Genome Research -- Table of Contents (13 [9])

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Volume 13, Issue 9: September 2003 [Index by Author] [Cover Caption]

Other Issues:

REVIEWS

ARTICLES

LETTERS

METHODS

RESOURCES

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REVIEWS:

Jef D. Boeke: The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis
Genome Res. 2003 13: 1975-1983. [Abstract] [Full Text]

ARTICLES:

Nathan J. Bowen, I. King Jordan, Jonathan A. Epstein, Valerie Wood, and Henry L. Levin: Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe
Genome Res. 2003 13: 1984-1997. [Abstract] [Full Text] [Supplemental Research Data]

Rogier Versteeg,, Barbera D.C. van Schaik, Marinus F. van Batenburg, Marco Roos, Ramin Monajemi, Huib Caron, Harmen J. Bussemaker, and Antoine H.C. van Kampen: The Human Transcriptome Map Reveals Extremes in Gene Density, Intron Length, GC Content, and Repeat Pattern for Domains of Highly and Weakly Expressed Genes
Genome Res. 2003 13: 1998-2004. Published in Advance August 12, 2003, 10.1101/gr.1649303 [Abstract] [Full Text] [Supplemental Research Data][Supplemental Research Data][Supplemental Research Data 3][Supplemental Research Data 4][Supplemental Research Data 5]

Ningxin Zhang, Annette L. Harrex, Barbara R. Holland, Lauren E. Fenton, Richard D. Cannon, and Jan Schmid: Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus
Genome Res. 2003 13: 2005-2017. [Abstract] [Full Text] [Supplemental Research Data]

LETTERS:

Stewart J. Hinchliffe, Karen E. Isherwood, Richard A. Stabler, Michael B. Prentice, Alexander Rakin, Richard A. Nichols, Petra C.F. Oyston, Jason Hinds, Richard W. Titball, and Brendan W. Wren: Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis
Genome Res. 2003 13: 2018-2029. [Abstract] [Full Text] [Supplemental Research Data]

Dan Choffnes Inada, Ali Bashir, Chunghau Lee, Brian C. Thomas, Cynthia Ko, Stephen A. Goff, and Michael Freeling: Conserved Noncoding Sequences in the Grasses
Genome Res. 2003 13: 2030-2041. [Abstract] [Full Text] [Supplemental Research Data][Supplemental Research Data][Supplemental Research Data][Supplemental Research Data]

Luba Katz and Christopher B. Burge: Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes
Genome Res. 2003 13: 2042-2051. [Abstract] [Full Text] [Supplemental Research Data]

Gavin C. Conant and Andreas Wagner: Asymmetric Sequence Divergence of Duplicate Genes
Genome Res. 2003 13: 2052-2058. [Abstract] [Full Text] [Supplemental Research Data]

Mario Ventura, Jonathan M. Mudge, Valeria Palumbo, Sally Burn, Elisabeth Blennow, Mauro Pierluigi, Roberto Giorda, Orsetta Zuffardi, Nicoletta Archidiacono, Michael S. Jackson, and Mariano Rocchi: Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25
Genome Res. 2003 13: 2059-2068. Published in Advance August 12, 2003, 10.1101/gr.1155103 [Abstract] [Full Text] [Supplemental Research Data]

Douglas P. Mortlock, Catherine Guenther, and David M. Kingsley: A General Approach for Identifying Distant Regulatory Elements Applied to the Gdf6 Gene
Genome Res. 2003 13: 2069-2081. Published in Advance August 12, 2003, 10.1101/gr.1306003 [Abstract] [Full Text]

Joseph H. Nadeau, Lindsay C. Burrage, Joe Restivo, Yoh-Han Pao, Gary Churchill, and Brian D. Hoit: Pleiotropy, Homeostasis, and Functional Networks Based on Assays of Cardiovascular Traits in Genetically Randomized Populations
Genome Res. 2003 13: 2082-2091. [Abstract] [Full Text]

Kuang-Yu Jen and Vivian G. Cheung: Transcriptional Response of Lymphoblastoid Cells to Ionizing Radiation
Genome Res. 2003 13: 2092-2100. Published in Advance August 12, 2003, 10.1101/gr.1240103 [Abstract] [Full Text] [Supplemental Research Data]

