Genómica comparativa
Our main line of research is centered on the discovery of the extent of all kinds of genome variation within phenotypically different genomes. Specifically, we study genome variation (centered on CNVs), gene expression and epigenetic differences in the human species in the context of great ape evolution and other mammalian genomes such as canids. Our goal is to create an integrated view of genome evolution by studying changes in the composition, frequency, size and location at every major branch point of recent human evolution.
Genomic variation in ape genomes
Characterizing the variation of thousands of human genomes is standard today. However, primates (our closest relatives) are the ideal set of species for studying the evolution of these features from both mechanistic and adaptive points of view. In this line of research, we use genomic approaches in humans and primates to understand the impact of variants in the evolution of every species to provide a proper perspective to the differences among species.
Epigenetics and transcriptomics of non-human primates
DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of DNA methylation changes between humans and their closest relatives is still poorly understood. In this project, we evaluate methylation patterns in recent human evolution. We identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level.
Canid evolution
The domestic dog has been widely recognized as an important organism for studying the relationship between selection, genome variation and phenotypic diversity. Both dogs and wolves have been extensively surveyed using mtDNA, microsatellites and SNPs, but structural variation, including variation in multicopy gene families, has not been fully characterized in canines.
Lab website: Comparative Genomics Lab
Wilder AP, Supple MA, Subramanian A, Mudide A, Swofford R, Serres-Armero A, Steiner C, Koepfli KP, Genereux DP, Karlsson EK, Lindblad-Toh K, Marques-Bonet T, Munoz Fuentes V, Foley K, Meyer WK; Zoonomia Consortium‡; Ryder OA, Shapiro B, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. 2023. The contribution of historical processes to contemporary extinction risk in placental mammals. Science, 380(6643). DOI:10.1126/science.abn5856
Murat F, Mbengue N, Winge SB, Trefzer T, Leushkin E, Sepp M, Cardoso-Moreira M, Schmidt J, Schneider C, Mößinger K, Brüning T, Lamanna F, Belles MR, Conrad C, Kondova I, Bontrop R, Behr R, Khaitovich P, Pääbo S, Marques-Bonet T, Grützner F, Almstrup K, Schierup MH, Kaessmann H. 2023. The molecular evolution of spermatogenesis across mammals. Nature, 613(7943):308-316. DOI:10.1038/s41586-022-05547-7
Juan D, Santpere G, Kelley JL, Cornejo OE, Marques-Bonet T. 2023. Current advances in primate genomics: novel approaches for understanding evolution and disease. Nature Reviews Genetics, 24(5):314-331. DOI:10.1038/s41576-022-00554-w
Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR; Zoonomia Consortium§; Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. 2023. Evolutionary constraint and innovation across hundreds of placental mammals. Science, 380(6643). DOI:10.1126/science.abn3943
Bentley BP, Carrasco-Valenzuela T, Ramos EKS, Pawar H, Souza Arantes L, Alexander A, Banerjee SM, Masterson P, Kuhlwilm M, Pippel M, Mountcastle J, Haase B, Uliano-Silva M, Formenti G, Howe K, Chow W, Tracey A, Sims Y, Pelan S, Wood J, Yetsko K, Perrault JR, Stewart K, Benson SR, Levy Y, Todd EV, Shaffer HB, Scott P, Henen BT, Murphy RW, Mohr DW, Scott AF, Duffy DJ, Gemmell NJ, Suh A, Winkler S, Thibaud-Nissen F, Nery MF, Marques-Bonet T, Antunes A, Tikochinski Y, Dutton PH, Fedrigo O, Myers EW, Jarvis ED, Mazzoni CJ, Komoroske LM. 2023. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Proceedings of the National Academy of Sciences, 120(7):2017. DOI:10.1073/pnas.2201076120
