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Forum: Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?
- Lutz Froenicke,
- Montserrat Garcia Caldés,
- Alexander Graphodatsky,
- Stefan Müller,
- Leslie A. Lyons,
- Terence J. Robinson,
- Marianne Volleth,
- Fengtang Yang,
- and Johannes Wienberg
Genome Res. March 2006 16: 306-310; doi:10.1101/gr.3955206
...and chicken s reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15 : 98 –110. ↵ Chowdhary, B.P., Raudsepp, T., Fronicke, L., and Scherthan, H. 1998 . Emerging patterns of comparative organization in some mammalian species as revealed by Zoo-FISH. Genome Res. 8 : 577...
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Forum: The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
- Guillaume Bourque,
- Glenn Tesler,
- and Pavel A. Pevzner
Genome Res. March 2006 16: 311-313; doi:10.1101/gr.4631806
...., Froenicke, L., and Scherthan, H. 1998 . Emerging patterns of comparative organization in some mammalian species as revealed by Zoo-FISH. Genome Res. 8 : 577 –589. ↵ Froenicke, L. 2005 . Origins of primate chromosomes—as delineated by Zoo-FISH and alignments of human and mouse draft sequences. Cytogenet...
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LETTER: Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation
- Shaying Zhao,
- Jyoti Shetty,
- Lihua Hou,
- Arthur Delcher,
- Baoli Zhu,
- Kazutoyo Osoegawa,
- Pieter de Jong,
- William C. Nierman,
- Robert L. Strausberg,
- and Claire M. Fraser
Genome Res. October 2004 14: 1851-1860; Published in Advance September 13, 2004, doi:10.1101/gr.2663304
.... A comparison of whole- shotgun-derived mouse chromosome 16 and the human . Science 296 : 1661 -1671. ↵ Murphy, W.J., Stanyon, R., and O'Brien, S.J. 2001 . Evolution of mammalian organization inferred from comparative gene mapping. Genome Biol. 2 : REVIEWS0005 . ↵ Murphy, W.J., Fronicke, L., O'Brien, S...
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LETTER: A Radiation Hybrid Map of the Cat Genome: Implications for Comparative Mapping
- William J. Murphy,
- Shan Sun,
- Zhang-qun Chen,
- Naoya Yuhki,
- Deborah Hirschmann,
- Marilyn Menotti-Raymond,
- and Stephen J. O'Brien
Genome Res. May 1, 2000 10: 691-702; doi:10.1101/gr.10.5.691
...light chain gene maps to chromosome D3p12– p11. Mamm. Genome 9 : 178 – 179 . ↵ Chowdhary B.P. , Raudsepp T. , Fronicke L. , Scherthan H. ( 1998 ) Emerging patterns of comparative organization in some mammalian species as revealed by Zoo-FISH. Genome Res 8 : 577 – 589 . ↵ Copeland N.G. , Jenkins N...
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RESOURCE: Integration of the Rat Recombination and EST Maps in the Rat Genomic Sequence and Comparative Mapping Analysis With the Mouse Genome
- Steven P. Wilder,
- Marie-Thérèse Bihoreau,
- Karène Argoud,
- Takeshi K. Watanabe,
- Mark Lathrop,
- and Dominique Gauguier
Genome Res. April 2004 14: 758-765; doi:10.1101/gr.2001604
...al. 2003 . Ensembl 2002: Accommodating comparative genomics. Nucleic Acids Res. 31 : 38 -42. ↵ Cooper, G.M., Brudno, M., Green, E.D., Batzoglou, S., and Sidow, A. 2003 . Quantitative estimates of sequence divergence for comparative analyses of mammalian s. Genome Res. 13 : 813 -820. ↵ Fakhrai-Rad, H...
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RESOURCE: The First-Generation Whole-Genome Radiation Hybrid Map in the Horse Identifies Conserved Segments in Human and Mouse Genomes
- Bhanu P. Chowdhary,
- Terje Raudsepp,
- Srinivas R. Kata,
- Glenda Goh,
- Lee V. Millon,
- Veronica Allan,
- François Piumi,
- Gérard Guérin,
- June Swinburne,
- Matthew Binns,
- Teri L. Lear,
- Jim Mickelson,
- James Murray,
- Douglas F. Antczak,
- James E. Womack,
- and Loren C. Skow
Genome Res. April 1, 2003 13: 742-751; doi:10.1101/gr.917503
....T. , Ruvinsky A. ( 2000 ) Cytogenetics and physical gene maps. In: in The genetics of the horse , eds Bowling A.T. , Ruvinsky A. ( CABI Publishing , New York, NY ), pp 171 – 243 . ↵ Chowdhary B.P. , Raudsepp T. , Fronicke L. , Scherthan H. ( 1998 ) Emerging patterns of comparative organization in some mammalian...
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LETTER: The Human Hox-bearing Chromosome Regions Did Arise by Block or Chromosome (or Even Genome) Duplications
- Dan Larhammar,
- Lars-Gustav Lundin,
- and Finn Hallböök
Genome Res. December 1, 2002 12: 1910-1920; doi:10.1101/gr.445702
...many chromosomal rearrangements are known to have taken place ( Chowdhary et al. 1998 ; Murphy et al. 2001 ; Gregory et al. 2002 ). This is particularly clear for two of the four human Hox-bearing chromosomes that differ from those of the mammalian ancestor. Hsa2 is the result of a fusion of two...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...of the genomic or epigenomic features. Herein we reconstructed the ancestral chromosome organization for several mammalian ancestral clades to investigate the functional role of EBRs in the context of changes that occurred for 60 million years (My) in the lineage leading to cattle.We used ruminants as a model...
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PERSPECTIVE: Advances in livestock genomics: Opening the barn door
- James E. Womack
Genome Res. December 2005 15: 1699-1705; doi:10.1101/gr.3809105
...identified in mammalian QTL studies beginning in 1999. These discoveries parallel the development of sequencing initiatives. The emergence of sequence from livestock species over the next few years bodes well for the discovery of genes underlying health and production traits in economically important species...
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LETTER: Phylogenetic Origin of Human Chromosomes 7, 16, and 19 and their Homologs in Placental Mammals
- Florence Richard,
- Martine Lombard,
- and Bernard Dutrillaux
Genome Res. May 1, 2000 10: 644-651; doi:10.1101/gr.10.5.644
...of the Indian Muntjac idiogram to align conserved chromosomal segments in sheep and human s by chromosome painting. Genomics 46 : 143 – 147 . ↵ Chowdhary B.P. , Raudsepp P. , Frönicke L. , Scherthan H. ( 1998 ) Emerging patterns of comparative organization in some mammalian species by Zoo-FISH. Genome Res. 8...

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