Genome Research Vol 19 Issue 3

Volume 19, Issue 3 | March 2009

Article
- - MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
    Hongjae Sunwoo
    Marcel E. Dinger
    Jeremy E. Wilusz
    Paulo P. Amaral
    John S. Mattick
    David L. Spector
    First Published December 22, 2008
  - A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome
    Bryan J. Venters
    B. Franklin Pugh
    First Published January 5, 2009
Letter
- - Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers
    Jérôme Eeckhoute
    Mathieu Lupien
    Clifford A. Meyer
    Michael P. Verzi
    Ramesh A. Shivdasani
    X. Shirley Liu
    Myles Brown
    First Published January 7, 2009
  - Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
    Jeremy R. Sanford
    Xin Wang
    Matthew Mort
    Natalia VanDuyn
    David N. Cooper
    Sean D. Mooney
    Howard J. Edenberg
    Yunlong Liu
    First Published December 30, 2008
  - HBEGF, SRA1, and IK: Three cosegregating genes as determinants of cardiomyopathy
    Frauke Friedrichs
    Christian Zugck
    Gerd-Jörg Rauch
    Boris Ivandic
    Dieter Weichenhan
    Margit Müller-Bardorff Benjamin Meder Nour Eddine El Mokhtari Vera Regitz-Zagrosek Roland Hetzer Arne Schäfer Stefan Schreiber Jian Chen Isaac Neuhaus Ruiru Ji Nathan O. Siemers
    ...[+11 authors]...,
    Norbert Frey
    Wolfgang Rottbauer
    Hugo A. Katus
    Monika Stoll
    First Published December 8, 2008
  - Histone H3.3 incorporation provides a unique and functionally essential telomeric chromatin in embryonic stem cells
    Lee H. Wong
    Hua Ren
    Evan Williams
    James McGhie
    Soyeon Ahn
    Marcus Sim Angela Tam
    ...[+2 authors]...,
    Elizabeth Earle
    Melissa A. Anderson
    Jeffrey Mann
    K.H. Andy Choo
    First Published February 5, 2009
  - Into the blue: Gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii
    Wayne L. Davies
    Livia S. Carvalho
    Boon-Hui Tay
    Sydney Brenner
    David M. Hunt
    Byrappa Venkatesh
    First Published February 4, 2009
  - Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa
    Zachary A. Lewis
    Shinji Honda
    Tamir K. Khlafallah
    Jennifer K. Jeffress
    Michael Freitag
    Fabio Mohn
    Dirk Schübeler
    Eric U. Selker
    First Published December 17, 2008
  - The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer
    Agustin F. Fernandez
    Cecilia Rosales
    Pilar Lopez-Nieva
    Osvaldo Graña
    Esteban Ballestar
    Santiago Ropero Jesus Espada Sonia A. Melo Amaia Lujambio Mario F. Fraga Irene Pino Biola Javierre Francisco J. Carmona Francesco Acquadro Renske D.M. Steenbergen Peter J.F. Snijders Chris J. Meijer Pascal Pineau Anne Dejean Belen Lloveras Gabriel Capella Josep Quer Maria Buti Juan-Ignacio Esteban Helena Allende Francisco Rodriguez-Frias Xavier Castellsague Janos Minarovits Jordi Ponce Daniela Capello Gianluca Gaidano Juan Cruz Cigudosa Gonzalo Gomez-Lopez David G. Pisano Alfonso Valencia Miguel Angel Piris
    ...[+31 authors]...,
    Francesc X. Bosch
    Ellen Cahir-McFarland
    Elliott Kieff
    Manel Esteller
    First Published February 10, 2009
  - Two duplicated P450 genes are associated with pyrethroid resistance in Anopheles funestus, a major malaria vector
    Charles S. Wondji
    Helen Irving
    John Morgan
    Neil F. Lobo
    Frank H. Collins
    Richard H. Hunt
    Maureen Coetzee
    Janet Hemingway
    Hilary Ranson
    First Published February 5, 2009
Methods
- - Genome-wide profiling of salt fractions maps physical properties of chromatin
    Steven Henikoff
    Jorja G. Henikoff
    Akiko Sakai
    Gabriel B. Loeb
    Kami Ahmad
    First Published December 16, 2008
  - Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
    Antoine Barrière
    Shiaw-Pyng Yang
    Elizabeth Pekarek
    Cristel G. Thomas
    Eric S. Haag
    Ilya Ruvinsky
    First Published February 9, 2009
Resource
- - MicroRNA target prediction by expression analysis of host genes
    Vincenzo Alessandro Gennarino
    Marco Sardiello
    Raffaella Avellino
    Nicola Meola
    Vincenza Maselli
    Santosh Anand
    Luisa Cutillo
    Andrea Ballabio
    Sandro Banfi
    First Published December 16, 2008
  - The genomic architecture of segmental duplications and associated copy number variants in dogs
    Thomas J. Nicholas
    Ze Cheng
    Mario Ventura
    Katrina Mealey
    Evan E. Eichler
    Joshua M. Akey
    First Published January 7, 2009
  - Mapping DNA structural variation in dogs
    Wei-Kang Chen
    Joshua D. Swartz
    Laura J. Rush
    Carlos E. Alvarez
    First Published November 17, 2008
  - A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate
    Martien A.M. Groenen
    Per Wahlberg
    Mario Foglio
    Hans H. Cheng
    Hendrik-Jan Megens
    Richard P.M.A. Crooijmans Francois Besnier Mark Lathrop
    ...[+3 authors]...,
    William M. Muir
    Gane Ka-Shu Wong
    Ivo Gut
    Leif Andersson
    First Published December 16, 2008
Erratum
- - Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy
    Edward F. Attiyeh
    Sharon J. Diskin
    Marc A. Attiyeh
    Yaël P. Mossé
    Cuiping Hou
    Eric M. Jackson Cecilia Kim
    ...[+2 authors]...,
    Joseph Glessner
    Hakon Hakonarson
    Jaclyn A. Biegel
    John M. Maris
    First Published March 2, 2009

Table of Contents

Volume 19, Issue 3 | March 2009

Article

MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome

Letter

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

HBEGF, SRA1, and IK: Three cosegregating genes as determinants of cardiomyopathy

Histone H3.3 incorporation provides a unique and functionally essential telomeric chromatin in embryonic stem cells

Into the blue: Gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii

Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer

Two duplicated P450 genes are associated with pyrethroid resistance in Anopheles funestus, a major malaria vector

Methods

Genome-wide profiling of salt fractions maps physical properties of chromatin

Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes

Resource

MicroRNA target prediction by expression analysis of host genes

The genomic architecture of segmental duplications and associated copy number variants in dogs

Mapping DNA structural variation in dogs

A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate

Erratum

Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy

Table of Contents

Volume 19, Issue 3 | March 2009

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