ARTICLES:

David S. Johnson, Qing Zhou, Kasumi Yagi, Nori Satoh, Wing Wong, and Arend Sidow

De novo discovery of a tissue-specific gene regulatory module in a chordate
Genome Res. 2005 15: 1315-1324. Published in Advance September 16, 2005, 10.1101/gr.4062605 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Claudine Médigue, Evelyne Krin, Géraldine Pascal, Valérie Barbe, Andreas Bernsel, Philippe N. Bertin, Frankie Cheung, Stéphane Cruveiller, Salvino D'Amico, Angela Duilio, Gang Fang, Georges Feller, Christine Ho, Sophie Mangenot, Gennaro Marino, Johan Nilsson, Ermenegilda Parrilli, Eduardo P.C. Rocha, Zoé Rouy, Agnieszka Sekowska, Maria Luisa Tutino, David Vallenet, Gunnar von Heijne, and Antoine Danchin

Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
Genome Res. 2005 15: 1325-1335. Published in Advance September 16, 2005, 10.1101/gr.4126905 [Abstract] [Full Text] [PDF] [Supplemental Reseach Data]  

Michaela Falb, Friedhelm Pfeiffer, Peter Palm, Karin Rodewald, Volker Hickmann, Jörg Tittor, and Dieter Oesterhelt

Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis
Genome Res. 2005 15: 1336-1343. Published in Advance September 16, 2005, 10.1101/gr.3952905 [Abstract] [Full Text] [PDF] [Supplemental Reseach Data]  

LETTERS:

Tera L. Newman, Eray Tuzun, V. Anne Morrison, Karen E. Hayden, Mario Ventura, Sean D. McGrath, Mariano Rocchi, and Evan E. Eichler

A genome-wide survey of structural variation between human and chimpanzee
Genome Res. 2005 15: 1344-1356. Published in Advance September 16, 2005, 10.1101/gr.4338005 [Abstract] [Full Text] [PDF] [Supplemental Reseach Data]  

Igor Mokrousov, Ho Minh Ly, Tatiana Otten, Nguyen Ngoc Lan, Boris Vyshnevskyi, Sven Hoffner, and Olga Narvskaya

Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: Clues from human phylogeography
Genome Res. 2005 15: 1357-1364. Published in Advance September 16, 2005, 10.1101/gr.3840605 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Stephen S. Fong, Andrew R. Joyce, and Bernhard Ø. Palsson

Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
Genome Res. 2005 15: 1365-1372. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Peter D. Keightley, Gregory V. Kryukov, Shamil Sunyaev, Daniel L. Halligan, and Daniel J. Gaffney

Evolutionary constraints in conserved nongenic sequences of mammals
Genome Res. 2005 15: 1373-1378. [Abstract] [Full Text] [PDF]  

Florian M. Pauler, Stefan H. Stricker, Katarzyna E. Warczok, and Denise P. Barlow

Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements
Genome Res. 2005 15: 1379-1387. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Martin Bengtsson, Anders Ståhlberg, Patrik Rorsman, and Mikael Kubista

Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels
Genome Res. 2005 15: 1388-1392. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Doris Bachtrog

Sex chromosome evolution: Molecular aspects of Y-chromosome degeneration in Drosophila
Genome Res. 2005 15: 1393-1401. Published in Advance September 16, 2005, 10.1101/gr.3543605 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Olivier Zugasti, Jeena Rajan, and Patricia E. Kuwabara

The function and expansion of the Patched- and Hedgehog-related homologs in C. elegans
Genome Res. 2005 15: 1402-1410. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Michaël Bekaert, Hugues Richard, Bernard Prum, and Jean-Pierre Rousset

Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae
Genome Res. 2005 15: 1411-1420. [Abstract] [Full Text] [PDF]  

Lars Kuepfer, Uwe Sauer, and Lars M. Blank

Metabolic functions of duplicate genes in Saccharomyces cerevisiae
Genome Res. 2005 15: 1421-1430. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Pablo D. Rabinowicz, Robert Citek, Muhammad A. Budiman, Andrew Nunberg, Joseph A. Bedell, Nathan Lakey, Andrew L. O'Shaughnessy, Lidia U. Nascimento, W. Richard McCombie, and Robert A. Martienssen

Differential methylation of genes and repeats in land plants
Genome Res. 2005 15: 1431-1440. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

METHODS:

John Emberton, Jianxin Ma, Yinan Yuan, Phillip SanMiguel, and Jeffrey L. Bennetzen

Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries
Genome Res. 2005 15: 1441-1446. [Abstract] [Full Text] [PDF]  

Duane E. Smailus, Andre Marziali, Philip Dextras, Marco A. Marra, and Robert A. Holt

Simple, robust methods for high-throughput nanoliter-scale DNA sequencing
Genome Res. 2005 15: 1447-1450. Published in Advance September 16, 2005, 10.1101/gr.4221805 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

RESOURCES:

Belinda Giardine, Cathy Riemer, Ross C. Hardison, Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, Daniel Blankenberg, Istvan Albert, James Taylor, Webb Miller, W. James Kent, and Anton Nekrutenko

Galaxy: A platform for interactive large-scale genome analysis
Genome Res. 2005 15: 1451-1455. Published in Advance September 16, 2005, 10.1101/gr.4086505 [Abstract] [Full Text] [PDF] [Supplemental Reseach Data]  

Kevin P. Byrne and Kenneth H. Wolfe

The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
Genome Res. 2005 15: 1456-1461. Published in Advance September 16, 2005, 10.1101/gr.3672305 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

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