Recurrent inversion toggling and great ape genome evolution

[1]  Victor Guryev,et al.  breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data , 2019, Bioinform..

[2]  Mark J. P. Chaisson,et al.  Human-specific tandem repeat expansion and differential gene expression during primate evolution , 2019, Proceedings of the National Academy of Sciences.

[3]  S. Pääbo,et al.  Organoid single-cell genomic atlas uncovers human-specific features of brain development , 2019, Nature.

[4]  P. O’Reilly,et al.  Evolutionary and functional impact of common polymorphic inversions in the human genome , 2019, Nature Communications.

[5]  E. Furlong,et al.  Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression , 2019, Nature Genetics.

[6]  Li Zhang,et al.  Current potentials for cancer pain management , 2018 .

[7]  Mitchell R. Vollger,et al.  Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus , 2019, PLoS genetics.

[8]  Heini M. Natri,et al.  The evolution of sex determination associated with a chromosomal inversion , 2019, Nature Communications.

[9]  Ian T. Fiddes,et al.  Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution , 2018, Cell.

[10]  Evan E. Eichler,et al.  Long-read sequence and assembly of segmental duplications , 2018, Nature Methods.

[11]  Lachlan James M. Coin,et al.  npInv: accurate detection and genotyping of inversions using long read sub-alignment , 2018, BMC Bioinformatics.

[12]  S. Schaeffer,et al.  Ancestral polymorphisms explain the role of chromosomal inversions in speciation , 2018, PLoS genetics.

[13]  S. Mundlos,et al.  Structural variation in the 3D genome , 2018, Nature Reviews Genetics.

[14]  David Haussler,et al.  High-resolution comparative analysis of great ape genomes , 2018, Science.

[15]  Francesca Antonacci,et al.  Inversion variants in human and primate genomes , 2018, Genome research.

[16]  A. Katsarou,et al.  Reporting for specific materials, systems and methods , 2018 .

[17]  M. Gerstein,et al.  Molecular and cellular reorganization of neural circuits in the human lineage , 2017, Science.

[18]  Ryan L. Collins,et al.  Multi-platform discovery of haplotype-resolved structural variation in human genomes , 2017, bioRxiv.

[19]  Mark Hills,et al.  Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs , 2017, Nature Protocols.

[20]  Doron Lancet,et al.  GeneHancer: genome-wide integration of enhancers and target genes in GeneCards , 2017, Database J. Biol. Databases Curation.

[21]  Victor Guryev,et al.  Dense and accurate whole-chromosome haplotyping of individual genomes , 2017, Nature Communications.

[22]  Alexander Lex,et al.  UpSetR: an R package for the visualization of intersecting sets and their properties , 2017, bioRxiv.

[23]  X. Estivill,et al.  Detailed analysis of inversions predicted between two human genomes: errors, real polymorphisms, and their origin and population distribution , 2016, Human molecular genetics.

[24]  Beryl B. Cummings,et al.  Landscape of X chromosome inactivation across human tissues , 2016, Nature.

[25]  E. Eichler,et al.  Discovery of large genomic inversions using long range information , 2017, BMC Genomics.

[26]  Zev N. Kronenberg,et al.  Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region , 2016, Genome research.

[27]  Victor Guryev,et al.  Direct chromosome-length haplotyping by single-cell sequencing , 2016, Genome research.

[28]  Victor Guryev,et al.  Characterizing polymorphic inversions in human genomes by single-cell sequencing , 2016, Genome research.

[29]  Fred H. Gage,et al.  Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility , 2016, Nature.

[30]  Bernat Gel,et al.  regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests , 2015, Bioinform..

[31]  Evan E. Eichler,et al.  Genetic variation and the de novo assembly of human genomes , 2015, Nature Reviews Genetics.

[32]  Tyson A. Clark,et al.  Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing , 2015, Nucleic acids research.

[33]  A. Visel,et al.  Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions , 2015, Cell.

[34]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[35]  Peter H. Sudmant,et al.  Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability , 2014, Nature Genetics.

[36]  Kali T. Witherspoon,et al.  Refining analyses of copy number variation identifies specific genes associated with developmental delay , 2014, Nature Genetics.

[37]  John G. Cleary,et al.  Joint Variant and De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data , 2014, bioRxiv.

[38]  Carl Baker,et al.  Evolution and diversity of copy number variation in the great ape lineage , 2013, Genome research.

