The general topics that the Genomics of Individuality lab is interested in revolve around the genomics of individuality: What is there in our genomes that makes us the way we are? What does it tell us about our ancestry? How does it affect our susceptibility to diseases? How can this be applied in practical settings (i.e., in forensic genetics)? In particular, its research focuses on populations on both sides of the western Mediterranean, looking at genetic structure, and contacts, and, in particular, populations that are geographically or socially isolated.

Lab website: Calafell Lab

 

Principal Investigator

Francesc Calafell Majó

Calafell Majó, Francesc
UPF Associate Professor
Genomics of Individuality Lab

Current members

Marco Antinucci

Antinucci, Marco
Predoctoral Researcher
Genomics of Individuality

Ongoing projects

Publications

Riyahi S, Carrillo-Ortiz JG, Uribe F, Calafell F, Senar JC. 2022. Risk-taking coping style correlates with SERT SNP290 polymorphisms in free-living great tits. Journal of Experimental Biology, 225(9). DOI:10.1242/jeb.243342

Font-Porterias N, García-Fernández C, Aizpurua-Iraola J, Comas D, Torrents D, de Cid R, Calafell F. 2022. Sequence diversity of the uniparentally transmitted portions of the genome in the resident population of Catalonia. Forensic Science International: Genetics, 61(September):102783. DOI:10.1016/j.fsigen.2022.102783

Casals F, Rasal R, Anglada R, Tormo M, Bonet N, Rivas N, Vásquez P, Calafell F. 2022. A forensic population database in El Salvador: 58 STRs and 94 SNPs. Forensic Science International: Genetics, 57:102646. DOI:10.1016/j.fsigen.2021.102646

Aguilar-Velázquez JA, Duran-Salazar MÁ, Córdoba-Mercado MF, Coronado-Avila CE, Salas-Salas O, Martinez-Cortés G, Casals F, Calafell F, Ramos-González B, Rangel-Villalobos H. 2022. Characterization of 58 STRs and 94 SNPs with the ForenSeqTM DNA signature prep kit in Mexican-Mestizos from the Monterrey city (Northeast, Mexico). Molecular Biology Reports, 49(8):7601-7609. DOI:10.1007/s11033-022-07575-y

Vullo CM, Catelli L, Ibarra Rodriguez AA, Papaioannou A, Merino JCÁ, Lopez-Parra AM, Gaviria A, Baeza-Richer C, Romanini C, González-Moya E, Casals F, Calafell F, Berardi G, Iannacone GC, Vicuña Giraldo GC, Zorba GK, Boschi I, Olarte JV, Ruiz Gomez JE, Acierno JP, Soto ML, Miranda MV, García King MD, Marrucci MA, Porto MJ, Piñero MH, Aler M, Stephenson Ojea MM, Navarrete SC, Toscanini U, Saragoni VG, Bozzo W, Posada Posada YC, Bajunovic Z, Solla LP, Parsons T. 2021. Second GHEP-ISFG exercise for DVI: “DNA-led” victims’ identification in a simulated air crash. Forensic Science International: Genetics, 53(102527). DOI:10.1016/j.fsigen.2021.102527

Platt DE, Artinian H, Mouzaya F, Khalil W, Kamar FG, Matisoo-Smith E, Calafell F, Taleb NN, Zalloua P. 2021. Autosomal genetics and Y-chromosome haplogroup L1b-M317 reveal Mount Lebanon Maronites as a persistently non-emigrating population. European Journal of Human Genetics, 29(4):581-592. DOI:10.1038/s41431-020-00765-x

Lucas-Sánchez M, Font-Porterias N, Calafell F, Fadhlaoui-Zid K, Comas D. 2021. Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation. Scientific Reports, 11(1):21125. DOI:10.1038/s41598-021-00576-0

Font-Porterias N, Caro-Consuegra R, Lucas-Sánchez M, Lopez M, Giménez A, Carballo A, Bosch E, Calafell F, Quintana-Murci L, Comas D. 2021. The counteracting effects of demography on functional genomic variation: the Roma paradigm. Molecular Biology and Evolution, 38(7):2804-2817. DOI: 10.1093/molbev/msab070. 