Alvarez-Estape M, Pawar H, Fontsere C, Trujillo AE, Gunson JL, Bergl RA, Bermejo M, Linder JM, McFarland K, Oates JF, Sunderland-Groves JL, Orkin J, Higham JP, Viaud-Martinez KA, Lizano E, Marques-Bonet T. 2023. Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs. Genes, 14(3):743. DOI:10.3390/genes14030743
Wu DD, Qi XG, Yu L, Li M, Liu ZJ, Yoder AD, Roos C, Hayakawa T, Rogers J, Marques-Bonet T, Su B, Yao YG, Zhang YP, Zhang G. 2022. Initiation of the Primate Genome Project. Zoological Research, 43(2):147-149. DOI:10.24272/j.issn.2095-8137.2022.001
Ruiz‐Gartzia I, Lizano E, Marques‐Bonet T, Kelley JL. 2022. Recovering the genomes hidden in museum wet collections. Molecular Ecology Resources, 22(6): 2127-2129. DOI:10.1111/1755-0998.13631
Palmada-Flores M, Orkin JD, Haase B, Mountcastle J, Bertelsen MF, Fedrigo O, Kuderna LFK, Jarvis ED, Marques-Bonet T. 2022. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). GigaScience, 11:1-7. DOI:10.1093/gigascience/giac026
Paez S, Kraus RHS, Shapiro B, Gilbert MTP, Jarvis ED; Vertebrate Genomes Project Conservation Group, Al-Ajli FO, Ceballos G, Crawford AJ, Fedrigo O, Johnson RN, Johnson WE, Marques-Bonet T, Morin PA, Mueller RC, Ryder OA, Teeling EC, Venkatesh B. 2022. Reference genomes for conservation. Science, 377(6604):364-366. DOI:10.1126/science.abm8127
Lobon I, Solís-Moruno M, Juan D, Muhaisen A, Abascal F, Esteller-Cucala P, García-Pérez R, Martí MJ, Tolosa E, Ávila J, Rahbari R, Marques-Bonet T, Casals F, Soriano E. 2022. Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes. Frontiers in Aging, 3(April):1-14. DOI:10.3389/fragi.2022.851039
Janiak MC, Silva FE, Beck RMD, de Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès-Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, de Melo FR, Valsecchi J, Hrbek T, Boubli JP. 2022. 205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Molecular Ecology, 31(14):3888-3902. DOI:10.1111/mec.16554
Gopalakrishnan S, Ebenesersdóttir SS, Lundstrøm IKC, Turner-Walker G, Moore KHS, Luisi P, Margaryan A, Martin MD, Ellegaard MR, Magnússon ÓÞ, Sigurðsson Á, Snorradóttir S, Magnúsdóttir DN, Laffoon JE, van Dorp L, Liu X, Moltke I, Ávila-Arcos MC, Schraiber JG, Rasmussen S, Juan D, Gelabert P, de-Dios T, Fotakis AK, Iraeta-Orbegozo M, Vågene ÅJ, Denham SD, Christophersen A, Stenøien HK, Vieira FG, Liu S, Günther T, Kivisild T, Moseng OG, Skar B, Cheung C, Sandoval-Velasco M, Wales N, Schroeder H, Campos PF, Guðmundsdóttir VB, Sicheritz-Ponten T, Petersen B, Halgunset J, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Willerslev E, Balloux F, Marques-Bonet T, Lalueza-Fox C, Nielsen R, Stefánsson K, Helgason A, Gilbert MTP. 2022. The population genomic legacy of the second plague pandemic. Current Biology, 32(21):4743-4751. DOI:10.1016/j.cub.2022.09.023
Fontsere C, Kuhlwilm M, Morcillo-Suarez C, Alvarez-Estape M, Lester JD, Gratton P, Schmidt JM, Dieguez P, Aebischer T, Álvarez-Varona P, Agbor A, Angedakin S, Assumang AK, Ayimisin EA, Bailey E, Barubiyo D, Bessone M, Carretero-Alonso A, Chancellor R, Cohen H, Danquah E, Deschner T, Dunn A, Dupain J, Egbe VE, Feliu O, Goedmakers A, Granjon AC, Head J, Hedwig D, Hermans V, Hernandez-Aguilar RA, Imong I, Jones S, Junker J, Kadam P, Kaiser M, Kambere M, Kambale MV, Kalan AK, Kienast I, Kujirakwinja D, Langergraber K, Lapuente J, Larson B, Laudisoit A, Lee K, Llana M, Llorente M, Marrocoli S, Morgan D, Mulindahabi F, Murai M, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Pacheco L, Piel A, Riera L, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, Ton E, van Schijndel J, Vergnes V, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Zuberbuehler K, Hecht J, Vigilant L, Boesch C, Andrés AM, Hughes DA, Kühl HS, Lizano E, Arandjelovic M, Marques-Bonet T. 2022. Population dynamics and genetic connectivity in recent chimpanzee history. Cell Genomics, 2(6):100133. DOI:10.1016/j.xgen.2022.100133
