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


Principal Investigator Principal Investigator

Current members Current members

Ongoing projects Ongoing projects

Publications Publications

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

Domínguez-Andrés J, Kuijpers Y, Bakker OB, Jaeger M, Xu CJ, Van der Meer JW, Jakobsson M, Bertranpetit J, Joosten LA, Li Y, Netea MG. 2021. Evolution of cytokine production capacity in ancient and modern European populations. eLife, 10:1-30. DOI:10.7554/eLife.64971

Borsari B, Villegas-Mirón P, Pérez-Lluch S, Turpin I, Laayouni H, Segarra-Casas A, Bertranpetit J, Guigó R, Acosta S. 2021. Enhancers with tissue-specific activity are enriched in intronic regions. Genome Research, 31(8):1325-1336. DOI:10.1101/gr.270371.120

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

Nagle N, van Oven M, Wilcox S, van Holst Pellekaan S, Tyler-Smith C, Xue Y, Ballantyne KN, Wilcox L, Papac L, Cooke K, van Oorschot RA, McAllister P, Williams L, Kayser M, Mitchell RJ, Genographic Consortium. 2017. Aboriginal Australian mitochondrial genome variation - An increased understanding of population antiquity and diversity. Scientific Reports, 7:1-12. DOI:10.1038/srep43041

Mondal M, Bergström A, Xue Y, Calafell F, Laayouni H, Casals F, Majumder PP, Tyler-Smith C, Bertranpetit J. 2017. Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Human Genetics, 136(5):499-510. DOI:10.1007/s00439-017-1800-0

Jofré P, Das P, Bertranpetit J, Foley R. 2017. Cosmic phylogeny: Reconstructing the chemical history of the solar neighbourhood with an evolutionary tree. Monthly Notices of the Royal Astronomical Society, 467(1):1140-1153. DOI:10.1093/mnras/stx075

Mondal M, Casals F, Xu T, Dall'Olio GM, Pybus M, Netea MG, Comas D, Laayouni H, Li Q, Majumder PP, Bertranpetit J. 2016. Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nature Genetics, 48(9):1066-1070. DOI:10.1038/ng.3621

Martínez-Cruz B, Mendizabal I, Harmant C, de Pablo R, Ioana M, Angelicheva D, Kouvatsi A, Makukh H, Netea MG, Pamjav H, Zalán A, Tournev I, Marushiakova E, Popov V, Bertranpetit J, Kalaydjieva L, Quintana-Murci L, Comas D. 2016. Origins, admixture and founder lineages in European Roma. European Journal of Human Genetics, 24(6):937-943. DOI:10.1038/ejhg.2015.201

Julià A, González I, Fernández-Nebro A, Blanco F, Rodriguez L, González A, Cañete JD, Maymó J, Alperi-López M, Olivé A, Corominas H, Martínez-Taboada V, Erra A, Sánchez-Fernández S, Alonso A, Lopez-Lasanta M, Tortosa R, Codó L, Gelpi JL, García-Montero AC, Bertranpetit J, Absher D, Bridges SL Jr, Myers RM, Tornero J, Marsal S. 2016. A genome-wide association study identifies SLC8A3 as a susceptibility locus for ACPA-positive rheumatoid arthritis. Rheumatology (United Kingdom), 55(6):1106-1111. DOI:10.1093/rheumatology/kew035

Fernández-Sampedro MA, Invergo BM, Ramon E, Bertranpetit J, Garriga P. 2016. Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution. Scientific Reports, 6:1-13. 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, 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, 37(21):2841-2847. DOI:10.1002/elps.201600180

Cagan A, Theunert C, Laayouni H, Santpere G, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J, Andrés AM. 2016. Natural selection in the great apes. Molecular Biology and Evolution, 33(12):3268-3283. DOI:10.1093/molbev/msw215

Aterido A, Julià A, Ferrándiz C, Puig L, Fonseca E, Fernández-López E, Dauden E, Sánchez-Carazo JL, López-Estebaranz JL, Moreno-Ramírez D, Vanaclocha F, Herrera E, de la Cueva P, Dand N, Palau N, Alonso A, López-Lasanta M, Tortosa R, García-Montero A, Codó L, Gelpí JL, Bertranpetit J, Absher D, Capon F, Myers RM, Barker JN, Marsal S. 2016. Genome-Wide Pathway Analysis Identifies Genetic Pathways Associated with Psoriasis. Journal of Investigative Dermatology, 136(3):593-602. DOI:10.1016/j.jid.2015.11.026

Solé-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. DOI:10.1038/ejhg.2015.14

