Genome Research -- Table of Contents (13 [6a])

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Volume 13, Issue 6a: June 2003 [Index by Author] [Cover Caption]

Other Issues:

PERSPECTIVES

ARTICLES

LETTERS

METHODS

RESOURCES

ERRATA

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PERSPECTIVES:

Timothy P. O'Brien, Carol J. Bult, Christoph Cremer, Michael Grunze, Barbara B. Knowles, Jörg Langowski, James McNally, Thoru Pederson, Joan C. Politz, Ana Pombo, Günter Schmahl, Joachim P. Spatz, and Roel van Driel: Genome Function and Nuclear Architecture: From Gene Expression to Nanoscience
Genome Res. 2003 13: 1029-1041. Published in Advance May 12, 2003, 10.1101/gr.946403 [Abstract] [Full Text]

ARTICLES:

Ichiro Nakagawa, Ken Kurokawa, Atsushi Yamashita, Masanobu Nakata, Yusuke Tomiyasu, Nobuo Okahashi, Shigetada Kawabata, Kiyoshi Yamazaki, Tadayoshi Shiba, Teruo Yasunaga, Hideo Hayashi, Masahira Hattori, and Shigeyuki Hamada: Genome Sequence of an M3 Strain of Streptococcus pyogenes Reveals a Large-Scale Genomic Rearrangement in Invasive Strains and New Insights into Phage Evolution
Genome Res. 2003 13: 1042-1055. [Abstract] [Full Text] [Supplemental Research Data]

Georgia Panopoulou, Steffen Hennig, Detlef Groth, Antje Krause, Albert J. Poustka, Ralf Herwig, Martin Vingron, and Hans Lehrach: New Evidence for Genome-Wide Duplications at the Origin of Vertebrates Using an Amphioxus Gene Set and Completed Animal Genomes
Genome Res. 2003 13: 1056-1066. [Abstract] [Full Text] [Supplemental Research Data]

Christoph Winkler, Matthias Schäfer, Jutta Duschl, Manfred Schartl, and Jean-Nicolas Volff: Functional Divergence of Two Zebrafish Midkine Growth Factors Following Fish-Specific Gene Duplication
Genome Res. 2003 13: 1067-1081. Published in Advance May 12, 2003, 10.1101/gr.1097503 [Abstract] [Full Text]

LETTERS:

Steven A. Farber, Robert A. De Rose, Eric S. Olson, and Marnie E. Halpern: The Zebrafish Annexin Gene Family
Genome Res. 2003 13: 1082-1096. [Abstract] [Full Text]

Mark Shannon, Aaron T. Hamilton, Laurie Gordon, Elbert Branscomb, and Lisa Stubbs: Differential Expansion of Zinc-Finger Transcription Factor Loci in Homologous Human and Mouse Gene Clusters
Genome Res. 2003 13: 1097-1110. Published in Advance May 12, 2003, 10.1101/gr.963903 [Abstract] [Full Text]

Simona Santini, Jeffrey L. Boore, and Axel Meyer: Evolutionary Conservation of Regulatory Elements in Vertebrate Hox Gene Clusters
Genome Res. 2003 13: 1111-1122. [Abstract] [Full Text] [Supplemental Research Data]

Eduardo P.C. Rocha: An Appraisal of the Potential for Illegitimate Recombination in Bacterial Genomes and Its Consequences: From Duplications to Genome Reduction
Genome Res. 2003 13: 1123-1132. Published in Advance May 12, 2003, 10.1101/gr.966203 [Abstract] [Full Text] [Supplemental Research Data]

Sarit Cohen, Keren Yacobi, and Daniel Segal: Extrachromosomal Circular DNA of Tandemly Repeated Genomic Sequences in Drosophila
Genome Res. 2003 13: 1133-1145. [Abstract] [Full Text]

Long Lu, Adrian K. Arakaki, Hui Lu, and Jeffrey Skolnick: Multimeric Threading-Based Prediction of Protein–Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome
Genome Res. 2003 13: 1146-1154. [Abstract] [Full Text]