Ferrandez-Peral L, Zhan X, Alvarez-Estape M, Chiva C, Esteller-Cucala P, Garcia-Perez R, Julia E, Lizano E, Fornas O, Sabido E, Li Q, Marques-Bonet T, Juan D, Zhang G. 2022. Transcriptome innovations in primates revealed by single-molecule long-read sequencing. Genome Research, 32(8):1448-1462. DOI:10.1101/gr.276395.121
Alvarez-Estape M, Fontsere C, Serres-Armero A, Kuderna LFK, Dobrynin P, Guidara H, Pukazhenthi BS, Koepfli KP, Marques-Bonet T, Moreno E, Lizano E. 2022. Insights from the rescue and breeding management of Cuvier’s gazelle (Gazella cuvieri) through whole‐genome sequencing. Evolutionary Applications, 15(3):351-364. DOI:10.1111/eva.13336
White AE, de-Dios T, Carrión P, Bonora GL, Llovera L, Cilli E, Lizano E, Khabdulina MK, Tleugabulov DT, Olalde I, Marquès-Bonet T, Balloux F, Pettener D, van Dorp L, Luiselli D, Lalueza-Fox C. 2021. Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome. Biology, 10(12):1324. DOI:10.3390/biology10121324
Westbury MV, Barnett R, Sandoval-Velasco M, Gowe G, Vieira FG, de Manuel M, Hansen AJ, Yamaguch N, Werdelin L, Marques-Bonet T, Gilbert MTP, Lorenzen ED. 2021. A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives. Open Research Europe, 1:25. DOI:10.12688/openreseurope.13104.1
Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR; Brain Somatic Mosaicism Network, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A. 2021. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biology, 22(1): 1–32. DOI: 10.1186/s13059-021-02285-3
Solís-Moruno M, Mensa-Vilaró A, Batlle-Masó L, Lobón I, Bonet N, Marquès-Bonet T, Aróstegui JI, Casals F. 2021. Assessment of the gene mosaicism burden in blood and its implications for immune disorders. Scientific Reports, 11(1):12940. DOI:10.1038/s41598-021-92381-y
Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. 2021. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Research, 31(5): 762–774. DOI: 10.1101/gr.266049.120.762
Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, Westbury MV, de Manuel M, Margaryan A, Ciucani MM, Vieira FG, Patramanis Y, Kalthoff DC, Timmons Z, Sicheritz-Pontén T, Dalén L, Ryder OA, Zhang G, Marquès-Bonet T, Moodley Y, Gilbert MTP. 2021. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros ( Ceratotherium simum ). Molecular Ecology, 10(23):6355-6369. DOI:10.1111/mec.16043
Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW 3rd, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. 2021.Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856):737-746. DOI: 10.1038/s41586-021-03451-0.
Renom P, de-Dios T, Civit S, Llovera L, Sánchez-Gracia A, Lizano E, Rando JC, Marquès-Bonet T, Kergoat GJ, Casanovas-Vilar I, Lalueza-Fox C. 2021. Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives. Biology Letters, 17(12):0-5. DOI:10.1098/rsbl.2021.0533
Orkin JD, Montague MJ, Tejada-Martinez D, de Manuel M, Del Campo J, Cheves Hernandez S, Di Fiore A, Fontsere C, Hodgson JA, Janiak MC, Kuderna LFK, Lizano E, Martin MP, Niimura Y, Perry GH, Valverde CS, Tang J, Warren WC, de Magalhães JP, Kawamura S, Marquès-Bonet T, Krawetz R, Melin AD. 2021. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Proceedings of the National Academy of Sciences of the United States of America, 118(7). DOI: 10.1073/pnas.2010632118.
