This lab’s main line of research at present focuses on the understanding of natural selection and adaptation in humans and primates through the comparative analysis of genomes. Its purpose is to understand complex adaptations through genome-wide analyses of the footprints that natural selection has left in genomes and attempt to place selection in a functional molecular framework of molecular pathways. The Evolutionary Systems Biology Lab is studying differential adaptation among human populations, including several African populations, Roma (as compared to Romanians and Indians) and in Chimpanzees. It has launched a project with the analysis of the haploid sequences of several individuals from all known groups of Southeast Asian pygmies.

Other websites: Bertranpetit Lab

 

Investigador principal Investigador principal

Miembros del grupo Miembros del grupo

Proyectos en curso Proyectos en curso

Publicaciones Publicaciones

Flores-Bello A, Bauduer F, Salaberria J, Oyharçabal B, Calafell F, Bertranpetit J, Quintana-Murci L, Comas D. 2021. Genetic origins, singularity, and heterogeneity of Basques. Current Biology, 31: 1-11DOI: 10.1016/j.cub.2021.03.010


Walsh S, Izquierdo-Serra M, Acosta S, Edo A, Lloret M, Moret R, Bosch E, Oliva B, Bertranpetit J, Fernández-Fernández JM. 2020. Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population. Scientific Reports, 10(1):1-16. DOI:10.1038/s41598-020-78081-z


Walsh S, Pagani L, Xue Y, Laayouni H, Tyler-Smith C, Bertranpetit J. 2020. Positive selection in admixed populations from Ethiopia. BMC Genetics, 21(Suppl 1):1-17. DOI:10.1186/s12863-020-00908-5


Nye J, Mondal M, Bertranpetit J, Laayouni H. 2020. A fully integrated machine learning scan of selection in the chimpanzee genome. NAR Genomics and Bioinformatics, 2(3). DOI:10.1093/nargab/lqaa061


García-Fernández C, Font-Porterias N, Kučinskas V, Sukarova-Stefanovska E, Pamjav H, Makukh H, Dobon B, Bertranpetit J, Netea MG, Calafell F, Comas D. 2020. Sex-biased patterns shaped the genetic history of Roma. Scientific Reports, 10(1):14464. DOI: 10.1038/s41598-020-71066-y


Dobon B, Ter Horst R, Laayouni H, Mondal M, Bianco E, Comas D, Ioana M, Bosch E, Bertranpetit J, Netea MG. 2020. The shaping of immunological responses through natural selection after the Roma Diaspora. Scientific Reports, 10(1):1–12. DOI: 10.1038/s41598-020-73182-1


Bianco E, Laval G, Font-Porterias N, García-Fernández C, Dobon B, Sabido-Vera R, Sukarova Stefanovska E, Kučinskas V, Makukh H, Pamjav H, Quintana-Murci L, Netea MG, Bertranpetit J, Calafell F, Comas D. 2020. Recent common origin, reduced population size, and marked admixture have shaped European roma genomes. Molecular Biology and Evolution, 37(11):3175–3187. DOI: 10.1093/molbev/msaa156


Mondal M, Bertranpetit J, Lao O. 2019. Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania. Nature Communications. 2019;10(1). doi:10.1038/s41467-018-08089-7


Dobon B, Rossell C, Walsh S, Bertranpetit J. 2019. Is there adaptation in the human genome for taste perception and phase i biotransformation? BMC Evolutionary Biology, 19(1):1-10. DOI:10.1186/s12862-019-1366-7


Dobon B, Montanucci L, Peretó J, Bertranpetit J, Laayouni H. 2019. Gene connectivity and enzyme evolution in the human metabolic network. Biology Direct, 14(1):1-14. DOI:10.1186/s13062-019-0248-7


Nye J, Laayouni H, Kuhlwilm M, Mondal M, Marques-Bonet T, Bertranpetit J. 2018. Selection in the introgressed regions of the chimpanzee genome. Genome Biology and Evolution, 10(4):1132-1138. DOI:10.1093/gbe/evy077


Montanucci L, Laayouni H, Dobon B, Keys KL, Bertranpetit J, Peretó J. 2018. Influence of pathway topology and functional class on the molecular evolution of human metabolic genes. PLoS ONE, 13(12):1-17. DOI:10.1371/journal.pone.0208782


