Publication List

2017

Pablo Librado, Cristina Gamba, Charleen Gaunitz, Clio Der Sarkissian, Mélanie Pruvost, Anders Albrechtsen, Antoine Fages, Naveed Khan, Mikkel Schubert, Vidhya Jagannathan, Aitor Serres, Lukas Kuderna, Inna Povolotskaya, Andaine Seguin-Orlando, Sébastien Lepetz, Markus Neuditschko, Catherine Thèves, Melanie Scheu, Saleh Alquaraishi, Ahmed H Alfarhan, Khaled Al-Rasheid, Stefan Rieder, Zainullah Samashev, Paul-Henri Francfort, Joachim Burger, Norbert Benecke, Michael Hofreiter, Arne Ludwig, Christine Keyser, Tomas Marques-Bonet, Bertrand Ludes, Eric Crubézy, Tosso Leeb, Eske Willerslev, Ludovic Orlando. “First domestic horse genomes Ancient DNA reveal major changes reshaping the horse genome in early and late domestication stages” Science 2017

Meyer KA, Marques-Bonet T, Sestan N. “Differential Gene Expression in the Human Brain Is Associated with Conserved, but not Accelerated, Noncoding Sequences.” Mol Biol Evol. 2017 Feb 13. doi: 10.1093/

2016

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. “Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting.” PLoS Genet. 2016 Nov 11;12(11):e1006427. doi: 10.1371/journal.pgen.1006427.

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. “Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.” Genome Biol. 2016 Dec 14;17(1):251.

Nam K, Munch K, Mailund T, Nater A, Greminger MP, Krützen M, Marquès-Bonet T, Schierup MH.”Evidence that the rate of strong selective sweeps increases with population size in the great apes.” Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1613-1618. doi: 10.1073/pnas.1605660114.

Marc de Manuel, Martin Kuhlwilm, Peter Frandsen, Vitor C Sousa, Tariq Desai, Javier Prado-Martinez, Jessica Hernandez-Rodriguez, Isabelle Dupanloup, Oscar Lao, Pille Hallast, Joshua M Schmidt, José María Heredia-Genestar, Andrea Benazzo, Guido Barbujani, Benjamin M Peter, Lukas FK Kuderna, Ferran Casals, Samuel Angedakin, Mimi Arandjelovic, Christophe Boesch, Hjalmar Kühl, Linda Vigilant, Kevin Langergraber, John Novembre, Marta Gut, Ivo Gut, Arcadi Navarro, Frands Carlsen, Aida M Andrés, Hans R Siegismund, Aylwyn Scally, Laurent Excoffier, Chris Tyler-Smith, Sergi Castellano, Yali Xue, Christina Hvilsom, Tomas Marques-Bonet   Chimpanzee genomic diversity reveals ancient admixture with bonobos Science 2016

G Dayama, J Prado, JM Kidd, T Marques-Bonet, RE Mills. “Evolution of nuclear mitochondrial insertions in the genomes of primates” Mitochondrion 31, 116-117 2016

Alexander Cagan, Christoph Theunert, Hafid Laayouni, Gabriel Santpere, Marc Pybus, Ferran Casals, Kay Prüfer, Arcadi Navarro, Tomas Marques-Bonet, Jaume Bertranpetit, Aida M Andrés. “Natural Selection in the Great Apes” Molecular Biology and Evolution 2016

Marta Sanchez-Delgado, Franck Court, Enrique Vidal, Jose Medrano, Ana Monteagudo-Sánchez, Alex Martin-Trujillo, Chiharu Tayama, Isabel Iglesias-Platas, Ivanela Kondova, Ronald Bontrop, Maria Eugenia Poo-Llanillo, Tomas Marques-Bonet, Kazuhiko Nakabayashi, Carlos Simón, David Monk. “Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting” Plos Genetics 2016

Martin Kuhlwilm*, Marc de Manuel*, Alexander Nater*, Maja P. Greminger*, Michael Krützen, Tomas Marques-Bonet “Evolution and demography of the great apes.” Current Opinion in Genetics & Development  2016 (In press). 

Irene Lobon, Serena Tucci, Marc de Manuel, Silvia Ghirotto, Andrea Benazzo, Javier Prado-Martinez, Belen Lorente-Galdos, Kiwoong Nam, Marc Dabad, Jessica Hernandez-Rodriguez, David Comas, Arcadi Navarro, Mikkel H. Schierup, Aida M. Andres, Guido Barbujani, Christina Hvilsom, Tomas Marques-Bonet “Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions”.  Genome Biology and Evolution 2016 (In press). 

