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  1. Article

    Open Access

    Extracellular vesicles from dental pulp mesenchymal stem cells modulate macrophage phenotype during acute and chronic cardiac inflammation in athymic nude rats with myocardial infarction

    Extracellular vesicles (EVs) derived from dental pulp mesenchymal stem cells (DP-MSCs) are a promising therapeutic option for the treatment of myocardial ischemia. The aim of this study is to determine whether...

    Elena Amaro-Prellezo, Marta Gómez-Ferrer, Lusine Hakobyan in Inflammation and Regeneration (2024)

  2. Article

    Open Access

    acorde unravels functionally interpretable networks of isoform co-usage from single cell data

    Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to modulate isoform expression within genes and contribute to cell-type identity. However, the extent to which alternative i...

    Angeles Arzalluz-Luque, Pedro Salguero, Sonia Tarazona, Ana Conesa in Nature Communications (2022)

  3. No Access

    Article

    Undisclosed, unmet and neglected challenges in multi-omics studies

    Multi-omics approaches have become a reality in both large genomics projects and small laboratories. However, the multi-omics research community still faces a number of issues that have either not been suffici...

    Sonia Tarazona, Angeles Arzalluz-Luque, Ana Conesa in Nature Computational Science (2021)

  4. No Access

    Article

    A multi-omic study for uncovering molecular mechanisms associated with hyperammonemia-induced cerebellar function impairment in rats

    Patients with liver cirrhosis may develop covert or minimal hepatic encephalopathy (MHE). Hyperammonemia (HA) and peripheral inflammation play synergistic roles in inducing the cognitive and motor alterations ...

    Sonia Tarazona, Héctor Carmona, Ana Conesa, Marta Llansola in Cell Biology and Toxicology (2021)

  5. Article

    Open Access

    Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients

    Patients with liver cirrhosis may develop minimal hepatic encephalopathy (MHE) which affects their quality of life and life span. It has been proposed that a shift in peripheral inflammation triggers the appea...

    Teresa Rubio, Vicente Felipo, Sonia Tarazona, Roberta Pastorelli in Scientific Reports (2021)

  6. Article

    Open Access

    Harmonization of quality metrics and power calculation in multi-omic studies

    Multi-omic studies combine measurements at different molecular levels to build comprehensive models of cellular systems. The success of a multi-omic data analysis strategy depends largely on the adoption of ad...

    Sonia Tarazona, Leandro Balzano-Nogueira, David Gómez-Cabrero in Nature Communications (2020)

  7. Article

    Open Access

    tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

    Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isofor...

    Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila in Genome Biology (2020)

  8. Article

    Open Access

    A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6

    Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms hav...

    Carme Nuño-Cabanes, Manuel Ugidos, Sonia Tarazona in Scientific Data (2020)

  9. Article

    Open Access

    STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse

    Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive sys...

    David Gomez-Cabrero, Sonia Tarazona, Isabel Ferreirós-Vidal in Scientific Data (2019)

  10. Article

    Open Access

    RGmatch: matching genomic regions to proximal genes in omics data integration

    The integrative analysis of multiple genomics data often requires that genome coordinates-based signals have to be associated with proximal genes. The relative location of a genomic region with respect to the ...

    Pedro Furió-Tarí, Ana Conesa, Sonia Tarazona in BMC Bioinformatics (2016)

  11. Article

    Open Access

    Erratum to: A survey of best practices for RNA-seq data analysis

    Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero in Genome Biology (2016)

  12. Article

    Open Access

    A survey of best practices for RNA-seq data analysis

    RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, ...

    Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero in Genome Biology (2016)

  13. Article

    Open Access

    RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior

    Invasive aspergillosis is started after germination of Aspergillus fumigatus conidia that are inhaled by susceptible individuals. Fungal hyphae can grow in the lung through the epithelial tissue and disseminate h...

    Henriette Irmer, Sonia Tarazona, Christoph Sasse, Patrick Olbermann in BMC Genomics (2015)

  14. Article

    Open Access

    Understanding disease mechanisms with models of signaling pathway activities

    Understanding the aspects of the cell functionality that account for disease or drug action mechanisms is one of the main challenges in the analysis of genomic data and is on the basis of the future implementa...

    Patricia Sebastian-Leon, Enrique Vidal, Pablo Minguez, Ana Conesa in BMC Systems Biology (2014)

  15. Article

    Open Access

    Pathway network inference from gene expression data

    The development of high-throughput omics technologies enabled genome-wide measurements of the activity of cellular elements and provides the analytical resources for the progress of the Systems Biology discipl...

    Ignacio Ponzoni, María José Nueda, Sonia Tarazona, Stefan Götz in BMC Systems Biology (2014)

  16. Article

    Open Access

    Functional assessment of time course microarray data

    Time-course microarray experiments study the progress of gene expression along time across one or several experimental conditions. Most developed analysis methods focus on the clustering or the differential ex...

    María José Nueda, Patricia Sebastián, Sonia Tarazona in BMC Bioinformatics (2009)