Browsing by Author "Laayouni, Hafid, 1968-"

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  • 1000 Genomes Selection Browser 1.0: A genome browser dedicated to signatures of natural selection in modern humans
    Pybus Oliveras, Marc, 1985-; Dall'Olio, Giovanni Marco, 1983-; Luisi, Pierre, 1985-; Uzkudun, Manu; Carreño Torres, Angel; Pavlidis, Pavlos; Laayouni, Hafid, 1968-; Bertranpetit, Jaume, 1952-; Engelken, Johannes (Oxford University Press, 2014)
    Searching for Darwinian selection in natural populations has been the focus of a multitude of studies over the last decades. Here we present the 1000 Genomes Selection Browser 1.0 (http://hsb.upf.edu) as a resource for ...
  • 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 Comprehensive screening of X-linked and miRNA-driven signatures of positive selection and the role of cis-regulatory elements in the human genome
    Villegas Mirón, Pablo, 1991- (2021-07-19)
    The evolutionary history of the human genome has been shaped by the selection of multiple elements in response to different environmental pressures. The analysis of regulatory adaptations and the particularities of sexual ...
  • A fully integrated machine learning scan of selection in the chimpanzee genome
    Nye, Jessica, 1986-; Mondal, Mayukh, 1989-; Bertranpetit, Jaume, 1952-; Laayouni, Hafid, 1968- (Oxford University Press, 2020)
    After diverging, each chimpanzee subspecies has been the target of unique selective pressures. Here, we employ a machine learning approach to classify regions as under positive selection or neutrality genome-wide. The ...
  • A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations
    Sikora, Martin, 1976-; Laayouni, Hafid, 1968-; Calafell i Majó, Francesc; Comas, David, 1969-; Bertranpetit, Jaume, 1952- (Nature Publishing Group, 2011)
    Studies of large sets of SNP data have proven to be a powerful tool in the analysis of the genetic structure of human populations. In this work, we analyze genotyping data for 2,841 SNPs in 12 Sub-Saharan African populations, ...
  • A system-level, molecular evolutionary analysis of mammalian phototransduction
    Invergo, Brandon M., 1982-; Montanucci, Ludovica, 1978-; Laayouni, Hafid, 1968-; Bertranpetit, Jaume, 1952- (BioMed Central, 2013)
    Visual perception is initiated in the photoreceptor cells of the retina via the phototransduction system./nThis system has shown marked evolution during mammalian divergence in such complex attributes as activation time ...
  • A targeted association study of immunity genes and networks suggests novel associations with placental malaria infection
    Sikora, Martin, 1976-; Laayouni, Hafid, 1968-; Menéndez, Clara; Mayor, Alfredo; Bardaji, Azucena; Sigauque, Betuel; Netea, Mihai G; Casals López, Ferran; Bertranpetit, Jaume, 1952- (Public Library of Science (PLoS), 2011)
    A large proportion of the death toll associated with malaria is a consequence of malaria infection during pregnancy, causing up to 200,000 infant deaths annually. We previously published the first extensive genetic association ...
  • A variant in the gene FUT9 is associated with susceptibility to placental malaria infection
    Sikora, Martin, 1976-; Ferrer Admetlla, Anna; Laayouni, Hafid, 1968-; Menéndez, Clara; Mayor, Alfredo; Bardaji, Azucena; Sigauque, Betuel; Mandomando, Inacio; Alonso, Pedro L.; Bertranpetit, Jaume, 1952-; Casals López, Ferran (Oxford University Press, 2009)
    Malaria in pregnancy forms a substantial part of the worldwide burden of malaria, with an estimated annual death toll of up to 200,000 infants, as well as increased maternal morbidity and mortality. Studies of genetic ...
  • Adaptive history of the chimpanzee subspecies in the genomic era
    Nye, Jessica, 1986- (Universitat Pompeu Fabra, 2018-12-17)
    Although universal and unavoidable, aging does not occur in a uniform way. In this dissertation, we assessed the effects of early life exposure to pro-inflammatory risk factors (air pollution and obesity) on mitochondrial ...
  • Applications of network theory to human population genetics : from pathways to genotype networks
    Dall'Olio, Giovanni Marco, 1983- (Universitat Pompeu Fabra, 2013-10-28)
    In this thesis we developed two approaches to study positive selection and genetic adaptation in the human genome. Both approaches are based on applications of network theory. In the first approach, we studied how the ...
  • Assessing the digenic model in rare disorders using population sequencing data
    Moreno-Ruiz, Nerea; Genomics England Research Consortium; Lao Grueso, Oscar, 1976-; Aróstegui, Juan Ignacio; Laayouni, Hafid, 1968-; Casals López, Ferran (Nature Research, 2022)
    An important fraction of patients with rare disorders remains with no clear genetic diagnostic, even after whole-exome or whole-genome sequencing, posing a difficulty in giving adequate treatment and genetic counseling. ...