Font-Porterias N, Giménez A, Carballo-Mesa A, Calafell F, Comas D. 2021. Admixture Has Shaped Romani Genetic Diversity in Clinically Relevant Variants. Frontiers in Genetics, 12(June):1-12. DOI:10.3389/fgene.2021.683880

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

Calafell F. 2021. Uniparental markers and their role in the future of Molecular Anthropology Next questions in Molecular Anthropology. Journal of Anthropological Sciences, 99:1-4. DOI:10.4436/jass.99005

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

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

Biagini SA, Ramos-Luis E, Comas D, Calafell F. 2020. The place of metropolitan France in the European genomic landscape. Human Genetics, 139(8):1091–1105. DOI: 10.1007/s00439-020-02158-y

Urnikyte A.; Flores-Bello A.; Mondal M.; Molyte A.; Comas D.; Calafell F.; Bosch E.; Kučinskas V.   2019. Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data. Scientific Reports. 9163 doi: doi: 10.1038/s41598-019-45746-3

Urnikyte A, Flores-Bello A, Mondal M, Molyte A, Comas D, Calafell F, Bosch E, Kučinskas V. 2019. Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data. Scientific Reports, 9(1):1-11. DOI:10.1038/s41598-019-45746-3

Larmuseau MHD, van den Berg P, Claerhout S, Calafell F, Boattini A, Gruyters L, Vandenbosch M, Nivelle K, Decorte R, Wenseleers T. 2019. A Historical-Genetic Reconstruction of Human Extra-Pair Paternity. Current Biology, 29(23):4102-4107. DOI:10.1016/j.cub.2019.09.075

Font-Porterias N, Arauna LR, Poveda A, Bianco E, Rebato E, Prata MJ, Calafell F, Comas D. 2019. European Roma groups show complex West Eurasian admixture footprints and a common South Asian genetic origin. PLoS Genetics, 15(9):1-24. DOI:10.1371/journal.pgen.1008417

Biagini SA, Solé-Morata N, Matisoo-Smith E, Zalloua P, Comas D, Calafell F. 2019. People from Ibiza: an unexpected isolate in the Western Mediterranean. European Journal of Human Genetics, 27(6):941-951. DOI:10.1038/s41431-019-0361-1.

Zalloua P, Collins CJ, Gosling A, Biagini SA, Costa B, Kardailsky O, Nigro L, Khalil W, Calafell F, Matisoo-Smith E. 2018. Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza. Scientific Reports, 8(1):1-15. DOI:10.1038/s41598-018-35667-y

Larmuseau MHD, Calafell F, Princen SA, Decorte R, Soen V. 2018. The black legend on the Spanish presence in the low countries: Verifying shared beliefs on genetic ancestry. American Journal of Physical Anthropology, 166(1):219-227. DOI:10.1002/ajpa.23409

Font-Porterias N, Solé-Morata N, Serra-Vidal G, Bekada A, Fadhlaoui-Zid K, Zalloua P, Calafell F, Comas D. 2018. The genetic landscape of Mediterranean North African populations through complete mtDNA sequences. Annals of Human Biology, 45(1):98-104. DOI:10.1080/03014460.2017.1413133

Flores-Bello A, Mas-Ponte D, Rosu ME, Bosch E, Calafell F, Comas D. 2018. Sequence diversity of the Rh blood group system in Basques. European Journal of Human Genetics, 26(12):1859-1866. DOI:10.1038/s41431-018-0232-1

Villaescusa P, Illescas MJ, Valverde L, Baeta M, Nuñez C, Martínez-Jarreta B, Zarrabeitia MT, Calafell F, de Pancorbo MM. 2017. Characterization of the Iberian Y chromosome haplogroup R-DF27 in Northern Spain. Forensic Science International: Genetics, 27:142-148. DOI:10.1016/j.fsigen.2016.12.013