Orkin JD, Kuderna LFK, Marques-Bonet T. 2021. The Diversity of Primates: From Biomedicine to Conservation Genomics. Annual Review of Animal Biosciences, 9:103-124. DOI:10.1146/annurev-animal-061220-023138
Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Alan Harris R, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Le MD, Manu S, Rabarivola CJ, Zaramody A, Andriaholinirina N, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KK, Rogers J, Marques-Bonet T, Navarro A, Juan D, Arora PS, Higham JP. 2021. Variation in predicted COVID‐19 risk among lemurs and lorises. American Journal of Primatology, 83(6):1-12. DOI: 10.1002/ajp.23255
Liu S, Westbury MV, Dussex N, Mitchell KJ, Sinding MS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, van der Valk T, Moodley Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, Bruins-van Sonsbeek LGR, Vartanyan S, Guo C, Cooper A, Kosintsev P, Kirillova I, Lister AM, Marques-Bonet T, Gopalakrishnan S, Dunn RR, Lorenzen ED, Shapiro B, Zhang G, Antoine PO, Dalén L, Gilbert MTP. 2021. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell, 184(19):4874-4885. DOI:10.1016/j.cell.2021.07.032
Kuhlwilm M, Fontsere C, Han S, Alvarez-Estape M, Marques-Bonet T. 2021. HuConTest: Testing human contamination in great ape samples. Genome Biology and Evolution, 13(6). DOI:10.1093/gbe/evab117
García-Pérez R, Esteller-Cucala P, Mas G, Lobón I, Di Carlo V, Riera M, Kuhlwilm M, Navarro A, Blancher A, Di Croce L, Gómez-Skarmeta JL, Juan D, Marquès-Bonet T. 2021. Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures. Nature Communications, 12(1):1-17. DOI:10.1038/s41467-021-23397-1
Fontsere C, Alvarez-Estape M, Lester J, Arandjelovic M, Kuhlwilm M, Dieguez P, Agbor A, Angedakin S, Ayuk Ayimisin E, Bessone M, Brazzola G, Deschner T, Eno-Nku M, Granjon AC, Head J, Kadam P, Kalan AK, Kambi M, Langergraber K, Lapuente J, Maretti G, Jayne Ormsby L, Piel A, Robbins MM, Stewart F, Vergnes V, Wittig RM, Kühl HS, Marques-Bonet T, Hughes DA, Lizano E. 2021. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments. Molecular Ecology Resources, 21(3):745–761. DOI: 10.1111/1755-0998.13300.
Fontsere C, Frandsen P, Hernandez-Rodriguez J, Niemann J, Scharff-Olsen CH, Vallet D, Le Gouar P, Ménard N, Navarro A, Siegismund HR, Hvilsom C, Gilbert MTP, Kuhlwilm M, Hughes D, Marques-Bonet T. 2021. The genetic impact of an Ebola outbreak on a wild gorilla population. BMC Genomics, 22(1):735. DOI:10.1186/s12864-021-08025-y
de-Dios T, Carrión P, Olalde I, Nadal LL, Lizano E, Pàmies D, Marques-Bonet T, Balloux F, van Dorp L, Lalueza-Fox C. 2021. Salmonella enterica from a soldier from the 1652-siege of Barcelona (Spain) supports historical transatlantic epidemic contacts. iScience, 24(9):103021. DOI:10.1016/j.isci.2021.103021
Boubli JP, Janiak MC, Porter LM, Torre S, Cortés-Ortiz L, Da Silva MNF, Rylands AB, Nash S, Bertuol F, Byrne H, Silva FE, Rohe F, Vries D, Beck RMD, Ruiz-Gartzia I, Kuderna LFK, Marques-Bonet T, Hrbek T, Farias IP, Van Heteren AH, Roos C. 2021. Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum. Zoological Research, 42(6):761-771. DOI:10.24272/j.issn.2095-8137.2021.143
Welker F, Ramos-Madrigal J, Gutenbrunner P, Mackie M, Tiwary S, Rakownikow Jersie-Christensen R, Chiva C, Dickinson MR, Kuhlwilm M, de Manuel M, Gelabert P, Martinón-Torres M, Margvelashvili A, Arsuaga JL, Carbonell E, Marques-Bonet T, Penkman K, Sabidó E, Cox J, Olsen JV, Lordkipanidze D, Racimo F, Lalueza-Fox C, Bermúdez de Castro JM, Willerslev E, Cappellini E. 2020. The dental proteome of Homo antecessor. Nature, 580(7802):235-238. DOI:10.1038/s41586-020-2153-8
van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. 2020. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Molecular Biology and Evolution, 37(3):773–785. DOI: 10.1093/molbev/msz264
Sinding MS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Carøe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jørgensen MP, Dietz R, Sonne C, Meldgaard M, Dalén L, Larson G, Petersen B, Sicheritz-Pontén T, Bachmann L, Wiig Ø, Marques-Bonet T, Hansen AJ, Gilbert MTP. 2020. Arctic-adapted dogs emerged at the Pleistocene–Holocene transition. Science, 368(6498):1495-1499. DOI:10.1126/science.aaz8599
Kuderna LFK, Solís-Moruno M, Batlle-Masó L, Julià E, Lizano E, Anglada R, Ramírez E, Bote A, Tormo M, Marquès-Bonet T, Fornas Ò, Casals F. 2020. Flow Sorting Enrichment and Nanopore Sequencing of Chromosome 1 From a Chinese Individual. Frontiers in Genetics, 10(1315). DOI: 10.3389/fgene.2019.01315
Kuderna LF, Esteller-Cucala P, Marques-Bonet T. 2020. Branching out: what omics can tell us about primate evolution. Current Opinion in Genetics & Development, 62:65–71. DOI: 10.1016/j.gde.2020.06.006
Khan N, de Manuel M, Peyregne S, Do R, Prufer K, Marques-Bonet T, Varki N, Gagneux P, Varki A. 2020. Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins. Genome Biology and Evolution, 12(7):1040–1050. DOI: 10.1093/gbe/evaa125
Heredia-Genestar JM, Marquès-Bonet T, Juan D, Navarro A. 2020. Extreme differences between human germline and tumor mutation densities are driven by ancestral human-specific deviations. Nature Communications, 11(1):2512. DOI: 10.1038/s41467-020-16296-4.
Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, Housman G, García-Pérez R, Lizano E, Cheronet O, Mallick S, Nieves-Colón MA, Li H, Alpaslan-Roodenberg S, Novak M, Gu H, Osinski JM, Ferrando-Bernal M, Gelabert P, Lipende I, Mjungu D, Kondova I, Bontrop R, Kullmer O, Weber G, Shahar T, Dvir-Ginzberg M, Faerman M, Quillen EE, Meissner A, Lahav Y, Kandel L, Liebergall M, Prada ME, Vidal JM, Gronostajski RM, Stone AC, Yakir B, Lalueza-Fox C, Pinhasi R, Reich D, Marques-Bonet T, Meshorer E, Carmel L. 2020. Differential DNA methylation of vocal and facial anatomy genes in modern humans. Nature Communications, 11(1):1189. DOI: 10.1038/s41467-020-15020-6.
Gelabert P, Sandoval-Velasco M, Serres A, de Manuel M, Renom P, Margaryan A, Stiller J, de-Dios T, Fang Q, Feng S, Mañosa S, Pacheco G, Ferrando-Bernal M, Shi G, Hao F, Chen X, Petersen B, Olsen RA, Navarro A, Deng Y, Dalén L, Marquès-Bonet T, Zhang G, Antunes A, Gilbert MTP, Lalueza-Fox C. 2020. Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet. Current Biology, 30(1):108-114. DOI: 10.1016/j.cub.2019.10.066
Frandsen P, Fontsere C, Nielsen SV, Hanghøj K, Castejon-Fernandez N, Lizano E, Hughes D, Hernandez-Rodriguez J, Korneliussen TS, Carlsen F, Siegismund HR, Mailund T, Marques-Bonet T, Hvilsom C. 2020. Targeted conservation genetics of the endangered chimpanzee. Heredity, 125(1-2):15-27. DOI:10.1038/s41437-020-0313-0
de Manuel M, Barnett R, Sandoval-Velasco M, Yamaguchi N, Garrett Vieira F, Zepeda Mendoza ML, Liu S, Martin MD, Sinding MS, Mak SST, Carøe C, Liu S, Guo C, Zheng J, Zazula G, Baryshnikov G, Eizirik E, Koepfli KP, Johnson WE, Antunes A, Sicheritz-Ponten T, Gopalakrishnan S, Larson G, Yang H, O'Brien SJ, Hansen AJ, Zhang G, Marques-Bonet T, Gilbert MTP. 2020. The evolutionary history of extinct and living lions. Proceedings of the National Academy of Sciences of the United States of America, 117(20): 10927–10934. DOI: 10.1073/pnas.1919423117
Dehasque M, Ávila‐Arcos MC, Díez‐del‐Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas A, Marques‐Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. 2020. Inference of natural selection from ancient DNA. Evolution Letters, 4(2):94–108. DOI: 10.1002/evl3.165
Chicote JU, López-Sánchez M, Marquès-Bonet T, Callizo J, Pérez-Jurado LA, García-España A. 2020. Circular DNA intermediates in the generation of large human segmental duplications. BMC Genomics, 21(1):1–11. DOI: 10.1186/s12864-020-06998-w
Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Alan Harris R, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. 2020. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genetics, 16(5). DOI: 10.1371/journal.pgen.1008742
Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Perez RG, Hsiao CJ, Eres I, Cuevas C, Marques-Bonet T, Gilad Y. 2020. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Research, 30(2):250–262. DOI: 10.1101/gr.254904.119
Batlle-Masó L, Mensa-Vilaró A, Solís-Moruno M, Marquès-Bonet T, Arostegui JI, Casals F. 2020. Genetic diagnosis of autoinflammatory disease patients using clinical exome sequencing. European Journal of Medical Genetics, 63(5):103920. DOI: 10.1016/j.ejmg.2020.103920