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

Tomàs Marquès Bonet

Marquès Bonet, Tomàs
ICREA Research Professor
Comparative Genomics Lab

Alejandro Valenzuela Seba

Valenzuela Seba, Alejandro
Predoctoral Researcher
Genómica comparativa

Sandra Ruibal Puertas

Ruibal Puertas, Sandra
Laboratory Technician
Comparative Genomics

Marc Palmada Flores

Palmada Flores, Marc
Predoctoral Researcher-INPhINIT " La Caixa "
Comparative genomics

Cira Martinez de Pablo

Martinez de Pablo, Cira
Senior Scientific Support Personnel
Comparative Genomics

ESTHER LIZANO GONZALEZ

LIZANO GONZALEZ, ESTHER
Postdoctoral Researcher
Comparative Genomics

Johanna Krueger

Krueger , Johanna
Predoctoral Researcher
Comparative Genomics

David Alejandro Juan Sopeña

Juan Sopeña, David Alejandro
Postdoctoral Researcher
Comparative Genomics

Meyer KA, Marques-Bonet T, Sestan N. 2017. Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences. Molecular Biology and Evolution, 34(5):1217-1229. DOI:10.1093/molbev/msx076

Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP. 2017. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. GigaScience, 6(8):1-13. DOI:10.1093/gigascience/gix049

Maibach V, Hans JB, Hvilsom C, Marques-Bonet T, Vigilant L. 2017. MHC class I diversity in chimpanzees and bonobos. Immunogenetics, 69(10):661-676. DOI:10.1007/s00251-017-0990-x

Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. 2017. Ancient genomic changes associated with domestication of the horse. Science, 356(6336):442-445. DOI:10.1126/science.aam5298.

Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Garcia Perez R, Povolotskaya I, Serres Armero A, Gómez Garrido J, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T. 2017. A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome. GigaScience,6(11):1-6. DOI:10.1093/gigascience/gix098

Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, Kuderna LFK, Räikkönen J, Petersen B, Sicheritz-Ponten T, Larson G, Orlando L, Marques-Bonet T, Hansen AJ, Dalén L, Gilbert MTP. 2017. The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics. BMC Genomics, 18(1):1-11. DOI:10.1186/s12864-017-3883-3

Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A; BLUEPRINT Consortium. 2017. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Research, 45(16):9244-9259. DOI:10.1093/nar/gkx618

Valles-Ibáñez G de, Hernandez-Rodriguez J, Prado-Martinez J, Luisi P, Marquès-Bonet T, Casals F. 2016. Genetic Load of Loss-of-Function Polymorphic Variants in Great Apes. Genome Biology and Evolution, 8(3):871-877. DOI:10.1093/gbe/evw040

Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF; Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD. 2016. The time scale of recombination rate evolution in great apes. Molecular Biology and Evolution, 33(4):928-945. DOI:10.1093/molbev/msv331

Sanchez-Delgado M, Court F, Vidal E, Medrano J, Monteagudo-Sánchez A, Martin-Trujillo A, Tayama C, Iglesias-Platas I, Kondova I, Bontrop R, Poo-Llanillo ME, Marques-Bonet T, Nakabayashi K, Simón C, Monk D. 2016. Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting. PLoS Genetics, 12(11):1-23. DOI:10.1371/journal.pgen.1006427

Morgan PPG. 2016. Mitochondria Research Society/United Mitochondrial Disease Foundation Meeting Abstracts. Mitochondrion, 31:89-117. DOI:10.1016/j.mito.2016.08.010

Marsden CD, Ortega-Del Vecchyo D, O'Brien DP, Taylor JF, Ramirez O, Vilà C, Marques-Bonet T, Schnabel RD, Wayne RK, Lohmueller KE. 2016. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. Proceedings of the National Academy of Sciences of the United States of America, 113(1):152-157. DOI:10.1073/pnas.1512501113

Lobon I, Tucci S, de Manuel M, Ghirotto S, Benazzo A, Prado-Martinez J, Lorente-Galdos B, Nam K, Dabad M, Hernandez-Rodriguez J, Comas D, Navarro A, Schierup MH, Andres AM, Barbujani G, Hvilsom C, Marques-Bonet T. 2016. Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions. Genome Biology and Evolution, 8(6):2020-2030. DOI:10.1093/gbe/evw124

