Photo of Lucia Carbone, Ph.D.

Lucia Carbone Ph.D.

  • (503) 494-7342
    • Assistant Professor of Medicine, Division of Cardiovascular Medicine School of Medicine
    • Assistant Professor of Molecular and Medical Genetics School of Medicine
    • Assistant Professor of Medical Informatics and Clinical Epidemiology School of Medicine

BIO

Dr. Carbone received her Masters in Biology and PhD in Genetics and Molecular Evolution at the University of Bari (Italy) under the mentorship of Prof. Mariano Rocchi. During this pre-genomic era, she specialized in comparative cytogenetics and focused her research on chromosome evolution. She also spent two years of her graduate training in Pieter de Jong's lab at the Children's Hospital of Oakland Research Institute (CA) where then she carried out her her postdoctoral training. She joined OHSU as an Assistant Professor in September 2010.

RESEARCH

Large-scale chromosomal rearrangements are key drivers of mammalian genome evolution. These events are a major source of genetic variation, bring about speciation, and are hallmarks of human disease, but the mechanisms underlying their occurrence and subsequent fixation are not entirely understood. My research program strives to investigate the following major questions: What are the mechanisms through which specific genomic and epigenetic features lead to chromosomal rearrangements? What is the outcome of rearrangements on the genomic landscape? Although fundamental, these questions remain unanswered. I use comparative genomics to investigate this question and leverage on one particular non-human primate model: the gibbons.

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Publications

  • "Sequencing thousands of single-cell genomes with combinatorial indexing." Nature Methods  In: , Vol. 14, No. 3, 28.02.2017, p. 302-308.
  • "Endogenous retroviruses : With us and against us." Frontiers in Chemistry In: , Vol. 5, No. APR, 23, 2017.
  • "IFPA meeting 2016 workshop report I : Genomic communication, bioinformatics, trophoblast biology and transport systems." Placenta In: , 12.12.2016.
  • "Investigating somatic aneuploidy in the brain : why we need a new model." Chromosoma  In: , 16.09.2016, p. 1-14.
  • "Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons." Molecular Ecology  In: , Vol. 25, No. 14, 01.07.2016, p. 3469-3483.
  • "Transcriptomic and epigenomic characterization of the developing bat wing." Nature Genetics  In: , Vol. 48, No. 5, 01.05.2016, p. 528-536.
  • "The flow of the gibbon LAVA element is facilitated by the LINE-1 retrotransposition machinery." Genome Biology and Evolution In: , Vol. 8, No. 10, 2016, p. 3209-3225.
  • "Whole-genome characterization in pedigreed non-human primates using genotyping-by-sequencing (GBS) and imputation." BMC Genomics  In: , Vol. 17, No. 1, 676, 2016.
  • "Mammalian pre-implantation chromosomal instability : Species comparison, evolutionary considerations, and pathological correlations." Systems Biology in Reproductive Medicine In: , Vol. 61, No. 6, 02.11.2015, p. 321-335.
  • "Response to Hron et al." Genome Biology In: , Vol. 16, No. 1, 165, 18.08.2015.
  • "Ring chromosomes, breakpoint clusters, and neocentromeres in sarcomas." Genes Chromosomes and Cancer  In: , Vol. 54, No. 3, 01.03.2015, p. 156-167.
  • "Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach." Genetics In: , Vol. 200, No. 1, 01.01.2015, p. 295-308.
  • "Gibbon genome and the fast karyotype evolution of small apes." Nature In: , Vol. 513, No. 7517, 11.09.2014, p. 195-201.
  • "Inference of Transposable Element Ancestry." PLoS Genetics In: , Vol. 10, No. 8, e1004482, 14.08.2014.
  • "Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer." Nucleic Acids Research  In: , Vol. 42, No. 14, 2014, p. 9131-9145.
  • "Conserved syntenic clusters of protein coding genes are missing in birds." Genome Biology In: , Vol. 15, No. 12, 2014, p. 565.
  • "Metabolic consequences of incorrect insulin administration techniques in aging subjects with diabetes." Diabetes Technology and Therapeutics In: , Vol. 15, No. SUPPL.1, 01.06.2013.
  • "Incomplete Lineage Sorting Is Common in Extant Gibbon Genera." PLoS One  In: , Vol. 8, No. 1, e53682, 18.01.2013.
  • "A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons." Genome Research  In: , Vol. 22, No. 12, 12.2012, p. 2520-2528.
  • "An alu-based phylogeny of gibbons (hylobatidae)." Molecular Biology and Evolution In: , Vol. 29, No. 11, 11.2012, p. 3441-3450.
  • "Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons." Genome Biology and Evolution In: , Vol. 4, No. 7, 2012, p. 648-658.
  • "Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines." Cancer genetics  In: , Vol. 204, No. 8, 08.2011, p. 447-457.
  • "Patterns of genetic variation within and between gibbon species." Molecular Biology and Evolution In: , Vol. 28, No. 8, 08.2011, p. 2211-2218.
  • "Metabolic consequences of incorrect insulin administration techniques in aging subjects with diabetes." Acta Diabetologica  In: , Vol. 48, No. 2, 06.2011, p. 121-125.
  • "Isolation of specific clones from nonarrayed BAC libraries through homologous recombination." Journal of Biomedicine and Biotechnology In: , Vol. 2011, 560124, 2011.
  • "A small, variable, and irregular killer cell Ig-like receptor locus accompanies the absence of MHC-C and MHC-G in gibbons." Journal of Immunology  In: , Vol. 184, No. 3, 01.02.2010, p. 1379-1391.
  • "Genomics through the lens of next-generation sequencing." Genome Biology In: , Vol. 11, No. 6, 2010, p. 306.
  • "Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution." PLoS Genetics In: , Vol. 5, No. 6, e1000538, 06.2009.
  • "A chromosomal inversion unique to the northern white-cheeked gibbon." PLoS One In: , Vol. 4, No. 3, e4999, 25.03.2009.
  • "A satellite-like sequence, representing a "clone gap" in the human genome, was likely involved in the seeding of a novel centromere in macaque." Chromosoma  In: , Vol. 118, No. 2, 2009, p. 269-277.

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