Mondal M, Casals F, Majumder PP, Bertranpetit J. 2018. Reply to ‘No evidence for unknown archaic ancestry in South Asia.’ Nature Genetics, 50(12):1637-1639. DOI:10.1038/s41588-018-0280-z


Mattle-Greminger MP, Bilgin Sonay T, Nater A, Pybus M, Desai T, de Valles G, Casals F, Scally A, Bertranpetit J, Marques-Bonet T, van Schaik CP, Anisimova M, Krützen M. 2018. Genomes reveal marked differences in the adaptive evolution between orangutan species. Genome Biology, 19(1):193. DOI:10.1186/s13059-018-1562-6


Casillas S, Mulet R, Villegas-Mirón P, Hervas S, Sanz E, Velasco D, Bertranpetit J, Laayouni H, Barbadilla A. 2018. PopHuman: the human population genomics browser. Nucleic Acids Research, 46(D1):D1003-D1010. DOI:10.1093/nar/gkx943


Nater, A.Email Author;Mattle-Greminger, M.P.;Nurcahyo, A.;Nowak, M.G.;de Manuel, M.;Desai, T.;Groves, C.;Pybus, M.;Sonay, T.B.;Roos, C.;Lameira, A.R.;Wich, S.A.;Askew, J.;Davila-Ross, M.;Fredriksson, G.;de Valles, G.;Casals, F.;Prado-Martinez, J.;Goossens, B.;Verschoor, E.J.;Warren, K.S.;Singleton, I.;Marques, D.A.;Pamungkas, J.;Perwitasari-Farajallah, D.;Rianti, P.;Tuuga, A.;Gut, I.G.;Gut, M.;Orozco-terWengel, P.;van Schaik, C.P.;Bertranpetit, J.;Anisimova, M.;Scally, A.;Marques-Bonet, T.;Meijaard, E. 2017. Erratum: Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species (Current Biology (2017) 27(22) (3487–3498.e10) (S0960982217312459)(10.1016/j.cub.2017.09.047). Current Biology. 27(22):3576-3577

Nagle N.;Van Oven M.;Wilcox S.;[17 authors];Comas D.;Cooper A;[30 authors];Wells R.S.;Zalloua P.A.;Ziegle J.S. 2017. Aboriginal Australian mitochondrial genome variation - An increased understanding of population antiquity and diversity. Scientific Reports . 7:artículo 43041


Mondal, M.; Bergström, A.; Xue, Y.; Calafell, F.; Laayouni, H.; Casals, F.; Majumder, P.P.; Tyler-Smith, C.; Bertranpetit, J. 2017. Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Hum Genet. Epub ahead of print]

Jofré, P.; Das, P.; Bertranpetit, J.; and Foley, R. 2017. Cosmic phylogeny: reconstructing the chemical history of the solar neighbourhood with an evolutionary tree. Mon Not R Astron Soc 467 (1): 1140-1153.

Mondal, M.; Casals, F.; Xu, T.; Dall'Olio, G.M.; Pybus, M.; Netea, M.G.; Comas, D.; Laayouni, H.; Li, Q.; Majumder, P.P.; Bertranpetit, J. 2016. Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptationNature Genetics 48(9):1066-70.

Martinez-Cruz, B.; Mendizabal, I.; Harmant, C.; de Pablo, R.; Ioana, M.; Angelicheva, D.; Kouvatsi, A.; Makukh, H.; Netea, M. G.; Pamjav, H.; Zalan, A.; Tournev, I.; Marushiakova, E.; Popov, V.; Bertranpetit, J.; Kalaydjieva, L.; Quintana-Murci, L.; and Comas, D. 2016. Origins, admixture and founder lineages in European RomaEuropean Journal of Human Genetics 24, 937-943

Martinez-Cruz, B.; Mendizabal, I.; Harmant, C.; [11 authors]; Bertranpetit, J.; Kalaydjieva, L.; Quintana-Murci, L.; Comas, D. 2016. Origins, admixture and founder lineages in European RomaEur J Hum Genet. 24(6):937-43.


