Research Topics
Genomes and Genes
Species | Francesc CalafellSummaryAffiliation: Universitat Pompeu Fabra Country: Spain Publications
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Detail Information
Publications
Minimizing recombinations in consensus networks for phylogeographic studiesLaxmi Parida
Computational Biology Center, IBM T J Watson Research, Yorktown, USA
BMC Bioinformatics 10:S72. 2009..To date, this is the best known result for a network consensus problem...
Evolutionary dynamics of the human ABO geneFrancesc Calafell
Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader, 80, 08003, Barcelona, Catalonia, Spain
Hum Genet 124:123-35. 2008..The time depth of the genealogy was also incompatible with neutral evolution, particularly in the region from exons 6 to 7, which codes for most of the catalytic domain...- [Genetic factors in severe cases of (H1N1) 2009 influenza]Francesc Calafell i Majó
Institut de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra Consejo Superior de Investigaciones Cientificas, Doctor Aiguader 88, Barcelona
Rev Esp Salud Publica 85:33-6. 2011.... 
Comparative genetics of functional trinucleotide tandem repeats in humans and apesAida M Andres
Unitat de Biologia Evolutiva, Facultat de Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
J Mol Evol 59:329-39. 2004..Only two loci (SCA1 and SCA8) show a human specific distribution, with larger alleles than the rest of species. This could account, at the same time, for a human-specific trait and a predisposition to disease through expansion...- A natural history of FUT2 polymorphism in humansAnna Ferrer-Admetlla
Institut de Biologia Evolutiva CSIC UPF, CEXS UPF PRBB, Barcelona, Catalonia, Spain
Mol Biol Evol 26:1993-2003. 2009..Thus, a convergent phenotype composition has been achieved through different mutations with different evolutionary histories... - Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LDElena Bosch
Institut de Biologia Evolutiva UPF CSIC, Departament de Ciències Experimentals i de Salut, Universitat Pompeu Fabra, Parc de Recerca Biomedica de Barcelona, Barcelona, Spain
BMC Genomics 10:338. 2009..Within each gene region and population we use r2 between all possible single nucleotide polymorphism (SNP) pairs as a measure of linkage disequilibrium and focus on the proportion of SNP pairs with r2 greater than 0.8... - Interrogating 11 fast-evolving genes for signatures of recent positive selection in worldwide human populationsAndres Moreno-Estrada
Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva UPF CSIC, Universitat Pompeu Fabra, Barcelona, Spain
Mol Biol Evol 26:2285-97. 2009..Based on these data, it therefore appears that adaptation for human-specific and for population-specific traits may have involved different genes... - Human pseudogenes of the ABO family show a complex evolutionary dynamics and loss of functionFerran Casals
Institut de Biologia Evolutiva CSIC UPF, CEXS UPF PRBB, Barcelona, Catalonia, Spain
Glycobiology 19:583-91. 2009.... - Mitochondrial DNA of an Iberian Neandertal suggests a population affinity with other European NeandertalsCarles Lalueza-Fox
, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
Curr Biol 16:R629-30. 2006 - Signatures of selection in the human olfactory receptor OR5I1 geneAndres Moreno-Estrada
Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
Mol Biol Evol 25:144-54. 2008..These results are compatible with positive selection having modeled the pattern of variation found in the OR5I1 gene and with a relatively ancient, mild selective sweep predating the "Out of Africa" expansion of modern humans... - The prion protein gene in humans revisited: lessons from a worldwide resequencing studyMarta Soldevila
Unitat de Biologia Evolutiva, , Universitat Pompeu Fabra, 08003 Barcelona, Spain
Genome Res 16:231-9. 2006.... - The portability of tagSNPs across populations: a worldwide surveyAnna Gonzalez-Neira
Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
Genome Res 16:323-30. 2006..This high degree of portability lends promise to the search for disease association in different populations, once tagSNPs are defined in a few reference populations like those analyzed in the HapMap initiative... - Geographic stratification of linkage disequilibrium: a worldwide population study in a region of chromosome 22Anna Gonzalez-Neira
Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
Hum Genomics 1:399-409. 2004.... - Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineagesDavid Comas
Unitat de Biologia Evolutiva, Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona 08003, Spain
Eur J Hum Genet 12:495-504. 2004.... - Association study between Alzheimer's disease and genes involved in Abeta biosynthesis, aggregation and degradation: suggestive results with BACE1Jordi Clarimon
Unitat de Biologia Evolutiva, Facultat de Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, Doctor Aiguader 80, 08003 Barcelona, Spain
J Neurol 250:956-61. 2003.... - Balancing selection is the main force shaping the evolution of innate immunity genesAnna Ferrer-Admetlla
Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Unitat de Biologia Evolutiva, Barcelona, Catalonia, Spain
J Immunol 181:1315-22. 2008..However, we also describe evidence from African populations, which may reflect parallel or long-term selective forces acting in different geographic areas... - Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the AmericasKarla Sandoval
