Table of Contents

ARTICLES

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Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation
- Lili Milani,
- Anders Lundmark,
- Jessica Nordlund,
- Anna Kiialainen,
- Trond Flaegstad,
- Gudmundur Jonmundsson,
- Jukka Kanerva,
- Kjeld Schmiegelow,
- Kevin L. Gunderson,
- Gudmar Lönnerholm,
- and Ann-Christine Syvänen
Genome Res. January 2009 19: 1-11; Published in Advance November 7, 2008, doi:10.1101/gr.083931.108
OPEN ACCESS ARTICLE
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Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa
- Craig Winstanley,
- Morgan G.I. Langille,
- Joanne L. Fothergill,
- Irena Kukavica-Ibrulj,
- Catherine Paradis-Bleau,
- François Sanschagrin,
- Nicholas R. Thomson,
- Geoff L. Winsor,
- Michael A. Quail,
- Nicola Lennard,
- Alexandra Bignell,
- Louise Clarke,
- Kathy Seeger,
- David Saunders,
- David Harris,
- Julian Parkhill,
- Robert E.W. Hancock,
- Fiona S.L. Brinkman,
- and Roger C. Levesque
Genome Res. January 2009 19: 12-23; Published in Advance December 1, 2008, doi:10.1101/gr.086082.108
OPEN ACCESS ARTICLE

LETTERS

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Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
- Suresh Cuddapah,
- Raja Jothi,
- Dustin E. Schones,
- Tae-Young Roh,
- Kairong Cui,
- and Keji Zhao
Genome Res. January 2009 19: 24-32; Published in Advance December 3, 2008, doi:10.1101/gr.082800.108
OPEN ACCESS ARTICLE
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Comparative sequence analysis of primate subtelomeres originating from a chromosome fission event
- M. Katharine Rudd,
- RaeLynn M. Endicott,
- Cynthia Friedman,
- Megan Walker,
- Janet M. Young,
- Kazutoyo Osoegawa,
- NISC Comparative Sequencing Program,
- Pieter J. de Jong,
- Eric D. Green,
- and Barbara J. Trask
Genome Res. January 2009 19: 33-41; Published in Advance October 24, 2008, doi:10.1101/gr.083170.108
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Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs
- Hanhui Kuang,
- Chellappan Padmanabhan,
- Feng Li,
- Ayako Kamei,
- Pudota B. Bhaskar,
- Shu Ouyang,
- Jiming Jiang,
- C. Robin Buell,
- and Barbara Baker
Genome Res. January 2009 19: 42-56; Published in Advance November 26, 2008, doi:10.1101/gr.078196.108
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Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
- Besma Ben Amor,
- Sonia Wirth,
- Francisco Merchan,
- Philippe Laporte,
- Yves d’Aubenton-Carafa,
- Judith Hirsch,
- Alexis Maizel,
- Allison Mallory,
- Antoine Lucas,
- Jean Marc Deragon,
- Herve Vaucheret,
- Claude Thermes,
- and Martin Crespi
Genome Res. January 2009 19: 57-69; Published in Advance November 7, 2008, doi:10.1101/gr.080275.108
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Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa
- Xuefeng Zhou,
- Ramanjulu Sunkar,
- Hailing Jin,
- Jian-Kang Zhu,
- and Weixiong Zhang
Genome Res. January 2009 19: 70-78; Published in Advance October 29, 2008, doi:10.1101/gr.084806.108
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Principles of transcriptional regulation and evolution of the metabolic system in E. coli
- Aswin S.N. Seshasayee,
- Gillian M. Fraser,
- M. Madan Babu,
- and Nicholas M. Luscombe
Genome Res. January 2009 19: 79-91; Published in Advance October 3, 2008, doi:10.1101/gr.079715.108

