REVIEW:

Rohan B.H. Williams, Eva K.F. Chan, Mark J. Cowley, and Peter F.R. Little

The influence of genetic variation on gene expression
Genome Res. 2007 17: 1707-1716. [Abstract] [Full Text] [PDF]  

LETTERS:

Christiane Robbins, Jada Benn Torres, Stanley Hooker, Carolina Bonilla, Wenndy Hernandez, Angela Candreva, Chiledum Ahaghotu, Rick Kittles, and John Carpten

Confirmation study of prostate cancer risk variants at 8q24 in African Americans identifies a novel risk locus
Genome Res. 2007 17: 1717-1722. Published in Advance October 31, 2007, 10.1101/gr.6782707 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Philippe P. Luedi, Fred S. Dietrich, Jennifer R. Weidman, Jason M. Bosko, Randy L. Jirtle, and Alexander J. Hartemink

Computational and experimental identification of novel human imprinted genes
Genome Res. 2007 17: 1723-1730. Published in Advance November 30, 2007, 10.1101/gr.6584707 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Kee-Pyo Kim, Alexandra Thurston, Christine Mummery, Dorien Ward-van Oostwaard, Helen Priddle, Cinzia Allegrucci, Chris Denning, and Lorraine Young

Gene-specific vulnerability to imprinting variability in human embryonic stem cell lines
Genome Res. 2007 17: 1731-1742. Published in Advance November 7, 2007, 10.1101/gr.6609207 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Gene Cutler, Lisa A. Marshall, Ni Chin, Helene Baribault, and Paul D. Kassner

Significant gene content variation characterizes the genomes of inbred mouse strains
Genome Res. 2007 17: 1743-1754. Published in Advance November 7, 2007, 10.1101/gr.6754607 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Peter Andolfatto

Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
Genome Res. 2007 17: 1755-1762. Published in Advance November 7, 2007, 10.1101/gr.6691007 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

METHODS:

Adam Siepel, Mark Diekhans, Brona Brejová, Laura Langton, Michael Stevens, Charles L.G. Comstock, Colleen Davis, Brent Ewing, Shelly Oommen, Christopher Lau, Hung-Chun Yu, Jianfeng Li, Bruce A. Roe, Phil Green, Daniela S. Gerhard, Gary Temple, David Haussler, and Michael R. Brent

Targeted discovery of novel human exons by comparative genomics
Genome Res. 2007 17: 1763-1773. Published in Advance November 7, 2007, 10.1101/gr.7128207 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Bernhard Suter, Michael J. Fetchko, Ralph Imhof, Christopher I. Graham, Ingrid Stoffel-Studer, Caroline Zbinden, Maanasa Raghavan, Lianet Lopez, Lucija Beneti, Jacqueline Hort, Jeffrey Fillingham, Jack F. Greenblatt, Guri Giaever, Corey Nislow, and Igor Stagljar

Examining protein–protein interactions using endogenously tagged yeast arrays: The Cross-and-Capture system
Genome Res. 2007 17: 1774-1782. Published in Advance November 7, 2007, 10.1101/gr.6667007 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

RESOURCES:

Tara C. Matise, Fang Chen, Wenwei Chen, Francisco M. De La Vega, Mark Hansen, Chunsheng He, Fiona C.L. Hyland, Giulia C. Kennedy, Xiangyang Kong, Sarah S. Murray, Janet S. Ziegle, William C.L. Stewart, and Steven Buyske

A second-generation combined linkage–physical map of the human genome
Genome Res. 2007 17: 1783-1786. Published in Advance November 7, 2007, 10.1101/gr.7156307 [Abstract] [Full Text] [PDF]  

