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Species | Evan E EichlerSummaryAffiliation: Case Western Reserve University Country: USA Publications
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Publications
Hotspots of mammalian chromosomal evolutionJeffrey A Bailey
Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA
Genome Biol 5:R23. 2004....
An assessment of the sequence gaps: unfinished business in a finished human genomeEvan E Eichler
Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, BRB720, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
Nat Rev Genet 5:345-54. 2004- Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication clusterDevin P Locke
Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine, University Hospitals of Cleveland, Cleveland, OH 44106, USA
Genome Biol 4:R50. 2003..Reproductive isolation and subsequent speciation are thought to be the potential result of pericentric inversions, as reproductive boundaries form as a result of hybrid sterility... - The structure and evolution of centromeric transition regions within the human genomeXinwei She
Department of Genetics, Center for Computational Genomics and the Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
Nature 430:857-64. 2004..The distribution of these duplicated segments is nonrandom among pericentromeric regions, suggesting that some regions have served as preferential acceptors of euchromatic DNA... - The DNA sequence and comparative analysis of human chromosome 5Jeremy Schmutz
Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Ave, Palo Alto, California 94304, USA
Nature 431:268-74. 2004..These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy... - Punctuated duplication seeding events during the evolution of human chromosome 2p11Julie E Horvath
Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
Genome Res 15:914-27. 2005..The data further indicate that factors other than sequence are important determinants for such bursts of duplicative transposition from the euchromatin to pericentromeric regions... - Analysis of segmental duplications and genome assembly in the mouseJeffrey A Bailey
Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 4410, USA
Genome Res 14:789-801. 2004..In addition, our unique method provides the means for improving whole-genome shotgun sequence assembly of mouse and future mammalian genomes... - Large-scale variation among human and great ape genomes determined by array comparative genomic hybridizationDevin P Locke
Department of Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
Genome Res 13:347-57. 2003..In contrast to previous cytogenetic and comparative mapping studies, these results indicate extensive local repatterning of hominoid chromosomes in euchromatic regions through a duplication-driven mechanism of genome evolution... - Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutansChris T Yohn
Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
PLoS Biol 3:e110. 2005..We speculate on the potential impact of such recent events on the evolution of humans and great apes... - Recent segmental duplications in the human genomeJeffrey A Bailey
Department of Genetics, Center for Computational Genomics, and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA
Science 297:1003-7. 2002..Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity... - The role of unequal crossover in alpha-satellite DNA evolution: a computational analysisCan Alkan
Department of EECS, Case Western Reserve University, Cleveland, OH 44106, USA
J Comput Biol 11:933-44. 2004..It is likely that the higher order repeats developed independently in distinct regions of the genome and were carried into their current locations through an unknown mechanism of transposition... - Manipulating multiple sequence alignments via MaM and WebMaMCan Alkan
Department of EECS, Case Western Reserve University, Cleveland, OH, USA
Nucleic Acids Res 33:W295-8. 2005..MaM source code is freely available for non-commercial use at http://compbio.cs.sfu.ca/MAM.htm; and the web interface WebMaM is hosted at http://atgc.lirmm.fr/mam... - Structural dynamics of eukaryotic chromosome evolutionEvan E Eichler
Department of Genetics, Center for Human Genetics and Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA
Science 301:793-7. 2003..Computational algorithms that take into account these dynamic forces along with traditional models of chromosomal rearrangement show promise for reconstructing the natural history of eukaryotic chromosomes... - An Alu transposition model for the origin and expansion of human segmental duplicationsJeffrey A Bailey
Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH, 44106, USA
Am J Hum Genet 73:823-34. 2003.... - Recent segmental duplications in the working draft assembly of the brown Norway ratEray Tuzun
Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
Genome Res 14:493-506. 2004..2 Mb), indicating that segmental duplications have been problematic for sequence and assembly of the rat genome. Further targeted efforts are required to resolve the organization and complexity of these regions... - Analysis of primate genomic variation reveals a repeat-driven expansion of the human genomeGe Liu
Department of Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
Genome Res 13:358-68. 2003..Assuming that the primate genome sequence we have sampled is representative, we estimate that human euchromatin has expanded 30 Mb and 550 Mb compared to the primate genomes of chimpanzee and lemur, respectively... - Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22Jeffrey A Bailey
Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, OH, USA
Am J Hum Genet 70:83-100. 2002.... - Linkage disequilibrium between two high-frequency deletion polymorphisms: implications for association studies involving the glutathione-S transferase (GST) genesYongzhong Zhao
Department of Molecular Genetics, Cleveland Clinic, Cleveland, OH, USA
PLoS Genet 5:e1000472. 2009..These results show a complex genomic organization and unexpected biological functions of CNVs within segmental duplications and emphasize the importance of detailed structural characterization for disease association studies... - An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolutionCan Alkan
Department of EECS, Center for Computational Genomics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
Genome Inform 13:93-102. 2002..It is likely that the higher order repeats developed independently in distinct regions of the genome and were carried into their current locations through an unknown mechanism of transposition... - Segmental duplications and the evolution of the primate genomeRhea Vallente Samonte
