As senior author:

Adrián Talavera, Marc Palmada-Flores, Bernat Burriel-Carranza, Emilio Valbuena-Ureña, Gabriel Mochales-Riaño, Dean C Adams, Héctor Tejero-Cicuéndez, Anna Soler-Membrives, Fèlix Amat, Daniel Guinart, Francesc Carbonell, Elena Obon, Marques-Bonet T+, Salvador Carranza “Genomic insights into the Montseny brook newt (Calotriton arnoldi), a Critically Endangered glacial relict” Iscience 2024 27 (1), 108665

D Juan, G Santpere, JL Kelley, OE Cornejo+, Marques-Bonet T+ “Current advances in primate genomics: novel approaches for understanding evolution and disease” Nature Reviews Genetics, 2023 1-18

Luis Ferrández-Peral, Xiaoyu Zhan, Marina Alvarez-Estape, Cristina Chiva, Paula Esteller-Cucala, Raquel García-Pérez, Eva Julià, Esther Lizano, Òscar Fornas, Eduard Sabidó, Qiye Li, Marques-Bonet T+,  David Juan+, Guojie Zhang+ “Transcriptome innovations in primates revealed by single-molecule long-read sequencing” Genome research 32 (8), 1448-1462

Clàudia Fontseré Alemany, Martin Kuhlwilm, Carlos Morcillo Suárez, Marina Alvarez-Estape, Jack de Lester, Paolo Gratton, Joshua M Schmidt, Paula Diéguez, Thierry Aebischer, Paula Álvarez-Varona, Anthony Agbor, Samuel Angedakin, Alfred K Assumang, Emmanuel A Ayimisin, Emma Bailey, Donatienne Barubiyo, Mattia Bessone, Andrea Carretero-Alonso, Rebecca Chancellor, Heather Cohen, Emmanuel Danquah, Tobias Deschner, Andrew Dunn, Jef Dupain, Villard E Egbe, Olga Feliu, Annemarie Goedmakers, Anne-Céline Granjon, Josephine Head, Daniela Hedwig, Veerle Hermans, Adriana Hernández Aguilar, Inaoyom Imong, Sorrel Jones, Jessica Junker, Parag Kadam, Mike Kaiser, Mbangi Kambere, Magloire V Kambale, Ammie K Kalan, Ivonne Kienast, Deo Kujirakwinja, Kevin Langergraber, Juan Lapuente, Bradley Larson, Anne Laudisoit, Kevin Lee, Manuel Llana, Miquel Llorente Espino, Sergio Marrocoli, David Morgan, Felix Mulindahabi, Mizuki Murai, Emily Neil, Sonia Nicholl, Stuart Nixon, Emma Normand, Chris Orbell, Lucy J Ormsby, Liliana Pacheco, Alex Piel, Laura Riera, Martha M Robbins, Aaron Rundus, Crickette Sanz, Lilah Sciaky, Volker Sommer, Fiona A Stewart, Nikki Tagg, Luc Roscelin Tédonzong, Els Ton, Joost van Schijndel, Virginie Vergnes, Erin G Wessling, Jacob Willie, Roman M Wittig, Yisa G Yuh, Kyle Yurkiw, Klaus Zuberbuehler, Jochen Hecht, Linda Vigilant, Christophe Boesch, Aida M Andrés, David A Hughes, Hjalmar S Kühl, Esther Lizano, Mimi Arandjelovic, Marques-Bonet T “Population dynamics and genetic connectivity in recent chimpanzee history” Cell Genomics, 2022, vol. 2, núm. 6, p. 100133

Palmada-Flores M, Orkin JD, Haase B, Mountcastle J, Bertelsen MF, Fedrigo O, Kuderna LFK, Jarvis ED, Marques-Bonet T. “A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)” Gigascience. 2022 Apr 1;11:giac026. doi: 10.1093/gigascience/giac026.

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*. “Insights from the rescue and breeding management of Cuvier’s gazelle ( Gazella cuvieri) through whole-genome sequencing” Evol Appl. 2022 Feb 22;15(3):351-364. doi: 10.1111/eva.13336. eCollection 2022 Mar.

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. “The genetic impact of an Ebola outbreak on a wild gorilla population” BMC Genomics. 2021 Oct 11;22(1):735. doi: 10.1186/s12864-021-08025-y.

Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. “Copy number variation underlies complex phenotypes in domestic dog breeds and other canids” Genome Research 2021 May;31(5):762-774. doi: 10.1101/gr.266049.120. Epub 2021 Apr 16.

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, Marques-Bonet T. “Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures” Nat Commun. 2021 May 25;12(1):3116. doi: 10.1038/s41467-021-23397-1.

Lukas FK Kuderna, Paula Esteller-Cucala, Tomas Marques-Bonet. “Branching out: what omics can tell us about primate evolution” Current Opinion in Genetics & Development Volume 62, June 2020, Pages 65-71

Lukas FK Kuderna, Joseph Orkin, Tomas Marques-Bonet. “The Diversity of Primates: From Biomedicine to Conservation Genomics”Annual Review of Animal Biosciences Vol. 9:- (Volume publication date February 2021)

Claudia Fontsere, Marina Alvarez‐Estape, Jack Lester, Mimi Arandjelovic, Martin Kuhlwilm, Paula Dieguez, Anthony Agbor, Samuel Angedakin, Emmanuel Ayuk Ayimisin, Mattia Bessone, Gregory Brazzola, Tobias Deschner, Manasseh Eno‐Nku, Anne‐Céline Granjon, Josephine Head, Parag Kadam, Ammie K Kalan, Mohamed Kambi, Kevin Langergraber, Juan Lapuente, Giovanna Maretti, Lucy Jayne Ormsby, Alex Piel, Martha M Robbins, Fiona Stewart, Virginie Vergnes, Roman M Wittig, Hjalmar S Kühl, Tomas Marques-Bonet+, David A Hughes+, Esther Lizano+ “Maximizing Improving data acquisitionthe acquisition of unique reads in non-invasive capture sequencing experiments” Molecular Ecology Resources 2020

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, Tomas Marques-Bonet+, Hansen AJ+, Gilbert MTP+. “Arctic-adapted Dogs Emerged at the Pleistocene-Holocene Transition” Science. 2020 Jun 26;368(6498):1495-1499. doi: 10.1126/science.aaz8599.

Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Tomas Marques-Bonet+, Rogers J+, Juan D+. “Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta)” PLoS Genet. 2020 May 11;16(5):e1008742. doi: 10.1371/journal.pgen.1008742. eCollection 2020 May.

Marc de Manuel+, Ross Barnett+, Marcela Sandoval-Velasco, Nobuyuki Yamaguchi, Filipe Garrett Vieira, M. Lisandra Zepeda Mendoza, Shiping Liu, Michael D. Martin, Mikkel-Holger S. Sinding, Sarah S. T. Mak, Christian Carøe, Shanlin Liu, Chunxue Guo, Jiao Zheng, Grant Zazula, Gennady Baryshnikov, Eduardo Eizirik, Klaus-Peter Koepfli,  Warren E. Johnson,  Agostinho Antunes,  Thomas Sicheritz-Ponten, Shyam Gopalakrishnan, Greger Larson, Huanming Yang, Stephen J. O’Brien, Anders J. Hansen, Guojie Zhang, Tomas Marques-Bonet+, and  M. Thomas P. Gilbert+ “The evolutionary history of extinct and living lions” PNAS May 4, 2020 https://doi.org/10.1073/pnas.1919423117

Peter Frandsen+, Claudia Fontsere+, Svend Vendelbo Nielsen, Kristian Hanghøj, Natalia Castejon-Fernandez, Esther Lizano, David Hughes, Jessica Hernandez-Rodriguez, Thorfinn Sand Korneliussen, Frands Carlsen, Hans Redlef Siegismund, Thomas Mailund, Tomas Marques-Bonet+, Christina Hvilsom+ “Targeted conservation genetics of the endangered chimpanzee” Heredity, 1-13 2020

Frido Welker, Jazmín Ramos-Madrigal, Martin Kuhlwilm, Wei Liao, Petra Gutenbrunner, Marc de Manuel, Diana Samodova, Meaghan Mackie, Morten E Allentoft, Anne-Marie Bacon, Matthew J Collins, Jürgen Cox, Carles Lalueza-Fox, Jesper V Olsen, Fabrice Demeter, Wei Wang*, Tomas Marques-Bonet *, Enrico Cappellini* “Enamel proteome shows that Gigantopithecus was an early diverging pongine”  Nature 576 (7786), 262-265

M Kuhlwilm, S Han, VC Sousa, L Excoffier, Tomas Marques-Bonet “Ancient admixture from an extinct ape lineage into bonobos”. Nature ecology & evolution, 2019 10.1038_s41559-019-0881-7

Sojung Han, Aida M. Andrés, Tomas Marques-Bonet+ and Martin Kuhlwilm+   “Genetic variation in Pan species is shaped by demographic history and harbors lineage-specific functions” Genome Biology and Evolution 2019, evz047, https://doi.org/10.1093/gbe/evz047  07 March 2019

Marques-Bonet and Hvilsom. “Genomic variation of the great apes and the application to conservation” International Zoo Yearbook 2018.

J Hernandez-Rodriguez, M Arandjelovic, J Lester, C de Filippo, A Weihmann, M Meyer, S Angedakin, F Casals, A Navarro, L Vigilant, HS Kühl, K Langergraber, C Boesch, D Hughes and T Marques-Bonet “The impact of endogenous content, replicates and pooling on genome capture from fecal samples” Molecular Ecology Resources, 2018 10:46AM EST | DOI: 10.1111/1755-0998.12728

Manuel Solis-Moruno, Marc de Manuel , Jessica Hernandez-Rodriguez , Claudia Fontsere , Alba Gomara-Castaño , Cristina Valsera-Naranjo , Dietmar Crailsheim , Arcadi Navarro , Miquel Llorente , Laura Riera , Olga Feliu-Olleta , Tomas Marques-Bonet.“Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation” Scientific Reports, 2017

Lukas F. K. Kuderna; Chad Tomlinson; LaDeana W. Hillier; Annabel Tran; Ian Fiddes; Joel Armstrong; Hafid Laayouni; David Gordon; John Huddleston; Raquel Garcia Perez; Inna Povolotskaya; Aitor Serres Armero; Jèssica Gómez Garrido; Daniel Ho; Paolo Ribeca; Tyler Alioto; Richard E. Green; Benedict Paten; Arcadi Navarro; Jaume Betranpetit; Javier Herrero; Evan E. Eichler; Andrew J. Sharp; Lars Feuk; Wesley C. Warren; Tomas Marques-Bonet. “A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan_tro_3.0)” GigaScience 2017

Aitor Serres-Armero, Inna S Povolotskaya, Javier Quilez, Oscar Ramirez, Gabriel Santpere, Lukas FK Kuderna, Jessica Hernandez-Rodriguez, Marcos Fernandez-Callejo, Daniel Gomez-Sanchez, Adam H Freedman, Zhenxin Fan, John Novembre, Arcadi Navarro, Adam Boyko, Robert Wayne, Carles Vilà, Belen Lorente-Galdos, Tomas Marques-Bonet. “Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing“ BMC genomics 2017 18 (1), 977

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 354 (6311), 477-481

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.

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   8 (6), 2020-2030.

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

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

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.

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.” Scientific Reports 2014 Apr 24;4:4666. doi: 10.1038/srep04666.

Irene Hernando-Herraez, Javier Prado-Martinez, Paras Garg, Marcos Fernandez-Callejo, Holger Heyn, Christina Hvilsom, Arcadi Navarro, Manel Esteller, Andrew J. Sharp, Tomas Marques-Bonet “Dynamics 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..

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.

