnan Ros, Carme; Polidori, Taisia; Hermoso Pulido, Antonio; Palumbo, Emilio; Ponomarenko, Julia; Guigó Serra, Roderic; Johnson, Rory (Public Library of Science (PLoS), 2017)
    CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, ...
  • Scalable workflows and reproducible data analysis for genomics
    Strozzi, Francesco; Jansenn, Roel; Wurmus, Ricardo; Crusoe, Michael R.; Githinji, George; Di Tommaso, Paolo; Belhachemi, Dominique; Möller, Steffen; Smant, Geert; de Ligt, Joep; Prins, Pjotr (Springer, 2019)
    Biological, clinical, and pharmacological research now often involves analyses of genomes, transcriptomes, proteomes, and interactomes, within and between individuals and across species. Due to large volumes, the analysis ...
  • Scatter search applied to the inference of a development gene network
    Abdol, Amir Masoud; Cicin Sain, Damjan; Kaandorp, Jaap A.; Crombach, Anton (MDPI, 2017)
    Efficient network inference is one of the challenges of current-day biology. Its application to the study of development has seen noteworthy success, yet a multicellular context, tissue growth, and cellular rearrangements ...
  • scDrugPrio: a framework for the analysis of single-cell transcriptomics to address multiple problems in precision medicine in immune-mediated inflammatory diseases
    Schäfer, Samuel; Smelik, Martin; Sysoev, Oleg; Zhao, Yelin; Eklund, Desiré; Lilja, Sandra; Gustafsson, Mika; Heyn, Holger; Julià, Antonio; Kovács, István A.; Loscalzo, Joseph; Marsal Barril, Sara; Zhang, Huan; Li, Xinxiu; Gawel, Danuta; Wang, Hui; Benson, Mikael (BioMed Central, 2024)
    Background: Ineffective drug treatment is a major problem for many patients with immune-mediated inflammatory diseases (IMIDs). Important reasons are the lack of systematic solutions for drug prioritisation and repurposing ...
  • Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells
    Kobayashi-Ishihara, Mie; Smutná, Katarína, 1991-; Alonso, Florencia E.; Argilaguet Marqués, Jordi, 1977-; Esteve-Codina, Anna; Geiger, Kerstin; Rogenmoser, Selina; Oliva Miguel, Baldomero; Martinez, Javier P.; Díez Antón, Juana, 1962-; Meyerhans, Andreas (Nature Research, 2023)
    Latency is a major barrier towards virus elimination in HIV-1-infected individuals. Yet, the mechanisms that contribute to the maintenance of HIV-1 latency are incompletely understood. Here we describe the Schlafen 12 ...
  • Science during lockdown - from virtual seminars to sustainable online communities
    Bottanelli, Francesca; Cadot, Bruno; Campelo, Felix; Curran, Scott; Davidson, Patricia M.; Dey, Gautam; Raote, Ishier; Straube, Anne; Swaffer, Matthew P. (Company of Biologists, 2020)
    The COVID-19 pandemic has disrupted traditional modes of scientific communication. In-person conferences and seminars have been cancelled and most scientists around the world have been confined to their homes. Although ...
  • scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
    Bianchi, Agostina; Scherer, Michael; Zaurín Quer, Roser; Quililan, Kimberly; Velten, Lars; Beekman, Renée (BioMed Central, 2022)
    Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We developed scTAM-seq, a targeted bisulfite-free method for profiling up to 650 CpGs in up to 10,000 cells ...
  • SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences
    Agostini, Federico, 1985-; Cirillo, Davide; Delli Ponti, Riccardo, 1987-; Tartaglia, Gian Gaetano (BioMed Central, 2014)
    BACKGROUND: The large amount of data produced by high-throughput sequencing poses new computational challenges. In the last decade, several tools have been developed for the identification of transcription and splicing ...
  • SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins
    Mariotti, Marco, 1984-; Lobanov, Alexei V.; Guigó Serra, Roderic; Gladyshev, Vadim N. (Oxford University Press, 2013)
    Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at the 3' UTR of selenoprotein ...
  • Second ISCB Latin American Student Council Symposium (LA-SCS) 2016
    Monzon, Alexander Miguel; Hasenahuer, Marcia A.; Mancini, Estefanía; Coimbra, Nilson; Cravero, Fiorella; Cáceres Molina, Javier; Ramírez Sarmiento, César A.; Palopoli, Nicolas; Meysman, Pieter; Parra, R. Gonzalo (F1000Research, 2017)
    This report summarizes the scientific content and activities of the second edition of the Latin American Symposium (LA-SCS), organized by the Student Council (SC) of the International Society for Computational Biology ...

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