Volume 16, Issue 3 | March 2006

In this Issue
- - Open Forum
    Hillary E. Sussman
    First Published March 1, 2006
Forum
- - Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?
    Lutz Froenicke
    Montserrat Garcia Caldés
    Alexander Graphodatsky
    Stefan Müller
    Leslie A. Lyons
    First Published March 1, 2006
  - The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
    Guillaume Bourque
    Glenn Tesler
    Pavel A. Pevzner
    First Published March 1, 2006
COMMENTARY
- - Small open reading frames: Not so small anymore
    Richelle Sopko
    Brenda Andrews
    First Published March 1, 2006
PERSPECTIVE
- - Application of sequence-based methods in human microbial ecology
    Li Weng
    Edward M. Rubin
    James Bristow
    First Published February 6, 2006
LETTERS
- - The portability of tagSNPs across populations: A worldwide survey
    Anna González-Neira
    Xiayi Ke
    Oscar Lao
    Francesc Calafell
    Arcadi Navarro
    David Comas Howard Cann Suzannah Bumpstead Jilur Ghori Sarah Hunt
    ...[+5 authors]...,
    Panos Deloukas
    Ian Dunham
    Lon R. Cardon
    Jaume Bertranpetit
    First Published February 8, 2006
  - Analysis of allelic differential expression in human white blood cells
    P.V. Krishna Pant
    Heng Tao
    Erica J. Beilharz
    Dennis G. Ballinger
    David R. Cox
    First Published February 8, 2006
  - Callipyge mutation affects gene expression in cis: A potential role for chromatin structure
    Susan K. Murphy
    Catherine M. Nolan
    Zhiqing Huang
    Katerina S. Kucera
    Brad A. Freking
    First Published January 13, 2006
  - “Genome design” model: Evidence from conserved intronic sequence in human–mouse comparison
    Alexander E. Vinogradov
    First Published February 3, 2006
  - Dynamic evolution at pericentromeres
    Anne E. Hall
    Gregory C. Kettler
    Daphne Preuss
    First Published February 6, 2006
  - Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
    James P. Kastenmayer
    Li Ni
    Angela Chu
    Lauren E. Kitchen
    Wei-Chun Au
    Hui Yang Carole D. Carter David Wheeler
    ...[+3 authors]...,
    Ronald W. Davis
    Jef D. Boeke
    Michael A. Snyder
    Munira A. Basrai
    First Published March 1, 2006
  - Identification and analysis of evolutionarily cohesive functional modules in protein networks
    Mónica Campillos
    Christian von Mering
    Lars Juhl Jensen
    Peer Bork
    First Published January 31, 2006
Methods
- - High-throughput DNA methylation profiling using universal bead arrays
    Marina Bibikova
    Zhenwu Lin
    Lixin Zhou
    Eugene Chudin
    Eliza Wickham Garcia
    Bonnie Wu Dennis Doucet Neal J. Thomas Yunhua Wang Ekkehard Vollmer Torsten Goldmann Carola Seifart Wei Jiang
    ...[+8 authors]...,
    David L. Barker
    Mark S. Chee
    Joanna Floros
    Jian-Bing Fan
    First Published January 31, 2006
  - Decoding the fine-scale structure of a breast cancer genome and transcriptome
    Stanislav Volik
    Benjamin J. Raphael
    Guiqing Huang
    Michael R. Stratton
    Graham Bignel
    John Murnane John H. Brebner Krystyna Bajsarowicz Pamela L. Paris Quanzhou Tao David Kowbel Anna Lapuk Dmitri A. Shagin Irina A. Shagina Joe W. Gray
    ...[+10 authors]...,
    Jan-Fang Cheng
    Pieter J. de Jong
    Pavel Pevzner
    Colin Collins
    First Published February 3, 2006
  - A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles
    Li-Wei Chang
    Rakesh Nagarajan
    Jeffrey A. Magee
    Jeffrey Milbrandt
    Gary D. Stormo
    First Published January 31, 2006
  - Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine
    Yunhai Li
    Kee Khoon Lee
    Sean Walsh
    Caroline Smith
    Sophie Hadingham
    First Published January 19, 2006
  - Systematic identification of functional orthologs based on protein network comparison
    Sourav Bandyopadhyay
    Roded Sharan
    Trey Ideker
    First Published April 4, 2006
RESOURCES
- - Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse
    Jennifer L. Moran
    Andrew D. Bolton
    Pamela V. Tran
    Alison Brown
    Noelle D. Dwyer
    Danielle K. Manning Bryan C. Bjork Cheng Li Kate Montgomery Sandra M. Siepka Martha Hotz Vitaterna Joseph S. Takahashi
    ...[+7 authors]...,
    Tim Wiltshire
    David J. Kwiatkowski
    Raju Kucherlapati
    David R. Beier
    First Published February 3, 2006
  - A global assembly of cotton ESTs
    Joshua A. Udall
    Jordan M. Swanson
    Karl Haller
    Ryan A. Rapp
    Michael E. Sparks
    Jamie Hatfield Yeisoo Yu Yingru Wu Caitriona Dowd Aladdin B. Arpat Brad A. Sickler Thea A. Wilkins Jin Ying Guo Xiao Ya Chen Jodi Scheffler Earl Taliercio Ricky Turley Helen McFadden Paxton Payton Natalya Klueva Randell Allen Deshui Zhang Candace Haigler Curtis Wilkerson Jinfeng Suo Stefan R. Schulze Margaret L. Pierce Margaret Essenberg HyeRan Kim Danny J. Llewellyn Elizabeth S. Dennis David Kudrna
    ...[+27 authors]...,
    Rod Wing
    Andrew H. Paterson
    Cari Soderlund
    Jonathan F. Wendel
    First Published February 14, 2006

Table of Contents

Volume 16, Issue 3 | March 2006

In this Issue

Open Forum

Forum

Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?

The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction

COMMENTARY

Small open reading frames: Not so small anymore

PERSPECTIVE

Application of sequence-based methods in human microbial ecology

LETTERS

The portability of tagSNPs across populations: A worldwide survey

Analysis of allelic differential expression in human white blood cells

Callipyge mutation affects gene expression in cis: A potential role for chromatin structure

“Genome design” model: Evidence from conserved intronic sequence in human–mouse comparison

Dynamic evolution at pericentromeres

Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae

Identification and analysis of evolutionarily cohesive functional modules in protein networks

Methods

High-throughput DNA methylation profiling using universal bead arrays

Decoding the fine-scale structure of a breast cancer genome and transcriptome

A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles

Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine

Systematic identification of functional orthologs based on protein network comparison

RESOURCES

Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse

A global assembly of cotton ESTs

Table of Contents

Volume 16, Issue 3 | March 2006

Share this issue

In this Issue

Forum

COMMENTARY

PERSPECTIVE

LETTERS

Methods

RESOURCES