Kuhlwilm M, de Manuel M, Nater A, Greminger MP, Krützen M, Marques-Bonet T. 2016. Evolution and demography of the great apes. Current Opinion in Genetics and Development, 41:124-129. DOI:10.1016/j.gde.2016.09.005

Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Marques-Bonet T, Andrés AM, Viola B, Pääbo S, Meyer M, Siepel A, Castellano S. 2016. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530(7591):429-433. DOI:10.1038/nature16544

Koblmüller S, Vilà C, Lorente-Galdos B, Dabad M, Ramirez O, Marques-Bonet T, Wayne RK, Leonard JA. 2016. Whole mitochondrial genomes illuminate ancient intercontinental dispersals of grey wolves (Canis lupus). Journal of Biogeography, 43(9):1728-1738. DOI:10.1111/jbi.12765

Gallego A, Melé M, Balcells I, García-Ramallo E, Torruella-Loran I, Fernández-Bellon H, Abelló T, Kondova I, Bontrop R, Hvilsom C, Navarro A, Marquès-Bonet T, Espinosa-Parrilla Y. 2016. Functional Implications of Human-Specific Changes in Great Ape microRNAs. PLoS ONE, 11(4):1-20. DOI:10.1371/journal.pone.0154194

Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J. 2016. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. PLoS Genetics, 12(3):1-23. DOI:10.1371/journal.pgen.1005851

Fan Z, Silva P, Gronau I, Wang S, Armero AS, Schweizer RM, Ramirez O, Pollinger J, Galaverni M, Ortega Del-Vecchyo D, Du L, Zhang W, Zhang Z, Xing J, Vilà C, Marques-Bonet T, Godinho R, Yue B, Wayne RK. 2016. Worldwide patterns of genomic variation and admixture in gray wolves. Genome Research, 26(2):163-173. DOI:10.1101/gr.197517.115

de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T, Prado-Martinez J, Hernandez-Rodriguez J, Dupanloup I, Lao O, Hallast P, Schmidt JM, Heredia-Genestar JM, Benazzo A, Barbujani G, Peter BM, Kuderna LF, Casals F, Angedakin S, Arandjelovic M, Boesch C, Kühl H, Vigilant L, Langergraber K, Novembre J, Gut M, Gut I, Navarro A, Carlsen F, Andrés AM, Siegismund HR, Scally A, Excoffier L, Tyler-Smith C, Castellano S, Xue Y, Hvilsom C, Marques-Bonet T. 2016. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science, 354(6311):477-481. DOI:10.1126/science.aag2602

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

Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA. 2016. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology, 17(1). DOI:10.1186/s13059-016-1090-1

Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN, de Manuel M, Hernandez-Rodriguez J, Lobon I, Siegismund HR, Pagani L, Quail MA, Hvilsom C, Mudakikwa A, Eichler EE, Cranfield MR, Marques-Bonet T, Tyler-Smith C, Scally A. 2015. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. Science, 348(6231):242-245. DOI:10.1126/science.aaa3952

Veeramah KR, Woerner AE, Johnstone L, Gut I, Gut M, Marques-Bonet T, Carbone L, Wall JD, Hammer MF. 2015. Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach. Genetics, 200(1):295-308. DOI:10.1534/genetics.115.174425

Ruiz S, Lopez-Contreras AJ, Gabut M, Marion RM, Gutierrez-Martinez P, Bua S, Ramirez O, Olalde I, Rodrigo-Perez S, Li H, Marques-Bonet T, Serrano M, Blasco MA, Batada NN, Fernandez-Capetillo O. 2015. Limiting replication stress during somatic cell reprogramming reduces genomic instability in induced pluripotent stem cells. Nature Communications, 6:1-8. DOI:10.1038/ncomms9036

Olalde I, Schroeder H, Sandoval-Velasco M, Vinner L, Lobón I, Ramirez O, Civit S, García Borja P, Salazar-García DC, Talamo S, María Fullola J, Xavier Oms F, Pedro M, Martínez P, Sanz M, Daura J, Zilhão J, Marquès-Bonet T, Gilbert MT, Lalueza-Fox C. 2015. A common genetic origin for early farmers from mediterranean cardial and central european LBK cultures. Molecular Biology and Evolution, 32(12):3132-3142. DOI:10.1093/molbev/msv181