Alicia Gallego, Marta Melé, Ingrid Balcells, Eva García-Ramallo, Ignasi Torruella-Loran, Teresa Abelló, Christina Hvilsom, Tomàs Marquès-Bonet, Yolanda Espinosa-Parrilla. “Functional Implications of Human-Specific Changes in Great Ape microRNAs” Plos One 2016.

Stephan Koblmüller, Carles Vilà, Belen Lorente-Galdos, Marc Dabad, Oscar Ramirez, Tomas Marques-Bonet, Robert K. Wayne, Jennifer A. Leonard. “Whole mitochondrial genomes illuminate ancient intercontinental dispersals of grey wolves (Canis lupus)”. Journal of Biogeography 2016.

Adam H. Freedman , Rena M. Schweizer, Diego Ortega-Del Vecchyo, Eunjung Han, Brian W. Davis, Ilan Gronau, Pedro M. Silva, Marco Galaverni, Zhenxin Fan, Peter Marx, Belen Lorente-Galdos, Oscar Ramirez, Farhad Hormozdiari, Can Alkan, Carles Vilà, Kevin Squire, Eli Geffen, Josip Kusak, Adam R. Boyko, Heidi G. Parker, Clarence Lee, Vasisht Tadigotla, Adam Siepel, Carlos D. Bustamante, Timothy T. Harkins, Stanley F. Nelson, Tomas Marques-Bonet, Elaine A. Ostrander, Robert K. Wayne, John Novembre. “Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs” Plos Genetics 2016. March 4, 2016DOI: 10.1371/journal.pgen.1005851

Guillem de Valles-Ibáñez, Jessica Hernandez-Rodriguez, Javier Prado-Martinez, Pierre Luisi, Tomàs Marquès-Bonet, and Ferran Casals “Genetic load of loss-of-function polymorphic variants in great apes” Genome Biol Evol February 24, 2016 doi:10.1093/gbe/evw040

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. “Ancient gene flow from early modern humans into Eastern Neanderthals.” Nature. 2016 Feb 17. doi: 10.1038/nature16544.

Marsden CD, Ortega-Del Vecchyo D, O’Brien DP, Taylor JF, Ramirez O, Vilà C, Marques-Bonet T, Schnabel RD, Wayne RK, Lohmueller KE. “Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.” Proc Natl Acad Sci U S A. 2015 2016 Jan 5;113(1):152-7. doi: 10.1073/pnas.1512501113.

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, Vilá C, Marques-Bonet T, Godinho R, Yue B, Wayne RK. “Worldwide patterns of genomic variation and admixture in gray wolves.”  Genome Res. 2016 Feb;26(2):163-73. doi: 10.1101/gr.197517.115.

2015

Jorge Ruiz-Orera, Jessica Hernandez-Rodriguez, Cristina Chiva, Eduard Sabidó, Ivanela Kondova, Ronald Bontrop, Tomas Marques-Bonet, M.Mar Albà. “De novo gene emergence in human and chimpanzee” Plos Genetics 2015 Dec 31;11(12):e1005721. doi: 10.1371/journal.pgen.1005721. eCollection 2015 Dec. PMID: 26720152

Laurie S Stevison, August E Woerner, Jeffrey M Kidd, Joanna L Kelley, Krishna R Veeramah, Kimberly F. McManus, Great Ape Genome Project, Carlos D Bustamante, Michael F Hammer and Jeffrey D Wall. “The Time-Scale Of Recombination Rate Evolution In Great Apes.” Mol Biol Evol (2015) doi: 10.1093/molbev/msv331

Hernando-Herraez I*, Raquel Garcia-Perez*, Andrew J. Sharp*, Tomas Marques-Bonet*DNA methylation: insights into human evolution” Plos Genetics 2015 doi: 10.1371/journal.pgen.1005661

Irene Hernando-Herraez, Holger Heyn, Marcos Fernandez-Callejo, Enrique Vidal, Hugo Fernandez-Bellon, Javier Prado-Martinez, Andrew J Sharp, Manel Esteller, Tomas Marques-Bonet. “The interplay between DNA methylation and sequence divergence in recent human evolution”. Nucleic Acid Research  2015 July 13, doi: 10.1093/nar/gkv693

Pavel Dobrynin, Shiping Liu, Aleksey Komissarov, Gaik Tamazian, Alexey Makunin, Ksenia Krasheninnikova, Andrey Yurchenko, Sergey Kliver, Ricardo Godinez, Klaus-Peter Koepfli, Warren Johnson, Lukas Kuderna, Raquel Garcia-Perez, Marc Manuel Montero, Carlos Driscoll, Agostinho Antunes, Taras Oleksyk,David Wildt, Mark Diekhans, Tomas Marques-Bonet, Laurie Marker, Anne Schmidt-Kuntzel, Xiong Zijun, Guojie Zhang & Stephen J O’Brien. “Genomic Legacy of the African Cheetah, Acinonyx jubatus.” Genome Biology 2015 Dec 10;16:277. doi: 10.1186/s13059-015-0837-4.

Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L. “Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.” Proc Natl Acad Sci U S A. 2015 Nov 23. pii: 201513696.

Wesley C Warren, Anna J Jasinska, Raquel Garcia-perez, Hannes Svardal, Chad Tomlinson, Mariano Rocchi, Nicoletta Archidiacono, Oronzo Capozzi, Patrick Minx, Michael J Montague, Kim Kyung, LaDeana W Hillier, Milinn Kremitzki, Tina Graves, Colby Chiang, Jennifer Hughes, Nam Tran, Yu Wang, Vasily Ramensky, Oi-wa Choi, Yoon J Jung, Christopher A Schmitt, Nikoleta Juretic, Jessica Wasserscheid, Trudy R Turner, Roger W Wiseman, Jennifer J Tuscher, Julie A Karl, Jöern E Schmitz, Roland Zahn, David H O’Connor, Eugene Redmond, Alex Nisbett, Béatrice Jacquelin, Michaela C Müller-Trutwin, Jason M Brenchley, Michel Dione, Martin Antonio, Gary P Schroth, Jay R Kaplan, Matthew J Jorgensen, Gregg WC Thomas, Matthew W Hahn, Brian Raney, Bronwen Aken, Juergen Schmitz, Gennady Churakov, Angela Noll, Roscoe Stanyon, David Webb, Francoise Thibaud-Nissen, Magnus Nordborg, Tomas Marques-Bonet, Ken Dewar, George M Weinstock, Richard K Wilson, and Nelson B Freimer. “The genome of the vervet (Chlorocebus aethiops sabaeus)Genome Research 2015  doi:10.1101/gr.192922.115

Tugce Bilgin Sonay, Tiago Carvalho, Mark Robinson, Maja Greminger, Michael Krützen, David Comas, Gareth Highnam, David Mittelman, Andrew Sharp, Tomas Marques-Bonet*, Andreas Wagner*. “Tandem repeat variation in human and great ape populations and its impact on gene expression divergence”. Genome Research , 2015 August 19, 2015, doi:10.1101/gr.190868.115

Clio Der Sarkissian, Luca Ermini, Mikkel Schubert, Melinda A. Yang, Pablo Librado, Matteo Fumagalli, Hákon Jónsson, Gila Kahila Bar-Gal, Anders Albrechtsen, Filipe G. Vieira, Bent Petersen, Aurélien Ginolhac, Andaine Seguin-Orlando, Kim Magnussen, Antoine Fages, Cristina Gamba, Belen Lorente, Sagi Polani, Cynthia Steiner, Markus Neuditschko, Vidhya Jagannathan, Claudia Feh, Charles L. Greenblatt, Arne Ludwig, Natalia Abramson, Waltraut Zimmermann, Renate Schafberg, Alexei Tikhonov, Thomas Sicheritz-Ponten, Eske Willerslev, Tomas Marques-Bonet, Oliver A. Ryder, Molly McCue, Stefan Rieder, Tosso Leeb, Montgomery Slatkin, Ludovic Orlando. “Evolutionary genomics and conservation of the endangered Przewalski’s horsesCurrent Biology 2015 Oct 5;25(19):2577-83. doi: 10.1016/j.cub.2015.08.032. Epub 2015 Sep 24.

Iñigo Olalde, Hannes Schroeder, Marcela Sandoval-Velasco, Lasse Vinner, Irene Lobón, Oscar Ramirez, Sergi Civit, Pablo García Borja, Domingo C. Salazar-García, Sahra Talamo, Josep María Fullola, Francesc Xavier Oms, Mireia Pedro, Pablo Martínez, Montserrat Sanz, Joan Daura, João Zilhão, Tomàs Marquès-Bonet, M. Thomas P. Gilbert, Carles Lalueza-Fox. “A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK culturesMol. Biol. Evol.  2015 doi: 10.1093/molbev/msv181

Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Zhou X, Ward MC, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Friedrich Ben-Nun I, Li Y, Sabatini K, Leonardo TR, Parast M, Marques-Bonet T, Laurent LC, Loring JF, Gilad Y. “A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics.” Elife. 2015 Jun 23;4. doi: 10.7554/eLife.07103. [Epub ahead of print]

Nam K, Munch K, Hobolth A, Dutheil JY, Veeramah KR, Woerner AE, Hammer MF; Great Ape Genome Diversity Project, Mailund T, Schierup MH.“Extreme selective sweeps independently targeted the X chromosomes of the great apes.” Proc Natl Acad Sci U S A.. 2015 May 19;112(20):6413-8. doi: 10.1073/pnas.1419306112. Epub 2015 May 4.

