Volume 12, Issue 1 | January 2002

COMMENTARY
- - Testing the Parsimony Test of Genome Duplications: A Counterexample
    Xun Gu
    Wei Huang
    First Published January 1, 2002
REPORT
- - Generation and Comparative Analysis of ∼3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome
    Udaya DeSilva
    Laura Elnitski
    Jacquelyn R. Idol
    Johannah L. Doyle
    Weiniu Gan
    James W. Thomas Scott Schwartz Nicole L. Dietrich Stephen M. Beckstrom-Sternberg Jennifer C. McDowell Robert W. Blakesley Gerard G. Bouffard
    ...[+7 authors]...,
    Pamela J. Thomas
    Jeffrey W. Touchman
    Webb Miller
    Eric D. Green
    First Published January 1, 2002
ARTICLE
- - Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content
    Snel Berend
    Bork Peer
    Huynen Martijn A.
    First Published December 14, 2001
LETTERS
- - Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species
    Guillaume Bourque
    Pavel A. Pevzner
    First Published January 1, 2002
  - Relating Whole-Genome Expression Data with Protein-Protein Interactions
    Ronald Jansen
    Dov Greenbaum
    Mark Gerstein
    First Published January 1, 2002
  - Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions
    Tobias Doerks
    Richard R. Copley
    Jörg Schultz
    Chris P. Ponting
    Peer Bork
    First Published January 1, 2002
  - A Comparative Genomic Analysis of Two Distant Diptera, the Fruit Fly, Drosophila melanogaster, and the Malaria Mosquito, Anopheles gambiae
    Viacheslav N. Bolshakov
    Pantelis Topalis
    Claudia Blass
    Elena Kokoza
    Alessandra della Torre
    Fotis C. Kafatos
    Christos Louis
    First Published January 1, 2002
  - Human Paralogs of KIAA0187 Were Created through Independent Pericentromeric-Directed and Chromosome-Specific Duplication Mechanisms
    Moira Crosier
    Luigi Viggiano
    Jane Guy
    Doriana Misceo
    Robert Stones
    Wenbin Wei Tom Hearn
    ...[+2 authors]...,
    Mario Ventura
    Nicoletta Archidiacono
    Mariano Rocchi
    Michael S. Jackson
    First Published January 1, 2002
  - Genomic Analysis of the Olfactory Receptor Region of the Mouse and Human T-Cell Receptor α/δ Loci
    Robert P. Lane
    Jared C. Roach
    Inyoul Y. Lee
    Cecilie Boysen
    Arian Smit
    Barbara J. Trask
    Leroy Hood
    First Published January 1, 2002
  - Identification of the Modifier of Min 2 (Mom2) Locus, a New Mutation That Influences Apc-Induced Intestinal Neoplasia
    Karen A. Silverman
    Revati Koratkar
    Linda D. Siracusa
    Arthur M. Buchberg
    First Published January 1, 2002
  - Changes in Gene Expression Profiles in Developing B Cells of Murine Bone Marrow
    Reinhard Hoffmann
    Thomas Seidl
    Martin Neeb
    Antonius Rolink
    Fritz Melchers
    First Published January 1, 2002
  - Expression Profiles of 290 ESTs Mapped to Chromosome 3 in Human Epithelial Ovarian Cancer Cell Lines Using DNA Expression Oligonucleotide Microarrays
    Emily N. Manderson
    Anne-Marie Mes-Masson
    Jaroslav Novak
    Peter D. Lee
    Diane Provencher
    Thomas J. Hudson
    Patricia N. Tonin
    First Published January 1, 2002
  - Athila4 of Arabidopsis and Calypso of Soybean Define a Lineage of Endogenous Plant Retroviruses
    David A. Wright
    Daniel F. Voytas
    First Published December 14, 2001
  - Analysis of the 5S RNA Pool in Arabidopsis thaliana: RNAs Are Heterogeneous and Only Two of the Genomic 5S Loci Produce Mature 5S RNA
    Catherine Cloix
    Sylvie Tutois
    Yasushi Yukawa
    Olivier Mathieu
    Claudine Cuvillier
    Marie-Claude Espagnol
    Georges Picard
    Sylvette Tourmente
    First Published December 14, 2001
METHODS
- - Gene Expression Analysis with Universal n-mer Arrays
    R. Michael van Dam
    Stephen R. Quake
    First Published January 1, 2002
  - Enzymatic Regional Methylation Assay: A Novel Method to Quantify Regional CpG Methylation Density
    Oliver Galm
    Michael R. Rountree
    Kurtis E. Bachman
    Kam-Wing Jair
    Stephen B. Baylin
    James G. Herman
    First Published December 14, 2001
  - Methylation-Specific Oligonucleotide Microarray: A New Potential for High-Throughput Methylation Analysis
    Raad S. Gitan
    Huidong Shi
    Chuan-Mu Chen
    Pearlly S. Yan
    Tim Hui-Ming Huang
    First Published December 14, 2001
  - Finding Genes in the C2C12 Osteogenic Pathway by k-Nearest-Neighbor Classification of Expression Data
    Joachim Theilhaber
    Timothy Connolly
    Sergio Roman-Roman
    Steven Bushnell
    Amanda Jackson
    Kathy Call
    Teresa Garcia
    Roland Baron
    First Published January 1, 2002
  - ARACHNE: A Whole-Genome Shotgun Assembler
    Serafim Batzoglou
    David B. Jaffe
    Ken Stanley
    Jonathan Butler
    Sante Gnerre
    Evan Mauceli
    Bonnie Berger
    Jill P. Mesirov
    Eric S. Lander
    First Published January 1, 2002
  - Linker-Mediated Recombinational Subcloning of Large DNA Fragments Using Yeast
    Christopher K. Raymond
    Elizabeth H. Sims
    Maynard V. Olson
    First Published January 1, 2002
  - The K A/K S Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study
    Anton Nekrutenko
    Kateryna D. Makova
    Wen-Hsiung Li
    First Published December 14, 2001
  - Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical Literature
    Soumya Raychaudhuri
    Jeffrey T. Chang
    Patrick D. Sutphin
    Russ B. Altman
    First Published January 1, 2002