Solé-Morata N, Villaescusa P, García-Fernández C, Font-Porterias N, Illescas MJ, Valverde L, Tassi F, Ghirotto S, Férec C, Rouault K, Jiménez-Moreno S, Martínez-Jarreta B, Pinheiro MF, Zarrabeitia MT, Carracedo Á, de Pancorbo MM, Calafell F. 2017. Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ. Scientific Reports, 7(1):1-13. DOI:10.1038/s41598-017-07710-x

Solé-Morata N, García-Fernández C, Urasin V, Bekada A, Fadhlaoui-Zid K, Zalloua P, Comas D, Calafell F. 2017. Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81). Scientific Reports, 7(1):1-11. DOI:10.1038/s41598-017-16271-y

Pérez de Los Cobos J, Alcaraz S, Siñol N, Arranz MJ, Trujols J, Batlle F, Calafell F, Durán-Sindreu S, Salazar J. 2017. Satisfaction With Methadone and Opioid Receptor Genes Polymorphisms in Treatment-Refractory Heroin-Dependent Patients. Journal of Clinical Psychopharmacology, 37(3):378-380. DOI:10.1097/JCP.0000000000000698

Moreno F, Indakoetxea B, Barandiaran M, Caballero MC, Gorostidi A, Calafell F, Gabilondo A, Tainta M, Zulaica M, Martí Massó JF, López de Munain A, Sánchez-Juan P, Lee SE. 2017. The unexpected co-occurrence of GRN and MAPT p.A152T in Basque families: Clinical and pathological characteristics. PLoS ONE, 12(6):1-15. DOI:10.1371/journal.pone.0178093

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

Casals F, Anglada R, Bonet N, Rasal R, van der Gaag KJ, Hoogenboom J, Solé-Morata N, Comas D, Calafell F. 2017. Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations. Forensic Science International: Genetics, 30:66-70. DOI:10.1016/j.fsigen.2017.06.006

Calafell F, Larmuseau MHD. 2017. The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research. Human Genetics, 136(5):559-573. DOI:10.1007/s00439-016-1740-0

Engelken J, Espadas G, Mancuso FM, Bonet N, Scherr AL, Jímenez-Álvarez V, Codina-Solà M, Medina-Stacey D, Spataro N, Stoneking M, Calafell F, Sabidó E, Bosch E. 2016. Signatures of evolutionary adaptation in quantitative trait loci influencing trace element homeostasis in liver. Molecular Biology and Evolution, 33(3):738-754. DOI:10.1093/molbev/msv267

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

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

Riyahi S, Sánchez-Delgado M, Calafell F, Monk D, Senar JC. 2015. Combined epigenetic and intraspecific variation of the DRD4 and SERT genes influence novelty seeking behavior in great tit Parus major. Epigenetics, 10(6):516-525. DOI:10.1080/15592294.2015.1046027

Garcia-Etxebarria K, Bracho MA, Galán JC, Pumarola T, Castilla J, Ortiz de Lejarazu R, Rodríguez-Dominguez M, Quintela I, Bonet N, Garcia-Garcerà M, Domínguez A, González-Candelas F, Calafell F; CIBERESP Cases and Controls in Pandemic Influenza Working Group. 2015. No major host genetic risk factor contributed to A(H1N1)2009 influenza severity. PLoS ONE, 10(9):1-10. DOI:10.1371/journal.pone.0135983

Bekada A, Arauna LR, Deba T, Calafell F, Benhamamouch S, Comas D. 2015. Genetic heterogeneity in Algerian human populations. PLoS ONE, 10(9):1-15. DOI:10.1371/journal.pone.0138453

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.