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. “Limiting replication stress during somatic cell reprogramming reduces genomic instability in induced pluripotent stem cells.” Nat Commun. 2015 Aug 21;6:8036. doi: 10.1038/ncomms9036. PMID: 26292731

Yali Xue*, Javier Prado-Martinez*, Peter H Sudmant*, Vagheesh Narasimhan, Qasim Ayub, Michal Szpak, Peter Frandsen, Yuan Chen, Bryndis Yngvadottir, David N Cooper, Marc de Manuel, Jessica Hernandez-Rodriguez, Irene Lobon, Hans R Siegismund, Luca Pagani, Michael A Quail, Christina Hvilsom, Antoine Mudakikwa, Evan E Eichler, Michael R Cranfield, Tomas Marques-Bonet, Chris Tyler-Smith*, Aylwyn Scally*. “Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding”Science 348 (6231), 242-245

Krishna R Veeramah, August E Woerner, Laurel Johnstone, Ivo Gut, Marta Gut, Tomas Marques-Bonet, Lucia Carbone, Jeff D Wall, Michael F Hammer. “Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach”. Genetics, 115.174425

Klaus-Peter Koepfli, Benedict Paten, G10K consortium, Stephen J O’Brien. “The Genome 10K Project: A Way Forward”. Annu. Rev. Anim. Biosci., 2015 3 (1), 57-111

2014

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. “Prehistoric genomes reveal the genetic foundation and cost of horse domestication” PNAS 2014 Dec 15. pii: 201416991

Michael J. Montague, Gang Li, Barbara Gandolfi, Razib Khan, Bronwen L. Aken, Steven M. J. Searle, Patrick Minx, LaDeana Hillier, Daniel C. Koboldt, Brian W. Davis, Carlos A. Driscoll, Christina S. Barr, Kevin Blackiston, Javier Quilez, Belen Lorente-Galdos, Tomas Marques-Bonet, Can Alkan, Gregg W. C. Thomas, Matthew W. Hahn, Marilyn Menotti-Raymond, Stephen J. O’Brien, Richard Wilson, Leslie A. Lyons, William J. Murphy and Wesley C. Warren. “Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication”  PNAS  2014 Dec 2;111(48):17230-17235.

Tamazian et al. “Annotated features of domestic cat – Felis catus genome” (including  Javier Quilez, Belen Lorente-Galdos and Tomas Marques-Bonet) Gigascience 2014  Aug 5;3:13. doi: 10.1186/2047-217X-3-13. eCollection 2014.

Carbone et al. The Gibbon Genome Sequencing and Analysis Consortium (including  Marcos Fernandez-Callejo, Jéssica Hernández-Rodríguez, Javier Quilez, Belen Lorente-Galdos and Tomas Marques-Bonet). The gibbon genome provides a novel perspective on the accelerated karyotype evolution of small apes Nature 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679..

Worley et al. The Marmoset Genome Sequencing and Analysis Consortium (including Belen Lorente-Galdos and Tomas Marques-Bonet). “The common marmoset genome provides insight into primate biology and evolution” Nature Genetics 2014  Aug;46(8):850-7. doi: 10.1038/ng.3042. Epub 2014 Jul 20..

Oscar Ramirez, Iñigo Olalde, Jonas Berglund, Belen Lorente-Galdos, Matthew T. Webster, Robert K. Wayne, Carles Lalueza-Fox, Carles Vilà, Tomas Marques-Bonet. “Analysis of structural diversity in wolf-like canids reveals post-domestication variants.” BMC Genomics 2014  Jun 12;15:465. doi: 10.1186/1471-2164-15-465.

Watson CT, Marques-Bonet T, Sharp AJ, Mefford HC. “The Genetics of Microdeletion and Microduplication Syndromes: An Update.” Annu Rev Genomics Hum Genet. 2014 Apr 16.

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. “Genomic analysis of the blood attributed to Louis XVI (1754-1793), king of France.” Sci Rep. 2014 Apr 24;4:4666. 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. “Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.” Nature. 2014 Jan 26. doi: 10.1038/nature12960.

