Browsing by Author "Dabad, Marc"

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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 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 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 Stenotrophomonas maltophilia TetR-like transcriptional regulator involved in fatty acid metabolism is controlled by quorum sensing signals
    Coves, Xavier; Bravo, Marc; Huedo, Pol; Conchillo-Solé, Òscar; Gómez, Andromeda-Celeste; Esteve-Codina, Anna; Dabad, Marc; Gut, Marta; Daura, Xavier; Yero, Daniel; Gibert, Isidre (American Society for Microbiology, 2023)
    Stenotrophomonas maltophilia is an environmental bacterium as well as an emerging opportunistic multidrug-resistant pathogen. They use the endogenous diffusible signal factor (DSF) quorum sensing (QS) system to coordinate ...
  • Alteration in the Culex pipiens transcriptome reveals diverse mechanisms of the mosquito immune system implicated upon Rift Valley fever phlebovirus exposure
    Núñez, Ana I.; Esteve-Codina, Anna; Gómez-Garrido, Jèssica; Brustolin, Marco; Talavera, Sandra; Berdugo, Miguel; Dabad, Marc; Alioto, Tyler; Bensaid, Albert; Busquets, Núria (Public Library of Science (PLoS), 2020)
    Rift Valley fever phlebovirus (RVFV) causes an emerging zoonotic disease and is mainly transmitted by Culex and Aedes mosquitoes. While Aedes aegypti-dengue virus (DENV) is the most studied model, less is known about the ...
  • Cross-protection against African swine fever virus upon intranasal vaccination is associated with an adaptive-innate immune crosstalk
    Bosch-Camós, Laia; Alonso, Uxía; Esteve-Codina, Anna; Chang, Chia-Yu; Martín-Mur, Beatriz; Accensi, Francesc; Muñoz, Marta; Navas, María J.; Dabad, Marc; Vidal Barba, Enric; Pina-Pedrero, Sonia; Pleguezuelos, Patricia; Caratù, Ginevra; Salas, María L.; Liu, Lihong; Bataklieva, Stanimira; Gavrilov, Boris; Rodríguez, Fernando; Argilaguet Marqués, Jordi, 1977- (Public Library of Science (PLoS), 2022)
    African swine fever virus (ASFV) is causing a worldwide pandemic affecting the porcine industry and leading to important global economic consequences. The virus causes a highly lethal hemorrhagic disease in wild boars and ...
  • 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 ...
  • De novo transcriptome sequencing and gene co-expression reveal a genomic basis for drought sensitivity and evidence of a rapid local adaptation on Atlas cedar (Cedrus atlantica)
    Cobo-Simón, Irene; Gómez-Garrido, Jèssica; Esteve-Codina, Anna; Dabad, Marc; Alioto, Tyler; Maloof, Julin N.; Méndez-Cea, Belén; Seco, José Ignacio; Linares, Juan Carlos; Gallego, Francisco Javier (Frontiers, 2023)
    Introduction: Understanding the adaptive capacity to current climate change of drought-sensitive tree species is mandatory, given their limited prospect of migration and adaptation as long-lived, sessile organisms. Knowledge ...
  • Deep analysis of acquired resistance to FGFR1 inhibitor identifies MET and AKT activation and an expansion of AKT1 mutant cells
    Giménez Xavier, Pol; Pros, Eva; Aza, Ana; Moran, Sebastian; Tonda, Raúl; Esteve-Codina, Anna; Dabad, Marc; Sánchez Céspedes, Montse (Impact Journals, 2018)
    The development of acquired resistance (AR) to tyrosine kinase inhibitors (TKIs) of FGFR1 activation is currently not well understood. To gain a deeper insight into this matter in lung cancer, we used the FGFR1-amplified ...
  • 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 ...
  • Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions
    Lobon Garcia, Irene; Tucci, Serena; de Manuel, Marc; Ghirotto, Silvia; Benazzo, Andrea; Prado Martínez, Javier, 1987-; Lorente-Galdós, Belén, 1981-; Nam, Kiwoong; Dabad, Marc; Hernández Rodríguez, Jéssica, 1983-; Comas, David, 1969-; Navarro i Cuartiellas, Arcadi, 1969-; Schierup, Mikkel H.; Andrés Morán, Aida, 1976-; Barbujani, Guido; Hvilsom, Christina; Marquès i Bonet, Tomàs, 1975- (Oxford University Press, 2016)
    The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan ...
  • Developmental RNA-Seq transcriptomics of haploid germ cells and spermatozoa uncovers novel pathways associated with teleost spermiogenesis
    Castro-Arnau, Júlia; Chauvigné, François; Gómez-Garrido, Jèssica; Esteve-Codina, Anna; Dabad, Marc; Alioto, Tyler; Finn, Roderick Nigel; Cerdà, Joan (Nature Research, 2022)
    In non-mammalian vertebrates, the molecular mechanisms involved in the transformation of haploid germ cells (HGCs) into spermatozoa (spermiogenesis) are largely unknown. Here, we investigated this process in the marine ...