Julià, A.; González, I.; Fernández-Nebro, A.; [17 authors]; Bertranpetit, J.; Absher, D.; Bridges, SL Jr.; Myers, RM.; Tornero, J. and Marsal, S. 2016. A genome-wide association study identifies SLC8A3 as a susceptibility locus for ACPA-positive rheumatoid arthritis. Rheumatology (Oxford) 55(6):1106-11.


Julià A.; Blanco F.; Fernández-Gutierrez.; B.; [17 authors]; Bertranpetit J.; Absher, D.; Myers R.M.; Tornero, J. and Marsal, S. 2016. Genome-Wide Association Study Identifies IRX1 as a Risk Locus for Rheumatoid Factor Positivity in Rheumatoid Arthritis. Arthritis Rheumatol 68(6):1384-91.


Fernández-Sampedro, M.A.; Invergo, B.M.; Ramon, E.; Bertranpetit, J.; and Garriga, P. (2016). Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolutionScientific Reports 6:21570. doi: 10.1038/srep21570.

Calafell, F.; Anglada, R.; Bonet, N.; González-Ruiz, M.; Prats-Muñoz, G.; Rasal, R.; Lalueza-Fox, C.; Bertranpetit, J.; Malgosa, A.; and Casals, F. (2016). An assessment of a massively parallel sequencing approach for the identification of individuals from mass graves of the Spanish Civil War (1936-1939)Electrophoresis [Epub ahead of print]

Cagan, A.; Theunert, C.; Laayouni, H.; Santpere, G.; Pybus, M.; Casals, F.; Prüfer, K.; Navarro, A.; Marques-Bonet, T.; Bertranpetit, J.; and Andres, A.M. (2016). Natural Selection in the Great Apes. Molecular Biology and Evolution 33 (12): 3268-3283.

Aterido, A.; Julià A.; Ferrándiz, C.; [18 authors]; Bertranpetit J.; Absher D.; Capon F.; Myers RM.; Barker J.N. and Marsal S. 2016. Genome-wide pathway analysis identifies new genetic pathways associated with psoriasis. J Invest Dermatol 136(3):593-602.


Sole-Morata, N.; Bertranpetit, J.; Comas, D.; Calafell, F. 2015. Y-chromosome diversity in Catalan surname samples: insights into surname origin and frequency. European Journal of Human Genetics 23(11): 1549-1557.


Pybus, M.; Luisi, P.; Dall'Olio, G.M.; Uzkudun, M.; Laayouni; H.; Bertranpetit, J.; Engelken, J. 2015. Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations. Bioinformatics 31(24): 3946-3952.


Luisi, P.; Alvarez-Ponce, D.; Pybus, M.; Fares, M. A.; Bertranpetit, J.; Laayouni, H. 2015. Recent Positive Selection Has Acted on Genes Encoding Proteins with More Interactions within the Whole Human Interactome. Genome Biology and Evolution 7(4): 1141-1154.


Gineau, L. Luisi, P.; Castelli, E. C.;[4 authors]; Laayouni, H.; Moreau, P.; Donadi, E. A.; Garcia, A.; Sabbagh, A. 2015. Balancing immunity and tolerance: genetic footprint of natural selection in the transcriptional regulatory region of HLA-G. Genes& Immunity 16(1): 57-70.


Dobon, B.; Hassan, H.Y.; Laayouni, H.; Luisi, P.; Ricaño-Ponce, I.; Zhernakova, A.; Wijmenga, C.; Tahir, H.; Comas, D.; Netea, M.G.; Bertranpetit, J. 2015. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscapeScientific Reports. 5.


Dall'Olio, G. M.; Vhadati, A. R.; Bertranpetit, J.; Wagner, A.; Laayouni, H. 2015. VCF2Networks: applying genotype networks to single-nucleotide variants data. Bioinformatics 31(3): 438-439

Yamamoto, F.; Cid, E.; Yamamoto, M.; Saitou, N.; Bertranpetit, J.; and Blancher, A. 2014. An integrative evolution theory of histo-blood group ABO and related genes. Scientific Reports 4:6601.


Solé-Morata, N.; Bertranpetit, J.; Comas, D.; and Calafell, F. 2014. Recent Radiation of R-M269 and High Y-STR Haplotype Resemblance Confirmed. Annals of Human Genetics 78 (4):253-254.