Methods

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Most mammalian mRNAs are conserved targets of microRNAs
- Robin C. Friedman,
- Kyle Kai-How Farh,
- Christopher B. Burge,
- and David P. Bartel
Genome Res. January 2009 19: 92-105; Published in Advance October 27, 2008, doi:10.1101/gr.082701.108
OPEN ACCESS ARTICLE
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MSB: A mean-shift-based approach for the analysis of structural variation in the genome
- Lu-yong Wang,
- Alexej Abyzov,
- Jan O. Korbel,
- Michael Snyder,
- and Mark Gerstein
Genome Res. January 2009 19: 106-117; Published in Advance November 26, 2008, doi:10.1101/gr.080069.108
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Targeted screening of cis-regulatory variation in human haplotypes
- Dominique J. Verlaan,
- Bing Ge,
- Elin Grundberg,
- Rose Hoberman,
- Kevin C.L. Lam,
- Vonda Koka,
- Joana Dias,
- Scott Gurd,
- Nicolas W. Martin,
- Hans Mallmin,
- Olof Nilsson,
- Eef Harmsen,
- Ken Dewar,
- Tony Kwan,
- and Tomi Pastinen
Genome Res. January 2009 19: 118-127; Published in Advance October 29, 2008, doi:10.1101/gr.084798.108
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Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol
- Sébastien Gallien,
- Emmanuel Perrodou,
- Christine Carapito,
- Caroline Deshayes,
- Jean-Marc Reyrat,
- Alain Van Dorsselaer,
- Olivier Poch,
- Christine Schaeffer,
- and Odile Lecompte
Genome Res. January 2009 19: 128-135; Published in Advance October 27, 2008, doi:10.1101/gr.081901.108

RESOURCES

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Fast and flexible simulation of DNA sequence data
- Gary K. Chen,
- Paul Marjoram,
- and Jeffrey D. Wall
Genome Res. January 2009 19: 136-142; Published in Advance November 24, 2008, doi:10.1101/gr.083634.108
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genBlastA: Enabling BLAST to identify homologous gene sequences
- Rong She,
- Jeffrey S.-C. Chu,
- Ke Wang,
- Jian Pei,
- and Nansheng Chen
Genome Res. January 2009 19: 143-149; Published in Advance October 6, 2008, doi:10.1101/gr.082081.108
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A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: The NIH heterogeneous stock
- Martina Johannesson,
- Regina Lopez-Aumatell,
- Pernilla Stridh,
- Margarita Diez,
- Jonatan Tuncel,
- Gloria Blázquez,
- Esther Martinez-Membrives,
- Toni Cañete,
- Elia Vicens-Costa,
- Delyth Graham,
- Richard R. Copley,
- Polinka Hernandez-Pliego,
- Amennai D. Beyeen,
- Johan Öckinger,
- Cristina Fernández-Santamaría,
- Percio S. Gulko,
- Max Brenner,
- Adolf Tobeña,
- Marc Guitart-Masip,
- Lydia Giménez-Llort,
- Anna Dominiczak,
- Rikard Holmdahl,
- Dominique Gauguier,
- Tomas Olsson,
- Richard Mott,
- William Valdar,
- Eva E. Redei,
- Alberto Fernández-Teruel,
- and Jonathan Flint
Genome Res. January 2009 19: 150-158; Published in Advance October 29, 2008, doi:10.1101/gr.081497.108
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Dissecting the effects of mtDNA variations on complex traits using mouse conplastic strains
- Xinhua Yu,
- Ulrike Gimsa,
- Lena Wester-Rosenlöf,
- Ellen Kanitz,
- Winfried Otten,
- Manfred Kunz,
- and Saleh M. Ibrahim
Genome Res. January 2009 19: 159-165; Published in Advance November 26, 2008, doi:10.1101/gr.078865.108

ARTICLES

Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation

Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

LETTERS

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

Comparative sequence analysis of primate subtelomeres originating from a chromosome fission event

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa

Principles of transcriptional regulation and evolution of the metabolic system in E. coli

Methods

Most mammalian mRNAs are conserved targets of microRNAs

MSB: A mean-shift-based approach for the analysis of structural variation in the genome

Targeted screening of cis-regulatory variation in human haplotypes

Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol

RESOURCES

Fast and flexible simulation of DNA sequence data

genBlastA: Enabling BLAST to identify homologous gene sequences

A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: The NIH heterogeneous stock

Dissecting the effects of mtDNA variations on complex traits using mouse conplastic strains

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