ARTICLES:

Stephen Richards, Yue Liu, Brian R. Bettencourt, Pavel Hradecky, Stan Letovsky, Rasmus Nielsen, Kevin Thornton, Melissa J. Hubisz, Rui Chen, Richard P. Meisel, Olivier Couronne, Sujun Hua, Mark A. Smith, Peili Zhang, Jing Liu, Harmen J. Bussemaker, Marinus F. van Batenburg, Sally L. Howells, Steven E. Scherer, Erica Sodergren, Beverly B. Matthews, Madeline A. Crosby, Andrew J. Schroeder, Daniel Ortiz-Barrientos, Catharine M. Rives, Michael L. Metzker, Donna M. Muzny, Graham Scott, David Steffen, David A. Wheeler, Kim C. Worley, Paul Havlak, K. James Durbin, Amy Egan, Rachel Gill, Jennifer Hume, Margaret B. Morgan, George Miner, Cerissa Hamilton, Yanmei Huang, Lenée Waldron, Daniel Verduzco, Kerstin P. Clerc-Blankenburg, Inna Dubchak, Mohamed A.F. Noor, Wyatt Anderson, Kevin P. White, Andrew G. Clark, Stephen W. Schaeffer, William Gelbart, George M. Weinstock, and Richard A. Gibbs

Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
Genome Res. 2005 15: 1-18. [Abstract] [Full Text] [PDF] [Suppplemental Research Data] OPEN ACCESS ARTICLE  

LETTERS:

Luísa Pereira, Martin Richards, Ana Goios, Antonio Alonso, Cristina Albarrán, Oscar Garcia, Doron M. Behar, Mukaddes Gölge, Jiri Hatina, Lihadh Al-Gazali, Daniel G. Bradley, Vincent Macaulay, and António Amorim

High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium
Genome Res. 2005 15: 19-24. [Abstract] [Full Text] [PDF]  

Jennifer G. Sambrook, Arman Bashirova, Sophie Palmer, Sarah Sims, John Trowsdale, Laurent Abi-Rached, Peter Parham, Mary Carrington, and Stephan Beck

Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates
Genome Res. 2005 15: 25-35. [Abstract] [Full Text] [PDF]  

Samson O. Obado, Martin C. Taylor, Shane R. Wilkinson, Elizabeth V. Bromley, and John M. Kelly

Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional "strand-switch" domain as a major feature
Genome Res. 2005 15: 36-43. [Abstract] [Full Text] [PDF]  

METHODS:

Eric Chiao, Jeff Leonard, Kari Dickinson, and Julie C. Baker

High-throughput functional screen of mouse gastrula cDNA libraries reveals new components of endoderm and mesoderm specification
Genome Res. 2005 15: 44-53. [Abstract] [Full Text] [PDF]  

Liliana Florea, Valentina Di Francesco, Jason Miller, Russell Turner, Alison Yao, Michael Harris, Brian Walenz, Clark Mobarry, Gennady V. Merkulov, Rosane Charlab, Ian Dew, Zuoming Deng, Sorin Istrail, Peter Li, and Granger Sutton

Gene and alternative splicing annotation with AIR
Genome Res. 2005 15: 54-66. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Analabha Basu, Probal Chaudhuri, and Partha P. Majumder

Identification of polymorphic motifs using probabilistic search algorithms
Genome Res. 2005 15: 67-77. [Abstract] [Full Text] [PDF] [Suppplemental Research Data]  

Alex Adai, Cameron Johnson, Sizolwenkosi Mlotshwa, Sarah Archer-Evans, Varun Manocha, Vicki Vance, and Venkatesan Sundaresan

Computational prediction of miRNAs in Arabidopsis thaliana
Genome Res. 2005 15: 78-91. [Abstract] [Full Text] [PDF] [Suppplemental Research Data]  

Richard Culleton, Axel Martinelli, Paul Hunt, and Richard Carter

Linkage group selection: Rapid gene discovery in malaria parasites
Genome Res. 2005 15: 92-97. [Abstract] [Full Text] [PDF]  

CHICKEN SPECIAL/LETTERS:

Guillaume Bourque, Evgeny M. Zdobnov, Peer Bork, Pavel A. Pevzner, and Glenn Tesler

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
Genome Res. 2005 15: 98-110. Published in Advance December 8, 2004, 10.1101/gr.3002305 [Abstract] [Full Text] [PDF] [Supplemental Research Data] [The Chicken Genome]  