Adam H. Freedman, Rena M. Schweizer, Ilan Gronau, Eunjung Han, Diego Ortega-Del Vecchyo, Pedro Silva, Marco Galaverni, Zhenxin Fan, Peter Marx, Belen Lorente-Galdos, Holly Beale, Oscar Ramirez, Farhad Hormozdiari, Can Alkan, Carles Vilà, Kevin Squire, Eli Geffen, Josip Kusak, Adam R. Boyko, Heidi Parker, Clarence Lee, Vasisht Tadigotla, Adam Siepel, Carlos Bustamante, Timothy Harkins, Stanley F. Nelson, Elaine A. Ostrander, Tomas Marques-Bonet, Robert K. Wayne, John Novembre. “Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs.” Plos Genetics 2014   Jan;10(1):e1004016.   doi:10.1371/journal.pgen.1004016. Epub 2014 Jan 16.

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 JMarques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC. “Elephant shark genome provides unique insights into gnathostome evolution.” Nature. 2014 Jan 9;505(7482):174-9. doi: 10.1038/nature12826. (Cover)

2013

Daniel Rico, Alfonso Valencia, David Juan, Tomas Marques-Bonet, and Óscar Fernández-Capetillo. “Late-replicating CNVs as a source of new genes”. Biology Open 2013 Dec 15;2(12):1402-11. doi: 10.1242/bio.20136924.

Irene Hernando-Herraez, Javier Prado-Martinez, Paras Garg, Marcos Fernandez-Callejo, Holger Heyn, Christina Hvilsom, Arcadi Navarro, Manel Esteller, Andrew J. Sharp, Tomas Marques-BonetDynamics of DNA Methylation in Recent Human and Great Apes Evolution” Plos Genetics 2013 Sep;9(9):e1003763. doi: 10.1371/journal.pgen.1003763. Epub 2013 Sep 5..

Holger Heyn, Sebastian Moran, Irene Hernando-Herraez, Sergi Sayols, Antonio Gomez, Juan Sandoval, Dave Monk, Kazuhiko Nakabayashi,  Tomas Marques Bonet, Liewei Wang and Manel Esteller. “DNA methylation contributes to natural human variation”. Genome Research 2013 Sep;23(9):1363-72. doi: 10.1101/gr.154187.112. Epub 2013 Aug 1.

Javier Prado-Martinez*, Peter H. Sudmant*, Jeffrey M. Kidd, Heng Li, Joanna L. Kelley, Belen LorenteGaldos, Krishna R. Veeramah, August Woerner, Timothy D. O’Connor, Gabriel Santpere, Alexander Cagan, Christoph Theunert, Ferran Casals, Hafid Laayouni, Kasper Munch, Asger Hobolth, Anders E. Halager, Maika Malig, Jessica Hernandez-Rodriguez, Irene Hernando-Herraez, Kay Prüfer, Marc Pybus, Laurel Johnstone, Michael Lachmann, Can Alkan, Dorina Twigg, Natalia Petit, Carl Baker, Fereydoun Hormozdiari, Marcos Fernandez-Callejo, Marc Dabad, Michael L. Wilson, Laurie Stevison, Cristina Camprubí, Tiago Carvalho, Aurora Ruiz-Herrera, Laura Vives, Marta Mele, Teresa Abello, Ivanela Kondova, Ronald E. Bontrop, Anne Pusey, Felix Lankester, John A. Kiyang, Richard A. Berg, Elizabeth Lonsdorf, Simon Myers, Mario Ventura, Pascal Gagneux, David Comas, Hans Siegismund, Julie Blanc,Lidia Agueda-Calpena, Marta Gut, Lucinda Fulton, Sarah A. Tishkoff, James C. Mullikin, Richard K. Wilson, Ivo G. Gut, Mary Katherine Gonder, Oliver A. Ryder, Beatrice H. Hahn, Arcadi Navarro, Joshua M. Akey, Jaume Bertranpetit, David Reich, Thomas Mailund, Mikkel H. Schierup, Christina Hvilsom, Aida M. Andrés, Jeff Wall, Carlos D. Bustamante, Mike Hammer, Evan E. Eichler+, Tomas Marques-Bonet +. (2013). “Great ape genetic diversity and population history.” Nature 2013 Jul 25;499(7459):471-5. doi: 10.1038/nature12228. Epub 2013 Jul 3.

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. Rates and patterns of great ape retrotransposition.” Proc Natl Acad Sci U S A. 2013  Aug 13;110(33):13457-62. doi: 10.1073/pnas.1310914110. Epub 2013 Jul 24.

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. “Evolution and diversity of copy number variation in the great ape lineage.” Genome Res. 2013  Sep;23(9):1373-82. doi: 10.1101/gr.158543.113. Epub 2013 Jul 3.

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. “The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.” BMC Genomics. 2013 May 31;14:363. doi: 10.1186/1471-2164-14-363.

