ARTICLES:

Patrick H. Degnan, Adam B. Lazarus, and Jennifer J. Wernegreen

Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects
Genome Res. 2005 15: 1023-1033. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

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

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Genome Res. 2005 15: 1034-1050. Published in Advance July 15, 2005, 10.1101/gr.3715005 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

LETTERS:

David C. King, James Taylor, Laura Elnitski, Francesca Chiaromonte, Webb Miller, and Ross C. Hardison

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
Genome Res. 2005 15: 1051-1060. Published in Advance July 15, 2005, 10.1101/gr.3642605 [Abstract] [Full Text] [PDF]  

Elisa de la Calle-Mustienes, Cármen Gloria Feijóo, Miguel Manzanares, Juan J. Tena, Elisa Rodríguez-Seguel, Annalisa Letizia, Miguel L. Allende, and José Luis Gómez-Skarmeta

A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts
Genome Res. 2005 15: 1061-1072. Published in Advance July 15, 2005, 10.1101/gr.4004805 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Sarah J. Wheelan, Yasunori Aizawa, Jeffrey S. Han, and Jef D. Boeke

Gene-breaking: A new paradigm for human retrotransposon-mediated gene evolution
Genome Res. 2005 15: 1073-1078. Published in Advance July 15, 2005, 10.1101/gr.3688905 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Sandrine Caburet, Chiara Conti, Catherine Schurra, Ronald Lebofsky, Stuart J. Edelstein, and Aaron Bensimon

Human ribosomal RNA gene arrays display a broad range of palindromic structures
Genome Res. 2005 15: 1079-1085. Published in Advance July 15, 2005, 10.1101/gr.3970105 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Daniel J. Gaffney and Peter D. Keightley

The scale of mutational variation in the murid genome
Genome Res. 2005 15: 1086-1094. Published in Advance July 15, 2005, 10.1101/gr.3895005 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Lawriston Wilson, Yung-Hao Ching, Michael Farias, Suzanne A. Hartford, Gareth Howell, Hongguang Shao, Maja Bucan, and John C. Schimenti

Random mutagenesis of proximal mouse chromosome 5 uncovers predominantly embryonic lethal mutations
Genome Res. 2005 15: 1095-1105. Published in Advance July 15, 2005, 10.1101/gr.3826505 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Kenji K. Kojima and Haruhiko Fujiwara

An extraordinary retrotransposon family encoding dual endonucleases
Genome Res. 2005 15: 1106-1117. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Rong Wang, John T. Prince, and Edward M. Marcotte

Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias
Genome Res. 2005 15: 1118-1126. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

METHODS:

Jade P. Vinson, David B. Jaffe, Keith O'Neill, Elinor K. Karlsson, Nicole Stange-Thomann, Scott Anderson, Jill P. Mesirov, Nori Satoh, Yutaka Satou, Chad Nusbaum, Bruce Birren, James E. Galagan, and Eric S. Lander

Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Genome Res. 2005 15: 1127-1135. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Josephine N. Harada, Kristen E. Bower, Anthony P. Orth, Scott Callaway, Christian G. Nelson, Casey Laris, John B. Hogenesch, Peter K. Vogt, and Sumit K. Chanda

Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis
Genome Res. 2005 15: 1136-1144. Published in Advance July 15, 2005, 10.1101/gr.3889305 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Jason Gertz, Linda Riles, Peter Turnbaugh, Su-Wen Ho, and Barak A. Cohen

Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics
Genome Res. 2005 15: 1145-1152. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Matthew W. Hahn, Tijl De Bie, Jason E. Stajich, Chi Nguyen, and Nello Cristianini

Estimating the tempo and mode of gene family evolution from comparative genomic data
Genome Res. 2005 15: 1153-1160. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Nicolas Ray, Mathias Currat, Pierre Berthier, and Laurent Excoffier

Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations
Genome Res. 2005 15: 1161-1167. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

John M. Maris, George Hii, Craig A. Gelfand, Shobha Varde, Peter S. White, Eric Rappaport, Saul Surrey, and Paolo Fortina

Region-specific detection of neuroblastoma loss of heterozygosity at multiple loci simultaneously using a SNP-based tag-array platform
Genome Res. 2005 15: 1168-1176. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

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