Tomas Marques-Bonet

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
    Tomas Marques-Bonet
    Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    BMC Genomics 9:384. 2008
  2. pmc Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses
    Belen Hurle
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Evol Biol 11:23. 2011
  3. doi request reprint Sequencing primate genomes: what have we learned?
    Tomas Marques-Bonet
    Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98105, USA
    Annu Rev Genomics Hum Genet 10:355-86. 2009
  4. pmc The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2
    Mario Ventura
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
    Genome Res 22:1036-49. 2012
  5. ncbi request reprint Balancing selection is the main force shaping the evolution of innate immunity genes
    Anna Ferrer-Admetlla
    Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Unitat de Biologia Evolutiva, Barcelona, Catalonia, Spain
    J Immunol 181:1315-22. 2008
  6. pmc A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk
    Francesca Antonacci
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 42:745-50. 2010
  7. ncbi request reprint Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
    Zhaoshi Jiang
    Department of Genome Sciences, University of Washington School of Medicine and the Howard Hughes Medical Institute, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nat Genet 39:1361-8. 2007
  8. pmc Rates and patterns of great ape retrotransposition
    Fereydoun Hormozdiari
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 110:13457-62. 2013
  9. pmc A burst of segmental duplications in the genome of the African great ape ancestor
    Tomas Marques-Bonet
    Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98195, USA
    Nature 457:877-81. 2009
  10. pmc Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee
    Mario Ventura
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Genome Res 21:1640-9. 2011

