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LETTER: Analyses of the Extent of Shared Synteny and Conserved Gene Orders between the Genome of Fugu rubripes and Human 20q
- Sarah F. Smith,
- Philip Snell,
- Frank Gruetzner,
- Anthony J. Bench,
- Thomas Haaf,
- Judith A. Metcalfe,
- Anthony R. Green,
- and Greg Elgar
Genome Res. May 1, 2002 12: 776-784; Published in Advance April 12, 2002, doi:10.1101/gr.221802
.... Development 123 : 37 – 46 . ↵ Elgar G. , Clark M.S. , Meek S. , Smith S. , Warner S. , Edwards Y.J. , Bouchireb N. , Cottage A. , Yeo G.S. , Umrania Y. , et al. ( 1999 ) Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res. 9 : 960 – 971 . ↵ Gates...
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LETTER: Genome Size Evolution in Pufferfish: A Comparative Analysis of Diodontid and Tetraodontid Pufferfish Genomes
- Daniel E. Neafsey and
- Stephen R. Palumbi
Genome Res. May 1, 2003 13: 821-830; doi:10.1101/gr.841703
...of the Tetraodon nigroviridis . Proc. Natl. Acad. Sci. 99 : 13636 – 13641 . ↵ Elgar G. , Clark M.S. , Meek S. , Smith S. , Warner S. , Edwards Y.J. , Bouchireb N. , Cottage A. , Yeo G.S. , Umrania Y. , et al. ( 1999 ) Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence...
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ARTICLE: Developmental Roles of Pufferfish Hox Clusters and Genome Evolution in Ray-Fin Fish
- Angel Amores,
- Tohru Suzuki,
- Yi-Lin Yan,
- Jordan Pomeroy,
- Amy Singer,
- Chris Amemiya,
- and John H. Postlethwait
Genome Res. January 2004 14: 1-10; doi:10.1101/gr.1717804
.... ↵ Elgar, G., Clark, M.S., Meek, S., Smith, S., Warner, S., Edwards, Y.J.K., Bouchireb, N., Cottage, A., Yeo, G.S.H., Umrania, Y., et al. 1999 . Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res. 9 : 960 -971. ↵ Escriva, H., Manzon, L...
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LETTER: Characterization and Repeat Analysis of the Compact Genome of the Freshwater Pufferfish Tetraodon nigroviridis
- H. Roest Crollius,
- O. Jaillon,
- C. Dasilva,
- C. Ozouf-Costaz,
- C. Fizames,
- C. Fischer,
- L. Bouneau,
- A. Billault,
- F. Quetier,
- W. Saurin,
- A. Bernot,
- and J. Weissenbach
Genome Res. July 1, 2000 10: 939-949; doi:10.1101/gr.10.7.939
...of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res. 9 : 960 – 71 . ↵ Ewing B. , Green P. ( 1998 ) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8 : 186 – 94 . ↵ Finnegan D.J. ( 1989 ) Eukaryotic transposable elements and evolution...
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REPORT: Is “Junk” DNA Mostly Intron DNA?
- Gane Ka-Shu Wong,
- Douglas A. Passey,
- Ying-zong Huang,
- Zhiyong Yang,
- and Jun Yu
Genome Res. November 1, 2000 10: 1672-1678; doi:10.1101/gr.148900
.... ( 1996 ) Small is beautiful: Comparative genomics with the pufferfish (Fugu rubripes). Trends Genet. 12 : 145 – 150 . ↵ Ewing B. , Green P. ( 2000 ) Analysis of expressed sequence tags indicates 35,000 human genes. Nat. Genet. 25 : 232 – 234 . ↵ Fields C. , Adams M.D. , White O. , Venter J.C. ( 1994...
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ARTICLE: Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
- Gayle K. McEwen,
- Adam Woolfe,
- Debbie Goode,
- Tanya Vavouri,
- Heather Callaway,
- and Greg Elgar
Genome Res. April 2006 16: 451-465; Published in Advance March 13, 2006, doi:10.1101/gr.4143406
...noncoding sequences most likely to be functional has been through fish–mammal comparisons using the compact of the pufferfish Fugu rubripes ( Boffelli et al. 2004 ). Mammals and fish, being the most evolutionary distant extant vertebrates for which whole information is available, provide high stringency...
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LETTER: Comparative Genomic Analysis of the Interferon/Interleukin-10 Receptor Gene Cluster
- Jérôme Reboul,
- Katheleen Gardiner,
- Danièle Monneron,
- Gilles Uzé,
- and Georges Lutfalla
Genome Res. March 1, 1999 9: 242-250; doi:10.1101/gr.9.3.242
...content of this GART–cytokine receptor gene cluster and the use of comparative genomic analysis to identify chicken IFNAR1, IFNAR2 , and IL10R2 . We show that the large-scale structure of this locus is conserved in human and chicken but not in the pufferfish Fugu rubripes . This establishes...
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LETTER: Human and Mouse α-Synuclein Genes: Comparative Genomic Sequence Analysis and Identification of a Novel Gene Regulatory Element
- Jeffrey W. Touchman,
- Anindya Dehejia,
- Ornit Chiba-Falek,
- Deborah E. Cabin,
- Jody R. Schwartz,
- Bonnie M. Orrison,
- Mihael H. Polymeropoulos,
- and Robert L. Nussbaum
Genome Res. January 1, 2001 11: 78-86; doi:10.1101/gr.165801
...: 425 – 427 . ↵ Davidson H. , Taylor M.S. , Doherty A. , Boyd A.C. , Porteous D.J. ( 2000 ) Genomic sequence analysis of fugu rubripes CFTR and flanking genes in a 60 kb region conserving synteny with 800 kb of human chromosome 7. Genome Res. 10 : 1194 – 1203 . ↵ Dubchak I. , Brudno M. , Loots G...
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LETTER: A Random Sequencing Approach for the Analysis of the Trypanosoma cruzi Genome: General Structure, Large Gene and Repetitive DNA Families, and Gene Discovery
- Fernán Agüero,
- Ramiro E. Verdún,
- Alberto Carlos C. Frasch,
- and Daniel O. Sánchez
Genome Res. December 1, 2000 10: 1996-2005; Published in Advance November 21, 2000, doi:10.1101/gr.146300
.... Parasitol. 84 : 167 – 178 . ↵ Elgar G. , Clark M.S. , Meek S. , Smith S. , Warner S. , Edwards Y.J.K. , Bouchireb N. , Cottage A. , Yeo G.S.H. , Umrania Y. , et al. ( 1999 ) Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res. 9 : 960 – 971...
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ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
...) neutrally evolving DNA in mammals ( Cooper et al. 2004 ), but were not accurate representations of the neutral substitution process in all respects. In particular, the branches to the more distant species (chicken and Fugu ) were significantly underestimated, because the s of these species are, in general...

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