Department of Genetics and Center for Human Genetics, School of Medicine and University Hospitals of Cleveland, Case Western Reserve University, Cleveland, Ohio 44106, USA
Nat Rev Genet 3:65-72. 2002..Although the precise fraction is unknown, some of these duplicated segments have recently been shown to be associated with rapid gene innovation and chromosomal rearrangement in the genomes of man and the great apes... - Primate segmental duplications: crucibles of evolution, diversity and diseaseJeffrey A Bailey
Department of Pathology, Case Western University School of Medicine and University Hospitals of Cleveland, Ohio 44106, USA
Nat Rev Genet 7:552-64. 2006..A growing number of examples link natural human genetic variation of these regions to susceptibility to common disease... - Biomedical applications and studies of molecular evolution: a proposal for a primate genomic library resourceEvan E Eichler
Department of Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
Genome Res 12:673-8. 2002..Based on existing BAC library resources, we propose the construction of a panel of primate BAC libraries from phylogenetic anchor species for the purpose of comparative medicine as well as studies of genome evolution... - Detection of deletions in de novo "balanced" chromosome rearrangements: further evidence for their role in phenotypic abnormalitiesCaroline Astbury
Center for Human Genetics and Department of Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106-9959, USA
Genet Med 6:81-9. 2004.... - The DNA sequence and biology of human chromosome 19Jane Grimwood
Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, California 94304, USA
Nature 428:529-35. 2004.... - The nature, pattern and function of human sequence variationEvan E Eichler
Department of Genetics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
Genome Biol 5:318. 2004 
Genetic history of an archaic hominin group from Denisova Cave in SiberiaDavid Reich
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 468:1053-60. 2010..This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans...- Demographic history and rare allele sharing among human populationsSimon Gravel
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
Proc Natl Acad Sci U S A 108:11983-8. 2011..Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence... - Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplicationMaria Francesca Cardone
Department of Genetics and Microbiology, University of Bari, Via Amendola, Bari, 70126, Italy
Genome Biol 9:R28. 2008.... - Closing gaps in the human genome with fosmid resources generated from multiple individualsDonald Bovee
Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195, USA
Nat Genet 40:96-101. 2008.... - Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolutionZhaoshi 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.... - Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence dataCan Alkan
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
PLoS Comput Biol 3:1807-18. 2007..Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution... - Mutational and selective effects on copy-number variants in the human genomeGregory M Cooper
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nat Genet 39:S22-9. 2007..Although defining these variants with nucleotide-level precision remains a largely unmet but critical challenge, our understanding of their potential medical impact and evolutionary importance is rapidly emerging... - Evolutionary and biomedical insights from the rhesus macaque genomeRichard A Gibbs
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
Science 316:222-34. 2007..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species... - Evolutionary formation of new centromeres in macaqueMario Ventura
Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
Science 316:243-6. 2007..Our results suggest that novel centromeres may trigger only local duplication activity and that the absence of genes in the seeding region may have been important in ENC maintenance and progression... - Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regionsStefan Kirsch
Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
Genome Res 18:1030-42. 2008.... - Explaining human uniqueness: genome interactions with environment, behaviour and cultureAjit Varki
Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California 92093, USA
Nat Rev Genet 9:749-63. 2008.... - Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypesHeather C Mefford
University of Washington School of Medicine, Seattle 98195, USA
N Engl J Med 359:1685-99. 2008..Advances in technologies to detect these changes allow for the routine identification of submicroscopic imbalances in large numbers of patients... - Systematic assessment of copy number variant detection via genome-wide SNP genotypingGregory M Cooper
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nat Genet 40:1199-203. 2008.... - Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21Robert Lyle
Department of Genetic Medicine and Development, University of Geneva Medical School, and University Hospitals, 1211 Geneva, Switzerland
Genome Res 17:1690-6. 2007..The sequencing of the "heterochromatic" regions of the human genome is likely to reveal many additional functional elements and provide important evolutionary information... - The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangementsTomas 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.... - DupMasker: a tool for annotating primate segmental duplicationsZhaoshi Jiang
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
Genome Res 18:1362-8. 2008..We predict this tool will be valuable in the annotation of large-insert sequence clones, allowing putative unique and duplicated regions of the genomes to be annotated prior to whole genome assembly comparisons... - Mouse segmental duplication and copy number variationXinwei She
Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195, USA
Nat Genet 40:909-14. 2008..We show large and complex patterns of interstrain copy number variation restricted to large gene families associated with spermatogenesis, pregnancy, viviparity, pheromone signaling and immune response... - Genome analysis of the platypus reveals unique signatures of evolutionWesley C Warren
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 453:175-83. 2008..Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation... - Mapping and sequencing of structural variation from eight human genomesJeffrey M Kidd
Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
