Browsing by Author "Hernandez-Ferrer, Carles, 1987-"

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  • affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.
    Hernandez-Ferrer, Carles, 1987-; Quintela Garcia, Ines; Danielski, Katharina; Carracedo, Ángel; Pérez Jurado, Luis Alberto; González Ruiz, Juan Ramón (BioMed Central , 2015)
    Background:The well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveriesusing SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other ...
  • Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk
    Rubio Martínez, Mercedes, 1980-; Bustamante Pineda, Mariona; Hernandez-Ferrer, Carles, 1987-; Fernández-Orth, Dietmar; Pantano Rubiño, Lorena, 1982-; Sarria-Trujillo, Yaris; Piqué-Borras, Maria; Vellve del Amo, Kilian; Agramunt, Silvia; Carreras Collado, Ramón; Estivill, Xavier, 1955-; González Ruiz, Juan Ramón; Mayor, Alfredo (Public Library of Science (PLoS), 2018)
    Circulating small RNAs, including miRNAs but also isomiRs and other RNA species, have the potential to be used as non-invasive biomarkers for communicable and non-communicable diseases. This study aims to characterize and ...
  • CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
    Hernandez-Ferrer, Carles, 1987-; González Ruiz, Juan Ramón (Oxford University Press, 2018)
    SUMMARY: Biomedical studies currently include a large volume of genomic and environmental factors for studying the etiology of human diseases. R/Bioconductor projects provide several tools for performing enrichment analysis ...
  • Dose and time effects of solar-simulated ultraviolet radiation on the in vivo human skin transcriptome
    Bustamante Pineda, Mariona; Hernandez-Ferrer, Carles, 1987-; Tewari, Angela; Sarria-Trujillo, Yaris; Harrison, Graham I.; Puigdecanet Riubugent, Eulàlia; Nonell Mazelón, Lara; Kang, Wenjing; Friedländer, Marc R.; Estivill, Xavier, 1955-; González, Juan Ramón; Nieuwenhuijsen, Mark J.; Young, Antony R. (Wiley, 2019)
    BACKGROUND: Terrestrial ultraviolet (UV) radiation causes erythema, oxidative stress, DNA mutations and skin cancer. Skin can adapt to these adverse effects by DNA repair, apoptosis, keratinization and tanning. OBJECTIVES: ...
  • Early life multiple exposures and child cognitive function: A multi-centric birth cohort study in six European countries
    Julvez, Jordi; López Vicente, Mònica, 1988-; Warembourg, Charline; Maitre, Léa; Philippat, Claire; Gützkow, Kristine B.; Guxens Junyent, Mònica; Evandt, Jorunn; Andrušaitytė, Sandra; Burgaleta Díaz, Miguel, 1981-; Casas Sanahuja, Maribel; Chatzi, Leda; de Castro, Montserrat; Donaire González, David; Gražulevičienė, Regina; Hernandez-Ferrer, Carles, 1987-; Heude, Barbara; McEachan, Rosie; Mon-Williams, Mark; Nieuwenhuijsen, Mark J.; Robinson, Oliver; Sakhi, Amrit Kaur; Sebastián Gallés, Núria; Slama, Rémy; Sunyer Deu, Jordi; Tamayo-Uria, Ibon; Thomsen, Cathrine; Urquiza, José M.; Vafeiadi, Marina, 1983-; Basagaña Flores, Xavier; Vrijheid, Martine (Elsevier, 2021)
    Epidemiological studies mostly focus on single environmental exposures. This study aims to systematically assess associations between a wide range of prenatal and childhood environmental exposures and cognition. The study ...
  • Early-life environmental exposure determinants of child behavior in Europe: A longitudinal, population-based study
    Maitre, Léa; Júlvez Calvo, Jordi; López Vicente, Mònica, 1988-; Warembourg, Charline; Tamayo-Uria, Ibon; Guxens Junyent, Mònica; Basagaña Flores, Xavier; Casas Sanahuja, Maribel; de Castro, Montserrat; González, Juan Ramón; Hernandez-Ferrer, Carles, 1987-; Márquez, Sandra; Nieuwenhuijsen, Mark J.; Urquiza, José M.; Vrijheid, Martine (Elsevier, 2021)
    Background: Environmental exposures in early life influence the development of behavioral outcomes in children, but research has not considered multiple exposures. We therefore aimed to investigate the impact of a broad ...