Lorente-Galdos B, Bleyhl J, Santpere G, Vives L, Ramirez O, Hernandez J, Anglada R, Cooper GM, Navarro A, Eichler EE, Marques-Bonet T. “Accelerated exon evolution within primate segmental duplications.”

Genome Biol. 2013 Jan 29;14(1):R9. [Epub ahead of print]

Giannuzzi G, Siswara P, Malig M, Marques-Bonet T; NISC Comparative Sequencing Program, Mullikin JC, Ventura M, Eichler EE. “Evolutionary dynamism of the primate LRRC37 gene family.” Genome Res. 2013 Jan;23(1):46-59. doi: 10.1101/gr.138842.112. Epub 2012 Oct 11.

2012

Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutiérrez S, Blanca J, Cañizares J, Ziarsolo P, Gonzalez-Ibeas D, Rodríguez-Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente-Galdos B, Melé M, Yang L, Weng Y, Navarro A, Marques-Bonet T, Aranda MA, Nuez F, Picó B, Gabaldón T, Roma G, Guigó R, Casacuberta JM, Arús P, Puigdomènech P. “The genome of melon (Cucumis melo L.)Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11872-7. Epub 2012 Jul 2.

Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S. “The bonobo genome compared with the chimpanzee and human genomes” Nature. 2012 Jun 28;486(7404):527-31.

Scally A, et al. Gorilla genome Consortium. “Insights into hominid evolution from the gorilla genome sequence.” Nature. 2012 Mar 7;483(7388):169-75.

Ventura M, Catacchio C, Sajjadian S, Vives L, Sudmant P,Marques-Bonet T, Graves TA, Wilson RK, Eichler EE. “The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2” Genome Research 2012 Mar 14

2011

Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, Graves TA, Hormozdiari F, Navarro A, Malig M, Baker C, Lee C, Turner EH, Chen L, Kidd JM, Archidiacono N, Shendure J, Wilson RK, Eichler EE. “Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee” Genome Res. 2011 Jun 21.

Gazave E, Darré F, Morcillo-Suarez C, Petit-Marty N, Carreño A, Marigorta UM, Ryder OA, Blancher A, Rocchi M, Bosch E, Baker C, Marquès-Bonet T, Eichler EE, Navarro A. “Copy number variation analysis in the great apes reveals species-specific patterns of structural variation” Genome Res. 2011 Oct;21(10):1626-39. Epub 2011 Aug 8.

Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF; NISC Comparative Sequencing Program, Eichler EE, Ornitz DM, Green ED. “Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analysesBMC Evol Biol. 2011 Jan 24;11:23.

Devin P. Locke, et al. Orangutan Consortium.Comparative and demographic analysis of orang-utan genomes” Nature 2011 Volume:469, Pages:529–533 Date published:(27 January 2011) DOI:doi:10.1038/nature09687 (Cover)

2010

David Reich, Richard E. Green, Martin Kircher, Johannes Krause, Nick Patterson, Bence Viola, Adrian W. Briggs, Eric Y. Durand, Udo Stenzel, Philip L.F. Johnson, Jeffrey M. Good, Tomas Marques-Bonet, Can Alkan, Qiao-mei Fu, Heng Li, Weiwei Zhai, Rasmus Nielsen, Matthias Meyer, Rigo Schultz, Evan E. Eichler, Mark Stoneking, Michael V. Shunkovz, Anatoli P. Dereviankoz,  Jean-Jacques Hublinx, Janet Kelso, Montgomery  Slatkin, Svante Pääbo. “A Draft Genome Sequence and Dental Morphology of an Archaic Hominin group from Denisova Cave, Russia”.Nature 2010 Volume:468, Pages: 1053-1060(23 December 2010) DOI:doi:10.1038/nature09710

Al-Shahrour F, Minguez P, Marques-Bonet T, Gazave, E., Navarro A, Dopazo, J. “Selection upon genome architecture: conservation of functional neighborhoods with changing genes” PLoS Computational Biology, 2010 Oct 7;6(10):e1000953.

Fernando CA, Conrad PA, Bartels CF, Marques-Bonet T, To M, Balow SA, Nakamura Y, Warman ML. “Temporal and Spatial Expression of CCN Genes in Zebrafish”. Developmental dynamics, 2010 Jun;239(6):1755-67.

Francesca Antonacci, Jeffrey M. Kidd, Tomas Marques-Bonet, Brian O’Roak, Mario Ventura, Santhosh Girirajan, Can Alkan, Laura Vives, Maika Malig, Jill A. Rosenberg,  Lisa G. Shaffer, Tina A. Graves, Richard K. Wilson, David G. Schwartz and Evan E Eichler. A large, complex structural polymorphism at 16p12.1 underlies microdeletion disease risk” Nature Genetics, 2010 Sep;42(9):745-50. Epub 2010 Aug 22.