Josep F. Abril, Robert Castelo, and Roderic Guigó

Comparison of splice sites in mammals and chicken
Genome Res. 2005 15: 111-119. Published in Advance December 8, 2004, 10.1101/gr.3108805 [Abstract] [Full Text] [PDF] [Supplemental Research Data] [The Chicken Genome]  

Erik Axelsson, Matthew T. Webster, Nick G.C. Smith, David W. Burt, and Hans Ellegren

Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes
Genome Res. 2005 15: 120-125. Published in Advance December 8, 2004, 10.1101/gr.3021305 [Abstract] [Full Text] [PDF] [Supplemental Research Data] [The Chicken Genome]  

Thomas Wicker, Jon S. Robertson, Stefan R. Schulze, F. Alex Feltus, Vincent Magrini, Jason A. Morrison, Elaine R. Mardis, Richard K. Wilson, Daniel G. Peterson, Andrew H. Paterson, and Robert Ivarie

The repetitive landscape of the chicken genome
Genome Res. 2005 15: 126-136. Published in Advance July 15, 2004, 10.1101/gr.2438004 [Abstract] [Full Text] [PDF] [Supplemental Research Data] [The Chicken Genome]  

Ivan Ovcharenko, Gabriela G. Loots, Marcelo A. Nobrega, Ross C. Hardison, Webb Miller, and Lisa Stubbs

Evolution and functional classification of vertebrate gene deserts
Genome Res. 2005 15: 137-145. Published in Advance December 8, 2004, 10.1101/gr.3015505 [Abstract] [Full Text] [PDF] [Supplemental Research Data] [The Chicken Genome]  

Martina Paulsen, Tarang Khare, Christopher Burgard, Sascha Tierling, and Jörn Walter

Evolution of the Beckwith-Wiedemann syndrome region in vertebrates
Genome Res. 2005 15: 146-153. Published in Advance December 8, 2004, 10.1101/gr.2689805 [Abstract] [Full Text] [PDF] [Supplemental Research Data] [The Chicken Genome]  

Takaaki Yokomine, Hisao Shirohzu, Wahyu Purbowasito, Atsushi Toyoda, Hisakazu Iwama, Kazuho Ikeo, Tetsuya Hori, Shigeki Mizuno, Masaoki Tsudzuki, Yoh-ichi Matsuda, Masahira Hattori, Yoshiyuki Sakaki, and Hiroyuki Sasaki

Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2–Igf2–H19 region
Genome Res. 2005 15: 154-165. Published in Advance December 8, 2004, 10.1101/gr.2609605 [Abstract] [Full Text] [PDF] [The Chicken Genome]  

CHICKEN SPECIAL/RESOURCES:

Wendy A. Kellner, Robert T. Sullivan, Brian H. Carlson, NISC Comparative Sequencing Program, and James W. Thomas

Uprobe: A genome-wide universal probe resource for comparative physical mapping in vertebrates
Genome Res. 2005 15: 166-173. Published in Advance December 8, 2004, 10.1101/gr.3066805 [Abstract] [Full Text] [PDF] [Supplemental Research Data] [The Chicken Genome]  

Simon J. Hubbard, Darren V. Grafham, Kevin J. Beattie, Ian M. Overton, Stuart R. McLaren, Michael D.R. Croning, Paul E. Boardman, James K. Bonfield, Joan Burnside, Robert M. Davies, Elizabeth R. Farrell, Matthew D. Francis, Sam Griffiths-Jones, Sean J. Humphray, Christopher Hyland, Carol E. Scott, Haizhou Tang, Ruth G. Taylor, Cheryll Tickle, William R.A. Brown, Ewan Birney, Jane Rogers, and Stuart A. Wilson

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
Genome Res. 2005 15: 174-183. Published in Advance December 8, 2004, 10.1101/gr.3011405 [Abstract] [Full Text] [PDF] [The Chicken Genome]  

Ivan Ovcharenko, Gabriela G. Loots, Belinda M. Giardine, Minmei Hou, Jian Ma, Ross C. Hardison, Lisa Stubbs, and Webb Miller

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Genome Res. 2005 15: 184-194. Published in Advance December 8, 2004, 10.1101/gr.3007205 [Abstract] [Full Text] [PDF] [The Chicken Genome]  

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