John D.H. Stead, Matthew E. Hurles, and Alec J. Jeffreys: Global Haplotype Diversity in the Human Insulin Gene Region
Genome Res. 2003 13: 2101-2111. [Abstract] [Full Text] [Supplemental Research Data]

Xin Lu, Tianhua Niu, and Jun S. Liu: Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms
Genome Res. 2003 13: 2112-2117. [Abstract] [Full Text]

Huaiyu Mi, Jody Vandergriff, Michael Campbell, Apurva Narechania, William Majoros, Suzanna Lewis, Paul D. Thomas, and Michael Ashburner: Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster
Genome Res. 2003 13: 2118-2128. [Abstract] [Full Text]

METHODS:

Paul D. Thomas, Michael J. Campbell, Anish Kejariwal, Huaiyu Mi, Brian Karlak, Robin Daverman, Karen Diemer, Anushya Muruganujan, and Apurva Narechania: PANTHER: A Library of Protein Families and Subfamilies Indexed by Function
Genome Res. 2003 13: 2129-2141. [Abstract] [Full Text]

Shiguo Zhou, Erika Kvikstad, Andrew Kile, Jessica Severin, Dan Forrest, Rod Runnheim, Chris Churas, Jason W. Hickman, Chris Mackenzie, Madhusudan Choudhary, Timothy Donohue, Samuel Kaplan, and David C. Schwartz: Whole-Genome Shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and Its Use for Whole-Genome Shotgun Sequence Assembly
Genome Res. 2003 13: 2142-2151. [Abstract] [Full Text]

Friedrich W. Engler, James Hatfield, William Nelson, and Carol A. Soderlund: Locating Sequence on FPC Maps and Selecting a Minimal Tiling Path
Genome Res. 2003 13: 2152-2163. Published in Advance August 12, 2003, 10.1101/gr.1068603 [Abstract] [Full Text] [Supplemental Research Data]

Xiaoqiu Huang, Jianmin Wang, Srinivas Aluru, Shiaw-Pyng Yang, and LaDeana Hillier: PCAP: A Whole-Genome Assembly Program
Genome Res. 2003 13: 2164-2170. [Abstract] [Full Text]

Gerli Pielberg, Andy E. Day, Graham S. Plastow, and Leif Andersson: A Sensitive Method for Detecting Variation in Copy Numbers of Duplicated Genes
Genome Res. 2003 13: 2171-2177. [Abstract] [Full Text]

Li Li, Christian J. Stoeckert, Jr., and David S. Roos: OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Genome Res. 2003 13: 2178-2189. [Abstract] [Full Text]

Vinícius Cotta-de-Almeida, Susan Schonhoff, Tomoyuki Shibata, Andrew Leiter, and Scott B. Snapper: A New Method for Rapidly Generating Gene-Targeting Vectors by Engineering BACs Through Homologous Recombination in Bacteria
Genome Res. 2003 13: 2190-2194. Published in Advance August 12, 2003, 10.1101/gr.1356503 [Abstract] [Full Text]

RESOURCES:

Derek Huntley, Holger Hummerich, Damian Smedley, Sasivimol Kittivoravitkul, Mark McCarthy, Peter Little, and Marek Sergot: GANESH: Software for Customized Annotation of Genome Regions
Genome Res. 2003 13: 2195-2202. [Abstract] [Full Text]

Carmela Gissi and Graziano Pesole: Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data
Genome Res. 2003 13: 2203-2212. Published in Advance August 12, 2003, 10.1101/gr.1227803 [Abstract] [Full Text]

Cover Caption:

Cover Cover An analysis of the genome sequence of Schizosaccharomyces pombe for transposons identified 186 insertions of long terminal repeat (LTR) retrotransposons. Although the vast majority of these recombined to form single LTRs, they comprise 1.1% of the genome. A phylogenetic study revealed nine families of LTRs all related to Tf1 and Tf2, the transposons that multiplied most recently. Interestingly, most of the 186 insertions occurred 100 to 400 nucleotides upstream of protein coding sequences, suggesting a mechanism that inserts the transposons at pol II promoters. (For details, see Bowen et al., pp. 1984-1997.)