Institut de Biologia Evolutiva, CEXS UPF PRBB, Barcelona, Catalonia, Spain
Am J Phys Anthropol 148:395-405. 2012..This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas... - African signatures of recent positive selection in human FOXI1Andres Moreno-Estrada
Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva UPF CSIC, Parc de Recerca Biomedica de Barcelona, 08003 Barcelona, Spain
BMC Evol Biol 10:267. 2010.... - Extreme individual marker F(ST )values do not imply population-specific selection in humans: the NRG1 exampleMichelle Gardner
Unitat de Biologia Evolutiva, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
Hum Genet 121:759-62. 2007..In the present study we show evidence that high F(ST) values may not necessarily imply the action of selection, in particular positive selection, neither globally nor regionally, using the example of the NRG1 gene... - Insights into the western Bantu dispersal: mtDNA lineage analysis in AngolaStéphanie Plaza
Unitat de Biologia Evolutiva, Facultat de Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, Doctor Aiguader 80, 08003, Barcelona, Spain
Hum Genet 115:439-47. 2004.... - PKLR- GBA region shows almost complete linkage disequilibrium over 70 kb in a set of worldwide populationsEva Mateu
Unitat de Biologia Evolutiva, Facultat de Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, Doctor Aiguader 80, 08003 Barcelona, Spain
Hum Genet 110:532-44. 2002..LD and STRP variability in non-Africans are approximately 87% of those in Africans, in contrast with other loci; this implies that the "out of Africa" bottleneck may have had a broad distribution of effects across loci... - Linguistic and maternal genetic diversity are not correlated in Native MexicansKarla Sandoval
Institute of Evolutionary Biology UPF CSIC, CEXS UPF PRBB, 08003 Barcelona, Catalonia, Spain
Hum Genet 126:521-31. 2009.... - The Mediterranean paradox for susceptibility factors in coronary heart disease extends to geneticsOscar Lao
Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
Ann Hum Genet 72:48-56. 2008.... - Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in CubaIsabel Mendizabal
Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
BMC Evol Biol 8:213. 2008.... - A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populationsMartin Sikora
Institut de Biologia Evolutiva UPF CSIC, CEXS UPF PRBB, Barcelona, Catalonia, Spain
Eur J Hum Genet 19:84-8. 2011..Finally, we find a strong differentiation of the southeastern Bantu population from Mozambique, which suggests an assimilation of a pre-Bantu substrate by Bantu speakers in the region... - Genetic adaptation of the antibacterial human innate immunity networkFerran Casals
Institute of Evolutionary Biology UPF CSIC, CEXS UPF PRBB, Barcelona, Catalonia, Spain
BMC Evol Biol 11:202. 2011..The evolution of the immune system has therefore been influenced by these pressures. Genomic scans have revealed that immune system is one of the functions enriched with genes under adaptive selection... - Recent human evolution has shaped geographical differences in susceptibility to diseaseUrko M Marigorta
Institute of Evolutionary Biology UPF CSIC, PRBB, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
BMC Genomics 12:55. 2011..Here, we focus on the world-wide patterns of replicability of published association studies... - Genetic and demographic implications of the Bantu expansion: insights from human paternal lineagesGemma Berniell-Lee
Institute of Evolutionary Biology, Consejo Superior de Investigaciones Cientificas UPF, CEXS UPF PRBB, Barcelona, Catalonia, Spain
Mol Biol Evol 26:1581-9. 2009..We also find the intriguing presence of paternal lineages belonging to Eurasian haplogroup R1b1*, which might represent footprints of demographic expansions in central Africa not directly related to the Bantu expansion... - The west side story: MEFV haplotype in Spanish FMF patients and controls, and evidence of high LD and a recombination "hot-spot" at the MEFV locusAnna Aldea
Servei d Immunologia, Institut d Investigacions Biomèdiques Agustí Pi i Sunyer, Hospital Clinic, Barcelona, Catalonia, Spain
Hum Mutat 23:399. 2004..On the contrary, the Chueta spectrum was poorer and closer to that of North African Jews, suggesting a direct connection with the Jewish diaspora... - Spatial patterns of cystic fibrosis mutation spectra in European populationsOscar Lao
Unitat de Biologia Evolutiva, , Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
Eur J Hum Genet 11:385-94. 2003..CF-based distances correlated with mtDNA but not with Y-chromosome-based distances, which may be a consequence of the relatively homogeneous CF mutation frequencies in European populations... - Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombinationAnna Ramírez-Soriano
Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
Genetics 179:555-67. 2008..Nevertheless, they are strongly affected by misestimations of recombination, so they should not be used when recombination levels are unknown. Instead, class I tests, particularly Tajima's D or R2, are recommended... - Prion susceptibility and protective alleles exhibit marked geographic differencesMarta Soldevila
Unitat de Biologia Evolutiva, , Universitat Pompeu Fabra, Barcelona, Spain