Collaborators

Detail Information

Publications28

  1. pmc The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
    Tomas Marques-Bonet
    Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    BMC Genomics 9:384. 2008
    ....
  2. pmc Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses
    Belen Hurle
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Evol Biol 11:23. 2011
    ....
  3. doi request reprint Sequencing primate genomes: what have we learned?
    Tomas Marques-Bonet
    Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98105, USA
    Annu Rev Genomics Hum Genet 10:355-86. 2009
    ....
  4. pmc The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2
    Mario Ventura
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
    Genome Res 22:1036-49. 2012
    ..Our findings highlight the complex interplay between duplicated sequences and chromosomal rearrangements that rapidly alter the cytogenetic landscape in a short period of evolutionary time...
  5. ncbi request reprint Balancing selection is the main force shaping the evolution of innate immunity genes
    Anna Ferrer-Admetlla
    Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Unitat de Biologia Evolutiva, Barcelona, Catalonia, Spain
    J Immunol 181:1315-22. 2008
    ..However, we also describe evidence from African populations, which may reflect parallel or long-term selective forces acting in different geographic areas...
  6. pmc A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk
    Francesca Antonacci
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 42:745-50. 2010
    ..Notably, we show that the S2 configuration harbors directly oriented duplications, specifically predisposing this chromosome to disease-associated rearrangement...
  7. ncbi request reprint Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
    Zhaoshi Jiang
    Department of Genome Sciences, University of Washington School of Medicine and the Howard Hughes Medical Institute, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nat Genet 39:1361-8. 2007
    ....
  8. pmc Rates and patterns of great ape retrotransposition
    Fereydoun Hormozdiari
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 110:13457-62. 2013
    ..We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time...
  9. pmc A burst of segmental duplications in the genome of the African great ape ancestor
    Tomas Marques-Bonet
    Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98195, USA
    Nature 457:877-81. 2009
    ....
  10. pmc Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee
    Mario Ventura
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Genome Res 21:1640-9. 2011
    ..Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes...
  11. pmc Death and resurrection of the human IRGM gene
    Cemalettin Bekpen
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 5:e1000403. 2009
    ..Such dynamism in structure and evolution may be critical for a gene family locked in an arms race with an ever-changing repertoire of intracellular parasites...
  12. pmc On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees
    Tomas Marques-Bonet
    Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomedica de Barcelona, Catalonia, Spain
    Genome Biol 8:R230. 2007
    ..To date, however, results are contradictory. Here we revisit this issue by making use of the available human and chimpanzee genome sequence to study the relationship between chromosomal rearrangements and rates of DNA sequence evolution...
  13. ncbi request reprint Murine segmental duplications are hot spots for chromosome and gene evolution
    Lluis Armengol
    Genes and Disease Program, Center for Genomic Regulation, Passeig Maritim 37 49, 08003 Barcelona, Catalonia, Spain
    Genomics 86:692-700. 2005
    ....
  14. pmc Evolution and diversity of copy number variation in the great ape lineage
    Peter H Sudmant
    Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
    Genome Res 23:1373-82. 2013
    ....
  15. pmc Personalized copy number and segmental duplication maps using next-generation sequencing
    Can Alkan
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Genet 41:1061-7. 2009
    ..2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology...
  16. pmc The origins and impact of primate segmental duplications
    Tomas Marques-Bonet
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
    Trends Genet 25:443-54. 2009
    ..Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses...
  17. pmc Patterns and rates of intron divergence between humans and chimpanzees
    Elodie Gazave
    Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
    Genome Biol 8:R21. 2007
    ..Several studies have investigated levels of evolutionary constraint along introns and across classes of introns of different length and location within genes. However, thus far these studies have yielded contradictory results...
  18. doi request reprint Human pseudogenes of the ABO family show a complex evolutionary dynamics and loss of function
    Ferran Casals
    Institut de Biologia Evolutiva CSIC UPF, CEXS UPF PRBB, Barcelona, Catalonia, Spain
    Glycobiology 19:583-91. 2009
    ....
  19. pmc The prion protein gene in humans revisited: lessons from a worldwide resequencing study
    Marta Soldevila
    Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
    Genome Res 16:231-9. 2006
    ....
  20. ncbi request reprint Chromosomal rearrangements and the genomic distribution of gene-expression divergence in humans and chimpanzees
    Tomas Marques-Bonet
    Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader, 80 08003 Barcelona, Catalonia, Spain
    Trends Genet 20:524-9. 2004
    ..In addition, our results are consistent with a role for some rearrangements in the original speciation events that separated the human and chimpanzee lineages...
  21. pmc Great ape genetic diversity and population history
    Javier Prado-Martinez
    Institut de Biologia Evolutiva, CSIC Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
    Nature 499:471-5. 2013
    ..This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations. ..
  22. ncbi request reprint Association Cluster Detector: a tool for heuristic detection of significance clusters in whole-genome scans
    Tomas Marques-Bonet
    Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
    Bioinformatics 21:ii180-1. 2005
    ....
  23. pmc Dynamics of DNA methylation in recent human and great ape evolution
    Irene Hernando-Herraez
    Institute of Evolutionary Biology UPF CSIC, PRBB, Barcelona, Spain
    PLoS Genet 9:e1003763. 2013
    ..We conclude that epigenetic alterations are an important force during primate evolution and have been under-explored in evolutionary comparative genomics. ..
  24. doi request reprint Interrogating 11 fast-evolving genes for signatures of recent positive selection in worldwide human populations
    Andres Moreno-Estrada
    Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva UPF CSIC, Universitat Pompeu Fabra, Barcelona, Spain
    Mol Biol Evol 26:2285-97. 2009
    ..Based on these data, it therefore appears that adaptation for human-specific and for population-specific traits may have involved different genes...
  25. ncbi request reprint Chromosomal rearrangements are associated with higher rates of molecular evolution in mammals
    Tomas Marques-Bonet
    Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 80, 08003 Barcelona, Spain
    Gene 353:147-54. 2005
    ..Still, there are other possible causes and further research is needed to properly explore them...
  26. pmc Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal
    Carles Lalueza-Fox
    Unitat de Biologia Evolutiva, Facultat de Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, Doctor Aiguader 80, 08003 Barcelona, Spain
    BMC Evol Biol 5:70. 2005
    ..35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs...
  27. pmc Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
    Santhosh Girirajan
    Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Genome Res 19:178-90. 2009
    ....
  28. pmc Characterization of six human disease-associated inversion polymorphisms
    Francesca Antonacci
    Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    Hum Mol Genet 18:2555-66. 2009
    ..In these cases, discovery and genotyping methods based on SNPs may be confounded and molecular cytogenetics remains the only method to genotype these inversions...