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]

Other publications:

2023

​KL Moon, HJ Huson, K Morrill, MS Wang, X Li, K Srikanth, … (including Tomas Marques-Bonet, Zoonomia Consortium)“Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs” Science 380 (6643), eabn5887 1 2023

AP Wilder, MA Supple, A Subramanian, A Mudide, R Swofford, … (including Tomas Marques-Bonet, Zoonomia Consortium) “The contribution of historical processes to contemporary extinction risk in placental mammals” Science 380 (6643), eabn5856 2 2023

JR Xue, A Mackay-Smith, K Mouri, MF Garcia, MX Dong, JF Akers, … (including Tomas Marques-Bonet, Zoonomia Consortium) “The functional and evolutionary impacts of human-specific deletions in conserved elements” Science 380 (6643), eabn2253 3 2023

AB Osmanski, NS Paulat, J Korstian, JR Grimshaw, M Halsey, … (including Tomas Marques-Bonet, Zoonomia Consortium) “Insights into mammalian TE diversity through the curation of 248 genome assemblies” Science 380 (6643), eabn1430 2 2023

PF Sullivan, JRS Meadows, S Gazal, BDN Phan, X Li, DP Genereux, … (including Tomas Marques-Bonet, Zoonomia Consortium) “Leveraging base-pair mammalian constraint to understand genetic variation and human disease” Science 380 (6643), eabn2937 7 2023

NM Foley, VC Mason, AJ Harris, KR Bredemeyer, J Damas, HA Lewin, …  (including Tomas Marques-Bonet, Zoonomia Consortium) “A genomic timescale for placental mammal evolution” Science 380 (6643), eabl8189 7 2023

BM Kirilenko, C Munegowda, E Osipova, D Jebb, V Sharma, M Blumer, …  (including Tomas Marques-Bonet, Zoonomia Consortium) “Integrating gene annotation with orthology inference at scale” Science 380 (6643), eabn3107 7 2023

KC Keough, S Whalen, F Inoue, PF Przytycki, T Fair, C Deng, M Steyert, …  (including Tomas Marques-Bonet, Zoonomia Consortium) “Three-dimensional genome rewiring in loci with human accelerated regions” Science 380 (6643), eabm1696 3 2023

G Andrews, K Fan, HE Pratt, N Phalke, … (including Tomas Marques-Bonet, Zoonomia Consortium) “Mammalian evolution of human cis-regulatory elements and transcription factor binding sites” Science 380 (6643), eabn7930 2 2023

IM Kaplow, AJ Lawler, DE Schäffer, C Srinivasan, HH Sestili, ME Wirthlin, …(including Tomas Marques-Bonet, Zoonomia Consortium) “Relating enhancer genetic variation across mammals to complex phenotypes using machine learning” Science 380 (6643), eabm7993 3 2023

MJ Christmas, IM Kaplow, DP Genereux, MX Dong, GM Hughes, X Li, … (including Tomas Marques-Bonet, Zoonomia Consortium) “Evolutionary constraint and innovation  across hundreds of placental mammals” Science 380 (6643), eabn3943

K Theissinger, C Fernandes, G Formenti, I Bista, PR Berg, C Bleidorn, …  (including Tomas Marques-Bonet) “How genomics can help biodiversity conservation” Trends in Genetics 2 2023

BP Bentley, T Carrasco-Valenzuela, EKS Ramos, H Pawar, … (including Tomas Marques-Bonet, H Pawar) “Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories” Proceedings of the National Academy of Sciences 120 (7), e2201076120

F Murat, N Mbengue, SB Winge, T Trefzer, E Leushkin, M Sepp, … (including Tomas Marques-Bonet) “The molecular evolution of spermatogenesis across mammals” Nature 613 (7943), 308-316 9 2023

2022

Shyam Gopalakrishnan, S Sunna Ebenesersdóttir, Inge KC Lundstrøm, Gordon Turner-Walker, Kristjan HS Moore, Pierre Luisi, Ashot Margaryan, Michael D Martin, Martin Rene Ellegaard, Ásgeir Sigurðsson, Steinunn Snorradóttir, Droplaug N Magnúsdóttir, Jason E Laffoon, Lucy van Dorp, Xiaodong Liu, Ida Moltke, María C Ávila-Arcos, Joshua G Schraiber, Simon Rasmussen, David Juan, Pere Gelabert, Toni de-Dios, Anna K Fotakis, Miren Iraeta-Orbegozo, Åshild J Vågene, Sean Dexter Denham, Axel Christophersen, Hans K Stenøien, Filipe G Vieira, Shanlin Liu, Torsten Günther, Toomas Kivisild, Ole Georg Moseng, Birgitte Skar, Christina Cheung, Marcela Sandoval-Velasco, Nathan Wales, Hannes Schroeder, Paula F Campos, Valdís B Guðmundsdóttir, Thomas Sicheritz-Ponten, Bent Petersen, Jostein Halgunset, Edmund Gilbert, Gianpiero L Cavalleri, Eivind Hovig, Ingrid Kockum, Tomas Olsson, Lars Alfredsson, Thomas F Hansen, Thomas Werge, Eske Willerslev, Francois Balloux, Tomas Marques-Bonet, Carles Lalueza-Fox, Rasmus Nielsen, Kári Stefánsson, Agnar Helgason, M Thomas P Gilbert “The population genomic legacy of the second plague pandemic”  Current Biology 2022.

I Ruiz‐Gartzia, E Lizano, T Marques‐Bonet, JL Kelley “Recovering the genomes hidden in museum wet collections” Molecular Ecology Resources. 2022 May 16. doi: 10.1111/1755-0998.13631.

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. “205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates” Molecular Ecology 2022 May 31. doi: 10.1111/mec.16554. 

Irene Lobon, Manuel Solís-Moruno, David Juan, Ashraf Muhaisen, Federico Abascal, Paula Esteller-Cucala, Raquel García-Pérez, Maria Josep Martí, Eduardo Tolosa, Jesús Ávila, Raheleh Rahbari, Tomas Marques-Bonet,, Ferran Casals, Eduardo Soriano “Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes” Frontiers in Aging 2022

Breuss MW, Yang X, Schlachetzki JCM, Antaki D, Lana AJ, Xu X, Chung C, Chai G, Stanley V, Song Q, Newmeyer TF, Nguyen A, O’Brien S, Hoeksema MA, Cao B, Nott A, McEvoy-Venneri J, Pasillas MP, Barton ST, Copeland BR, Nahas S, Van Der Kraan L, Ding Y; NIMH Brain Somatic Mosaicism Network, Glass CK, Gleeson JG. “Somatic mosaicism reveals clonal distributions of neocortical development.” Nature. 2022 Apr;604(7907):689-696. doi: 10.1038/s41586-022-04602-7. Epub 2022 Apr 20.

