Volume 13, Issue 9 | September 2003

REVIEW
- - The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis
    Jef D. Boeke
    First Published September 2, 2003
ARTICLES
- - Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe
    Nathan J. Bowen
    I. King Jordan
    Jonathan A. Epstein
    Valerie Wood
    Henry L. Levin
    First Published September 2, 2003
  - The Human Transcriptome Map Reveals Extremes in Gene Density, Intron Length, GC Content, and Repeat Pattern for Domains of Highly and Weakly Expressed Genes
    Rogier Versteeg,
    Barbera D.C. van Schaik
    Marinus F. van Batenburg
    Marco Roos
    Ramin Monajemi
    First Published January 1, 2003
  - Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus
    Ningxin Zhang
    Annette L. Harrex
    Barbara R. Holland
    Lauren E. Fenton
    Richard D. Cannon
    First Published September 2, 2003
LETTERS
- - Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis
    Stewart J. Hinchliffe
    Karen E. Isherwood
    Richard A. Stabler
    Michael B. Prentice
    Alexander Rakin
    Richard A. Nichols
    ...[+1 authors]...,
    Petra C.F. Oyston
    Jason Hinds
    Richard W. Titball
    Brendan W. Wren
    First Published September 2, 2003
  - Conserved Noncoding Sequences in the Grasses4
    Dan Choffnes Inada
    Ali Bashir
    Chunghau Lee
    Brian C. Thomas
    Cynthia Ko
    First Published September 2, 2003
  - Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes
    Luba Katz
    Christopher B. Burge
    First Published September 2, 2003
  - Asymmetric Sequence Divergence of Duplicate Genes
    Gavin C. Conant
    Andreas Wagner
    First Published September 2, 2003
  - Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25
    Mario Ventura
    Jonathan M. Mudge
    Valeria Palumbo
    Sally Burn
    Elisabeth Blennow
    Mauro Pierluigi Roberto Giorda
    ...[+2 authors]...,
    Orsetta Zuffardi
    Nicoletta Archidiacono
    Michael S. Jackson
    Mariano Rocchi
    First Published January 1, 2003
  - A General Approach for Identifying Distant Regulatory Elements Applied to the Gdf6 Gene
    Douglas P. Mortlock
    Catherine Guenther
    David M. Kingsley
    First Published January 1, 2003
  - Pleiotropy, Homeostasis, and Functional Networks Based on Assays of Cardiovascular Traits in Genetically Randomized Populations
    Joseph H. Nadeau
    Lindsay C. Burrage
    Joe Restivo
    Yoh-Han Pao
    Gary Churchill
    First Published September 2, 2003
  - Transcriptional Response of Lymphoblastoid Cells to Ionizing Radiation
    Kuang-Yu Jen
    Vivian G. Cheung
    First Published January 1, 2003
  - Global Haplotype Diversity in the Human Insulin Gene Region
    John D.H. Stead
    Matthew E. Hurles
    Alec J. Jeffreys
    First Published September 2, 2003
  - Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms
    Xin Lu
    Tianhua Niu
    Jun S. Liu
    First Published September 2, 2003
  - Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster
    Huaiyu Mi
    Jody Vandergriff
    Michael Campbell
    Apurva Narechania
    William Majoros
    First Published September 2, 2003
Methods
- - PANTHER: A Library of Protein Families and Subfamilies Indexed by Function
    Paul D. Thomas
    Michael J. Campbell
    Anish Kejariwal
    Huaiyu Mi
    Brian Karlak
    First Published September 2, 2003
  - Whole-Genome Shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and Its Use for Whole-Genome Shotgun Sequence Assembly
    Shiguo Zhou
    Erika Kvikstad
    Andrew Kile
    Jessica Severin
    Dan Forrest
    Rod Runnheim Chris Churas Jason W. Hickman Chris Mackenzie
    ...[+4 authors]...,
    Madhusudan Choudhary
    Timothy Donohue
    Samuel Kaplan
    David C. Schwartz
    First Published September 2, 2003
  - Locating Sequence on FPC Maps and Selecting a Minimal Tiling Path
    Friedrich W. Engler
    James Hatfield
    William Nelson
    Carol A. Soderlund
    First Published January 1, 2003
  - PCAP: A Whole-Genome Assembly Program
    Xiaoqiu Huang
    Jianmin Wang
    Srinivas Aluru
    Shiaw-Pyng Yang
    LaDeana Hillier
    First Published September 2, 2003
  - A Sensitive Method for Detecting Variation in Copy Numbers of Duplicated Genes
    Gerli Pielberg
    Andy E. Day
    Graham S. Plastow
    Leif Andersson
    First Published September 2, 2003
  - OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
    Li Li
    Christian J. Stoeckert
    David S. Roos
    First Published September 2, 2003
  - A New Method for Rapidly Generating Gene-Targeting Vectors by Engineering BACs Through Homologous Recombination in Bacteria
    Vinícius Cotta-de-Almeida
    Susan Schonhoff
    Tomoyuki Shibata
    Andrew Leiter
    Scott B. Snapper
    First Published January 1, 2003
RESOURCE
- - GANESH: Software for Customized Annotation of Genome Regions
    Derek Huntley
    Holger Hummerich
    Damian Smedley
    Sasivimol Kittivoravitkul
    Mark McCarthy
    First Published September 2, 2003
RESOURCE
- - Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data
    Carmela Gissi
    Graziano Pesole
    First Published January 1, 2003

Table of Contents

Volume 13, Issue 9 | September 2003

REVIEW

The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis

ARTICLES

Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe

The Human Transcriptome Map Reveals Extremes in Gene Density, Intron Length, GC Content, and Repeat Pattern for Domains of Highly and Weakly Expressed Genes

Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus

LETTERS

Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis

Conserved Noncoding Sequences in the Grasses4

Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes

Asymmetric Sequence Divergence of Duplicate Genes

Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25

A General Approach for Identifying Distant Regulatory Elements Applied to the Gdf6 Gene

Pleiotropy, Homeostasis, and Functional Networks Based on Assays of Cardiovascular Traits in Genetically Randomized Populations

Transcriptional Response of Lymphoblastoid Cells to Ionizing Radiation

Global Haplotype Diversity in the Human Insulin Gene Region

Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms

Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster

Methods

PANTHER: A Library of Protein Families and Subfamilies Indexed by Function

Whole-Genome Shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and Its Use for Whole-Genome Shotgun Sequence Assembly

Locating Sequence on FPC Maps and Selecting a Minimal Tiling Path

PCAP: A Whole-Genome Assembly Program

A Sensitive Method for Detecting Variation in Copy Numbers of Duplicated Genes

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

A New Method for Rapidly Generating Gene-Targeting Vectors by Engineering BACs Through Homologous Recombination in Bacteria

RESOURCE

GANESH: Software for Customized Annotation of Genome Regions

RESOURCE

Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data

Table of Contents

Volume 13, Issue 9 | September 2003

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