Volume 18, Issue 12 | December 2008

Insight/Outlook
- - Ethical, legal, and social considerations in conducting the Human Microbiome Project
    Amy L. McGuire
    James Colgrove
    Simon N. Whitney
    Christina M. Diaz
    Daniel Bustillos
    First Published October 29, 2008
LETTERS
- - Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history
    Philip M. Kim
    Hugo Y.K. Lam
    Alexander E. Urban
    Jan O. Korbel
    Jason Affourtit
    Fabian Grubert
    ...[+1 authors]...,
    Xueying Chen
    Sherman Weissman
    Michael Snyder
    Mark B. Gerstein
    First Published October 8, 2008
  - Active Alu retrotransposons in the human genome
    E. Andrew Bennett
    Heiko Keller
    Ryan E. Mills
    Steffen Schmidt
    John V. Moran
    First Published October 3, 2008
  - Characterization of the bovine pseudoautosomal boundary: Documenting the evolutionary history of mammalian sex chromosomes
    Anne-Sophie Van Laere
    Wouter Coppieters
    Michel Georges
    First Published November 3, 2008
  - Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
    Yong Cheng
    David C. King
    Louis C. Dore
    Xinmin Zhang
    Yuepin Zhou
    Ying Zhang Christine Dorman Demesew Abebe Swathi A. Kumar Francesca Chiaromonte
    ...[+5 authors]...,
    Webb Miller
    Roland D. Green
    Mitchell J. Weiss
    Ross C. Hardison
    First Published September 25, 2008
  - Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
    A. Gordon Robertson
    Mikhail Bilenky
    Angela Tam
    Yongjun Zhao
    Thomas Zeng
    Nina Thiessen Timothee Cezard Anthony P. Fejes Elizabeth D. Wederell Rebecca Cullum Ghia Euskirchen Martin Krzywinski Inanc Birol Michael Snyder
    ...[+9 authors]...,
    Pamela A. Hoodless
    Martin Hirst
    Marco A. Marra
    Steven J.M. Jones
    First Published September 11, 2008
  - Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster
    Ervin D. Nagy
    Jeffrey L. Bennetzen
    First Published August 21, 2008
  - Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
    Michael Freeling
    Eric Lyons
    Brent Pedersen
    Maqsudul Alam
    Ray Ming
    First Published October 3, 2008
  - DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya
    Wenli Zhang
    Xiue Wang
    Qingyi Yu
    Ray Ming
    Jiming Jiang
    First Published July 1, 2008
Methods
- - Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
    Haibao Tang
    Xiyin Wang
    John E. Bowers
    Ray Ming
    Maqsudul Alam
    First Published October 2, 2008
  - Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
    Steven G. Kuntz
    Erich M. Schwarz
    John A. DeModena
    Tristan De Buysscher
    Diane Trout
    First Published November 3, 2008
  - DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression
    Shintaro Yagi
    Keiji Hirabayashi
    Shinya Sato
    Wei Li
    Yoko Takahashi
    Tsutomu Hirakawa Guoying Wu Naoko Hattori Naka Hattori
    ...[+4 authors]...,
    Jun Ohgane
    Satoshi Tanaka
    X. Shirley Liu
    Kunio Shiota
    First Published October 29, 2008
  - Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
    Vardges Ter-Hovhannisyan
    Alexandre Lomsadze
    Yury O. Chernoff
    Mark Borodovsky
    First Published August 29, 2008
  - Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions
    Yan Qi
    Yasir Suhail
    Yu-yi Lin
    Jef D. Boeke
    Joel S. Bader
    First Published October 2, 2008
RESOURCES
- - Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
    Natalia J. Martinez
    Maria C. Ow
    John S. Reece-Hoyes
    M. Inmaculada Barrasa
    Victor R. Ambros
    First Published November 3, 2008
  - Haplotype sorting using human fosmid clone end-sequence pairs
    Jeffrey M. Kidd
    Ze Cheng
    Tina Graves
    Bob Fulton
    Richard K. Wilson
    First Published October 3, 2008
  - Sequencing of natural strains of Arabidopsis thaliana with short reads
    Stephan Ossowski
    Korbinian Schneeberger
    Richard M. Clark
    Christa Lanz
    Norman Warthmann
    First Published September 25, 2008

Table of Contents

Volume 18, Issue 12 | December 2008

Insight/Outlook

Ethical, legal, and social considerations in conducting the Human Microbiome Project

LETTERS

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

Active Alu retrotransposons in the human genome

Characterization of the bovine pseudoautosomal boundary: Documenting the evolutionary history of mammalian sex chromosomes

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster

Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya

Methods

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

Multigenome DNA sequence conservation identifies Hox cis-regulatory elements

DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions

RESOURCES

Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity

Haplotype sorting using human fosmid clone end-sequence pairs

Sequencing of natural strains of Arabidopsis thaliana with short reads

Table of Contents

Volume 18, Issue 12 | December 2008

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Insight/Outlook

LETTERS

Methods

RESOURCES