Matthieu Legendre, Nathalie Pochet, Theodore Pak, and Kevin J. Verstrepen

Sequence-based estimation of minisatellite and microsatellite repeat variability
Genome Res. 2007 17: 1787-1796. Published in Advance October 31, 2007, 10.1101/gr.6554007 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Webb Miller, Kate Rosenbloom, Ross C. Hardison, Minmei Hou, James Taylor, Brian Raney, Richard Burhans, David C. King, Robert Baertsch, Daniel Blankenberg, Sergei L. Kosakovsky Pond, Anton Nekrutenko, Belinda Giardine, Robert S. Harris, Svitlana Tyekucheva, Mark Diekhans, Thomas H. Pringle, William J. Murphy, Arthur Lesk, George M. Weinstock, Kerstin Lindblad-Toh, Richard A. Gibbs, Eric S. Lander, Adam Siepel, David Haussler, and W. James Kent

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
Genome Res. 2007 17: 1797-1808. Published in Advance November 5, 2007, 10.1101/gr.6761107 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Michael J. Cornell, Intikhab Alam, Darren M. Soanes, Han Min Wong, Cornelia Hedeler, Norman W. Paton, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, and Stephen G. Oliver

Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi
Genome Res. 2007 17: 1809-1822. Published in Advance November 5, 2007, 10.1101/gr.6531807 [Abstract] [Full Text] [PDF] [HTML Page - index.htslp] OPEN ACCESS ARTICLE  

12 DROSOPHILA GENOMES/LETTER:

Michael F. Lin, Joseph W. Carlson, Madeline A. Crosby, Beverley B. Matthews, Charles Yu, Soo Park, Kenneth H. Wan, Andrew J. Schroeder, L. Sian Gramates, Susan E. St. Pierre, Margaret Roark, Kenneth L. Wiley, Jr., Rob J. Kulathinal, Peili Zhang, Kyl V. Myrick, Jerry V. Antone, Susan E. Celniker, William M. Gelbart, and Manolis Kellis

Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
Genome Res. 2007 17: 1823-1836. Published in Advance November 7, 2007, 10.1101/gr.6679507 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Andreas Heger and Chris P. Ponting

Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
Genome Res. 2007 17: 1837-1849. Published in Advance November 7, 2007, 10.1101/gr.6249707 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

J. Graham Ruby, Alexander Stark, Wendy K. Johnston, Manolis Kellis, David P. Bartel, and Eric C. Lai

Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
Genome Res. 2007 17: 1850-1864. Published in Advance November 7, 2007, 10.1101/gr.6597907 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Alexander Stark, Pouya Kheradpour, Leopold Parts, Julius Brennecke, Emily Hodges, Gregory J. Hannon, and Manolis Kellis

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
Genome Res. 2007 17: 1865-1879. Published in Advance November 7, 2007, 10.1101/gr.6593807 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Arjun Bhutkar, Susan M. Russo, Temple F. Smith, and William M. Gelbart

Genome-scale analysis of positionally relocated genes
Genome Res. 2007 17: 1880-1887. Published in Advance November 7, 2007, 10.1101/gr.7062307 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Deborah E. Stage and Thomas H. Eickbush

Sequence variation within the rRNA gene loci of 12 Drosophila species
Genome Res. 2007 17: 1888-1897. Published in Advance November 7, 2007, 10.1101/gr.6376807 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Pär G. Engström, Shannan J. Ho Sui, Øyvind Drivenes, Thomas S. Becker, and Boris Lenhard

Genomic regulatory blocks underlie extensive microsynteny conservation in insects
Genome Res. 2007 17: 1898-1908. Published in Advance November 7, 2007, 10.1101/gr.6669607 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Alfredo Villasante, José P. Abad, Rosario Planelló, María Méndez-Lago, Susan E. Celniker, and Beatriz de Pablos

Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase
Genome Res. 2007 17: 1909-1918. Published in Advance November 7, 2007, 10.1101/gr.6365107 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

12 DROSOPHILA GENOMES/METHODS:

Pouya Kheradpour, Alexander Stark, Sushmita Roy, and Manolis Kellis

Reliable prediction of regulator targets using 12 Drosophila genomes
Genome Res. 2007 17: 1919-1931. Published in Advance November 7, 2007, 10.1101/gr.7090407 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Matthew D. Rasmussen and Manolis Kellis

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
Genome Res. 2007 17: 1932-1942. Published in Advance November 7, 2007, 10.1101/gr.7105007 [Abstract] [Full Text] [PDF] [Drosophila 12 Genomes] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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