Volume 13, Issue 7 | July 2003

ARTICLES
- - An Evolutionarily Structured Universe of Protein Architecture
    Gustavo Caetano-Anollés
    Derek Caetano-Anollés
    First Published July 1, 2003
  - 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
    ...[+2 authors]...,
    Akihiko Yamagishi
    Hisashi Kikuchi
    Kazuho Ikeo
    Takashi Gojobori
    First Published July 1, 2003
  - 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
    ...[+16 authors]...,
    Frank Larimer
    Loren Hauser
    Miriam Land
    Ricardo Cavicchioli
    First Published June 12, 2003
LETTERS
- - The Balance of Driving Forces During Genome Evolution in Prokaryotes
    Victor Kunin
    Christos A. Ouzounis
    First Published July 1, 2003
  - Assessing the Drosophila melanogaster and Anopheles gambiae Genome Annotations Using Genome-Wide Sequence Comparisons
    Olivier Jaillon
    Carole Dossat
    Ralph Eckenberg
    Karin Eiglmeier
    Béatrice Segurens
    Jean-Marc Aury Charles W. Roth
    ...[+2 authors]...,
    Claude Scarpelli
    Paul T. Brey
    Jean Weissenbach
    Patrick Wincker
    First Published July 1, 2003
  - Mitochondrial Genome Variation and Evolutionary History of Australian and New Guinean Aborigines
    Max Ingman
    Ulf Gyllensten
    First Published July 1, 2003
  - Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms
    W. Scott Watkins
    Alan R. Rogers
    Christopher T. Ostler
    Steve Wooding
    Michael J. Bamshad
    Anna-Marie E. Brassington Marion L. Carroll Son V. Nguyen Jerilyn A. Walker B.V. Ravi Prasad
    ...[+5 authors]...,
    P. Govinda Reddy
    Pradipta K. Das
    Mark A. Batzer
    Lynn B. Jorde
    First Published June 12, 2003
  - Comparative Analysis of Gene-Expression Patterns in Human and African Great Ape Cultured Fibroblasts
    Mazen W. Karaman
    Marlys L. Houck
    Leona G. Chemnick
    Shailender Nagpal
    Daniel Chawannakul
    Dominick Sudano
    ...[+1 authors]...,
    Brian L. Pike
    Vincent V. Ho
    Oliver A. Ryder
    Joseph G. Hacia
    First Published July 1, 2003
  - Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse
    Rotem Sorek
    Gil Ast
    First Published July 1, 2003
  - Divergence in the Spatial Pattern of Gene Expression Between Human Duplicate Genes
    Kateryna D. Makova
    Wen-Hsiung Li
    First Published July 1, 2003
  - Quantitative Assessment of Transcriptome Differences Between Brain Territories
    Michel de Chaldée
    Marie-Claude Gaillard
    Nicolas Bizat
    Jean-Marie Buhler
    Olivier Manzoni
    First Published July 1, 2003
  - Using Advanced Intercross Lines for High-Resolution Mapping of HDL Cholesterol Quantitative Trait Loci
    Xiaosong Wang
    Isabelle Le Roy
    Edwige Nicodeme
    Renhua Li
    Richard Wagner
    Christina Petros Gary A. Churchill Stephen Harris
    ...[+3 authors]...,
    Ariel Darvasi
    Jorge Kirilovsky
    Pierre L. Roubertoux
    Beverly Paigen
    First Published June 12, 2003
  - Systematic Cloning of Treponema pallidum Open Reading Frames for Protein Expression and Antigen Discovery
    Matthew McKevitt
    Krupa Patel
    David Smajs
    Michael Marsh
    Melanie McLoughlin
    First Published June 12, 2003
  - EST Mining and Functional Expression Assays Identify Extracellular Effector Proteins From the Plant Pathogen Phytophthora
    Trudy A. Torto
    Shuang Li
    Allison Styer
    Edgar Huitema
    Antonino Testa
    First Published July 1, 2003
  - An Active Non-LTR Retrotransposon With Tandem Structure in the Compact Genome of the Pufferfish Tetraodon nigroviridis
    Laurence Bouneau
    Cécile Fischer
    Catherine Ozouf-Costaz
    Alexander Froschauer
    Olivier Jaillon
    Jean-Pierre Coutanceau
    ...[+1 authors]...,
    Cornelia Körting
    Jean Weissenbach
    Alain Bernot
    Jean-Nicolas Volff
    First Published June 12, 2003
  - Identification of a Large Novel Imprinted Gene Cluster on Mouse Proximal Chromosome 6
    Ryuichi Ono
    Hirosuke Shiura
    Hiroyuki Aburatani
    Takashi Kohda
    Tomoko Kaneko-Ishino
    First Published July 1, 2003
Methods
- - Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data
    Philip M. Kim
    Bruce Tidor
    First Published July 1, 2003
  - Customized Molecular Phenotyping by Quantitative Gene Expression and Pattern Recognition Analysis
    Shreeram Akilesh
    Daniel J. Shaffer
    Derry Roopenian
    First Published July 1, 2003
  - 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
    First Published June 12, 2003
  - 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
    K.H. Andy Choo
    First Published July 1, 2003
  - Identification of Novel ErbB3-Interacting Factors Using the Split-Ubiquitin Membrane Yeast Two-Hybrid System
    Safia Thaminy
    Daniel Auerbach
    Anthony Arnoldo
    Igor Stagljar
    First Published July 1, 2003
  - Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring
    Qinghong Yang
    Alla Lishanski
    Wendy Yang
    Sandra Hatcher
    Henrietta Seet
    First Published July 1, 2003
  - 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
    First Published June 12, 2003
  - Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis
    Andrea Barczak
    Madeleine Willkom Rodriguez
    Kristina Hanspers
    Laura L. Koth
    Yu Chuan Tai
    First Published June 12, 2003

Table of Contents

Volume 13, Issue 7 | July 2003

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

Table of Contents

Volume 13, Issue 7 | July 2003

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ARTICLES

LETTERS

Methods