Publications by authors named "Tomas Marques-Bonet"

100Publications

Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.

Curr Biol 2020 Oct 9. Epub 2020 Oct 9.

Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2020.09.051DOI Listing
October 2020

Circular DNA intermediates in the generation of large human segmental duplications.

BMC Genomics 2020 Aug 26;21(1):593. Epub 2020 Aug 26.

Research Unit, Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43005, Tarragona, Spain.

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http://dx.doi.org/10.1186/s12864-020-06998-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7450558PMC
August 2020

Branching out: what omics can tell us about primate evolution.

Curr Opin Genet Dev 2020 Jun 4;62:65-71. Epub 2020 Jul 4.

Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2020.06.006DOI Listing
June 2020

Extreme differences between human germline and tumor mutation densities are driven by ancestral human-specific deviations.

Nat Commun 2020 05 19;11(1):2512. Epub 2020 May 19.

Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain.

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http://dx.doi.org/10.1038/s41467-020-16296-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237693PMC
May 2020

Genetic diagnosis of autoinflammatory disease patients using clinical exome sequencing.

Eur J Med Genet 2020 May 25;63(5):103920. Epub 2020 Mar 25.

Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.ejmg.2020.103920DOI Listing
May 2020

Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793).

Infect Genet Evol 2020 06 29;80:104209. Epub 2020 Jan 29.

Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain.

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http://dx.doi.org/10.1016/j.meegid.2020.104209DOI Listing
June 2020

Flow Sorting Enrichment and Nanopore Sequencing of Chromosome 1 From a Chinese Individual.

Front Genet 2019 9;10:1315. Epub 2020 Jan 9.

Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain.

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http://dx.doi.org/10.3389/fgene.2019.01315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962354PMC
January 2020

The impact of genetic adaptation on chimpanzee subspecies differentiation.

PLoS Genet 2019 11 25;15(11):e1008485. Epub 2019 Nov 25.

UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1008485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901233PMC
November 2019

Admixture in Mammals and How to Understand Its Functional Implications: On the Abundance of Gene Flow in Mammalian Species, Its Impact on the Genome, and Roads into a Functional Understanding.

Bioessays 2019 12 30;41(12):e1900123. Epub 2019 Oct 30.

Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, 08003, Barcelona, Spain.

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http://dx.doi.org/10.1002/bies.201900123DOI Listing
December 2019

Reconstructing Denisovan Anatomy Using DNA Methylation Maps.

Cell 2019 Sep;179(1):180-192.e10

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.08.035DOI Listing
September 2019

Author Correction: Ancient admixture from an extinct ape lineage into bonobos.

Nat Ecol Evol 2019 Jun;3(6):988

Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1038/s41559-019-0919-xDOI Listing
June 2019

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.

Authors:
Antoine Fages Kristian Hanghøj Naveed Khan Charleen Gaunitz Andaine Seguin-Orlando Michela Leonardi Christian McCrory Constantz Cristina Gamba Khaled A S 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 Y de Villa-Ceballos 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 Monchalov 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

Cell 2019 05 2;177(6):1419-1435.e31. Epub 2019 May 2.

Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.03.049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547883PMC
May 2019

Ancient admixture from an extinct ape lineage into bonobos.

Nat Ecol Evol 2019 06 29;3(6):957-965. Epub 2019 Apr 29.

Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.

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http://www.nature.com/articles/s41559-019-0881-7
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http://dx.doi.org/10.1038/s41559-019-0881-7DOI Listing
June 2019

Genetic Variation in Pan Species Is Shaped by Demographic History and Harbors Lineage-Specific Functions.

Genome Biol Evol 2019 04;11(4):1178-1191

Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra, Barcelona, Spain.

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http://dx.doi.org/10.1093/gbe/evz047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482415PMC
April 2019

Direct estimation of mutations in great apes reconciles phylogenetic dating.

Nat Ecol Evol 2019 02 21;3(2):286-292. Epub 2019 Jan 21.

Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1038/s41559-018-0778-xDOI Listing
February 2019

The Genomic Footprints of the Fall and Recovery of the Crested Ibis.

Curr Biol 2019 01 10;29(2):340-349.e7. Epub 2019 Jan 10.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2018.12.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345625PMC
January 2019

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas.

Curr Biol 2019 01 27;29(1):165-170.e6. Epub 2018 Dec 27.

Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2018.11.055DOI Listing
January 2019

On the path to extinction: Inbreeding and admixture in a declining grey wolf population.

Mol Ecol 2018 09 4;27(18):3599-3612. Epub 2018 Sep 4.

Ciencies Experimetals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC), Barcelona, Spain.

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http://dx.doi.org/10.1111/mec.14824DOI Listing
September 2018

Whole genome sequencing in the search for genes associated with the control of SIV infection in the Mauritian macaque model.

Sci Rep 2018 05 8;8(1):7131. Epub 2018 May 8.

Laboratoire d'immunogénétique moléculaire (LIMT, EA 3034, Faculté de médecine Purpan, Université Toulouse 3 (Université Paul Sabatier, UPS), Toulouse, France.

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http://dx.doi.org/10.1038/s41598-018-25071-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940699PMC
May 2018

Selection in the Introgressed Regions of the Chimpanzee Genome.

Genome Biol Evol 2018 04;10(4):1132-1138

Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.