Table of Contents

Volume 12, Issue 1 | January 2002

COMMENTARY

Testing the Parsimony Test of Genome Duplications: A Counterexample

REPORT

Generation and Comparative Analysis of ∼3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome

ARTICLE

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content

LETTERS

Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species

Relating Whole-Genome Expression Data with Protein-Protein Interactions

Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions

A Comparative Genomic Analysis of Two Distant Diptera, the Fruit Fly, Drosophila melanogaster, and the Malaria Mosquito, Anopheles gambiae

Human Paralogs of KIAA0187 Were Created through Independent Pericentromeric-Directed and Chromosome-Specific Duplication Mechanisms

Genomic Analysis of the Olfactory Receptor Region of the Mouse and Human T-Cell Receptor α/δ Loci

Identification of the Modifier of Min 2 (Mom2) Locus, a New Mutation That Influences Apc-Induced Intestinal Neoplasia

Changes in Gene Expression Profiles in Developing B Cells of Murine Bone Marrow

Expression Profiles of 290 ESTs Mapped to Chromosome 3 in Human Epithelial Ovarian Cancer Cell Lines Using DNA Expression Oligonucleotide Microarrays

Athila4 of Arabidopsis and Calypso of Soybean Define a Lineage of Endogenous Plant Retroviruses

Analysis of the 5S RNA Pool in Arabidopsis thaliana: RNAs Are Heterogeneous and Only Two of the Genomic 5S Loci Produce Mature 5S RNA

METHODS

Gene Expression Analysis with Universal n-mer Arrays

Enzymatic Regional Methylation Assay: A Novel Method to Quantify Regional CpG Methylation Density

Methylation-Specific Oligonucleotide Microarray: A New Potential for High-Throughput Methylation Analysis

Finding Genes in the C2C12 Osteogenic Pathway by k-Nearest-Neighbor Classification of Expression Data

ARACHNE: A Whole-Genome Shotgun Assembler

Linker-Mediated Recombinational Subcloning of Large DNA Fragments Using Yeast

The K A/K S Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study

Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical Literature

Table of Contents

Volume 12, Issue 1 | January 2002

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COMMENTARY

REPORT

ARTICLE

LETTERS

METHODS