  • Chromosome X-wide analysis of positive selection in human populations: common and private signals of selection and its impact on inactivated genes and enhancers
    Villegas Mirón, Pablo; Acosta, Sandra; Nye, Jessica, 1986-; Bertranpetit, Jaume, 1952-; Laayouni, Hafid, 1968- (Frontiers, 2021)
    The ability of detecting adaptive (positive) selection in the genome has opened the possibility of understanding the genetic basis of population-specific adaptations genome-wide. Here, we present the analysis of recent ...
  • Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD
    Bosch Fusté, Elena; Laayouni, Hafid, 1968-; Morcillo Suárez, Carlos, 1969-; Casals López, Ferran; Moreno Estrada, Andrés; Ferrer Admetlla, Anna; Gardner, Michelle; Rosa, Araceli; Comas, David, 1969-; Graffelman, Jan; Calafell i Majó, Francesc; Bertranpetit, Jaume, 1952- (BioMed Central, 2009)
    Background: It is well known that the pattern of linkage disequilibrium varies between human populations, with remarkable geographical stratification. Indirect association studies routinely exploit linkage disequilibrium ...
  • Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation
    Dall'Olio, Giovanni Marco, 1983-; Laayouni, Hafid, 1968-; Luisi, Pierre, 1985-; Sikora, Martin, 1976-; Montanucci, Ludovica, 1978-; Bertranpetit, Jaume, 1952- (BioMed Central, 2012)
    Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving ...
  • Enhancers with tissue-specific activity are enriched in intronic regions
    Borsari, Beatrice, 1992-; Villegas Mirón, Pablo; Pérez-Lluch, Sílvia; Turpin, Isabel; Laayouni, Hafid, 1968-; Segarra Casas, Alba; Bertranpetit, Jaume, 1952-; Guigó Serra, Roderic; Acosta, Sandra (Cold Spring Harbor Laboratory Press (CSHL Press), 2021)
    Tissue function and homeostasis reflect the gene expression signature by which the combination of ubiquitous and tissue-specific genes contribute to the tissue maintenance and stimuli-responsive function. Enhancers are ...
  • Evaluating the genetics of common variable immunodeficiency: monogenetic model and beyond
    Valles Ibáñez, Guillem de, 1986-; Hernández Rodríguez, Jéssica, 1983-; Laayouni, Hafid, 1968-; Cuscó Martí, Ivon, 1973-; Codina i Solà, Marta, 1988-; Batlle Masó, Laura, 1993-; Solís Moruno, Manuel; Marquès i Bonet, Tomàs, 1975-; Bosch Fusté, Elena; Casals López, Ferran (Frontiers, 2018)
    Common variable immunodeficiency (CVID) is the most frequent symptomatic primary immunodeficiency characterized by recurrent infections, hypogammaglobulinemia and poor response to vaccines. Its diagnosis is made based on ...
  • From networks to population-specific adaptations : studying positive selection in humans
    Dobón Berenguer, Begoña, 1987- (Universitat Pompeu Fabra, 2018-11-23)
    The evolution of the genome is driven, among other factors, by the composition of the genome, the functional output of the gene products, and by environmental pressures. Among the environmental factors, pathogens are one ...
  • Gene connectivity and enzyme evolution in the human metabolic network
    Dobón Berenguer, Begoña, 1987-; Montanucci, Ludovica, 1978-; Peretó, Juli; Bertranpetit, Jaume, 1952-; Laayouni, Hafid, 1968- (BioMed Central, 2019)
    Background: Determining the factors involved in the likelihood of a gene being under adaptive selection is still a challenging goal in Evolutionary Biology. Here, we perform an evolutionary analysis of the human metabolic ...
  • Genetic adaptation of the antibacterial human innate immunity network
    Casals López, Ferran; Sikora, Martin, 1976-; Laayouni, Hafid, 1968-; Montanucci, Ludovica, 1978-; Muntasell i Castellví, Aura, 1972-; Lazarus, Ross; Calafell i Majó, Francesc; Awadalla, Philip; Netea, Mihai G; Bertranpetit, Jaume, 1952- (BioMed Central, 2011)
    Background: Pathogens have represented an important selective force during the adaptation of modern human populations to changing social and other environmental conditions. The evolution of the immune system has therefore ...
  • Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation
    Mondal, Mayukh, 1989-; Casals López, Ferran; Xu, Tina; Dall'Olio, Giovanni Marco, 1983-; Pybus Oliveras, Marc, 1985-; Netea, Mihai G; Comas, David, 1969-; Laayouni, Hafid, 1968-; Li, Qibin; Majumder, Partha P.; Bertranpetit, Jaume, 1952- (Nature Publishing Group, 2016)
    To shed light on the peopling of South Asia and the origins of the morphological adaptations found there, we analyzed whole-genome sequences from 10 Andamanese individuals and compared them with sequences for 60 individuals ...