Browsing by Author "Heath, Simon"

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  • A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples
    Esteve-Codina, Anna; Arpí Llucià, Oriol; Martínez-García, Maria; Pineda, Estela; Mallo, Mar; Gut, Marta; Carrato, Cristina; Rovira Guerín, Ana; Lopez, Raquel; Tortosa, Avelina; Dabad, Marc; del Barco, Sonia; Heath, Simon; Bagué, Silvia; Ribalta, Teresa; Alameda Quitllet, Francisco; de la Iglesia, Nuria; Balaña, Carmen; GLIOCAT Group (Public Library of Science (PLoS), 2017)
    The molecular classification of glioblastoma (GBM) based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time
    Feichtinger, Julia; Hernández, Inmaculada; Fischer, Christoph; Hanscho, Michael; Auer, Norbert; Hackl, Matthias; Jadhav, Vaibhav; Baumann, Martina; Krempl, Peter M.; Schmidl, Christian; Farlik, Matthias; Schuster, Michael; Merkel, Angelika; Sommer, Andreas; Heath, Simon; Rico, Daniel; Bock, Christoph; Thallinger, Gerhard R.; Borth, Nicole (Wiley, 2016)
    The most striking characteristic of CHO cells is their adaptability, which enables efficient production of proteins as well as growth under a variety of culture conditions, but also results in genomic and phenotypic ...
  • cvlr: finding heterogeneously methylated genomic regions using ONT reads
    Raineri, Emanuele; Alberola i Pla, Mariona; Dabad, Marc; Heath, Simon (Oxford University Press, 2023)
    Summary: Nanopore reads encode information on the methylation status of cytosines in CpG dinucleotides. The length of the reads makes it comparatively easy to look at patterns consisting of multiple loci; here, we exploit ...
  • 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 ...
  • DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data
    Bonet, Jose; Chen, Mandi; Dabad, Marc; Heath, Simon; Gonzalez-Perez, Abel; López Bigas, Núria; Lagergren, Jens (Oxford University Press, 2021)
    Motivation: DNA Methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational ...
  • 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 ...
  • Dynamics of transcription regulation in human bone marrow myeloid differentiation to mature blood neutrophils
    Grassi, Luigi; Ullrich, Sebastian, 1984-; Merkel, Angelika; Gut, Marta; Heath, Simon; Gut, Ivo Glynne; Kuijpers, Taco W. (Elsevier, 2018)
    Neutrophils are short-lived blood cells that play a critical role in host defense against infections. To better comprehend neutrophil functions and their regulation, we provide a complete epigenetic overview, assessing ...
  • Epigenetic regulation of gene expression in Chinese hamster ovary cells in response to the changing environment of a batch culture
    Hernandez, Inmaculada; Dhiman, Heena; Klanert, Gerald; Jadhav, Vaibhav; Auer, Norbert; Hanscho, Michael; Baumann, Martina; Esteve-Codina, Anna; Dabad, Marc; Gómez, Jessica; Alioto, Tyler; Merkel, Angelika; Raineri, Emanuele; Heath, Simon; Rico, Daniel; Borth, Nicole (Wiley, 2019)
    The existence of dynamic cellular phenotypes in changing environmental conditions is of major interest for cell biologists who aim to understand the mechanism and sequence of regulation of gene expression. In the context ...
  • Evaluation of circulating tumor DNA by electropherogram analysis and methylome profiling in high-risk neuroblastomas
    Trinidad, Eva María; Juan-Ribelles, Antonio; Pisano, Giulia; Castel, Victoria; Cañete, Adela; Gut, Marta; Heath, Simon; Font de Mora, Jaime (Frontiers, 2023)
    Background: Liquid biopsy has emerged as a promising, non-invasive diagnostic approach in oncology because the analysis of circulating tumor DNA (ctDNA) reflects the precise status of the disease at diagnosis, progression, ...