  • Epimutation detection in the clinical context: guidelines and a use case from a new Bioconductor package
    Ruiz-Arenas, Carlos; Abarrategui, Leire; Hernandez-Ferrer, Carles, 1987-; Pelegrí-Sisó, Dolors; Ryser-Welch, Patricia; Vrijheid, Martine; Bustamante Pineda, Mariona; Gražulevičienė, Regina; Lepeule, Johanna; Mathai, Mathew; Vafeiadi, Marina, 1983-; Beltran, Sergi; Pérez Jurado, Luis Alberto; González, Juan Ramón (Taylor & Francis, 2023)
    Epimutations are rare alterations of the normal DNA methylation pattern at specific loci, which can lead to rare diseases. Methylation microarrays enable genome-wide epimutation detection, but technical limitations prevent ...
  • Identification of autosomal cis expression quantitative trait methylation (cis eQTMs) in children's blood
    Ruiz-Arenas, Carlos; Hernandez-Ferrer, Carles, 1987-; Vives Usano, Marta, 1990-; Marí, Sergi; Casas Sanahuja, Maribel; Vafeiadi, Marina, 1983-; Vrijheid, Martine; González Ruiz, Juan Ramón; Bustamante Pineda, Mariona (eLife Sciences Publications, 2022)
    Background: The identification of expression quantitative trait methylation (eQTMs), defined as associations between DNA methylation levels and gene expression, might help the biological interpretation of epigenome-wide ...
  • MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
    Hernandez-Ferrer, Carles, 1987-; Ruiz-Arenas, Carlos; Beltran-Gomila, Alba; González Ruiz, Juan Ramón (BioMed Central, 2017)
    BACKGROUND: Reduction in the cost of genomic assays has generated large amounts of biomedical-related data. As a result, current studies perform multiple experiments in the same subjects. While Bioconductor's methods and ...
  • Prenatal particulate air pollution and DNA methylation in newborns: an epigenome-wide meta-analysis
    Gruzieva, Olena; Kogevinas, Manolis; Ruiz, José L.; Bustamante Pineda, Mariona; Antó i Boqué, Josep Maria; Sunyer Deu, Jordi; Vrijheid, Martine; Hernandez-Ferrer, Carles, 1987-; Melén, Erik (National Institute of Environmental Health Sciences (NIEHS), 2019)
    BACKGROUND: Prenatal exposure to air pollution has been associated with childhood respiratory disease and other adverse outcomes. Epigenetics is a suggested link between exposures and health outcomes. OBJECTIVES: We aimed ...
  • The acute effects of ultraviolet radiation on the blood transcriptome are independent
    Bustamante Pineda, Mariona; Hernandez-Ferrer, Carles, 1987-; Sarria-Trujillo, Yaris; Harrison, Graham I.; Nonell Mazelón, Lara; Kang, Wenjing; Friedländer, Marc R.; Estivill, Xavier, 1955-; González, Juan Ramón; Nieuwenhuijsen, Mark J.; Young, Antony R. (Elsevier, 2017)
    The molecular basis of many health outcomes attributed to solar ultraviolet radiation (UVR) is unknown. We tested the hypothesis that they may originate from transcriptional changes in blood cells. This was determined by ...
  • The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases
    Laurie, Steven, 1973-; Piscia, Davide; Matalonga, Leslie; Corvò, Alberto; Fernández Callejo, Marcos; Garcia-Linares, Carles; Hernandez-Ferrer, Carles, 1987-; Luengo, Cristina; Martínez, Inés; Papakonstantinou Ntalis, Anastasios; Picó-Amador, Daniel; Protasio, Joan; Tonda, Raúl; Bayés, Mònica; Bullich, Gemma; Camps-Puchadas, Jordi; Paramonov, Ida; Trotta, Jean-Remi; Pérez Jurado, Luis Alberto; Rambla de Argila, Jordi; Gut, Ivo Glynne; Lochmüller, Hanns; Beltran, Sergi (Wiley, 2022)
    Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, ...
  • WEScover: selection between clinical whole exome sequencing and gene panel testing
    Lee, In-Hee; Lin, Yufei; Jefferson Alvarez, William; Hernandez-Ferrer, Carles, 1987-; Mandl, Kenneth D.; Kong, Sek Won (BioMed Central, 2021)
    Background: Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for ...

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