ARTICLES:

Soochin Cho, Suk-Won Jin, Adam Cohen, and Ronald E. Ellis

A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution
Genome Res. 2004 14: 1207-1220. [Abstract] [Full Text] [Supplemental Research Data]  

Stéphane Boissinot, Ali Entezam, Lynn Young, Peter J. Munson, and Anthony V. Furano

The Insertional History of an Active Family of L1 Retrotransposons in Humans
Genome Res. 2004 14: 1221-1231. Published in Advance June 14, 2004, 10.1101/gr.2326704 [Abstract] [Full Text] [Supplemental Research Data]  

LETTERS:

Nurjana Bachman, Yolanda Eby, and Jef D. Boeke

Local Definition of Ty1 Target Preference by Long Terminal Repeats and Clustered tRNA Genes
Genome Res. 2004 14: 1232-1247. Published in Advance June 14, 2004, 10.1101/gr.2052904 [Abstract] [Full Text] [Supplemental Research Data]  

Yong Hwee Loh, Alan Christoffels, Sydney Brenner, Walter Hunziker, and Byrappa Venkatesh

Extensive Expansion of the Claudin Gene Family in the Teleost Fish, Fugu rubripes
Genome Res. 2004 14: 1248-1257. Published in Advance June 14, 2004, 10.1101/gr.2400004 [Abstract] [Full Text] [Supplemental Research Data]  

Pascal Kahlem, Marc Sultan, Ralf Herwig, Matthias Steinfath, Daniela Balzereit, Barbara Eppens, Nidhi G. Saran, Mathew T. Pletcher, Sarah T. South, Gail Stetten, Hans Lehrach, Roger H. Reeves, and Marie-Laure Yaspo

Transcript Level Alterations Reflect Gene Dosage Effects Across Multiple Tissues in a Mouse Model of Down Syndrome
Genome Res. 2004 14: 1258-1267. [Abstract] [Full Text] [Supplemental Research Data]  

Robert Lyle, Corinne Gehrig, Charlotte Neergaard-Henrichsen, Samuel Deutsch, and Stylianos E. Antonarakis

Gene Expression From the Aneuploid Chromosome in a Trisomy Mouse Model of Down Syndrome
Genome Res. 2004 14: 1268-1274. [Abstract] [Full Text] [Supplemental Research Data]  

Karen D. Tsuchiya, John M. Greally, Yajun Yi, Kevin P. Noel, Jean-Pierre Truong, and Christine M. Disteche

Comparative Sequence and X-Inactivation Analyses of a Domain of Escape in Human Xp11.2 and the Conserved Segment in Mouse
Genome Res. 2004 14: 1275-1284. Published in Advance June 14, 2004, 10.1101/gr.2575904 [Abstract] [Full Text] [Supplemental Research Data]  

Bart M.G. Smits, Bert F.M. van Zutphen, Ronald H.A. Plasterk, and Edwin Cuppen

Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains
Genome Res. 2004 14: 1285-1290. [Abstract] [Full Text] [Supplemental Research Data]  

Joseph Schacherer, Yves Tourrette, Jean-Luc Souciet, Serge Potier, and Jacky de Montigny

Recovery of a Function Involving Gene Duplication by Retroposition in Saccharomyces cerevisiae
Genome Res. 2004 14: 1291-1297. [Abstract] [Full Text]  

Natalie C. Duarte, Markus J. Herrgård, and Bernhard Ø. Palsson

Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model
Genome Res. 2004 14: 1298-1309. Published in Advance June 14, 2004, 10.1101/gr.2250904 [Abstract] [Full Text] [Supplemental Research Data]  

Stefan Wuchty

Evolution and Topology in the Yeast Protein Interaction Network
Genome Res. 2004 14: 1310-1314. [Abstract] [Full Text] [Supplemental Research Data]  

Ben Lehner and Christopher M. Sanderson

A Protein Interaction Framework for Human mRNA Degradation
Genome Res. 2004 14: 1315-1323. [Abstract] [Full Text] [Supplemental Research Data-1][Supplemental Research Data-2]  

Frédéric Colland, Xavier Jacq, Virginie Trouplin, Christelle Mougin, Caroline Groizeleau, Alexandre Hamburger, Alain Meil, Jérôme Wojcik, Pierre Legrain, and Jean-Michel Gauthier

Functional Proteomics Mapping of a Human Signaling Pathway
Genome Res. 2004 14: 1324-1332. [Abstract] [Full Text] [Supplemental Research Data]  

