Browsing by Author "Bertranpetit, Jaume, 1952-"

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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, 1989-; 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 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 ...
  • Aboriginal Australian mitochondrial genome variation – an increased understanding of population antiquity and diversity
    Nagle, Nano; van Oven, Mannis; Wilcox, Stephen; van Holst Pellekaan, Sheila; Tyler-Smith, Chris; Xue, Yali; Ballantyne, Kaye N.; Wilcox, Leah; Papac, Luka; Cooke, Karen; van Oorschot, Roland A. H.; McAllister, Peter; Williams, Lesley; Manfred, Kayser; Mitchell, R. John; Genographic Consortium; Bertranpetit, Jaume, 1952-; Comas, David, 1969-; Haber, Marc, 1980-; Martínez Cruz, Begoña; Melé Messeguer, Marta, 1982- (Nature Publishing Group, 2017)
    Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 ...
  • Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population
    Walsh Capdevila, Sandra, 1991-; Izquierdo Serra, Mercè; Acosta, Sandra; Edo, Albert; Lloret, María; Moret, Roser; Bosch Fusté, Elena; Oliva Miguel, Baldomero; Bertranpetit, Jaume, 1952-; Fernández-Fernández, José Manuel, 1967- (Nature Research, 2020)
    TRPP3 (also called PKD2L1) is a nonselective, cation-permeable channel activated by multiple stimuli, including extracellular pH changes. TRPP3 had been considered a candidate for sour sensor in humans, due to its high ...
  • Agta hunter–gatherer oral microbiomes are shaped by contact network structure
    Musciotto, Federico; Dobón Berenguer, Begoña, 1987-; Greenacre, Michael; Mira, Alex; Chaudhary, Nikhil; Salali, Gul Deniz; Gerbault, Pascale; Schlaepfer, Rodolph; Astete, Leonora H.; Ngales, Marilyn; Gomez-Gardenes, Jesus; Latora, Vito; Battiston, Federico; Bertranpetit, Jaume, 1952-; Vinicius, Lucio; Migliano, Andrea Bamberg (Cambridge University Press, 2023)
    Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter–gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar ...
  • An integrative evolution theory of histo-blood group ABO and related genes
    Yamamoto, Fumiichiro; Cid, Emili; Yamamoto, Miyako; Saitou, Naruya; Bertranpetit, Jaume, 1952-; Blancher, Antoine (Nature Research, 2014)
    The ABO system is one of the most important blood group systems in transfusion/transplantation medicine. However, the evolutionary significance of the ABO gene and its polymorphism remained unknown. We took an integrative ...
  • Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania
    Mondal, Mayukh, 1989-; Bertranpetit, Jaume, 1952-; Lao Grueso, Oscar, 1976- (Nature Research, 2019)
    Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified ...
  • 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 ...
  • Comparative analysis of cancer genes in the human and chimpanzee genomes
    Puente, Xosé S.; Velasco, Gloria; Gutiérrez Fernández, Ana; Bertranpetit, Jaume, 1952-; King, Mary Claire; López Otín, Carlos (BioMed Central, 2006)
    Background: Cancer is a major medical problem in modern societies. However, the incidence of this disease in non-human primates is very low. To study whether genetic differences between human and chimpanzee could contribute ...
  • A comprehensive model of the phototransduction cascade in mouse rod cells
    Invergo, Brandon M., 1982-; Dell'Orco, Daniele; Montanucci, Ludovica, 1978-; Koch, Karl-Wilhelm; Bertranpetit, Jaume, 1952- (Royal Society of Chemistry, 2014)
    Vertebrate visual phototransduction is perhaps the most well-studied G-protein signaling pathway. A wealth of available biochemical and electrophysiological data has resulted in a rich history of mathematical modeling of ...
  • Cosmic phylogeny: reconstructing the chemical history of the solar neighbourhood with an evolutionary tree
    Jofré, Paula; Das, Payel; Bertranpetit, Jaume, 1952-; Foley, Robert (Oxford University Press, 2017)
    Using 17 chemical elements as a proxy for stellar DNA, we present a full phylogenetic study of stars in the solar neighbourhood. This entails applying a clustering technique that is widely used in molecular biology to ...
  • 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 ...
  • Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins
    Invergo, Brandon M., 1982-; Montanucci, Ludovica, 1978-; Bertranpetit, Jaume, 1952- (Royal Society, 2015)
    Determining the influence of complex, molecular-system dynamics on the evolution of proteins is hindered by the significant challenge of quantifying the control exerted by the proteins on system output. We have employed a ...
  • 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 ...

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