Alexei Fedorov, Scott Roy, Xiaohong Cao, and Walter Gilbert: Phylogenetically Older Introns Strongly Correlate With Module Boundaries in Ancient Proteins
Genome Res. 2003 13: 1155-1157. Published in Advance May 12, 2003, 10.1101/gr.1008203 [Abstract] [Full Text]

Hideki Innan, Badri Padhukasahasram, and Magnus Nordborg: The Pattern of Polymorphism on Human Chromosome 21
Genome Res. 2003 13: 1158-1168. [Abstract] [Full Text]

Naoya Yuhki, Thomas Beck, Robert M. Stephens, Yoko Nishigaki, Kymberly Newmann, and Stephen J. O'Brien: Comparative Genome Organization of Human, Murine, and Feline MHC Class II Region
Genome Res. 2003 13: 1169-1179. Published in Advance May 12, 2003, 10.1101/gr.976103 [Abstract] [Full Text]

Vinayak Kapatral, Natalia Ivanova, Iain Anderson, Gary Reznik, Anamitra Bhattacharyya, Warren L. Gardner, Natalia Mikhailova, Alla Lapidus, Niels Larsen, Mark D'Souza, Theresa Walunas, Robert Haselkorn, Ross Overbeek, and Nikos Kyrpides: Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586
Genome Res. 2003 13: 1180-1189. [Abstract] [Full Text]

METHODS:

Lingang Zhang, Vladimir Pavlovic, Charles R Cantor, and Simon Kasif: Human–Mouse Gene Identification by Comparative Evidence Integration and Evolutionary Analysis
Genome Res. 2003 13: 1190-1202. Published in Advance May 12, 2003, 10.1101/gr.703903 [Abstract] [Full Text]

Erin D. Pleasance, Marco A. Marra, and Steven J.M. Jones: Assessment of SAGE in Transcript Identification
Genome Res. 2003 13: 1203-1215. Published in Advance May 12, 2003, 10.1101/gr.873003 [Abstract] [Full Text]

Natalia Volfovsky, Brian J. Haas, and Steven L. Salzberg: Computational Discovery of Internal Micro-Exons
Genome Res. 2003 13: 1216-1221. [Abstract] [Full Text] [Supplemental Research Data]

RESOURCES:

Janet Kelso, Johann Visagie, Gregory Theiler, Alan Christoffels, Soraya Bardien, Damian Smedley, Darren Otgaar, Gary Greyling, C. Victor Jongeneel, Mark I. McCarthy, Tania Hide, and Winston Hide: eVOC: A Controlled Vocabulary for Unifying Gene Expression Data
Genome Res. 2003 13: 1222-1230. [Abstract] [Full Text]

Asako Koike, Yoshiyuki Kobayashi, and Toshihisa Takagi: Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource
Genome Res. 2003 13: 1231-1243. [Abstract] [Full Text]

Christopher D. Fjell, Ian Bosdet, Jacqueline E. Schein, Steven J.M. Jones, and Marco A. Marra: Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps
Genome Res. 2003 13: 1244-1249. [Abstract] [Full Text]

Karl J. Schmid, Thomas Rosleff Sörensen, Ralf Stracke, Ottó Törjék, Thomas Altmann, Tom Mitchell-Olds, and Bernd Weisshaar: Large-Scale Identification and Analysis of Genome-Wide Single-Nucleotide Polymorphisms for Mapping in Arabidopsis thaliana
Genome Res. 2003 13: 1250-1257. [Abstract] [Full Text]

ERRATA:

: Correction for Volume 13, p. 742
Genome Res. 2003 13: 1258. [Full Text]

: Correction for Volume 13, p. 794
Genome Res. 2003 13: 1258. [Full Text]

Cover Caption:

Cover Cover The unique midkine (mdk) gene in higher vertebrates encodes a heparin-binding growth factor with neurotrophic activity that shows widespread expression duringembryonic development. In the teleost fish lineage, a large duplication resulted in the presence of two mdk genes. Functional analyses in zebrafish have now shown that duplicated mdkcopies display highly divergent expression patterns and distinct biological activities in the developingnervous system. In this figure, the expression of mdka in the central neural tube and somites (right) and mdkb in the dorsal neural tube (left) are shown together with their completely different effects on the development of floorplate and neural crest cells, respectively, after overexpression. (For details, see Winkler et al., pp. 1067-1081.)