Table of Contents

ARTICLES

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An Evolutionarily Structured Universe of Protein Architecture
- Gustavo Caetano-Anollés and
- Derek Caetano-Anollés
Genome Res. July 2003 13: 1563-1571; doi:10.1101/gr.1161903
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Comparative Complete Genome Sequence Analysis of the Amino Acid Replacements Responsible for the Thermostability of Corynebacterium efficiens
- Yousuke Nishio,
- Yoji Nakamura,
- Yutaka Kawarabayasi,
- Yoshihiro Usuda,
- Eiichiro Kimura,
- Shinichi Sugimoto,
- Kazuhiko Matsui,
- Akihiko Yamagishi,
- Hisashi Kikuchi,
- Kazuho Ikeo,
- and Takashi Gojobori
Genome Res. July 2003 13: 1572-1579; doi:10.1101/gr.1285603
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Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
- Neil F.W. Saunders,
- Torsten Thomas,
- Paul M.G. Curmi,
- John S. Mattick,
- Elizabeth Kuczek,
- Rob Slade,
- John Davis,
- Peter D. Franzmann,
- David Boone,
- Karl Rusterholtz,
- Robert Feldman,
- Chris Gates,
- Shellie Bench,
- Kevin Sowers,
- Kristen Kadner,
- Andrea Aerts,
- Paramvir Dehal,
- Chris Detter,
- Tijana Glavina,
- Susan Lucas,
- Paul Richardson,
- Frank Larimer,
- Loren Hauser,
- Miriam Land,
- and Ricardo Cavicchioli
Genome Res. July 2003 13: 1580-1588; Published in Advance June 12, 2003, doi:10.1101/gr.1180903

Methods

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Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data
- Philip M. Kim and
- Bruce Tidor
Genome Res. July 2003 13: 1706-1718; doi:10.1101/gr.903503
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Customized Molecular Phenotyping by Quantitative Gene Expression and Pattern Recognition Analysis
- Shreeram Akilesh,
- Daniel J. Shaffer,
- and Derry Roopenian
Genome Res. July 2003 13: 1719-1727; doi:10.1101/gr.533003
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Analysis of mRNA With Microsomal Fractionation Using a SAGE-Based DNA Microarray System Facilitates Identification of the Genes Encoding Secretory Proteins
- Nobuaki Toyoda ,
- Shigenori Nagai,
- Yuya Terashima,
- Kazushi Motomura,
- Makoto Haino,
- Shin-ichi Hashimoto,
- Hajime Takizawa,
- and Kouji Matsushima
Genome Res. July 2003 13: 1728-1736; Published in Advance June 12, 2003, doi:10.1101/gr.709603
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A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere
- Huseyin Sumer,
- Jeffrey M. Craig,
- Mandy Sibson,
- and K.H. Andy Choo
Genome Res. July 2003 13: 1737-1743; doi:10.1101/gr.1095903
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Identification of Novel ErbB3-Interacting Factors Using the Split-Ubiquitin Membrane Yeast Two-Hybrid System
- Safia Thaminy,
- Daniel Auerbach,
- Anthony Arnoldo,
- and Igor Stagljar
Genome Res. July 2003 13: 1744-1753; doi:10.1101/gr.1276503
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Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring
- Qinghong Yang,
- Alla Lishanski,
- Wendy Yang,
- Sandra Hatcher,
- Henrietta Seet,
- and Jeffrey P. Gregg
Genome Res. July 2003 13: 1754-1764; doi:10.1101/gr.997703
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Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay
- Shirin Khambata-Ford,
- Yueyi Liu,
- Christopher Gleason,
- Mark Dickson,
- Russ B. Altman,
- Serafim Batzoglou,
- and Richard M. Myers
Genome Res. July 2003 13: 1765-1774; Published in Advance June 12, 2003, doi:10.1101/gr.529803
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Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis
- Andrea Barczak,
- Madeleine Willkom Rodriguez,
- Kristina Hanspers,
- Laura L. Koth,
- Yu Chuan Tai,
- Benjamin M. Bolstad,
- Terence P. Speed,
- and David J. Erle
Genome Res. July 2003 13: 1775-1785; Published in Advance June 12, 2003, doi:10.1101/gr.1048803

ARTICLES

An Evolutionarily Structured Universe of Protein Architecture

Comparative Complete Genome Sequence Analysis of the Amino Acid Replacements Responsible for the Thermostability of Corynebacterium efficiens

Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii

LETTERS

The Balance of Driving Forces During Genome Evolution in Prokaryotes

Assessing the Drosophila melanogaster and Anopheles gambiae Genome Annotations Using Genome-Wide Sequence Comparisons

Mitochondrial Genome Variation and Evolutionary History of Australian and New Guinean Aborigines

Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms

Comparative Analysis of Gene-Expression Patterns in Human and African Great Ape Cultured Fibroblasts

Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse

Divergence in the Spatial Pattern of Gene Expression Between Human Duplicate Genes

Quantitative Assessment of Transcriptome Differences Between Brain Territories

Using Advanced Intercross Lines for High-Resolution Mapping of HDL Cholesterol Quantitative Trait Loci

Systematic Cloning of Treponema pallidum Open Reading Frames for Protein Expression and Antigen Discovery

EST Mining and Functional Expression Assays Identify Extracellular Effector Proteins From the Plant Pathogen Phytophthora

An Active Non-LTR Retrotransposon With Tandem Structure in the Compact Genome of the Pufferfish Tetraodon nigroviridis

Identification of a Large Novel Imprinted Gene Cluster on Mouse Proximal Chromosome 6

Methods

Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data

Customized Molecular Phenotyping by Quantitative Gene Expression and Pattern Recognition Analysis

Analysis of mRNA With Microsomal Fractionation Using a SAGE-Based DNA Microarray System Facilitates Identification of the Genes Encoding Secretory Proteins

A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere

Identification of Novel ErbB3-Interacting Factors Using the Split-Ubiquitin Membrane Yeast Two-Hybrid System

Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring

Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay

Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis

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