Pybus M, Luisi P, Dall'Olio GM, 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. DOI:10.1093/bioinformatics/btv493

Luisi P, Alvarez-Ponce D, Pybus M, Fares MA, 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. DOI:10.1093/gbe/evv055

Gineau L, Luisi P, Castelli EC, Milet J, Courtin D, Cagnin N, Patillon B, Laayouni H, Moreau P, Donadi EA, Garcia A, Sabbagh A. 2015. Balancing immunity and tolerance: Genetic footprint of natural selection in the transcriptional regulatory region of HLA-G. Genes and Immunity, 16(1):57-70. DOI:10.1038/gene.2014.63

Dobon B, Hassan HY, Laayouni H, Luisi P, Ricaño-Ponce I, Zhernakova A, Wijmenga C, Tahir H, Comas D, Netea MG, Bertranpetit J. 2015. The genetics of East African populations: A Nilo-Saharan component in the African genetic landscape. Scientific Reports, 5(November 2014):1-11. DOI:10.1038/srep09996

Dall’Olio GM, Vahdati AR, Bertranpetit J, Wagner A, Laayouni H. 2015. VCF2Networks: Applying genotype networks to single-nucleotide variants data. Bioinformatics, 31(3):438-439. DOI:10.1093/bioinformatics/btu650

Yamamoto F, Cid E, Yamamoto M, Saitou N, Bertranpetit J, Blancher A. 2014. An integrative evolution theory of histo-blood group ABO and related genes. Scientific Reports, 4:1-12. DOI:10.1038/srep06601

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 EC, Gineau L, Courtin D, Milet J, Massaro JD, Laayouni H, Moreau P, Donadi EA, Garcia A. 2014. Worldwide genetic variation at the 3′ untranslated region of the HLA-G gene: Balancing selection influencing genetic diversity. Genes and Immunity, 15(2):95-106. DOI:10.1038/gene.2013.67

Pybus M, Dall'Olio GM, Luisi P, Uzkudun M, Carreño-Torres A, Pavlidis P, Laayouni H, Bertranpetit J, 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):903-909. DOI:10.1093/nar/gkt1188

Laayouni H, Oosting M, Luisi P, Ioana M, Alonso S, Ricaño-Ponce I, Trynka G, Zhernakova A, Plantinga TS, Cheng SC, van der Meer JW, Popp R, Sood A, Thelma BK, Wijmenga C, Joosten LA, Bertranpetit J, Netea MG. 2014. Convergent evolution in European and Rroma populations reveals pressure exerted by plague on Toll-like receptors. Proceedings of the National Academy of Sciences of the United States of America, 111(7):2668-2673. DOI:10.1073/pnas.1317723111

Juyal G, Mondal M, Luisi P, Laayouni H, Sood A, Midha V, Heutink P, Bertranpetit J, Thelma BK, Casals F. 2014. Population and genomic lessons from genetic analysis of two Indian populations. Human genetics, 133(10):1273-1287. DOI:10.1007/s00439-014-1462-0

Invergo BM, Dell’Orco D, Montanucci L, Koch KW, Bertranpetit J. 2014. A comprehensive model of the phototransduction cascade in mouse rod cells. Molecular BioSystems, 10(6):1481-1489. DOI:10.1039/c3mb70584f

Dall’Olio GM, Bertranpetit J, Wagner A, Laayouni H. 2014. Human genome variation and the concept of genotype networks. PLoS ONE, 9(6). DOI:10.1371/journal.pone.0099424

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. 2014. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biology, 15(6):1-14. DOI:10.1186/gb-2014-15-6-r88

Colombo M, Laayouni H, Invergo BM, Bertranpetit J, Montanucci L. 2014. Metabolic flux is a determinant of the evolutionary rates of enzyme-encoding genes. Evolution, 68(2):605-613. DOI:10.1111/evo.12262

Clarke AC, Prost S, Stanton JA, White WT, Kaplan ME, Matisoo-Smith EA; 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):1-12. DOI:10.1186/1471-2164-15-68

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

Invergo, B.;  Montanucci, L.;  Laayouni , H.;  Bertranpetit. J. 2013. A system-level, molecular evolutionary analysis of mammalian phototransduction. BMC Evolutionary Biology. 13 (1):52

Haber, M.;  Gauguier, D.;  Youhanna, S.;  [7 authros];  Bertranpetit, J.;  Tyler-Smith, C.;  Comas, D.;  Zalloua. P.A. 2013. Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture. PLoS Genetic. 9 (2):e1003316

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