[39]  Mario Cáceres,et al.  On the Power and the Systematic Biases of the Detection of Chromosomal Inversions by Paired-End Genome Sequencing , 2013, PloS one.

[40]  Russell B. Corbett-Detig,et al.  Population Genomics of Inversion Polymorphisms in Drosophila melanogaster , 2012, PLoS genetics.

[41]  Yongjun Zhao,et al.  DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution , 2012, Nature Methods.

[42]  Thomas Zichner,et al.  DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..

[43]  Peter H. Sudmant,et al.  The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2 , 2012, Genome research.

[44]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[45]  S. Bergmann,et al.  The evolution of gene expression levels in mammalian organs , 2011, Nature.

[46]  Arcadi Navarro,et al.  Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. , 2011, Genome research.

[47]  Bradley P. Coe,et al.  Genome structural variation discovery and genotyping , 2011, Nature Reviews Genetics.

[48]  E. Eichler,et al.  A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms , 2010, Cell.

[49]  Peter H. Sudmant,et al.  Diversity of Human Copy Number Variation and Multicopy Genes , 2010, Science.

[50]  A. Gylfason,et al.  Fine-scale recombination rate differences between sexes, populations and individuals , 2010, Nature.

[51]  Zhaoshi Jiang,et al.  Characterization of six human disease-associated inversion polymorphisms , 2009, Human molecular genetics.

[52]  Richard M Myers,et al.  Population analysis of large copy number variants and hotspots of human genetic disease. , 2009, American journal of human genetics.

[53]  C. Baker,et al.  A burst of segmental duplications in the genome of the African great ape ancestor , 2009, Nature.

[54]  Zhaoshi Jiang,et al.  Evolutionary toggling of the MAPT 17q21.31 inversion region , 2008, Nature Genetics.

[55]  Joshua M. Korn,et al.  Mapping and sequencing of structural variation from eight human genomes , 2008, Nature.

[56]  Mario Cáceres,et al.  A recurrent inversion on the eutherian X chromosome , 2007, Proceedings of the National Academy of Sciences.

[57]  D. Cooper,et al.  The chimpanzee-specific pericentric inversions that distinguish humans and chimpanzees have identical breakpoints in Pan troglodytes and Pan paniscus. , 2006, Genomics.

[58]  E. Eichler,et al.  A genome-wide survey of structural variation between human and chimpanzee. , 2005, Genome research.

[59]  L. Feuk,et al.  Discovery of Human Inversion Polymorphisms by Comparative Analysis of Human and Chimpanzee DNA Sequence Assemblies , 2005, PLoS genetics.

[60]  E. Eichler,et al.  A genome-wide comparison of recent chimpanzee and human segmental duplications , 2005, Nature.

[61]  E. Eichler,et al.  Fine-scale structural variation of the human genome , 2005, Nature Genetics.

[62]  Matthias Platzer,et al.  Breakpoint analysis of the pericentric inversion distinguishing human chromosome 4 from the homologous chromosome in the chimpanzee (Pan troglodytes) , 2005, Human mutation.

[63]  H. Hameister,et al.  Breakpoint analysis of the pericentric inversion between chimpanzee chromosome 10 and the homologous chromosome 12 in humans , 2004, Cytogenetic and Genome Research.

[64]  J. Hey Speciation and inversions: chimps and humans. , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[65]  N. Barton,et al.  Chromosomal Speciation and Molecular Divergence--Accelerated Evolution in Rearranged Chromosomes , 2003, Science.

[66]  A. Dutra,et al.  The Chapel Hill hemophilia A dog colony exhibits a factor VIII gene inversion , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[67]  M. Adams,et al.  Recent Segmental Duplications in the Human Genome , 2002, Science.

[68]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[69]  Stephen W. Scherer,et al.  A 1.5 million–base pair inversion polymorphism in families with Williams-Beuren syndrome , 2001, Nature Genetics.

[70]  P. Lewis A likelihood approach to estimating phylogeny from discrete morphological character data. , 2001, Systematic biology.

[71]  J. Weber,et al.  Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements. , 2001, American journal of human genetics.

[72]  J. Yunis,et al.  The origin of man: a chromosomal pictorial legacy. , 1982, Science.

[73]  A. Sturtevant,et al.  Genetic Factors Affecting the Strength of Linkage in Drosophila. , 1917, Proceedings of the National Academy of Sciences of the United States of America.