Garcia-Etxebarria K, Garcia-Garcerà M, Calafell F. 2014. Consistency of metagenomic assignment programs in simulated and real data. BMC Bioinformatics, 15(1). DOI:10.1186/1471-2105-15-90

Džunková M, Garcia-Garcerà M, Martínez-Priego L, D’Auria G, Calafell F, Moya A. 2014. Direct squencing from the minimal number of DNA molecules needed to fill a 454 picotiterplate. PLoS ONE, 9(6):1-10. DOI:10.1371/journal.pone.0097379

Garcia-Garcerà M, Garcia-Etxebarria K, Coscollà M, Latorre A, Calafell F. 2013. A New Method for Extracting Skin Microbes Allows Metagenomic Analysis of Whole-Deep Skin. PLoS ONE, 8(9):1-12. DOI:10.1371/journal.pone.0074914

Charlier P, Olalde I, Solé N, Ramírez O, Babelon JP, Galland B, Calafell F, Lalueza-Fox C. 2013. Genetic comparison of the head of Henri IV and the presumptive blood from Louis XVI (both Kings of France). Forensic Science International, 226(1-3):38-40. DOI:10.1016/j.forsciint.2012.11.018

Sandoval K, Moreno-Estrada A, Mendizabal I, Underhill PA, Lopez-Valenzuela M, Peñaloza-Espinosa R, Lopez-Lopez M, Buentello-Malo L, Avelino H, Calafell F, Comas D. 2012. Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas. American Journal of Physical Anthropology, 148(3):395-405. DOI:10.1002/ajpa.22062

Melé M, Javed A, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Pitchappan RM, Arunkumar G, Parida L, Calafell F, Bertranpetit J; Genographic Consortium. 2012. Recombination gives a new insight in the effective population size and the history of the old world human populations. Molecular Biology and Evolution, 29(1):25-30. DOI:10.1093/molbev/msr213

Martínez-González LJ, Martínez-Espín E, Álvarez JC, Albardaner F, Rickards O, Martínez-Labarga C, Calafell F, Lorente JA. 2012. Surname and y chromosome in Southern Europe: A case study with Colom/Colombo. European Journal of Human Genetics, 20(2):211-216. DOI:10.1038/ejhg.2011.162

Martinez-Cruz B, Ioana M, Calafell F, Arauna LR, Sanz P, Ionescu R, Boengiu S, Kalaydjieva L, Pamjav H, Makukh H, Plantinga T, van der Meer JW, Comas D, Netea MG; Genographic Consortium. 2012. Y-chromosome analysis in individuals bearing the Basarab name of the first dynasty of Wallachian kings. PLoS ONE, 7(7). DOI:10.1371/journal.pone.0041803

Javed A, Melé M, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Arunkumar G, Pitchappan R, Bertranpetit J, Calafell F, Parida L; Genographic Consortium. 2012. Recombination networks as genetic markers in a human variation study of the Old World. Human Genetics, 131(4):601-613. DOI:10.1007/s00439-011-1104-8

Garcia-Garcerà M, Coscollà M, Garcia-Etxebarria K, Martín-Caballero J, González-Candelas F, Latorre A, Calafell F. 2012. Staphylococcus prevails in the skin microbiota of long-term immunodeficient mice. Environmental Microbiology, 14(8):2087-2098. DOI:10.1111/j.1462-2920.2012.02756.x

Bertinetto FE, Calafell F, Roggero S, Chidichimo R, Garino E, Marcuccio C, Coppo R, Scolari F, Frascá GM, Savoldi S, Schena FP, Amoroso A; European IgA Nephropathy Consortium. 2012. Search for genetic association between IgA nephropathy and candidate genes selected by function or by gene mapping at loci IGAN2 and IGAN3. Nephrology Dialysis Transplantation, 27(6):2328-2337. DOI:10.1093/ndt/gfr633

Sikora M, Laayouni H, Calafell F, Comas D, Bertranpetit J. 2011. A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations. European Journal of Human Genetics, 19(1):84-88. DOI:10.1038/ejhg.2010.141

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