Nicole Soranzo, Gianpiero L. Cavalleri, Michael E. Weale, Nicholas W. Wood, Chantal Depondt, Richard Marguerie, Sanjay M. Sisodiya, and David B. Goldstein

Identifying Candidate Causal Variants Responsible for Altered Activity of the ABCB1 Multidrug Resistance Gene
Genome Res. 2004 14: 1333-1344. Published in Advance June 14, 2004, 10.1101/gr.1965304 [Abstract] [Full Text] [Supplemental Research Data]  

YongYong Shi, XinZhi Zhao, Lan Yu, Ran Tao, JunXia Tang, YuJuan La, Yun Duan, Bo Gao, NiuFan Gu, YiFeng Xu, GuoYin Feng, ShaoMin Zhu, HuiJun Liu, Hugh Salter, and Lin He

Genetic Structure Adds Power to Detect Schizophrenia Susceptibility at SLIT3 in the Chinese Han Population
Genome Res. 2004 14: 1345-1349. [Abstract] [Full Text] [Supplemental Research Data]  

David J. Mulvihill and Yuh-Hwa Wang

Two Breakpoint Clusters at Fragile Site FRA3B Form Phased Nucleosomes
Genome Res. 2004 14: 1350-1357. [Abstract] [Full Text]  

Tiffany A. Greenwood, Brinda K. Rana, and Nicholas J. Schork

Human Haplotype Block Sizes Are Negatively Correlated With Recombination Rates
Genome Res. 2004 14: 1358-1361. [Abstract] [Full Text] [Supplemental Research Data]  

METHODS:

Wynand B.L. Alkema, Boris Lenhard, and Wyeth W. Wasserman

Regulog Analysis: Detection of Conserved Regulatory Networks Across Bacteria: Application to Staphylococcus aureus
Genome Res. 2004 14: 1362-1373. [Abstract] [Full Text]  

M. Ryan Weil, Piotr Widlak, John D. Minna, and Harold R. Garner

Global Survey of Chromatin Accessibility Using DNA Microarrays
Genome Res. 2004 14: 1374-1381. [Abstract] [Full Text] [Supplemental Research Data]  

Dieter Egli, Ernst Hafen, and Walter Schaffner

An Efficient Method to Generate Chromosomal Rearrangements by Targeted DNA Double-Strand Breaks in Drosophila melanogaster
Genome Res. 2004 14: 1382-1393. Published in Advance June 14, 2004, 10.1101/gr.2279804 [Abstract] [Full Text]  

Aaron C.E. Darling, Bob Mau, Frederick R. Blattner, and Nicole T. Perna

Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
Genome Res. 2004 14: 1394-1403. [Abstract] [Full Text] [Supplemental Research Data]  

Hossein Fakhrai-Rad, Jianbiao Zheng, Thomas D. Willis, Kee Wong, Kent Suyenaga, Martin Moorhead, Jim Eberle, Yvonne R. Thorstenson, Ted Jones, Ronald W. Davis, Eugeni Namsaraev, and Malek Faham

SNP Discovery in Pooled Samples With Mismatch Repair Detection
Genome Res. 2004 14: 1404-1412. [Abstract] [Full Text]  

The Ludwig–FAPESP Transcript Finishing Initiative, Mari Cleide Sogayar, and Anamaria A. Camargo

A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome
Genome Res. 2004 14: 1413-1423. Published in Advance June 14, 2004, 10.1101/gr.2111304 [Abstract] [Full Text] [Supplemental Research Data]  

RESOURCES:

Annelie Everts-van der Wind, Srinivas R. Kata, Mark R. Band, Mark Rebeiz, Denis M. Larkin, Robin E. Everts, Cheryl A. Green, Lei Liu, Shreedhar Natarajan, Tom Goldammer, Jun Heon Lee, Stephanie McKay, James E. Womack, and Harris A. Lewin

A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates
Genome Res. 2004 14: 1424-1437. [Abstract] [Full Text] [Supplemental Research Data]  

Victor Guryev, Eugene Berezikov, Rainer Malik, Ronald H.A. Plasterk, and Edwin Cuppen

Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
Genome Res. 2004 14: 1438-1443. [Abstract] [Full Text] [Supplemental Research Data]  

ERRATA:

Correction for Volume 14, p. 414
Genome Res. 2004 14: 1444. [Full Text]  

Correction for Volume 14, p. 742
Genome Res. 2004 14: 1444. [Full Text]  

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