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. “Initiation of the Primate Genome Project” Zool Res. 2022 Mar 18;43(2):147-149. doi: 10.24272/j.issn.2095-8137.2022.001.

Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JH, Kress WJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazzoni CJ, Myers EW, O’Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G. “The Earth BioGenome Project 2020: Starting the clock”  Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115635118. doi: 10.1073/pnas.2115635118.

Lawniczak MKN, Durbin R, Flicek P, Lindblad-Toh K, Wei X, Archibald JM, Baker WJ, Belov K, Blaxter ML, Marques Bonet T, Childers AK, Coddington JA, Crandall KA, Crawford AJ, Davey RP, Di Palma F, Fang Q, Haerty W, Hall N, Hoff KJ, Howe K, Jarvis ED, Johnson WE, Johnson RN, Kersey PJ, Liu X, Lopez JV, Myers EW, Pettersson OV, Phillippy AM, Poelchau MF, Pruitt KD, Rhie A, Castilla-Rubio JC, Sahu SK, Salmon NA, Soltis PS, Swarbreck D, Thibaud-Nissen F, Wang S, Wegrzyn JL, Zhang G, Zhang H, Lewin HA, Richards S. “Standards recommendations for the Earth BioGenome Project” Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115639118. doi: 10.1073/pnas.2115639118.

Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M; European Reference Genome Atlas (ERGA) Consortium. “The era of reference genomes in conservation genomics”  Trends Ecol Evol. 2022 Mar;37(3):197-202. doi: 10.1016/j.tree.2021.11.008. Epub 2022 Jan 24.

2021

Boubli JP, Janiak MC, Porter LM, de la Torre S, Cortés-Ortiz L, Da Silva MNF, Rylands AB, Nash S, Bertuol F, Byrne H, Silva FE, Rohe F, de Vries D, Beck RMD, Ruiz-Gartzia I, Kuderna LFK, Marques-Bonet T, Hrbek T, Farias IP, Van Heteren AH, Roos C. “Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum” Zool Res. 2021 Nov 18;42(6):761-771. doi: 10.24272/j.issn.2095-8137.2021.143.

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. “Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives” Biol Lett. 2021 Dec;17(12):20210533. doi: 10.1098/rsbl.2021.0533. Epub 2021 Dec 22.

Kuhlwilm M, Fontsere C, Han S, Alvarez-Estape M, Marques-Bonet T. “HuConTest: Testing human contamination in great ape samples” Genome Biol Evol. 2021 Jun 8;13(6):evab117. doi: 10.1093/gbe/evab117.

Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F 3rd, 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. “Variation in predicted COVID-19 risk among lemurs and lorises.” Am J Primatol. 2021 Jun;83(6):e23255. doi: 10.1002/ajp.23255. Epub 2021 Apr 1.

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. “Towards complete and error-free genome assemblies of all vertebrate species.”  Nature. 2021 Apr;592(7856):737-746. doi: 10.1038/s41586-021-03451-0. Epub 2021 Apr 28.

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. “The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS” Proc Natl Acad Sci U S A. 2021 Feb 16;118(7):e2010632118. doi: 10.1073/pnas.2010632118.

Zhu X, Zhou B, Pattni R, Gleason K, Tan C, Kalinowski A, Sloan S, Fiston-Lavier AS, Mariani J, Petrov D, Barres BA, Duncan L, Abyzov A, Vogel H; Brain Somatic Mosaicism Network, Moran JV, Vaccarino FM, Tamminga CA, Levinson DF, Urban AE. “Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia” Nat Neurosci. 2021 Feb;24(2):186-196. doi: 10.1038/s41593-020-00767-4. Epub 2021 Jan 11.

Rodin RE, Dou Y, Kwon M, Sherman MA, D’Gama AM, Doan RN, Rento LM, Girskis KM, Bohrson CL, Kim SN, Nadig A, Luquette LJ, Gulhan DC; Brain Somatic Mosaicism Network, Park PJ, Walsh CA “The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing.” Nat Neurosci. 2021 Feb;24(2):176-185. doi: 10.1038/s41593-020-00765-6. Epub 2021 Jan 11.

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. “Comprehensive identification of somatic nucleotide variants in human brain tissue” Genome Biol. 2021 Mar 29;22(1):92. doi: 10.1186/s13059-021-02285-3.

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. “Ancient and modern genomes unravel the evolutionary history of the rhinoceros family”  Cell. 2021 Sep 16;184(19):4874-4885.e16. doi: 10.1016/j.cell.2021.07.032. Epub 2021 Aug 24.

Michael Westbury; Ross Barnett; Marcela Sandoval-Velasco; Graham Gower; Filipe Garrett Vieira; Marc de Manuel; Anders J Hansen; Nobuyuki Yamaguchi; Lars Werdelin; Tomas Marques-Bonet; M Thomas P Gilbert; Eline D Lorenzen “A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives”  Open Research Europe 2021

Solís-Moruno M, Mensa-Vilaró A, Batlle-Masó L, Lobón I, Bonet N, Marquès-Bonet T, Aróstegui JI, Casals F. “Assessment of the gene mosaicism burden in blood and its implications for immune disorders” Sci Rep. 2021 Jun 21;11(1):12940. doi: 10.1038/s41598-021-92381-y.

de-Dios T, Carrión P, Olalde I, Llovera Nadal L, Lizano E, Pàmies D, Marques-Bonet T, Balloux F, van Dorp L, Lalueza-Fox C. “Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts” iScience. 2021 Aug 24;24(9):103021. doi: 10.1016/j.isci.2021.103021. eCollection 2021 Sep 24.

2020

Zoonomia Consortium. “A comparative genomics multitool for scientific discovery and conservation” Nature. 2020 Nov;587(7833):240-245. doi: 10.1038/s41586-020-2876-6. Epub 2020 Nov 11.

Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium. “Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.” Nat Commun. 2020 Sep 21;11(1):4748. doi: 10.1038/s41467-020-18151-y.

Khan N, de Manuel M, Peyregne S, Do R, Prufer K, Marques-Bonet T, Varki N, Gagneux P, Varki A. “Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins.” Genome Biol Evol. 2020 Jun 18:evaa125. doi: 10.1093/gbe/evaa125. Online ahead of print.

Heredia-Genestar JM, Marques-Bonet T, Juan D, Navarro A. “Extreme differences between human germline and tumor mutation densities are driven by ancestral human-specific deviations.” Nat Commun. 2020 May 19;11(1):2512. doi: 10.1038/s41467-020-16296-4.

Dehasque M, Ávila-Arcos MC, Díez-Del-Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas AS, Marques-Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. “Inference of natural selection from ancient DNA.” Evol Lett. 2020 Mar 18;4(2):94-108. doi: 10.1002/evl3.165. eCollection 2020 Apr.

Frido Welker, Jazmín Ramos-Madrigal, Petra Gutenbrunner, Meaghan Mackie, Shivani Tiwary, Rosa Rakownikow Jersie-Christensen, Cristina Chiva, Marc R Dickinson, Martin Kuhlwilm, Marc de Manuel, Pere Gelabert, María Martinón-Torres, Ann Margvelashvili, Juan Luis Arsuaga, Eudald Carbonell, Tomas Marques-Bonet, Kirsty Penkman, Eduard Sabidó, Jürgen Cox, Jesper V Olsen, David Lordkipanidze, Fernando Racimo, Carles Lalueza-Fox, José María Bermúdez de Castro, Eske Willerslev, Enrico Cappellini “The dental proteome of Homo antecessor”  Nature 580 (7802), 235-238

Marianne Dehasque, María C Ávila‐Arcos, David Díez‐del‐Molino, Matteo Fumagalli, Katerina Guschanski, Eline D Lorenzen, Anna‐Sapfo Malaspinas, Tomas Marques‐Bonet, Michael D Martin, Gemma GR Murray, Alexander ST Papadopulos, Nina Overgaard Therkildsen, Daniel Wegmann, Love Dalén, Andrew D Foote “Inference of natural selection from ancient DNA”  Evolution Letters 2020

Laura Batlle-Masó, Anna Mensa-Vilaró, Manuel Solís-Moruno, Tomas Marques-Bonet, Juan I Arostegui, Ferran Casals “Genetic diagnosis of autoinflammatory disease patients using clinical exome sequencing”  European Journal of Medical Genetics 2020, 103920

Toni de-Dios, Lucy van Dorp, Philippe Charlier, Sofia Morfopoulou, Esther Lizano, Celine Bon, Corinne Le Bitouzé, Marina Alvarez-Estape, Tomas Marques-Bonet, François Balloux, Carles Lalueza-Fox “Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743–1793)”  Infection, Genetics and Evolution 2020 80, 104209

David Gokhman, Malka Nissim-Rafinia, Lily Agranat-Tamir, Genevieve Housman, Raquel García-Pérez, Esther Lizano, Olivia Cheronet, Swapan Mallick, Maria A Nieves-Colón, Heng Li, Songül Alpaslan-Roodenberg, Mario Novak, Hongcang Gu, Jason M Osinski, Manuel Ferrando-Bernal, Pere Gelabert, Iddi Lipende, Deus Mjungu, Ivanela Kondova, Ronald Bontrop, Ottmar Kullmer, Gerhard Weber, Tal Shahar, Mona Dvir-Ginzberg, Marina Faerman, Ellen E Quillen, Alexander Meissner, Yonatan Lahav, Leonid Kandel, Meir Liebergall, María E Prada, Julio M Vidal, Richard M Gronostajski, Anne C Stone, Benjamin Yakir, Carles Lalueza-Fox, Ron Pinhasi, David Reich, Tomas Marques-Bonet, Eran Meshorer, Liran Carmel “Differential DNA methylation of vocal and facial anatomy genes in modern humans” Nature Communications 2020 11 (1), 1-21

Lauren E Blake, Julien Roux, Irene Hernando-Herraez, Nicholas E Banovich, Raquel Garcia Perez, Chiaowen Joyce Hsiao, Ittai Eres, Claudia Cuevas, Tomas Marques-Bonet, Yoav Gilad “A comparison of gene expression and DNA methylation patterns across tissues and species”  Genome Research 2020 30 (2), 250-262

Lukas FK Kuderna, Manuel Solís-Moruno, Laura Batlle-Masó, Eva Julià, Esther Lizano, Roger Anglada, Erika Ramírez, Alex Bote, Marc Tormo, Tomàs Marquès-Bonet, Òscar Fornas, Ferran Casals “Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual” Frontiers in genetics 2020 10, 1315

Pere Gelabert, Marcela Sandoval-Velasco, Aitor Serres, Marc de Manuel, Pere Renom, Ashot Margaryan, Josefin Stiller, Toni de-Dios, Qi Fang, Shaohong Feng, Santi Mañosa, George Pacheco, Manuel Ferrando-Bernal, Guolin Shi, Fei Hao, Xianqing Chen, Bent Petersen, Remi-André Olsen, Arcadi Navarro, Yuan Deng, Love Dalén, Tomàs Marquès-Bonet, Guojie Zhang, Agostinho Antunes, M Thomas P Gilbert, Carles Lalueza-Fox “Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet” Current Biology 2020 30 (1), 108-114. e5

TCGA Pan-Cancer Analysis of Whole Genomes Consortium “Pan-cancer analysis of whole genomes” Nature 2020 578 (7793), 82

2019

Pere Gelabert, Marcela Sandoval-Velasco, Aitor Serres, Marc de Manuel, Pere Renom, Ashot Margaryan, Josefin Stiller, Toni de-Dios, Qi Fang, Shaohong Feng, Santi Mañosa, George Pacheco, Manuel Ferrando-Bernal, Guolin Shi, Fei Hao, Xianqing Chen, Bent Petersen, Remi-André Olsen, Arcadi Navarro, Yuan Deng, Love Dalén, Tomàs Marquès-Bonet, Guojie Zhang, Agostinho Antunes, M Thomas P Gilbert, Carles Lalueza-Fox “Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet” Current Biology 30 (1), 108-114. e5

