ARTICLES:

Jeffrey A. Bailey, Deanna M. Church, Mario Ventura, Mariano Rocchi, and Evan E. Eichler

Analysis of Segmental Duplications and Genome Assembly in the Mouse
Genome Res. 2004 14: 789-801. [Abstract] [Full Text] [Supplemental Research Data]  

Cristian I. Castillo-Davis, Fyodor A. Kondrashov, Daniel L. Hartl, and Rob J. Kulathinal

The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint
Genome Res. 2004 14: 802-811. [Abstract] [Full Text] [Supplemental Research Data]  

LETTERS:

Anirban Maitra, Yoram Cohen, Susannah E.D. Gillespie, Elizabeth Mambo, Noriyoshi Fukushima, Mohammad O. Hoque, Nila Shah, Michael Goggins, Joseph Califano, David Sidransky, and Aravinda Chakravarti

The Human MitoChip: A High-Throughput Sequencing Microarray for Mitochondrial Mutation Detection
Genome Res. 2004 14: 812-819. [Abstract] [Full Text] [Supplemental Research Data]  

Kiyoshi Naruse, Minoru Tanaka, Kazuei Mita, Akihiro Shima, John Postlethwait, and Hiroshi Mitani

A Medaka Gene Map: The Trace of Ancestral Vertebrate Proto-Chromosomes Revealed by Comparative Gene Mapping
Genome Res. 2004 14: 820-828. Published in Advance April 12, 2004, 10.1101/gr.2004004 [Abstract] [Full Text] [Supplemental Research Data]  

Amos Tanay, Irit Gat-Viks, and Ron Shamir

A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation
Genome Res. 2004 14: 829-834. [Abstract] [Full Text] [Supplemental Research Data]  

Elena Bosch, Matthew E. Hurles, Arcadi Navarro, and Mark A. Jobling

Dynamics of a Human Interparalog Gene Conversion Hotspot
Genome Res. 2004 14: 835-844. [Abstract] [Full Text] [Supplemental Research Data]  

Jianzhi Zhang, Xiaoxia Wang, and Ondrej Podlaha

Testing the Chromosomal Speciation Hypothesis for Humans and Chimpanzees
Genome Res. 2004 14: 845-851. [Abstract] [Full Text] [Supplemental Research Data]  

Emmanouil T. Dermitzakis, Ewen Kirkness, Scott Schwarz, Ewan Birney, Alexandre Reymond, and Stylianos E. Antonarakis

Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment
Genome Res. 2004 14: 852-859. Published in Advance April 12, 2004, 10.1101/gr.1934904 [Abstract] [Full Text] [Supplemental Research Data]  

Jianxin Ma, Katrien M. Devos, and Jeffrey L. Bennetzen

Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice
Genome Res. 2004 14: 860-869. Published in Advance April 12, 2004, 10.1101/gr.1466204 [Abstract] [Full Text]  

METHODS:

Kevin L. Gunderson, Semyon Kruglyak, Michael S. Graige, Francisco Garcia, Bahram G. Kermani, Chanfeng Zhao, Diping Che, Todd Dickinson, Eliza Wickham, Jim Bierle, Dennis Doucet, Monika Milewski, Robert Yang, Chris Siegmund, Juergen Haas, Lixin Zhou, Arnold Oliphant, Jian-Bing Fan, Steven Barnard, and Mark S. Chee

Decoding Randomly Ordered DNA Arrays
Genome Res. 2004 14: 870-877. Published in Advance April 12, 2004, 10.1101/gr.2255804 [Abstract] [Full Text]  

Jian-Bing Fan, Joanne M. Yeakley, Marina Bibikova, Eugene Chudin, Eliza Wickham, Jing Chen, Dennis Doucet, Philippe Rigault, Baohong Zhang, Richard Shen, Celeste McBride, Hai-Ri Li, Xiang-Dong Fu, Arnold Oliphant, David L. Barker, and Mark S. Chee

A Versatile Assay for High-Throughput Gene Expression Profiling on Universal Array Matrices
Genome Res. 2004 14: 878-885. [Abstract] [Full Text]  

Stéphane Cruveiller, Kamel Jabbari, Oliver Clay, and Giorgio Bernardi

Compositional Gene Landscapes in Vertebrates
Genome Res. 2004 14: 886-892. [Abstract] [Full Text]  

Amy Bishop, Sue Fielding, Paul Dyson, and Paul Herron

Systematic Insertional Mutagenesis of a Streptomycete Genome: A Link Between Osmoadaptation and Antibiotic Production
Genome Res. 2004 14: 893-900. Published in Advance April 12, 2004, 10.1101/gr.1710304 [Abstract] [Full Text]  