Richard E. Green,et al. Neandertal Consortium. A draft sequence and preliminary analysis of the Neandertal genome” Science 7 May 2010: Vol. 328 no. 5979 pp. 710-722

2009

Tomas Marques-Bonet, Oliver Ryder, Evan Eichler. Primate Comparative Genomics: the evolution of our order.” Annu Rev Genomics Hum Genet. 2009;10:355-86. Review.

Tomas Marques-Bonet, Santhosh Girirajan, Evan Eichler. ­Origins and Impacts of Primate Segmental Duplications.” Trends Genet. 2009 Oct;25(10):443-54. Epub 2009 Sep 30. Review.

Tomas Marques-Bonet and Evan Eichler. The Evolution of Human Segmental Duplications and the Core Duplicon Hypothesis.” Cold Spring Harb Symp Quant Biol. 2009;74:355-62. Epub 2009 Aug 28.

Andres Moreno-Estrada, Ku Tang, Martin Sikora, Tomàs Marquès-Bonet, Ferran Casals, Arcadi Navarro, Francesc Calafell, Jaume Bertranpetit, Marc Stoneking, Elena Bosch. “Interrogating eleven fast-evolving genes for signatures ofrecent positive selection in worldwide human populations” Mol Biol Evol. 2009 Oct;26(10):2285-97. Epub 2009 Jul 3.

Francesca Antonacci, Jeffrey M. Kidd, Tomas Marques-Bonet, Mario Ventura, Priscillia Siswara, Zhaoshi Jiang and Evan E Eichler. Characterization of six human disease-associated inversion polymorphisms” Human Molecular Genetics 2009 18(14):2555-2566;.

Can Alkan, Jeffrey M. Kidd, Tomas Marques-Bonet, Gözde Aksay, Fereydoun Hormozdiari, Francesca Antonacci, Carl Baker, Onur Mutlu, S. Cenk Sahinalp, Richard A. Gibbs, Evan E. Eichler.”Personalized Copy-Number and Segmental Duplication Maps using Next-Gen Sequencing Technology. Nature Genet. 2009 Oct;41(10):1061-7. Epub 2009 Aug 30.

Tomas Marques-Bonet, Jeffrey M. Kidd, Mario Ventura, Tina A. Graves, Ze Cheng, LaDeanna W. Hillier, Zhaoshi Jiang, Carl Baker, Ray Malfavon-Borja, Lucinda A. Fulton, Can Alkan, Gozde Aksay, Priscillia Siswara, Lin Chen, Maria Francesca Cardone, Arcadi Navarro, Elaine R. Mardis, Richard K. Wilson, Evan E. Eichler. A Burst of Segmental Duplications in the African Great Ape Genome AncestorNature. 2009 Feb 12;457(7231):877-81.

Ferran Casals, Anna Ferrer-Admetlla, Martin Sikora, Anna Ramírez-Soriano, Tomàs Marquès-Bonet, Stéphanie Despiau, Francis Roubinet, Francesc Calafell,Jaume Bertranpetit and Antoine Blancher. “Human pseudogenes of the ABO family show a complex evolutionary dynamics and loss of function.” Glycobiology 2009 Feb 13.

Cemalettin Bekpen, Tomas Marques-Bonet, Can Alkan, Francesca Antonacci, Bruna Leogrande, Mario Ventura, Jeffrey M. Kidd, Priscillia Siswara, Jonathan C. Howard, Evan E. Eichler. The Death and Resurrection of the Human IRGM Gene”. PLOS Genetics 2009 Mar;5(3):e1000403.

2008

Santhosh Girirajan, Lin Chen, Tina Graves, Tomas Marques-Bonet, Mario Ventura, Elaine Mardis and Evan E. Eichler. Sequence analysis of human gibbon breakpoints provides insight into the genomic and phenotypic uniqueness of gibbons.” Genome Research. 2008 Nov 24. 2009. 19: 178-190

Ferrer-Admetlla A, Bosch E, Sikora M, Marquès-Bonet T, Ramírez-Soriano A, Muntasell A, Navarro A, Lazarus R, Calafell F, Bertranpetit J, Casals F. “Balancing selection is the main force shaping the evolution of innate immunity genes”. J Immunol. 2008 Jul 15;181(2):1315-22.

