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Browsing by Author "Navarro i Cuartiellas, Arcadi, 1969-"

Browsing by Author "Navarro i Cuartiellas, Arcadi, 1969-"

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  • 267 spanish exomes reveal population-specific differences in disease-related genetic variation
    Dopazo, Joaquín; Rodríguez, Juan Antonio; Daub, Josephine T.; Muntané, Gerard; Navarro i Cuartiellas, Arcadi, 1969-; Antiñolo, Guillermo (Oxford University Press, 2016)
    Recent results from large-scale genomic projects suggest that allele frequencies, which are highly relevant for medical purposes, differ considerably across different populations. The need for a detailed catalog of local ...
  • A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)
    Kuderna, Lukas F.K.; Laayouni, Hafid, 1968-; García Pérez, Raquel, 1989-; Povolotskaya, Inna, 1986-; Serres Armero, Aitor, 1992-; Gómez Garrido, Jèssica; Alioto, Tyler; Navarro i Cuartiellas, Arcadi, 1969-; Bertranpetit, Jaume, 1952-; Marquès i Bonet, Tomàs, 1975- (Oxford University Press, 2017)
    The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high-quality reference genome assembly; however, as with most mammalian genomes, the current ...
  • A burst of segmental duplications in the genome of the African great ape ancestor
    Marquès i Bonet, Tomàs, 1975-; Kidd, Jeffrey M.; Ventura, Mario; Graves, Tina A.; Cheng, Ze; Hillier, LeDeana W.; Jiang, Zhaoshi; Baker, Carl; Malfavon-Borja, Ray; Fulton, Lucinda; Alkan, Can; Aksay, Gozde; Girirajan, Santhosh; Siswara, Priscillia; Chen, Lin; Cardone, Maria Francesca; Navarro i Cuartiellas, Arcadi, 1969-; Mardis, Elaine R.; Wilson, Richard K.; Eichler, Evan E. (Nature Publishing Group, 2009)
    It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there ...
  • A new risk variant for multiple sclerosis at 11q23.3 locus is associated with expansion of CXCR5+ circulating regulatory T cells
    Gil-Varea, Elia; Bosch Fusté, Elena; Navarro i Cuartiellas, Arcadi, 1969-; Comabella López, Manuel (MDPI, 2020)
    Genome-wide association studies and meta-analysis have contributed to the identification of more than 200 loci associated with multiple sclerosis (MS). However, a proportion of MS heritability remains unknown. We aimed to ...
  • A quality control portal for sequencing data deposited at the European genome-phenome archive
    Fernández-Orth, Dietmar; Rueda, Manuel; Singh, Babita, 1986-; Moldes, Mauricio; Jene, Aina; Ferri, Marta; Vasallo, Claudia; Fromont, Lauren A.; Navarro i Cuartiellas, Arcadi, 1969-; Rambla de Argila, Jordi (Oxford University Press, 2022)
    Since its launch in 2008, the European Genome-Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data. In this regard, one of the community concerns is the potential usability ...
  • Accelerated exon evolution within primate segmental duplications
    Lorente-Galdós, Belén, 1981-; Bleyhl, Jonathan; Santpere Baró, Gabriel, 1981-; Vives, Laura; Ramírez, Oscar; Hernández Rodríguez, Jéssica, 1983-; Anglada Busquets, Roger; Cooper, Gregory M.; Navarro i Cuartiellas, Arcadi, 1969-; Eichler, Evan E.; Marquès i Bonet, Tomàs, 1975- (BioMed Central, 2013)
    BACKGROUND: The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most ...
  • Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements
    Santpere Baró, Gabriel, 1981-; Carnero-Montoro, Elena, 1985-; Petit, Natalia; Serra, François; Hvilsom, Christina; Rambla de Argila, Jordi; Heredia Genestar, José María, 1985-; Halligan, Daniel L.; Dopazo, Hernán; Navarro i Cuartiellas, Arcadi, 1969-; Bosch Fusté, Elena (Oxford University Press, 2015)
    We set out to investigate potential differences and similarities between the selective forces acting upon the coding and noncoding regions of five different sets of genes defined according to functional and evolutionary ...