  • 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 ...
  • 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 ...
  • Great ape genetic diversity and population history
    Prado Martínez, Javier, 1987-; Lorente-Galdós, Belén, 1981-; Santpere Baró, Gabriel, 1981-; Casals López, Ferran; Laayouni, Hafid, 1968-; Hernández Rodríguez, Jéssica, 1983-; Hernando Herráez, Irene, 1985-; Pybus Oliveras, Marc, 1985-; Petit, Natalia; Fernández Callejo, Marcos; Dabad, Marc; Carvalho, Tiago Loureiro de, 1987-; Melé Messeguer, Marta, 1982-; Comas, David, 1969-; Navarro i Cuartiellas, Arcadi, 1969-; Bertranpetit, Jaume, 1952-; Marquès i Bonet, Tomàs, 1975- (Nature Publishing Group, 2013)
    Most great ape genetic variation remains uncharacterized1, 2; however, its study is critical for understanding population history3, 4, 5, 6, recombination7, selection8 and susceptibility to disease9, 10. Here we sequence ...
  • Histone H1 depletion triggers an interferon response in cancer cells via activation of heterochromatic repeats
    Izquierdo Bouldstridge, Andrea; Bustillos, Alberto; Bonet-Costa, Carles; Aribau-Miralbés, Patricia; García-Gomis, Daniel; Dabad, Marc; Esteve-Codina, Anna; Pascual-Reguant, Laura, 1990-; Peiró Sales, Sandra; Esteller, Manel; Murtha, Matthew; Millán Ariño, Lluís, 1984-; Jordan Vallès, Albert (Oxford University Press, 2017)
    Histone H1 has seven variants in human somatic cells and contributes to chromatin compaction and transcriptional regulation. Knock-down (KD) of each H1 variant in breast cancer cells results in altered gene expression and ...
  • In silico validation of RNA-Seq results can identify gene fusions with oncogenic potential in glioblastoma
    Hernandez, Ainhoa; Muñoz-Mármol, Ana M.; Esteve-Codina, Anna; Alameda Quitllet, Francisco; Carrato, Cristina; Pineda, Estela; Arpí Llucià, Oriol; Martinez-García, Maria; Mallo, Mar; Gut, Marta; Barco Berrón, Sonia del; Gallego, Oscar; Dabad, Marc; Mesia, Carlos; Bellosillo Paricio, Beatriz; Domenech, Marta; Vidal, Noemí; Aldecoa, Iban; Iglesia, Nuria de la; Balana, Carmen (Nature Research, 2022)
    RNA-Sequencing (RNA-Seq) can identify gene fusions in tumors, but not all these fusions have functional consequences. Using multiple data bases, we have performed an in silico analysis of fusions detected by RNA-Seq in ...
  • Innate cell-mediated cytotoxic activity of European sea bass leucocytes against nodavirus-infected cells: a functional and RNA-seq study
    Chaves Pozo, Elena; Valero, Yulema; Esteve-Codina, Anna; Gómez Garrido, Jèssica; Dabad, Marc; Alioto, Tyler; Meseguer, José; Esteban, María Ángeles; Cuesta, Alberto (Nature Publishing Group, 2017)
    Nervous necrosis virus (NNV) causes high mortalities in several marine species. We aimed to evaluate the innate cell-mediated cytotoxic (CMC) activity of head-kidney leucocytes (HKLs) isolated from naïve European sea bass ...
  • Integrated single-base resolution maps of transcriptome, sRNAome and methylome of Tomato yellow leaf curl virus (TYLCV) in tomato
    Piedra Aguilera, Álvaro; Jiao, Chen; Luna, Ana P.; Villanueva, Francisco; Dabad, Marc; Esteve-Codina, Anna; Díaz Pendón, Juan Antonio; Fei, Zhangjun; Bejarano, Eduardo R.; Castillo, Araceli G. (Nature Research, 2019)
    Geminiviruses are plant ssDNA viruses that replicate through dsDNA intermediates and form minichromosomes which carry the same epigenetic marks as the host chromatin. During the infection, geminiviruses are targets of the ...
  • RNA-Sequencing and immunohistochemistry reveal ZFN7 as a stronger marker of survival than molecular subtypes in G-CIMP-negative glioblastoma
    Esteve-Codina, Anna; Alameda Quitllet, Francisco; Arpí Llucià, Oriol; Gut, Marta; Dabad, Marc; Balana, Carmen (American Association for Cancer Research (AACR), 2021)
    Purpose: Glioblastoma is the most aggressive brain tumor in adults and has few therapeutic options. The study of molecular subtype classifications may lead to improved prognostic classification and identification of new ...

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