George H. Perry, Fengtang Yang, Tomas Marques-Bonet, Carly Murphy, Tomas Fitzgerald, Arthur S. Lee, Courtney Hyland, Richard S. Smith, Anne C. Stone, Matthew E. Hurles, Chris Tyler-Smith, Evan E. Eichler, Nigel P. Carter, Charles Lee, Richard Redon. Copy number variation and genome evolution in humans and chimpanzees”. Genome Research 2008,18:1698-1710, (Cover).

Tomas Marques-Bonet, Ze Cheng, Xinwei She, Evan E. Eichler, Arcadi Navarro. The genomic distribution of intra and inter divergence of human SD”. BMC Genomics 2008, 9:384. 1.

2000-2007

Zhaoshi Jiang, Haixu Tang, Mario Ventura, Maria Francesca Cardone, Tomas Marques-Bonet,  Xinwei She, Pavel A. Pevzner, Evan E. Eichler. Ancestral Reconstruction of Segmental Duplications Reveals Punctuated Cores of Human Genome Evolution”. Nature Genetics 2007 Nov;39(11):1361-8.

Marques-Bonet T., Sanchez-Ruiz J., Armengol LL., Khaja R., Bertranpetit J., Rocchi M., Gazave E., Navarro A. On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees”. Genome Biology 2007 Oct 30;8(10):R230

Elodie Gazave, Tomàs Marquès-Bonet, Brian Charlesworth, Arcadi Navarro. Patterns and rates of intron divergence between human and chimpanzee”. Genome Biology 2007, 8:R21 (19 February 2007)

Kohji Okamura, Lars Feuk, Tomàs Marquès-Bonet, Arcadi Navarro, and Stephen W. Scherer. “Frequent appearance of novel protein-coding sequences by frameshift translation”. Genomics, 2006, Dec;88(6):690-7. Epub 2006 Aug 4.

Soldevila M., Calafell, F., Ramirez-Soriano, A, Marques-Bonet T., Navarro, A., Bertranpetit, B. “The prion protein gene in humans revisited: lessons from a worldwide resequencing study”. Genome Research 2006 16: 231-239.

Carles Lalueza-Fox, Jose Castresana, Lourdes Sampietro, Marques-Bonet T., Josep Antoni Alcover and Jaume Bertranpetit. Molecular dating  of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal.BMC Evolutionary Biology 2005,5:70 (6 December 2005).

Lluís Armengol, Marques-Bonet T., Joseph Cheung, Stephen W. Scherer, Arcadi Navarro, Xavier Estivill. Murine segmental duplications are hot spots for chromosome and gene evolution”. Genomics, Volume 86, Issue 6, 2005, Pages 692-700.

Marques-Bonet T., Arcadi Navarro. “Chromosomal rearrangements are associated with higher rates of molecular evolution in mammals”. Gene 2005 Jul 4;353(2):147-54. 

Marques-Bonet T., Oscar Lao, Robert Goertsches, Manuel Comabella, Xavier Montalban, Arcadi Navarro. Association Cluster Detector: a tool for heuristic detection of association clusters in whole-genome scans.” Bioinformatics 2005 , 21 (s2):180-181.

Marques-Bonet T., Cáceres M. , Bertranpetit J., Preuss T.M., Thomas J.W., Navarro A. “Genomic distribution of gene expression divergence in humans and chimpanzees.” Trends in Genetics, 2004 Nov;20(11):524-9

Navarro, A., Marques-Bonet T., and N.H. Barton,Response to comment on ” chromosomal speciation and molecular divergence – Accelerated evolution in rearranged chromosomes”. Science, 2003. 302(5647). 

Serra-Cobo, J., Lopez-Roig, M, Marques-Bonet T., Lahuerta, E., Rivers as possible landmarks in the orientation flight of Miniopterus schreibersii.” Acta Theriologica, 2000. 45(3): p. 347-352.

Serra-Cobo, J., Marques-Bonet T., and J.P. Martinez-Rica, Ecological segregation between Rana pyrenaica and Rana temporaria, and differential predation of Euproctus asper on their tadpoles.” Netherlands Journal of Zoology, 2000. 50(1): p. 65-73.

Serra-Cobo, J., Lopez-Roig, M., Marques-Bonet T., Martinez-Rica, J. P.Body condition changes of Miniopterus schreibersii in autumn and winter.” Revue D Ecologie-La Terre Et La Vie, 2000. 55(4): p. 351-360.

Books

  • “L’estructura del genoma”. Marques-bonet, T & Armengol, LL. “Cent cinquanta anys després de L’origen de les espècies, de Darwin”. Societat Catalana de Biologia 2008.

Non ISI Articles

  • “Diversitat”. Comas, D  & Marques-bonet, T. Omnis Cellula 2010.
  • “Tribuna”. Marques-bonet, T. Talencia 2010.