Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

[1]  Jens Stoye,et al.  On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios , 2008, RECOMB-CG.

[2]  Giorgio Bernardi,et al.  Mapping DNase-I hypersensitive sites on human isochores. , 2008, Gene.

[3]  Marie-France Sagot,et al.  Precise detection of rearrangement breakpoints in mammalian chromosomes , 2008, BMC Bioinformatics.

[4]  A. Bird,et al.  DNA methylation landscapes: provocative insights from epigenomics , 2008, Nature Reviews Genetics.

[5]  Z. Weng,et al.  High-Resolution Mapping and Characterization of Open Chromatin across the Genome , 2008, Cell.

[6]  S Nicolay,et al.  DNA replication timing data corroborate in silico human replication origin predictions. , 2007, Physical review letters.

[7]  Steven Henikoff,et al.  Genome-wide analysis of DNA methylation patterns , 2007, Development.

[8]  Ivan Ovcharenko,et al.  Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. , 2007, Genome research.

[9]  T. J. Robinson,et al.  Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies , 2007, BMC Evolutionary Biology.

[10]  Pavel A. Pevzner,et al.  Are There Rearrangement Hotspots in the Human Genome? , 2007, PLoS Comput. Biol..

[11]  Boris Lenhard,et al.  The random versus fragile breakage models of chromosome evolution: a matter of resolution , 2007, Molecular Genetics and Genomics.

[12]  Alain Arneodo,et al.  Human gene organization driven by the coordination of replication and transcription. , 2007, Genome research.

[13]  K. Howe,et al.  Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. , 2007, Genome research.

[14]  Elaine R Mardis,et al.  Molecular refinement of gibbon genome rearrangements. , 2007, Genome research.

[15]  Laurent Duret,et al.  A new perspective on isochore evolution. , 2006, Gene.

[16]  Andreas Prlic,et al.  Ensembl 2007 , 2006, Nucleic Acids Res..

[17]  Sridhar Hannenhalli,et al.  Recurring genomic breaks in independent lineages support genomic fragility , 2006, BMC Evolutionary Biology.

[18]  Hélène Hayes,et al.  High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution , 2006, BMC Genomics.

[19]  Davide Mantiero,et al.  The cellular response to chromosome breakage , 2006, Molecular microbiology.

[20]  David Sankoff,et al.  The Signal in the Genomes , 2006, PLoS Comput. Biol..

[21]  Pavel A Pevzner,et al.  The Fragile Breakage versus Random Breakage Models of Chromosome Evolution , 2006, PLoS Comput. Biol..

[22]  Readman Chiu,et al.  A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Caleb Webber,et al.  Hotspots of mutation and breakage in dog and human chromosomes. , 2005, Genome research.

[24]  Phil Trinh,et al.  Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement , 2005, J. Comput. Biol..

[25]  P. Pevzner,et al.  Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps , 2005, Science.

[26]  Alain Arneodo,et al.  Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[27]  S Nicolay,et al.  From DNA sequence analysis to modeling replication in the human genome. , 2005, Physical review letters.

[28]  A. Ruiz-Herrera,et al.  Evolutionary breakpoints are co-localized with fragile sites and intrachromosomal telomeric sequences in primates , 2004, Cytogenetic and Genome Research.

[29]  A. Delcher,et al.  Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. , 2004, Genome research.

[30]  Nick Gilbert,et al.  Chromatin Architecture of the Human Genome Gene-Rich Domains Are Enriched in Open Chromatin Fibers , 2004, Cell.

[31]  F Galibert,et al.  Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements. , 2004, Genomics.

[32]  P. Pevzner,et al.  Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. , 2004, Genome research.

[33]  D. Haussler,et al.  Hotspots of mammalian chromosomal evolution , 2004, Genome Biology.

[34]  D. Haussler,et al.  Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[35]  S. Scherer,et al.  Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. , 2003, Human molecular genetics.

[36]  E. Eichler,et al.  Structural Dynamics of Eukaryotic Chromosome Evolution , 2003, Science.

[37]  P. Pevzner,et al.  Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[38]  T. Cremer,et al.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells , 2001, Nature Reviews Genetics.

[39]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[40]  L. Duret,et al.  The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact. , 2000, Molecular biology and evolution.

[41]  W. Goedecke,et al.  Mechanisms of DNA double-strand break repair and their potential to induce chromosomal aberrations. , 2000, Mutagenesis.

[42]  G Bernardi,et al.  Isochores and the evolutionary genomics of vertebrates. , 2000, Gene.

[43]  David Waddington,et al.  The dynamics of chromosome evolution in birds and mammals , 1999, Nature.

[44]  A. Bird,et al.  Methylation-Induced Repression— Belts, Braces, and Chromatin , 1999, Cell.

[45]  N. Galtier,et al.  Isochore evolution in mammals: a human-like ancestral structure. , 1998, Genetics.

[46]  David Sankoff,et al.  The lengths of undiscovered conserved segments in comparative maps , 1998, Mammalian Genome.

[47]  G Bernardi,et al.  The gene distribution of the human genome. , 1996, Gene.

[48]  M. Seldin,et al.  Human/mouse homology relationships. , 1996, Genomics.

[49]  L. Duret,et al.  Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores , 1995, Journal of Molecular Evolution.

[50]  G. Bernardi,et al.  Compositional properties of coding sequences and mammalian phylogeny , 1993, Journal of Molecular Evolution.

[51]  G Bernardi,et al.  The distribution of genes in the human genome. , 1991, Gene.

[52]  A. Bird.  CpG-rich islands and the function of DNA methylation , 1986, Nature.

[53]  J. Nadeau,et al.  Lengths of chromosomal segments conserved since divergence of man and mouse. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[54]  A. Steinacker,et al.  A Spice Study of Silicon Sensor Strip Noise on Long Ladders , 2011 .

[55]  Bernard B. Suh,et al.  Reconstructing contiguous regions of an ancestral genome. , 2006, Genome research.

[56]  Peer Bork,et al.  Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. , 2005, Genome research.

[57]  Phil Trinh,et al.  Genomic features in the breakpoint regions between syntenic blocks , 2004, ISMB/ECCB.

[58]  P. Pevzner,et al.  Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. , 2003, Genome research.

[59]  A. Bird.  DNA methylation patterns and epigenetic memory. , 2002, Genes & development.

[60]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[61]  Distribution of , 2000 .

[62]  G. Sermonti.  The human genome. , 1988, Rivista di biologia.

[63]  D. Haussler,et al.  The Ucsc Genome Browser Database , 2022 .