Hum Mutat 22:104-5. 2003..The protective 219L allele was restricted to Asian and Pacific populations. Susceptibility alleles exhibit marked geographic differences in frequency, and thus, differences in probability to develop prion diseases... - SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP dataCarlos Morcillo-Suarez
Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona Biomedical Research Park PRBB, Barcelona, Spain
Bioinformatics 24:1643-4. 2008..Many different quality control and analysis procedures can be performed either by using built-in SNPator algorithms or by calling standard genetic software. AVAILABILITY: Access is granted from the SNPator webpage http://www.snpator.org... - Admixture and sexual bias in the population settlement of La Réunion Island (Indian Ocean)Gemma Berniell-Lee
Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
Am J Phys Anthropol 136:100-7. 2008..The absence of genetic diversity within these two major components of the mtDNA gene pool suggests these populations may have witnessed strong founder effects during the colonization process... - Sequence variation and genetic evolution at the human F12 locus: mapping quantitative trait nucleotides that influence FXII plasma levelsFrancesc Calafell
Departament de Ciencies Experimentals i de la Salut, Institute of Evolutionary Biology UPF CSIC, Universitat Pompeu Fabra, Barcelona, Spain
Hum Mol Genet 19:517-25. 2010..Our study provides a template for future genetic studies of human quantitative traits, as we move beyond QTL localization to the polymorphisms responsible for the variation of important biomedical phenotypes... - Similarity in recombination rate estimates highly correlates with genetic differentiation in humansHafid Laayouni
IBE, Institute of Evolutionary Biology UPF CSIC, CEXS UPF PRBB, Barcelona, Catalonia, Spain
PLoS ONE 6:e17913. 2011..This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans... - Reconstructing the Indian origin and dispersal of the European Roma: a maternal genetic perspectiveIsabel Mendizabal
Institute of Evolutionary Biology CSIC UPF, CEXS UPF PRBB, Barcelona, Spain
PLoS ONE 6:e15988. 2011.... - Joint analysis of candidate genes related to Alzheimer's disease in a Spanish populationJordi Clarimon
Unitat de Biologia Evolutiva, Facultat de Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
Psychiatr Genet 13:85-90. 2003..Most of these studies have examined only one or two polymorphisms in a defined population, which provides a lack of a general view of the Alzheimer's disease genetic component... - A new method to reconstruct recombination events at a genomic scaleMarta Mele
IBE, Institute of Evolutionary Biology UPF CSIC, CEXS UPF PRBB, Barcelona, Catalonia, Spain
PLoS Comput Biol 6:e1001010. 2010.... - FABSIM: a software for generating FST distributions with various ascertainment biasesAnna Ramírez-Soriano
IBE, Institute of Evolutionary Biology UPF CSIC, CEXS UPF PRBB Doctor Aiguader, 88 08003 Barcelona, Catalonia, Spain
Bioinformatics 24:2790-1. 2008..AVAILABILITY: FABSIM is available from http://www.snpator.com/public/downloads/aRamirez/FABSIM/... - A genome-wide survey does not show the genetic distinctiveness of BasquesHafid Laayouni
IBE, Institute of Evolutionary Biology UPF CSIC, CEXS UPF PRBB, Barcelona, Catalonia, Spain
Hum Genet 127:455-8. 2010..Thus, Basques cannot be considered a genetic outlier under a general genome scope and interpretations on their origin may have to be revised... - Neandertal evolutionary genetics: mitochondrial DNA data from the iberian peninsulaCarles Lalueza-Fox
Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
Mol Biol Evol 22:1077-81. 2005..250,000 years ago. This coincides with the full emergence of the "classical" Neandertal morphology and fits chronologically with a proposed speciation event of Homo neanderthalensis... - Dynamics of CAG repeat loci revealed by the analysis of their variabilityAida M Andres
Unitat de Biologia Evolutiva, Facultat de Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
Hum Mutat 21:61-70. 2003.... - Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomicsMarc García-Garcerà
Institut de Biologia Evolutiva, CSIC UPF, Barcelona, Spain
PLoS ONE 6:e24161. 2011..Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone... - Insights into the demographic history of African Pygmies from complete mitochondrial genomesChiara Batini
Institut de Biologia Evolutiva CSIC UPF, Department de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
Mol Biol Evol 28:1099-110. 2011.... - Why namesFrancesc Calafell
Unitat de Biologia Evolutiva, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
Genome Res 12:219-21. 2002 - Genetic analysis of the presumptive blood from Louis XVI, King of FranceCarles Lalueza-Fox
Institut de Biologia Evolutiva, CSIC UPF, Dr Aiguader 88, 08003 Barcelona, Spain
Forensic Sci Int Genet 5:459-63. 2011..To confirm the identity of the subject, an analysis of the dried heart of his son, Louis XVII, could be undertaken... - Y-chromosome analysis in individuals bearing the Basarab name of the first dynasty of Wallachian kingsBegoña Martínez-Cruz
Institut de Biologia Evolutiva CSIC UPF, Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
PLoS ONE 7:e41803. 2012..It can be therefore concluded that the Basarab dynasty was successful in spreading its name beyond the spread of its genes... - Can a place of origin of the main cystic fibrosis mutations be identified?Eva Mateu
Unitat de Biologia Evolutiva, Facultat de Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
Am J Hum Genet 70:257-64. 2002....