Nature 453:56-64. 2008..These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects... - Molecular refinement of gibbon genome rearrangementsRoberta Roberto
Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
Genome Res 17:249-57. 2007..Our data emphasize the synergistic effect of combining computational genomics and cytogenetics and provide a framework for ultimate sequence and assembly of the gibbon genome... - Recurrent duplication-driven transposition of DNA during hominoid evolutionMatthew E Johnson
Department of Genome Sciences and the Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 103:17626-31. 2006..Our data support a model of duplication where the probability that a segment of DNA becomes duplicated is determined by its proximity to core duplicons, such as LCR16a... - Generation and annotation of the DNA sequences of human chromosomes 2 and 4Ladeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St. Louis, Missouri 63108, USA
Nature 434:724-31. 2005..Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions... - Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosomeStefan Kirsch
Institute of Human Genetics, University of Heidelberg, INF 366, 69120 Heidelberg, Germany
Genome Res 15:195-204. 2005.... - The sequence and analysis of duplication-rich human chromosome 16Joel Martin
DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA
Nature 432:988-94. 2004.... - Recurrent sites for new centromere seedingMario Ventura
Sezione di Genetica-Dipartimento di Anatomia Patologica e Genetica, University of Bari, 70126 Bari, Italy
Genome Res 14:1696-703. 2004..We propose that the formation of neocentromeres in humans and the emergence of new centromeres during the course of evolution share a common mechanism... - Regional patterns of gene expression in human and chimpanzee brainsPhilipp Khaitovich
Max Planck Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
Genome Res 14:1462-73. 2004..Furthermore, genes that show an elevated expression level in humans are statistically significantly enriched in regions that are recently duplicated in humans... - Segmental duplications flank the multiple sclerosis locus on chromosome 17qDaniel C Chen
Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California 90095, USA
Genome Res 14:1483-92. 2004.... - A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomesMichel van Geel
Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, USA
Am J Hum Genet 70:269-78. 2002..Our analysis emphasizes the dynamic nature of duplication-mediated genome evolution and the delicate balance between gene acquisition and silencing... - Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRichard A Gibbs
Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA <http://www.hgsc.bcm.tmc.edu
Nature 428:493-521. 2004.... - Fine-scale structural variation of the human genomeEray Tuzun
Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
Nat Genet 37:727-32. 2005..These data provide a fine-scale structural variation map of the human genome and the requisite sequence precision for subsequent genetic studies of human disease... - Segmental duplications and copy-number variation in the human genomeAndrew J Sharp
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
Am J Hum Genet 77:78-88. 2005..Our specialized segmental duplication BAC microarray and associated database of structural polymorphisms will provide an important resource for the future characterization of human genomic disorders... - Shotgun sequence assembly and recent segmental duplications within the human genomeXinwei She
Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
Nature 431:927-30. 2004.... - Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigsMaria Francesca Cardone
Department of Genetics and Microbiology, University of Bari, Bari, Italy
Genome Biol 7:R91. 2006..Comparison of the pericentromeric organization of chromosome 13 in four Old World monkey species revealed many differences in sequence organization. The region contains clusters of duplicons showing peculiar features... - Discovery of previously unidentified genomic disorders from the duplication architecture of the human genomeAndrew J Sharp
Department of Genome Sciences and the Howard Hughes Medical Institute, University of Washington School of Medicine, 1705 NE Pacific St, Seattle, Washington 98195, USA
Nat Genet 38:1038-42. 2006..In common with the 17q21.31 deletion, these breakpoint regions are sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions... - Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genomeDevin P Locke
Department of Genome Sciences, University of Washington and Howard Hughes Medical Institute, Seattle, WA 98195, USA
Am J Hum Genet 79:275-90. 2006..Our results underscore the need for complete maps of genetic variation in duplication-rich regions of the genome... - Hotspots for copy number variation in chimpanzees and humansGeorge H Perry
School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
Proc Natl Acad Sci U S A 103:8006-11. 2006..Therefore, some of these regions may be unstable "hotspots" for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species... - A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplicationsXinwei She
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
Genome Res 16:576-83. 2006..These architectural shifts in genomic structure and elevated substitution rates have important implications for the emergence of new genes, gene-expression differences, and structural variation among humans and great apes... - Analysis of the DNA sequence and duplication history of human chromosome 15Michael C Zody
Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
Nature 440:671-5. 2006..Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome... - Chromosome evolution in eukaryotes: a multi-kingdom perspectiveAvril Coghlan
Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
Trends Genet 21:673-82. 2005..There is little evidence that chromosomal rearrangements cause speciation, but they probably intensify reproductive isolation between species that have formed by another route... - A genome-wide comparison of recent chimpanzee and human segmental duplicationsZe Cheng
Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
Nature 437:88-93. 2005..Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%)... - Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10pJane Guy
The Institute of Human Genetics, The International Centre For Life, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 3BZ, UK
Genome Res 13:159-72. 2003..This suggests that any novel gene structures formed by these interchromosomal events would require relocation to a more open chromatin environment to be expressed...