  • From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing
    Laurie, Steven, 1973-; Fernández Callejo, Marcos; Marco Sola, Santiago; Trotta, Jean-Remi; Camps-Puchadas, Jordi; Chacón, Alejandro; Espinosa, Antonio; Gut, Marta; Gut, Ivo Glynne; Heath, Simon; Beltran, Sergi (Wiley, 2016)
    As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics. However, computing cost–performance ratio is not ...
  • gemBS: high throughput processing for DNA methylation data from bisulfite sequencing
    Merkel, Angelika; Fernández Callejo, Marcos; Casals, Eloi; Marco Sola, Santiago; Schuyler, Ronald P.; Gut, Ivo Glynne; Heath, Simon (Oxford University Press, 2019)
    Motivation: DNA methylation is essential for normal embryogenesis and development in mammals and can be captured at single base pair resolution by whole genome bisulfite sequencing (WGBS). Current available analysis tools ...
  • Gender specific airway gene expression in COPD sub-phenotypes supports a role of mitochondria and of different types of leukocytes
    Esteve-Codina, Anna; Soler Artigas, María; Dabad, Marc; Fernández Callejo, Marcos; Griebel, Thasso; Heath, Simon; Gut, Ivo Glynne; Ziegler-Heitbrock, Loems (Nature Research, 2021)
    Chronic obstructive pulmonary disease (COPD) is a destructive inflammatory disease and the genes expressed within the lung are crucial to its pathophysiology. We have determined the RNAseq transcriptome of bronchial brush ...
  • Impact of DNA methylation on 3D genome structure
    Buitrago, Diana; Labrador, Mireia; Arcon, Juan Pablo; Lema, Rafael; Flores, Oscar; Esteve-Codina, Anna; Blanc, Julie; Villegas, Núria; Bellido, David; Gut, Marta; Dans, Pablo D.; Heath, Simon; Gut, Ivo Glynne; Brun-Heath, Isabelle; Orozco, Modesto (Nature Research, 2021)
    Determining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, ...
  • Increased DNA methylation variability in type 1 diabetes across three immune effector cell types
    Paul, Dirk S.; Heath, Simon; Gut, Marta; Gut, Ivo Glynne; Leslie, R. David (Nature Publishing Group, 2016)
    The incidence of type 1 diabetes (T1D) has substantially increased over the past decade, suggesting a role for non-genetic factors such as epigenetic mechanisms in disease development. Here we present an epigenome-wide ...
  • Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease
    Ventham, N. T.; Kennedy, N. A.; Adams, A. T.; Kalla, Rahul; Heath, Simon; O'Leary, K. R.; Drummond, H.; IBD BIOM consortium; IBD CHARACTER consortium; Wilson, D. C.; Gut, Ivo Glynne; Nimmo, E. R.; Satsangi, Jack (Nature Publishing Group, 2016)
    Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and ...
  • Linking cell dynamics with gene coexpression networks to characterize key events in chronic virus infections
    Pedragosa Marín, Mireia, 1988-; Riera Domínguez, María Graciela, 1987-; Casella, Valentina, 1991-; Esteve-Codina, Anna; Steuerman, Yael; Seth, Celina; Bocharov, Gennady A.; Heath, Simon; Gat-Viks, Irit; Argilaguet Marqués, Jordi, 1977-; Meyerhans, Andreas (Frontiers Media, 2019)
    The host immune response against infection requires the coordinated action of many diverse cell subsets that dynamically adapt to a pathogen threat. Due to the complexity of such a response, most immunological studies have ...
  • Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA
    Trinidad, Eva María; Vidal, Enrique; Coronado, Esther; Esteve-Codina, Anna; Castel, Victoria; Cañete, Adela; Gut, Marta; Heath, Simon; Font de Mora, Jaime (Oxford University Press, 2023)
    Analysis of the methylome of tumor cell-free deoxyribonucleic acid (DNA; cfDNA) has emerged as a powerful non-invasive technique for cancer subtyping and prognosis. However, its application is frequently hampered by the ...