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https://academic.oup.com/gbe/article/10/4/1132/4960011
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http://dx.doi.org/10.1093/gbe/evy077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905441PMC
April 2018

Stably expressed APOBEC3H forms a barrier for cross-species transmission of simian immunodeficiency virus of chimpanzee to humans.

PLoS Pathog 2017 12 21;13(12):e1006746. Epub 2017 Dec 21.

Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.

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http://dx.doi.org/10.1371/journal.ppat.1006746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739507PMC
December 2017

FOXP2 variation in great ape populations offers insight into the evolution of communication skills.

Sci Rep 2017 12 4;7(1):16866. Epub 2017 Dec 4.

Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, 800 22nd Street NW, Suite 6000, Washington, DC, 20052, USA.

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http://www.nature.com/articles/s41598-017-16844-x
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http://dx.doi.org/10.1038/s41598-017-16844-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5715162PMC
December 2017

Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation.

Sci Rep 2017 11 9;7(1):15224. Epub 2017 Nov 9.

Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1038/s41598-017-15544-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680330PMC
November 2017

MHC class I diversity in chimpanzees and bonobos.

Immunogenetics 2017 10 16;69(10):661-676. Epub 2017 Jun 16.

Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.

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http://dx.doi.org/10.1007/s00251-017-0990-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597694PMC
October 2017

An evolutionary medicine perspective on Neandertal extinction.

J Hum Evol 2017 07 16;108:62-71. Epub 2017 May 16.

Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jhevol.2017.03.004DOI Listing
July 2017

Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences.

Mol Biol Evol 2017 05;34(5):1217-1229

Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT.

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http://dx.doi.org/10.1093/molbev/msx076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400397PMC
May 2017

Evidence that the rate of strong selective sweeps increases with population size in the great apes.

Proc Natl Acad Sci U S A 2017 02 30;114(7):1613-1618. Epub 2017 Jan 30.

Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark;

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http://dx.doi.org/10.1073/pnas.1605660114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320968PMC
February 2017

Natural Selection in the Great Apes.

Mol Biol Evol 2016 12 30;33(12):3268-3283. Epub 2016 Oct 30.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

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http://dx.doi.org/10.1093/molbev/msw215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100057PMC
December 2016

Chimpanzee genomic diversity reveals ancient admixture with bonobos.

Science 2016 10 27;354(6311):477-481. Epub 2016 Oct 27.

Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.

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http://dx.doi.org/10.1126/science.aag2602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546212PMC
October 2016

Evolution and demography of the great apes.

Curr Opin Genet Dev 2016 Dec 4;41:124-129. Epub 2016 Oct 4.

Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2016.09.005DOI Listing
December 2016

Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

Genome Biol Evol 2016 07 3;8(6):2020-30. Epub 2016 Jul 3.

Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

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http://dx.doi.org/10.1093/gbe/evw124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943195PMC
July 2016

Genetic Load of Loss-of-Function Polymorphic Variants in Great Apes.

Genome Biol Evol 2016 Mar 26;8(3):871-7. Epub 2016 Mar 26.

Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain

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http://dx.doi.org/10.1093/gbe/evw040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824148PMC
March 2016

Origins of De Novo Genes in Human and Chimpanzee.

PLoS Genet 2015 Dec 31;11(12):e1005721. Epub 2015 Dec 31.

Evolutionary Genomics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pgen.1005721DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697840PMC
December 2015

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.

Proc Natl Acad Sci U S A 2016 01 22;113(1):152-7. Epub 2015 Dec 22.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095; Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095

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http://dx.doi.org/10.1073/pnas.1512501113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4711855PMC
January 2016

DNA Methylation: Insights into Human Evolution.

PLoS Genet 2015 Dec 10;11(12):e1005661. Epub 2015 Dec 10.

Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.

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http://public-files.prbb.org/publicacions/b51e74e0-86cc-0133
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http://dx.plos.org/10.1371/journal.pgen.1005661
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http://dx.doi.org/10.1371/journal.pgen.1005661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684328PMC
December 2015

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence.

Genome Res 2015 Nov 19;25(11):1591-9. Epub 2015 Aug 19.

Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-805 Zurich, Switzerland; The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; The Santa Fe Institute, Santa Fe, New Mexico 87501, USA.

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http://dx.doi.org/10.1101/gr.190868.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617956PMC
November 2015

The interplay between DNA methylation and sequence divergence in recent human evolution.

Nucleic Acids Res 2015 Sep 13;43(17):8204-14. Epub 2015 Jul 13.

Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona 08028, Spain Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gkv693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787803PMC
September 2015

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014

Analysis of structural diversity in wolf-like canids reveals post-domestication variants.

BMC Genomics 2014 Jun 12;15:465. Epub 2014 Jun 12.

Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC), Ciències Experimentals i de la Salut, Barcelona 08003, Spain.

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http://dx.doi.org/10.1186/1471-2164-15-465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070573PMC
June 2014

The genetics of microdeletion and microduplication syndromes: an update.

Annu Rev Genomics Hum Genet 2014 16;15:215-244. Epub 2014 Apr 16.

Department of Pediatrics, University of Washington, Seattle, Washington 98195.

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http://dx.doi.org/10.1146/annurev-genom-091212-153408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476258PMC
May 2015