Hernando-Herraez I, Heyn H, Fernandez-Callejo M, Vidal E, Fernandez-Bellon H, Prado-Martinez J, Sharp AJ, Esteller M, Marques-Bonet T. 2015. The interplay between DNA methylation and sequence divergence in recent human evolution. Nucleic Acids Research, 43(17):8204-8214. DOI:10.1093/nar/gkv693

Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L. 2015. Evolutionary genomics and conservation of the endangered Przewalski’s horse. Current Biology, 25(19):2577-2583. DOI:10.1016/j.cub.2015.08.032

Bilgin Sonay T, Carvalho T, Robinson MD, Greminger MP, Krützen M, Comas D, Highnam G, Mittelman D, Sharp A, Marques-Bonet T, Wagner A. 2015. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. Genome Research, 25(11):1591-1599. DOI:10.1101/gr.190868.115

Worley KC, Warren WC, Rogers J, Locke D, Muzny DM, Mardis ER, Weinstock GM, Tardif SD, Aagaard KM, Archidiacono N, Arul Rayan N, Batzer MA, Beal K, Brejova B, Capozzi O, Capuano SB, Casola C, Chandrabose MM, Cree A, Diep Dao M, De Jong PJ, Cruz-Herrera del Rosario R, Delehaunty KD, Dinh HH, Eichler EE, Fitzgerald S, Flicek P, Fontenot CC, Fowler G, Fronick C, Fulton LA, Fulton RS, Gabisi RA, Gerlac D, Graves TA, Gunaratne PH, Hahn MW, Haig D, Han Y, Harris A, Herrero J, Hillier LDW, Hubley R, Hughes JF, Hume J, Jhangiani SN, Jorde LB, Joshi V, Karakor E, Konkel MK, Kosiol C, LKovar C, Kriventseva EV, Lee SL, Lewis LR, Liu YS, Lopez J, Lopez-Otin C, Lorente-Galdos B, Mansfield KG, Marques-Bonet T, Minx P, Misceo D, Moncrieff JS, Morgan MB, Nazareth LV, Newsham I, Nguyen NB, Okwuonu GO, Prabhakar S, Perales L, Pu L, Puente XS, Quesada V, Ranck MC, Raney BJ, Raveendran M, Deiros DR, Rocchi M, Rodriguez D, Ross C, Ruffier M, Ruiz SJ, Sajjadian S, Santibanez J, Schrider DR, Searle S, Skaletsky H, Soibam B, Smit AFA, Tennakoon JB, Tomaska L, Ullmer B, Vejnar CE, Ventura M, Vilella AJ, Vinar T, Vogel JH, Walker JA, Wang Q, Warner CM, Wildman DE, Witherspoon DJ, Wright RA, Wu Y, Xiao W,Xing J, Zdobnov EM, Zhu B, Gibbs RA, Wilson RK. 2014. The common marmoset genome provides insight into primate biology and evolution. Nature Genetics, 46(8):850-857. DOI:10.1038/ng.3042

Watson CT, Marques-Bonet T, Sharp AJ, Mefford HC. 2014. The genetics of microdeletion and microduplication syndromes: An update. Annual Review of Genomics and Human Genetics, 15:215-244. DOI:10.1146/annurev-genom-091212-153408

Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC. 2014. Elephant shark genome provides unique insights into gnathostome evolution. Nature, 505(7482):174-179. DOI:10.1038/nature12826

Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A, Shevchenko A, Brukhin V, Cherkasov N, Svitin A, Koepfli KP, Pontius J, Driscoll CA, Blackistone K, Barr C, Goldman D, Antunes A, Quilez J, Lorente-Galdos B, Alkan C, Marques-Bonet T, Menotti-Raymond M, David VA, Narfström K, O'Brien SJ. 2014. Annotated features of domestic cat - Felis catus genome. GigaScience, 3(1):2-4. DOI:10.1186/2047-217X-3-13

Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L. 2014. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proceedings of the National Academy of Sciences of the United States of America, 111(52):E5661-E5669. DOI:10.1073/pnas.1416991111

Ramirez O, Olalde I, Berglund J, Lorente-Galdos B, Hernandez-Rodriguez J, Quilez J, Webster MT, Wayne RK, Lalueza-Fox C, Vilà C, Marques-Bonet T. 2014. Analysis of structural diversity in wolf-like canids reveals post-domestication variants. BMC Genomics, 15(1):465. DOI:10.1186/1471-2164-15-465

