Browsing by Author "Reverter, Ferran"

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  • A fast non-parametric test of association for multiple traits
    Garrido Martín, Diego, 1992-; Calvo, Miquel (Calvo Llorca); Reverter, Ferran; Guigó Serra, Roderic (BioMed Central, 2023)
    The increasing availability of multidimensional phenotypic data in large cohorts of genotyped individuals requires efficient methods to identify genetic effects on multiple traits. Permutational multivariate analysis of ...
  • A limited set of transcriptional programs define major cell types
    Breschi, Alessandra, 1988-; Muñoz-Aguirre, Manuel; Wucher, Valentin; Davis, Carrie A.; Garrido Martín, Diego, 1992-; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D.; Vlasova, Anna; Dobin, Alexander; Zaleski, Chris; Drenkow, Jorg; Danyko, Cassidy; Scavelli, Alexandra; Reverter, Ferran; Snyder, Michael; Gingeras, Thomas R.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, ...
  • CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis
    Ounzain, Samir; Micheletti, Rudi; Arnan Ros, Carme; Plaisance, Isabelle; Cecchi, Dario; Schroen, Blanche; Reverter, Ferran; Alexanian, Michael; Gonzales, Christine; Ng, Shi Yan; Bussotti, Giovanni, 1983-; Pezzuto, Iole; Notredame, Cedric; Heymans, Stephane; Guigó Serra, Roderic; Johnson, Rory; Pedrazzini, Thierry (Elsevier, 2015)
    Long noncoding RNAs (lncRNAs) are emerging as important regulators of developmental pathways. However, their roles in human cardiac precursor cell (CPC) remain unexplored. To characterize the long noncoding transcriptome ...
  • Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features
    Lanzos Camaioni, Andrés Arturo; Carlevaro-Fita, Joana; Mularoni, Loris; Reverter, Ferran; Palumbo, Emilio; Guigó Serra, Roderic; Johnson, Rory (Nature Publishing Group, 2017)
    Long noncoding RNAs (lncRNAs) represent a vast unexplored genetic space that may hold missing drivers of tumourigenesis, but few such “driver lncRNAs” are known. Until now, they have been discovered through changes in ...
  • Enhancing SVM for survival data using local invariances and weighting
    Sanz, Hector; Reverter, Ferran; Valim, Clarissa (BioMed Central, 2020)
    Background: The necessity to analyze medium-throughput data in epidemiological studies with small sample size, particularly when studying biomedical data may hinder the use of classical statistical methods. Support vector ...
  • Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
    Abascal, Federico; Corvelo, André; Cruz, Fernando; Villanueva Cañas, José Luis, 1984-; Vlasova, Anna; Marcet Houben, Marina; Prieto Barja, Pablo, 1986-; Quilez Oliete, Javier; Frias, Leonor; Ribeca, Paolo; Capella Gutiérrez, Salvador Jesús, 1985-; Câmara Ferreira, Francisco; Lowy Gallego, Ernesto; Cozzuto, Luca; Erb, Ionas; Rodríguez Ales, José Luis; Ruiz Orera, Jorge, 1988-; Reverter, Ferran; Derdak, Sophia; Blanc, Julie; Gut, Marta; Lorente-Galdós, Belén, 1981-; Gut, Ivo Glynne; Guigó Serra, Roderic; Gabaldón Estevan, Juan Antonio, 1973-; Godoy, José A. (BioMed Central, 2016)
    Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective ...
  • Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome
    Garrido Martín, Diego, 1992-; Borsari, Beatrice, 1992-; Calvo, Miquel (Calvo Llorca); Reverter, Ferran; Guigó Serra, Roderic (Nature Research, 2021)
    Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we develop an efficient and reproducible pipeline for the discovery of genetic variants that affect AS (splicing QTLs, sQTLs). We use it ...
  • Inferring differentially expressed pathways using kernel maximum mean discrepancy-based test
    Vegas Lozano, Esteban; Oller, Josep M.; Reverter, Ferran (BioMed Central, 2016)
    Background: Pathway expression is multivariate in nature. Thus, from a statistical perspective, to detect differentially expressed pathways between two conditions, methods for inferring differences between mean vectors ...
  • Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques
    Santus, Luisa; Sopena Rios, Maria; García Pérez, Raquel, 1989-; Lin, Aaron E.; Adams, Gordon C.; Barnes, Kayla G.; Siddle, Katherine J.; Wohl, Shirlee; Reverter, Ferran; Rinn, John L.; Bennett, Richard S.; Hensley, Lisa E.; Sabeti, Pardis C.; Melé Messeguer, Marta, 1982- (Nature Research, 2023)
    Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a ...
  • SVM-RFE: selection and visualization of the most relevant features through non-linear kernels
    Sanz, Hector; Valim, Clarissa; Vegas Lozano, Esteban; Oller, Josep M.; Reverter, Ferran (BioMed Central, 2018)
    Background: Support vector machines (SVM) are a powerful tool to analyze data with a number of predictors approximately equal or larger than the number of observations. However, originally, application of SVM to analyze ...
  • Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases
    Yang, Jialiang; Huang, Tao; Petralia, Francesca; Long, Quan; Zhang, Bin; Argmann, Carmen; Zhao, Yong; Mobbs, Charles V.; Schadt, Eric; Zhu, Jun; Tu, Zhidong; GTEx Consortium; Monlong, Jean; Sammeth, Michael; Mele, Marta; Reverter, Ferran; Goldmann, Jakob; Guigó Serra, Roderic (Nature Publishing Group, 2015)
    Aging is one of the most important biological processes and is a known risk factor for many age-related diseases in human. Studying age-related transcriptomic changes in tissues across the whole body can provide valuable ...
  • The effects of death and post-mortem cold ischemia on human tissue transcriptomes
    Ferreira, Pedro G.; Muñoz-Aguirre, Manuel; Reverter, Ferran; Godinho, Caio P. Sá; Sousa, Abel; Amadoz, Alicia; Sodaei, Reza, 1988-; Hidalgo, Marta R.; Pervouchine, Dmitri D.; Carbonell-Caballero, Jose; Nurtdinov, Ramil; Breschi, Alessandra, 1988-; Amador, Raziel; Oliveira, Patrícia; Çubut, Cankut; Curado, Joao; Aguet, François; Oliveira, Carla; Dopazo, Joaquín; Sammeth, Michael; Ardlie, Kristin G.; Guigó Serra, Roderic (Nature Publishing Group, 2018)
    Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA ...
  • The landscape of expression and alternative splicing variation across human traits
    García Pérez, Raquel, 1989-; Ramirez, Jose Miguel; Ripoll Cladellas, Aida; Chazarra-Gil, Ruben; Oliveros, Winona; Soldatkina, Oleksandra; Bosio, Mattia; Rognon, Paul Joris; Capella Gutiérrez, Salvador Jesús, 1985-; Calvo, Miquel (Calvo Llorca); Reverter, Ferran; Guigó Serra, Roderic; Aguet, François; Ferreira, Pedro G.; Ardlie, Kristin G.; Melé Messeguer, Marta, 1982- (Elsevier, 2022)
    Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as ...