  • Application of multi-SNP approaches Bayesian LASSO and AUC-RF to detect main effects of inflammatory-gene variants associated with bladder cancer risk
    López De Maturana, Evangelina; Ye, Yuanqing; Calle, M. Luz; Rothman, Nathaniel; Urrea, Víctor; Kogevinas, Manolis; Petrus, Sandra; Chanock, Stephen J.; Tardón, Adonina; García Closas, Montserrat; González Neira, Anna; Vellalta, Gemma; Carrato, Alfredo; Navarro i Cuartiellas, Arcadi, 1969-; Lorente-Galdós, Belén, 1981-; Silverman, Debra T.; Real, Francisco X.; Wu, Xifeng; Malats i Riera, Núria (Public Library of Science (PLoS), 2013)
    The relationship between inflammation and cancer is well established in several tumor types, including bladder cancer. We performed an association study between 886 inflammatory-gene variants and bladder cancer risk in ...
  • Assessing statistical significance in multivariable genome wide association analysis
    Buzdugan, Laura; Kalisch, Markus; Navarro i Cuartiellas, Arcadi, 1969-; Schunk, Daniel; Fehr, Ernst; Bühlmann, Peter (Oxford University Press, 2016)
    Motivation: Although Genome Wide Association Studies (GWAS) genotype a very large number of single nucleotide polymorphisms (SNPs), the data are often analyzed one SNP at a time. The low predictive power of single SNPs, ...
  • Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond
    Rambla de Argila, Jordi; Baudis, Michael; Ariosa, Roberto; Beck, Timothy; Fromont, Lauren A.; Navarro i Cuartiellas, Arcadi, 1969-; Paloots, Rahel; Rueda, Manuel; Saunders, Gary; Singh, Babita, 1986-; Spalding, J. Dylan; Törnoos, Juha; Vasallo, Claudia; Veal, Colin D.; Brookes, Anthony J. (Wiley, 2022)
    Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human ...
  • Biological processes modulating longevity across primates: a phylogenetic genome-phenome analysis
    Muntané, Gerard; Farré, Xavier; Rodríguez Pérez, Juan Antonio, 1985-; Pegueroles Queralt, Maria Cinta; Hughes, David; Magalhães, João Pedro de; Gabaldón Estevan, Juan Antonio, 1973-; Navarro i Cuartiellas, Arcadi, 1969- (Oxford University Press, 2018)
    Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and ...
  • Brain transcriptomic profiling reveals common alterations across neurodegenerative and psychiatric disorders
    Sadeghi, Iman; Gispert López, Juan Domingo; Palumbo, Emilio; Muñoz-Aguirre, Manuel; Wucher, Valentin; D'Argenio, Valeria; Santpere Baró, Gabriel, 1981-; Navarro i Cuartiellas, Arcadi, 1969-; Guigó Serra, Roderic; Vilor Tejedor, Natàlia, 1988- (Elsevier, 2022)
    Neurodegenerative and neuropsychiatric disorders (ND-NPs) are multifactorial, polygenic and complex behavioral phenotypes caused by brain abnormalities. Large-scale collaborative efforts have tried to identify the genetic ...
  • Chimpanzee genomic diversity reveals ancient admixture with bonobos
    de Manuel, Marc; Kuhlwilm, Martin; Sousa, Victor C.; Prado Martínez, Javier, 1987-; Hernández Rodríguez, Jéssica, 1983-; Dupanloup, Isabelle; Lao Grueso, Oscar, 1976-; Heredia Genestar, José María, 1985-; Kuderna, Lukas F.K.; Casals López, Ferran; Angedakin, Samuel; Arandjelovic, Mimi; Boesch, Christophe; Kühl, Hjalmar S.; Vigilant, Linda; Navarro i Cuartiellas, Arcadi, 1969-; Excoffier, Laurent; Marquès i Bonet, Tomàs, 1975- (American Association for the Advancement of Science (AAAS), 2016)
    Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that ...