David L. Barker, Mark S.T. Hansen, A. Fawad Faruqi, Diane Giannola, Orlando R. Irsula, Roger S. Lasken, Martin Latterich, Vladimir Makarov, Arnold Oliphant, Jonathon H. Pinter, Richard Shen, Irina Sleptsova, William Ziehler, and Eric Lai

Two Methods of Whole-Genome Amplification Enable Accurate Genotyping Across a 2320-SNP Linkage Panel
Genome Res. 2004 14: 901-907. [Abstract] [Full Text]  

Kui Zhang, Zhaohui S. Qin, Jun S. Liu, Ting Chen, Michael S. Waterman, and Fengzhu Sun

Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies
Genome Res. 2004 14: 908-916. Published in Advance April 12, 2004, 10.1101/gr.1837404 [Abstract] [Full Text]  

RESOURCES:

Iwei Yeh, Theodor Hanekamp, Sophia Tsoka, Peter D. Karp, and Russ B. Altman

Computational Analysis of Plasmodium falciparum Metabolism: Organizing Genomic Information to Facilitate Drug Discovery
Genome Res. 2004 14: 917-924. Published in Advance April 12, 2004, 10.1101/gr.2050304 [Abstract] [Full Text]  

ENSEMBL Special:

Ewan Birney, T. Daniel Andrews, Paul Bevan, Mario Caccamo, Yuan Chen, Laura Clarke, Guy Coates, James Cuff, Val Curwen, Tim Cutts, Thomas Down, Eduardo Eyras, Xose M. Fernandez-Suarez, Paul Gane, Brian Gibbins, James Gilbert, Martin Hammond, Hans-Rudolf Hotz, Vivek Iyer, Kerstin Jekosch, Andreas Kahari, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Heikki Lehvaslaiho, Graham McVicker, Craig Melsopp, Patrick Meidl, Emmanuel Mongin, Roger Pettett, Simon Potter, Glenn Proctor, Mark Rae, Steve Searle, Guy Slater, Damian Smedley, James Smith, Will Spooner, Arne Stabenau, James Stalker, Roy Storey, Abel Ureta-Vidal, K. Cara Woodwark, Graham Cameron, Richard Durbin, Anthony Cox, Tim Hubbard, and Michele Clamp

An Overview of Ensembl
Genome Res. 2004 14: 925-928. Published in Advance April 12, 2004, 10.1101/gr.1860604 [Abstract] [Full Text]  

Arne Stabenau, Graham McVicker, Craig Melsopp, Glenn Proctor, Michele Clamp, and Ewan Birney

The Ensembl Core Software Libraries
Genome Res. 2004 14: 929-933. [Abstract] [Full Text]  

Simon C. Potter, Laura Clarke, Val Curwen, Stephen Keenan, Emmanuel Mongin, Stephen M.J. Searle, Arne Stabenau, Roy Storey, and Michele Clamp

The Ensembl Analysis Pipeline
Genome Res. 2004 14: 934-941. [Abstract] [Full Text]  

Val Curwen, Eduardo Eyras, T. Daniel Andrews, Laura Clarke, Emmanuel Mongin, Steven M.J. Searle, and Michele Clamp

The Ensembl Automatic Gene Annotation System
Genome Res. 2004 14: 942-950. [Abstract] [Full Text]  

James Stalker, Brian Gibbins, Patrick Meidl, James Smith, William Spooner, Hans-Rudolf Hotz, and Antony V. Cox

The Ensembl Web Site: Mechanics of a Genome Browser
Genome Res. 2004 14: 951-955. [Abstract] [Full Text] [Supplemental Research Data]  

Stephen B. Montgomery, Tamara Astakhova, Mikhail Bilenky, Ewan Birney, Tony Fu, Maik Hassel, Craig Melsopp, Marcin Rak, A. Gordon Robertson, Monica Sleumer, Asim S. Siddiqui, and Steven J.M. Jones

Sockeye: A 3D Environment for Comparative Genomics
Genome Res. 2004 14: 956-962. [Abstract] [Full Text] [Supplemental Research Data]  

Stephen M.J. Searle, James Gilbert, Vivek Iyer, and Michele Clamp

The Otter Annotation System
Genome Res. 2004 14: 963-970. [Abstract] [Full Text] [Supplemental Research Data]  

James A. Cuff, Guy M.P. Coates, Tim J.R. Cutts, and Mark Rae

The Ensembl Computing Architecture
Genome Res. 2004 14: 971-975. [Abstract] [Full Text]  

Eduardo Eyras, Mario Caccamo, Val Curwen, and Michele Clamp

ESTGenes: Alternative Splicing From ESTs in Ensembl
Genome Res. 2004 14: 976-987. [Abstract] [Full Text] [Supplemental Research Data][URL INFO]  

Ewan Birney, Michele Clamp, and Richard Durbin

GeneWise and Genomewise
Genome Res. 2004 14: 988-995. [Abstract] [Full Text]  

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