Browsing by Author "Gut, Ivo Glynne"

Sort by: Order: Results:

  • A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
    Alioto, Tyler; Derdak, Sophia; Ribeca, Paolo; Castro Giner, Francesc; Beltran, Sergi; Raineri, Emanuele; Dabad, Marc; Heath, Simon; Gut, Marta; Gut, Ivo Glynne (Nature Research, 2015)
    As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different ...
  • A DNA methylation map of human cancer at single base-pair resolution
    Vidal Ocabo, Enrique; Sayols, Sergi; Moran, Sebastian; Guillaumet-Adkins, Amy; Schroeder, Michael Philipp, 1986-; Royo, Romina; Orozco, Modesto; Gut, Marta; Gut, Ivo Glynne; López Bigas, Núria; Heyn, Holger; Esteller, Manel (Nature Publishing Group, 2017)
    Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling ...
  • A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome
    Keraite, Ieva; Becker, Philipp; Canevazzi, Davide; Frias-López, Cristina; Dabad, Marc; Tonda, Raúl; Paramonov, Ida; Ingham, Matthew; Brun-Heath, Isabelle; Leno, Jordi; Abulí, Anna; García-Arumí, Elena; Heath, Simon; Gut, Marta; Gut, Ivo Glynne (Nature Research, 2022)
    Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple ...
  • A single-cell tumor immune atlas for precision oncology
    Nieto, Paula; Elosua-Bayés, Marc; Trincado Alonso, Juan Luis, 1987-; Marchese, Domenica, 1986-; Massoni-Badosa, Ramon; Nieto, Juan C.; Aguilar-Fernández, Sergio; Mereu, Elisabetta; Moutinho, Catia; Ruiz, Sara; Lorden, Patricia; Gut, Ivo Glynne; Heyn, Holger (Cold Spring Harbor Laboratory Press (CSHL Press), 2021)
    The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients, and biomarkers for prognosis ...
  • A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers
    Ferrari, Anthony; Gut, Ivo Glynne; Gut, Marta; Thomas, Gilles (Nature Research, 2016)
    HER2-positive breast cancer has long proven to be a clinically distinct class of breast cancers for which several targeted therapies are now available. However, resistance to the treatment associated with specific gene ...
  • Alternative enhancer usage and targeted polycomb marking hallmark promoter choice during T cell differentiation
    Maqbool, Muhammad Ahmad; Pioger, Léo; El Aabidine, Amal Zine; Karasu, Nezih; Molitor, Anne Marie; Dao, Lan T.M.; Charbonnier, Guillaume; van Laethem, François; Fenouil, Romain; Koch, Frederic; Lacaud, Georges; Gut, Ivo Glynne; Gut, Marta; Amigorena, Sebastian; Joffre, Olivier; Sexton, Thomas; Spicuglia, Salvatore; Andrau, Jean-Christophe (Elsevier, 2020)
    During thymic development and upon peripheral activation, T cells undergo extensive phenotypic and functional changes coordinated by lineage-specific developmental programs. To characterize the regulatory landscape controlling ...
  • Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
    Feliubadaló, Lídia; Tonda, Raúl; Trotta, Jean-Remi; Gut, Marta; Gut, Ivo Glynne; Beltran, Sergi; Lázaro García, Conxi (Nature Research, 2017)
    Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome ...
  • Benchmarking single-cell RNA sequencing protocols for cell atlas projects
    Mereu, Elisabetta; Lafzi, Atefeh; Moutinho, Catia; Gut, Marta; Gut, Ivo Glynne; Heyn, Holger (Nature Research, 2020)
    Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands of cells and are being used to compile ...
  • bigSCale: an analytical framework for big-scale single-cell data
    Iacono, Giovanni; Mereu, Elisabetta; Guillaumet-Adkins, Amy; Corominas, Roser; Cuscó Martí, Ivon, 1973-; Rodríguez Esteban, Gustavo; Gut, Marta; Pérez Jurado, Luis Alberto; Gut, Ivo Glynne; Heyn, Holger (Cold Spring Harbor Laboratory Press (CSHL Press), 2018)
    Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into complex tissues, with the latest techniques capable of processing tens of thousands of cells simultaneously. Analyzing increasing numbers ...
  • Blood eosinophil count and airway epithelial transcriptome relationships in COPD versus asthma
    George, Leena; Esteve-Codina, Anna; Soler Artigas, María; Thun, Gian Andri; Heath, Simon; Gut, Ivo Glynne; Brightling, Christopher E. (Wiley, 2020)
    BACKGROUND: Whether the clinical or pathophysiologic significance of the "treatable trait" high blood eosinophil count in COPD is the same as for asthma remains controversial. We sought to determine the relationship between ...
  • Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation
    Cieslak, Agata; Gut, Marta; Gut, Ivo Glynne; Asnafi, Vahid (Rockefeller University Press, 2020)
    Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an ...
  • Charting intra-tumoral heterogeneity dynamics through the integration of multi-modal single-cell profiles
    Elosua-Bayés, Marc (Universitat Pompeu Fabra, 2023-06-27)
    Understanding multicellular organisms depends on the advent of technologies capable of delivering unprecedented levels of resolution. With new technologies come novel data modalities, which require the development of tools ...
  • Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
    Ordóñez, Raquel; Gut, Ivo Glynne; Martín-Subero, José Ignacio (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    Multiple myeloma (MM) is a plasma cell neoplasm associated with a broad variety of genetic lesions. In spite of this genetic heterogeneity, MMs share a characteristic malignant phenotype whose underlying molecular basis ...
  • Clonal dynamics monitoring during clinical evolution in chronic lymphocytic leukaemia
    González-Rincón, Julia; Gómez, Sagrario; Martinez, Nerea; Troulé, Kevin; Perales-Patón, Javier; Derdak, Sophia; Beltran, Sergi; Fernández-Cuevas, Belén; Pérez-Sanz, Nuria; Nova-Gurumeta, Sara; Gut, Ivo Glynne; Al-Shahrour, Fátima; Piris, Miguel A.; García-Marco, J. A.; Sánchez-Beato, Margarita (Nature Research, 2019)
    Chronic lymphocytic leukaemia is the most prevalent leukaemia in Western countries. It is an incurable disease characterized by a highly variable clinical course. Chronic lymphocytic leukaemia is an ideal model for studying ...
  • Combined burden and functional impact tests for cancer driver discovery using DriverPower
    Shuai, Shimin; PCAWG Drivers and Functional Interpretation Working Group; Gallinger, Steven; Stein, Lincoln D.; PCAWG Consortium; Deu-Pons, Jordi; Gut, Ivo Glynne; Muiños, Ferran; Mularoni, Loris; Rubio Pérez, Carlota, 1990-; Tamborero Noguera, David (Nature Research, 2020)
    The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing ...
  • Combined HAT/EZH2 modulation leads to cancer-selective cell death
    Petraglia, Francesca; Heath, Simon; Gut, Ivo Glynne; Altucci, Lucia (Impact Journals, 2018)
    Epigenetic alterations have been associated with both pathogenesis and progression of cancer. By screening of library compounds, we identified a novel hybrid epi-drug MC2884, a HAT/EZH2 inhibitor, able to induce bona fide ...
  • Deciphering B lymphocyte dynamics in health and disease through the integrative analysis of multi-modal single-cell data
    Aguilar Fernández, Sergio (Universitat Pompeu Fabra, 2024-04-26)
    The intrinsic complexity and dynamic nature of B-lymphocytes make them ideal for in-depth analysis using single-cell technologies. Secondary lymphoid organs (SLOs) are central in B-lymphocyte activation and differentiation, ...
  • Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle
    Stefanini, Irene; Rizzetto, Lisa; Rivero, Damariz; Carbonell, Silvia; Gut, Marta; Heath, Simon; Gut, Ivo Glynne; Trabocchi, Andrea; Guarna, Antonio; Ben Ghazzi, Nagwa; Bowyer, Paul; Kapushesky, Misha; Cavalieri, Duccio (Nature Research, 2018)
    Fungal infections represent an increasingly relevant clinical problem, primarily because of the increased survival of severely immune-compromised patients. Despite the availability of active and selective drugs and of ...
  • Detection of early seeding of Richter transformation in chronic lymphocytic leukemia
    Nadeu, Ferran; Massoni-Badosa, Ramon; Ruiz Gil, Sara; Marchese, Domenica, 1986-; López Bigas, Núria; Gut, Ivo Glynne; Heyn, Holger; Campo, Elias (Nature Research, 2022)
    Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. ...
  • Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems
    Schuyler, Ronald P.; Merkel, Angelika; Raineri, Emanuele; Gut, Ivo Glynne; Heath, Simon (Elsevier, 2016)
    DNA methylation and the localization and post-translational modification of nucleosomes are interdependent factors that contribute to the generation of distinct phenotypes from genetically identical cells. With 112 ...

Search DSpace

Browse

My Account

In collaboration with Compliant to Partaking