Research:
The long-term goal of our laboratory is to understand the evolution, pathology and mechanisms of recent gene duplication and DNA transposition within the human genome.
Our research specifically addresses a new paradigm that has emerged in the past few years in which particular regions of the human genome have been shown active in the acquisition, duplication and dispersal of large gene-containing genomic segments.
We hypothesize that these 'jumping genomic segments' are part of an ongoing evolutionary process that results in a novel form of large-scale variation in human genomic DNA and contributes rapidly to primate gene evolution.
The large blocks of sequence similarity generated by this process, we further propose provide the substrates for aberrant recombination, thereby leading to recurrent and potentially pathogenic chromosomal structural rearrangements.
The general aims of our research are
1) to investigate the molecular mechanism(s) responsible for such duplications;
2) to evaluate their role in the evolution of the higher primate genome; and
3) to assess their impact in contributing to polymorphism of both normal human chromosomes and chromosomes associated with genetic instability diseases.
Our approach has been to combine bioinformatics, large-scale comparative sequencing, phylogenetics and high-resolution FISH methods to address these questions.
We are committed to the further characterization of these complex regions of the genome and the development of assays to correlate their dynamic structure with chromosome function, gene evolution and human disease. My research philosophy combines various disciplines (evolutionary biology, human genetics/genomics and bioinformatics) to understand the mechanisms and consequences of novel forms of variation in the human genome. Such a synergism of various disciplines provides a powerful strategy to address biological processes of genome evolution. The development of tools and the conditions required to pursue such a holistic approach, with respect to studies of genome evolution, are unprecedented. With the advent of the information age, current large-scale sequencing of genomes and the development of powerful bioinformatics tools, such 'complex' and mulitfaceted research objectives will become increasingly tractable endeavors.
My overall goal is to contribute to this new era of genomics sciences as it applies to evolution and medicine and to impart the value of this scientific design, through teaching and mentorship, to the next generation of scientists.
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Publications:
Yohn CT, Jiang Z, McGrath SD,Hayden KE, Khaitovich P, Johnson ME, Eichler MY, McPherson JD, Zhao S, P䤢o S, Eichler EE (2005). Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans. PLoS Biol 2005;3(4): e110.
She X, Jiang Z, Clark RA, Liu G, Cheng Z, Tuzun E, Church DM, Sutton G, Halpern AL, Eichler EE (2004). Shotgun sequence assembly and recent segmental duplications within the human genome. Nature. 2004 Oct 21;431(7011):927-930.
She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE. (2004) The structure and evolution of centromeric transition regions within the human genome. Nature. 2004 Aug 19;430(7002):857-864
Bailey JA, Liu G, Eichler EE. (2003) An alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet. 73:823-34
Eichler EE, Sankoff D. (2003) Structural dynamics of eukaryotic chromosome evolution. Science 301:793-7
additional publication listings available via PubMed
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