Sabbagh, A., Luisi, P., Castelli, E.C.; Gineau, L.; Courtin, D.; Milet, J.; Massaro, J.D.; Laayouni, H.; Moreau, P.; Donadi, E.A.; Garcia, A. 2014. Worldwide genetic variation at the 3[prime] untranslated region of the HLA-G gene: balancing selection influencing genetic diversity. Genes Immuity 15 (2):95-106


Pybus, M., Dall'Olio, G.M.; Luisi, P.; Uzkudun, M.; Carreño-Torres, A.; Pavlidis, P.; Laayouni, H.; Bertranpetit, J.; and Engelken, J. 2014. 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Research 42 (D1):D903-D909.


Laayouni, H.; Oosting, M.; Luisi, P.; Ioana, M.; Alonso, S.; Ricaño-Ponce, I.; Trynka, G.; Zhernakova, A.; Plantinga, T.S.; Cheng, S.; van der Meer, J.W.M.; Popp, R.; Sood, A.; Thelma, B.K.; Wijmenga, C.; Joosten, L.A.B.; Bertranpetit, J.; Netea, M.G. 2014. Convergent evolution in European and Rroma populations reveals pressure exerted by plague on Toll-like receptors. Proceedings of the National Academy of Sciences 111 (7):2668-2673.


Juyal, G.; Mondal, M.; Luisi, P.; Laayouni, H.; Sood, A.; Midha, V.; Heutink, P.; Bertranpetit, J.; Thelma, B.K.; and Casals, F. 2014. Population and genomic lessons from genetic analysis of two Indian populations. Human Genetics. 133 (10):1273-1287


Invergo, B.M.; Dell'Orco, D.; Montanucci, L.; Koch, K.-W.; and Bertranpetit, J. 2014. A comprehensive model of the phototransduction cascade in mouse rod cells. Molecular BioSystems 10 (6):1481-1489


Gineau, L.; Pierre, L.; Castelli, E.C.; Milet, J.; Courtin, D.; Cagnin, N.; Patillon, B.; Laayouni, H.; Moreau, P.; Donadi, E.A.; Garcia, A.; and Sabbagh, A. 2014.  Balancing immunity and tolerance: genetic footprint of natural selection in the transcriptional regulatory region of HLA-G. Genes and Immunity 16, 57-70


Dall'Olio, G.M.; Bertranpetit, J.; Wagner, A.; and Laayouni, H. 2014. Human Genome Variation and the Concept of Genotype Networks. Plos One 9 (6):e99424


Colonna, V.; Ayub, Q.; Chen, Y.; Pagani, L.; Luisi, P.; Pybus, M.; Garrison, E.; Xue, Y.; and Tyler-Smith, C. 2014. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biology. 15 (6):R88.


Colombo, M.; Laayouni H.; Invergo, B.M.; Bertranpetit, J.; and Montanucci, L. 2014. Metabolic flux is a determinant of the evolutionary rates of enzyme-encoding genes.Evolution. Evolution. 68 (2):605-613


Clarke, A.C.; Prost,S.; Stanton, J.A.; White, W.T.; Kaplan, M.E.; Matisoo-Smith, E.A.; and Genographic Consortium. 2014. From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. BMC Genomics 15(1): 68.


Utro, F.;  Pybus, M.; Parida, L. 2013. Sum of parts is greater than the whole: inference of common genetic history of populations. BMC Genomics. 14 (Suppl 1):S10


Prado-Martinez, J.;  Sudmant, P. H.; Kidd, J. M.;[46 authors]; Comas, D.; [12 authors]; Navarro, A.; Akey, J. M.; Bertranpetit, J.;[9 authors]; Marques-Bonet, T. 2013. Great ape genetic diversity and population history. Nature. 499 (7459):471-475


Prado-Martinez, J.; Hernando-Herraez, I.; Lorente-Galdos, B.; [20 authors]; Bertranpetit, J.; [4 authors].; Lalueza-Fox, C.; Navarro, A.; Marques-Bonet, T. 2013. The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. BMC Genomics. 14 (1):363


Invergo, B.;  Montanucci, L.; Koch, K.-W.; Bertranpetit, J.; DellOrco, D. 2013. Exploring the rate-limiting steps in visual phototransduction recovery by bottom-up kinetic modeling. Cell Communication and Signaling. 11 (1):36


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