Am M, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, Mj O. “Gene Fusions derived by transcriptional readthrough are Driven by Segmental Duplication in Human.” Genome Biol Evol. 2019 Aug 10. pii: evz163. doi: 10.1093/gbe/evz163. [Epub ahead of print]

Antoine Fages, Kristian Hanghøj, Naveed Khan, Charleen Gaunitz, Andaine Seguin-Orlando, Michela Leonardi, Christian McCrory Constantz, Cristina Gamba, Khaled AS Al-Rasheid, Silvia Albizuri, Ahmed H Alfarhan, Morten Allentoft, Saleh Alquraishi, David Anthony, Nurbol Baimukhanov, James H Barrett, Jamsranjav Bayarsaikhan, Norbert Benecke, Eloísa Bernáldez-Sánchez, Luis Berrocal-Rangel, Fereidoun Biglari, Sanne Boessenkool, Bazartseren Boldgiv, Gottfried Brem, Dorcas Brown, Joachim Burger, Eric Crubézy, Linas Daugnora, Hossein Davoudi, Peter de Barros Damgaard, María de los Ángeles de Chorro, Sabine Deschler-Erb, Cleia Detry, Nadine Dill, Maria do Mar Oom, Anna Dohr, Sturla Ellingvåg, Diimaajav Erdenebaatar, Homa Fathi, Sabine Felkel, Carlos Fernández-Rodríguez, Esteban García-Viñas, Mietje Germonpré, José D Granado, Jón H Hallsson, Helmut Hemmer, Michael Hofreiter, Aleksei Kasparov, Mutalib Khasanov, Roya Khazaeli, Pavel Kosintsev, Kristian Kristiansen, Tabaldiev Kubatbek, Lukas Kuderna, Pavel Kuznetsov, Haeedeh Laleh, Jennifer A Leonard, Johanna Lhuillier, Corina Liesau von Lettow-Vorbeck, Andrey Logvin, Lembi Lõugas, Arne Ludwig, Cristina Luis, Ana Margarida Arruda, Tomas Marques-Bonet, Raquel Matoso Silva, Victor Merz, Enkhbayar Mijiddorj, Bryan K Miller, Oleg Mochlov, Fatemeh A Mohaseb, Arturo Morales, Ariadna Nieto-Espinet, Heidi Nistelberger, Vedat Onar, Albína H Pálsdóttir, Vladimir Pitulko, Konstantin Pitskhelauri, Mélanie Pruvost, Petra Rajic Sikanjic, Anita Rapan Papeša, Natalia Roslyakova, Alireza Sardari, Eberhard Sauer, Renate Schafberg, Amelie Scheu, Jörg Schibler, Angela Schlumbaum, Nathalie Serrand, Aitor Serres-Armero, Beth Shapiro, Shiva Sheikhi Seno, Irina Shevnina, Sonia Shidrang, John Southon, Bastiaan Star, Naomi Sykes, Kamal Taheri, William Taylor, Wolf-Rüdiger Teegen, Tajana Trbojević Vukičević, Simon Trixl, Dashzeveg Tumen, Sainbileg Undrakhbold, Emma Usmanova, Ali Vahdati, Silvia Valenzuela-Lamas, Catarina Viegas, Barbara Wallner, Jaco Weinstock, Victor Zaibert, Benoit Clavel, Sébastien Lepetz, Marjan Mashkour, Agnar Helgason, Kári Stefánsson, Eric Barrey, Eske Willerslev, Alan K Outram, Pablo Librado, Ludovic Orlando “Tracking five millennia of horse management with extensive ancient genome time series” Cell 2019 ay 30;177(6):1419-1435.e31. doi: 10.1016/j.cell.2019.03.049. Epub 2019 May 2.

Marc Tollis, Jooke Robbins, Andrew E Webb, Lukas FK Kuderna, Aleah F Caulin, Jacinda D Garcia, Martine Bèrubè, Nader Pourmand, Tomas Marques-Bonet, Mary J O’Connell, Per J Palsbøll, Carlo C Maley “Return to the sea, get huge, beat cancer: an analysis of cetacean genomes including an assembly for the humpback whale (Megaptera novaeangliae)” Molecular biology and evolution 2019

Belen Lorente-Galdos; Oscar Lao; Gerard Serra-Vidal; Gabriel Santpere; Lukas FK Kuderna; Lara R Arauna; Karima Fadhlaoui-Zid; Ville N Pimenoff; Himla Soodyall; Pierre Zalloua; Tomas Marques-Bonet; David Comas “Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations” Genome Biology 2019

Jeffrey Rogers, Muthuswamy Raveendran, R Alan Harris, Thomas Mailund, Kalle Leppälä, Georgios Athanasiadis, Mikkel Heide Schierup, Jade Cheng, Kasper Munch, Jerilyn A Walker, Miriam K Konkel, Vallmer Jordan, Cody J Steely, Thomas O Beckstrom, Christina Bergey, Andrew Burrell, Dominik Schrempf, Angela Noll, Maximillian Kothe, Gisela H Kopp, Yue Liu, Shwetha Murali, Konstantinos Billis, Fergal J Martin, Matthieu Muffato, Laura Cox, James Else, Todd Disotell, Donna M Muzny, Jane Phillips-Conroy, Bronwen Aken, Evan E Eichler, Tomas Marques-Bonet, Carolin Kosiol, Mark A Batzer, Matthew W Hahn, Jenny Tung, Dietmar Zinner, Christian Roos, Clifford J Jolly, Richard A Gibbs, Kim C Worley, Baboon Genome Analysis Consortium “The comparative genomics and complex population history of Papio baboons” Science Advances 2019 5 (1), eaau6947