Olalde I, Sánchez-Quinto F, Datta D, Marigorta UM, Chiang CW, Rodríguez JA, Fernández-Callejo M, González I, Montfort M, Matas-Lalueza L, Civit S, Luiselli D, Charlier P, Pettener D, Ramírez O, Navarro A, Himmelbauer H, Marquès-Bonet T, Lalueza-Fox C. 2014. Genomic analysis of the blood attributed to Louis XVI (1754-1793), king of France. Scientific Reports, 4:1-7. DOI:10.1038/srep04666

Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW, DeGiorgio M, Prado-Martinez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández-Callejo M, Prada ME, Encinas JM, Nielsen R, Netea MG, Novembre J, Sturm RA, Sabeti P, Marquès-Bonet T, Navarro A, Willerslev E, Lalueza-Fox C. 2014. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature, 507(7491):225-228. DOI:10.1038/nature12960

Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, Marques-Bonet T, Alkan C, Thomas GW, Hahn MW, Menotti-Raymond M, O'Brien SJ, Wilson RK, Lyons LA, Murphy WJ, Warren WC. 2014. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proceedings of the National Academy of Sciences of the United States of America, 111(48):17230-17235. DOI:10.1073/pnas.1410083111

Juan D, Rico D, Marques-bonet T. 2014. Late-replicating CNVs as a source of new genes. Biology Open, 3(3):231. DOI:10.1242/bio.20147815

Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. 2014. Genome Sequencing Highlights the Dynamic Early History of Dogs. PLoS Genetics, 10(1). DOI:10.1371/journal.pgen.1004016

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA. 2014. Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517):195-201. DOI:10.1038/nature13679

Sudmant PH, Huddleston J, Catacchio CR, Malig M, Hillier LW, Baker C, Mohajeri K, Kondova I, Bontrop RE, Persengiev S, Antonacci F, Ventura M, Prado-Martinez J; Great Ape Genome Project, Marques-Bonet T, Eichler EE. 2013. Evolution and diversity of copy number variation in the great ape lineage. Genome Research, 23(9):1373-1382. DOI:10.1101/gr.158543.113

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. 2013. Great ape genetic diversity and population history. Nature, 499(7459):471-475. DOI:10.1038/nature12228

Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, de la Calle-Mustienes E, Casillas S, Rubio-Acero R, Melé M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Bertranpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, 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). DOI:10.1186/1471-2164-14-363

Lorente-Galdos B, Bleyhl J, Santpere G, Vives L, Ramírez O, Hernandez J, Anglada R, Cooper GM, Navarro A, Eichler EE, Marques-Bonet T. 2013. Accelerated exon evolution within primate segmental duplications. Genome Biology, 14(1):R9. DOI: 10.1186/gb-2013-14-1-r9

Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C; Great Ape Genome Project, Marques-Bonet T, Ventura M, Batzer MA, Eichler EE. 2013. Rates and patterns of great ape retrotransposition. Proceedings of the National Academy of Sciences of the United States of America, 110(33):13457-13462. DOI:10.1073/pnas.1310914110

Heyn H, Moran S, Hernando-Herraez I, Sayols S, Gomez A, Sandoval J, Monk D, Hata K, Marques-Bonet T, Wang L, Esteller M. 2013. DNA methylation contributes to natural human variation. Genome Research, 23(9):1363-1372. DOI:10.1101/gr.154187.112

Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom C, Navarro A, Esteller M, Sharp AJ, Marques-Bonet T. 2013. Dynamics of DNA Methylation in Recent Human and Great Ape Evolution. PLoS Genetics, 9(9). DOI:10.1371/journal.pgen.1003763

Giannuzzi G, Siswara P, Malig M, Marques-Bonet T; NISC Comparative Sequencing Program, Mullikin JC, Ventura M, Eichler EE. 2013. Evolutionary dynamism of the primate LRRC37 gene family. Genome Research, 23(1):46-59. DOI:10.1101/gr.138842.112

Ventura M, Catacchio CR, Sajjadian S, Vives L, Sudmant PH, Marques-Bonet T, Graves TA, Wilson RK, Eichler EE. 2012. The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2. Genome Research, 27(9):1621.1-1621.1. DOI:10.1101/gr.226878.117

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