  • Coexpression of the discoidin domain receptor 1 gene with oligodendrocyte-related and schizophrenia risk genes in the developing and adult human brain
    Muntané, Gerard; Chillida, Marc; Aranda, Selena; Navarro i Cuartiellas, Arcadi, 1969-; Vilella, Elisabet (Wiley, 2021)
    Background: Discoidin domain receptor tyrosine kinase 1 (DDR1) is present in multiple types of epithelial cells and is highly expressed in the nervous system. Previous studies have revealed that DDR1 is involved in ...
  • Combining Multiple Hypothesis Testing with Machine Learning Increases the Statistical Power of Genome-wide Association Studies
    Mieth, Bettina; Kloft, Marius; Rodríguez, Juan Antonio; Sonnenburg, Sören; Vobruba, Robin; Morcillo Suárez, Carlos, 1969-; Farré, Xavier; Marigorta, Urko M.; Fehr, Ernst; Dickhaus, Thorsten; Blanchard, Gilles; Schunk, Daniel; Navarro i Cuartiellas, Arcadi, 1969-; Müller, Klaus-Robert (Nature Publishing Group, 2016)
    The standard approach to the analysis of genome-wide association studies (GWAS) is based on testing each position in the genome individually for statistical significance of its association with the phenotype under ...
  • Comparative analysis of mammal genomes unveils key genomic variability for human life span
    Farré, Xavier; Molina, Ruben; Barteri, Fabio; Timmers, Paul R.H.J.; Joshi, Peter K.; Oliva Miguel, Baldomero; Acosta, Sandra; Esteve Altava, Borja; Navarro i Cuartiellas, Arcadi, 1969-; Muntané, Gerard (Oxford University Press, 2021)
    The enormous mammal's lifespan variation is the result of each species' adaptations to their own biological trade-offs and ecological conditions. Comparative genomics have demonstrated that genomic factors underlying both, ...
  • Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta)
    Brasó-Vives, Marina, 1990-; Povolotskaya, Inna, 1986-; Hartasánchez Frenk, Diego Andrés, 1982-; Farré, Xavier; Fernández Callejo, Marcos; Raveendran, Muthuswamy; Harris, R. Alan; Rosene, Douglas L.; Lorente Galdós, Maria Belén; Navarro i Cuartiellas, Arcadi, 1969-; Marquès i Bonet, Tomàs, 1975-; Rogers, Jeffrey; Juan Sopeña, David Alejandro, 1975- (Public Library of Science (PLoS), 2020)
    The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources ...
  • Copy number variation analysis in the great apes reveals species-specific patterns of structural variation
    Gazave, Elodie; Darre, Fleur; Morcillo Suárez, Carlos, 1969-; Petit, Natalia; Carreño Torres, Angel; Marigorta, Urko M.; Ryder, Oliver A.; Blancher, Antoine; Rocchi, Mariano; Bosch Fusté, Elena; Baker, Carl; Marquès i Bonet, Tomàs, 1975-; Eichler, Evan E.; Navarro i Cuartiellas, Arcadi, 1969- (Cold Spring Harbor Laboratory Press (CSHL Press), 2011)
    Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV ...
  • Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions
    Lobón, 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 ...
  • Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
    Olalde Marquínez, Íñigo, 1987-; Sánchez Quinto, Federico A, 1985-; Santpere Baró, Gabriel, 1981-; Rodríguez Pérez, Juan Antonio, 1985-; Quilez Oliete, Javier; Ramírez, Oscar; Marigorta, Urko M.; Fernández Callejo, Marcos; Marquès i Bonet, Tomàs, 1975-; Navarro i Cuartiellas, Arcadi, 1969-; Lalueza Fox, Carles, 1965- (Nature Research, 2014)
    Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the ...