Lauren C White, Claudia Fontsere, Esther Lizano, David A Hughes, Samuel Angedakin, Mimi Arandjelovic, Anne‐Céline Granjon, Jörg B Hans, Jack D Lester, M Timothy Rabanus‐Wallace, Carolyn Rowney, Veronika Städele, Tomas Marques‐Bonet, Kevin E Langergraber, Linda Vigilant “A roadmap for high‐throughput sequencing studies of wild animal populations using non‐invasive samples and hybridization capture” Molecular ecology resources 2019

Tom van der Valk, David Díez-del-Molino, Tomas Marques-Bonet, Katerina Guschanski, Love Dalén “Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas” Current Biology 2019 29 (1) 165-170. e6

Víctor Quesada, Sandra Freitas-Rodríguez, Joshua Miller, José Pérez-Silva, Zi-Feng Jiang, Washington Tapia, Olaya Santiago-Fernández, Diana Campos-Iglesias, Lukas Kuderna, Maud Quinzin, Miguel Álvarez, Dido Carrero, Luciano Beheregaray, James Gibbs, Ylenia Chiari, Scott Glaberman, Claudio Ciofi, Miguel Araujo-Voces, Pablo Mayoral, Javier Arango, Isaac Tamargo-Gómez, David Roiz-Valle, Maria Pascual-Torner, Benjamin Evans, Danielle Edwards, Ryan Garrick, Michael Russello, Nikos Poulakakis, Stephen Gaughran, Danny Rueda, Gabriel Bretones, Tomas Marques-Bonet, Kevin White, Adalgisa Caccone, and Carlos Lopez-Otin. “Giant tortoise genomes provide insights into longevity and age-related disease”  Nat Ecol Evol. 2019 Jan;3(1):87-95. doi: 10.1038/s41559-018-0733-x. Epub 2018 Dec 3.

Shaohong Feng, Qi Fang, Ross Barnett, Cai Li, Sojung Han, Martin Kuhlwilm, Long Zhou, Hailin Pan, Yuan Deng, Guangji Chen, Anita Gamauf, Friederike Woog, Robert Prys-Jones, Tomas Marques-Bonet, M Thomas P Gilbert, Guojie Zhang. “The Genomic Footprints of the Fall and Recovery of the Crested Ibis” Current Biology 2019  29 (2), 340-349. e7

2018

van der Valk T, Díez-Del-Molino D, Marques-Bonet T, Guschanski K, Dalén L. “Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas.”  Curr Biol. 2018 Dec 18. pii: S0960-9822(18)31554-9. doi: 10.1016/j.cub.2018.11.055.

Ying Zhu, André MM Sousa, Tianliuyun Gao, Mario Skarica, Mingfeng Li, Gabriel Santpere, Paula Esteller-Cucala, David Juan, Luis Ferrández-Peral, Forrest O Gulden, Mo Yang, Daniel J Miller, Tomas Marques-Bonet, Yuka Imamura Kawasawa, Hongyu Zhao, Nenad Sestan “Spatiotemporal transcriptomic divergence across human and macaque brain development” Science 2018, 362:6420.

Shyam Gopalakrishnan, Mikkel-Holger S. Sinding, Jazmín Ramos-Madrigal, Jonas Niemann, Jose A. Samaniego Castruita, Filipe G. Vieira, Christian Carøe, Marc de Manuel Montero, Lukas Kuderna, Aitor Serres, Víctor Manuel González-Basallote, Yan-Hu Liu, Guo-Dong Wang, Tomas Marques-Bonet, Siavash Mirarab, Carlos Fernandes, Philippe Gaubert, Klaus-Peter Koepfli, Jane Budd, Eli Knispel Rueness, Mads Peter Heide-Jørgensen, Bent Petersen, Thomas Sicheritz-Ponten, Lutz Bachmann, Øystein Wiig, Anders J. Hansen, M. Thomas P. Gilbert “Interspecific Gene Flow Shaped the Evolution of the Genus Canis” Current Biology 2018

Maja P. Mattle-Greminger, Tugce Bilgin Sonay, Alexander Nater, Marc Pybus, Tariq Desai, Guillem de Valles, Ferran Casals, Aylwyn Scally, Jaume Bertranpetit, Tomas Marques-Bonet, Carel P. van Schaik, Maria Anisimova, and Michael Krützen. “Genomes reveal marked differences in the adaptive evolution between orangutan species” Genome Biology 2018

D Gómez‐Sánchez, I Olalde, N Sastre, C Enseñat, R Carrasco, T Marques‐Bonet, C Lalueza‐Fox, JA Leonard, C Vilà, O Ramírez “On the path to extinction: inbreeding and admixture in a declining gray wolf population” Molecular ecology 2018

Marc de Manuel, Takashi Shiina, Shingo Suzuki, Nathalie Dereuddre-Bosquet, Henri-Jean Garchon, Masayuki Tanaka, Nicolas Congy-Jolivet, Alice Aarnink, Roger Le Grand, Tomas Marques-Bonet, Antoine Blancher “Whole genome sequencing in the search for genes associated with the control of SIV infection in the Mauritian macaque model“ Scientific Reports 2018

Jessica Nye, Hafid Laayouni, Martin Kuhlwilm, Mayukh Mondal, Tomas Marques-Bonet, Jaume Bertranpetit “Selection in the Introgressed Regions of the Chimpanzee Genome” Genome biology and evolution 10 (4), 1132-1138

Guillem de Valles-Ibáñez,   Ana Esteve-Sole, Mònica Piquer,   Azucena González-Navarro,   Jessica Hernández-Rodríguez, Hafid Laayouni, Eva González-Roca, Ana María Plaza-Martín, Angela Deyà-Martínez,   Andrea Martín-Nalda,   Mònica Martínez-Gallo,  Marina García-Prat,   Lucía del Pino, Ivon Cuscó, Marta Codina-Solà, Tomàs Marquès-Bonet, Elena Bosch,   Eduardo Lopez-Granados, Juan Ignacio Aróstegui, Pere Soler-Palacín,   Roger Colobrán4   Jordi Yague, Laia Alsina, Manel Juan and   Ferran Casals. “Evaluating the genetics of common variable immunodeficiency: monogenetic model and beyond” Front. Immunol. (2018)| doi: 10.3389/fimmu.2018.00636

Wesley C. Warren, Raquel García-Pérez, Sen Xu, Kathrin P. Lampert, Domitille Chalopin, Matthias Stöck, Laurence Loewe, Yuan Lu, Lukas Kuderna, Patrick Minx, Michael J. Montague, Chad Tomlinson, LaDeana W. Hillier, Daniel N. Murphy, John Wang, Zhongwei Wang, Constantino Macias Garcia, Gregg C. W. Thomas, Jean-Nicolas Volff, Fabiana Farias, Bronwen Aken, Ronald B. Walter, Kim D. Pruitt, Tomas Marques-Bonet, Matthew W. Hahn, Susanne Kneitz, Michael Lynch & Manfred Schartl “Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly” Nature Ecology & Evolution (2018) doi:10.1038/s41559-018-0473-y

2017

André MM Sousa, Ying Zhu, Mary Ann Raghanti, Robert R Kitchen, Marco Onorati, Andrew TN Tebbenkamp, Bernardo Stutz, Kyle A Meyer, Mingfeng Li, Yuka Imamura Kawasawa, Fuchen Liu, Raquel Garcia Perez, Marta Mele, Tiago Carvalho, Mario Skarica, Forrest O Gulden, Mihovil Pletikos, Akemi Shibata, Alexa R Stephenson, Melissa K Edler, John J Ely, John D Elsworth, Tamas L Horvath, Patrick R Hof, Thomas M Hyde, Joel E Kleinman, Daniel R Weinberger, Mark Reimers, Richard P Lifton, Shrikant M Mane, James P Noonan, Ed S Lein, James A Knowles, Tomas Marques-Bonet, Chet C Sherwood, Mark B Gerstein, Nenad Sestan “Molecular and cellular reorganization of neural circuits in the human lineage”  Science 358 (6366), 1027-1032

V Maibach, JB Hans, C Hvilsom, T Marques-Bonet, L Vigilant “MHC class I diversity in chimpanzees and bonobos“ Immunogenetics 69 (10), 661-676

Zeli Zhang, Qinyong Gu, Marc de Manuel Montero, Ignacio G Bravo, Tomas Marques-Bonet, Dieter Häussinger, Carsten Münk “Stably expressed APOBEC3H forms a barrier for cross-species transmission of simian immunodeficiency virus of chimpanzee to humans” PLoS pathogens 13 (12), e1006746

Nicky Staes, Chet C Sherwood, Katharine Wright, Marc Manuel, Elaine E Guevara, Tomas Marques-Bonet, Michael Krützen, Michael Massiah, William D Hopkins, John J Ely, Brenda J Bradley “FOXP2 variation in great ape populations offers insight into the evolution of communication skills” Scientific reports 7 (1), 16866

Alexander Nater, Maja P Mattle-Greminger, Anton Nurcahyo, Matthew G Nowak, Marc de Manuel, Tariq Desai, Colin Groves, Marc Pybus, Tugce Bilgin Sonay, Christian Roos, Adriano R Lameira, Serge A Wich, James Askew, Marina Davila-Ross, Gabriella Fredriksson, Guillem de Valles, Ferran Casals, Javier Prado-Martinez, Benoit Goossens, Ernst J Verschoor, Kristin S Warren, Ian Singleton, David A Marques, Joko Pamungkas, Dyah Perwitasari-Farajallah, Puji Rianti, Augustine Tuuga, Ivo G Gut, Marta Gut, Pablo Orozco-terWengel, Carel P Van Schaik, Jaume Bertranpetit, Maria Anisimova, Aylwyn Scally, Tomas Marques-Bonet, Erik Meijaard, Michael Krützen. “Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species” Current Biology 2017

Wesley C Warren, Lukas Kuderna, Alana Alexander, Julian Catchen, José G Pérez-Silva, Carlos López-Otín, Víctor Quesada, Patrick Minx, Chad Tomlinson, Michael J Montague, Fabiana HG Farias, Ronald B Walter, Tomas Marques-Bonet, Travis Glenn, Troy J Kieran, Sandra S Wise, John Pierce Wise Jr, Robert M Waterhouse, John Pierce Wise Sr  “The novel evolution of the sperm whale genome“ Genome Biology and Evolution, 2017 evx187

Sullivan AP, de Manuel M, Marques-Bonet T, Perry GH. “An evolutionary medicine perspective on Neandertal extinction.” J Hum Evol. 2017 Jul;108:62-71. doi: 10.1016/j.jhevol.2017.03.004. Epub 2017 May 16.

Shyam Gopalakrishnan; Jose Samaniego Castruita; Mikkel-Holger Sinding; Lukas Kuderna; Jannikke Räikkönen; Bent Petersen; Thomas SIcheritz-Ponten; Greger Larson; Ludovic Orlando; Tomas Marques-Bonet; Anders Hansen; Love Dalen; M Thomas Gilbert. “The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics” BMC Genomics 2017 18 (1), 495

Sarah Mak; Shyam Gopalakrishnan; Christian Carøe; Chunyu Geng; Shanlin Liu; Mikkel Sinding; Lukas Kuderna; Wenwei Zhang; Shujin Fu; Filipe Vieira; Mietje Germonpré; Hervé Bocherens; Sergej Fedorov; Bent Petersen; Thomas Sicheritz-Ponten; Tomas Marques-Bonet; Guojie Zhang; Hui Jiang; Marcus Thomas Pius Gilbert. “Comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing” GigaScience 2017  6 (8), 1-13

McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM; Brain Somatic Mosaicism Network (including Tomas Marques-Bonet). “Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.” Science. 2017 Apr 28;356(6336). pii: eaal1641. doi: 10.1126/science.aal1641. Epub 2017 Apr 27. Review

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 Apr 28;356(6336):442-445. doi: 10.1126/science.aam5298.

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/

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.

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.

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

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

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.

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 horses” Current 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 cultures” Mol. 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..

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, 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 J, Marques-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.

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.

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.

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

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 analyses“BMC 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 Ancestor” Nature. 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.

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