Volume 19, Issue 2 | February 2009

LETTERS
- - A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
    Oliver A. Hampton
    Petra Den Hollander
    Christopher A. Miller
    David A. Delgado
    Jian Li
    Cristian Coarfa Ronald A. Harris Stephen Richards Steven E. Scherer
    ...[+4 authors]...,
    Donna M. Muzny
    Richard A. Gibbs
    Adrian V. Lee
    Aleksandar Milosavljevic
    First Published December 3, 2008
  - Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
    Santhosh Girirajan
    Lin Chen
    Tina Graves
    Tomas Marques-Bonet
    Mario Ventura
    Catrina Fronick Lucinda Fulton Mariano Rocchi
    ...[+3 authors]...,
    Robert S. Fulton
    Richard K. Wilson
    Elaine R. Mardis
    Evan E. Eichler
    First Published November 24, 2008
  - Chromosomal instability mediated by non-B DNA: Cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans
    Hidehito Inagaki
    Tamae Ohye
    Hiroshi Kogo
    Takema Kato
    Hasbaira Bolor
    First Published November 7, 2008
  - Widespread balancing selection and pathogen-driven selection at blood group antigen genes
    Matteo Fumagalli
    Rachele Cagliani
    Uberto Pozzoli
    Stefania Riva
    Giacomo P. Comi
    First Published November 7, 2008
  - The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)
    Webb Miller
    Daniela I. Drautz
    Jan E. Janecka
    Arthur M. Lesk
    Aakrosh Ratan
    Lynn P. Tomsho Mike Packard Yeting Zhang Lindsay R. McClellan Ji Qi Fangqing Zhao M. Thomas P. Gilbert Love Dalén Juan Luis Arsuaga Per G.P. Ericson Daniel H. Huson
    ...[+11 authors]...,
    Kristofer M. Helgen
    William J. Murphy
    Anders Götherström
    Stephan C. Schuster
    First Published January 12, 2009
  - H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
    Florian M. Pauler
    Mathew A. Sloane
    Ru Huang
    Kakkad Regha
    Martha V. Koerner
    Ido Tamir
    ...[+1 authors]...,
    Andreas Sommer
    Andras Aszodi
    Thomas Jenuwein
    Denise P. Barlow
    First Published December 1, 2008
  - Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes
    David Alvarez-Ponce
    Montserrat Aguadé
    Julio Rozas
    First Published January 13, 2009
  - Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome
    Regina S. Baucom
    James C. Estill
    Jim Leebens-Mack
    Jeffrey L. Bennetzen
    First Published November 24, 2008
Methods
- - Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
    Eivind Valen
    Giovanni Pascarella
    Alistair Chalk
    Norihiro Maeda
    Miki Kojima
    Chika Kawazu Mitsuyoshi Murata Hiromi Nishiyori Dejan Lazarevic Dario Motti Troels Torben Marstrand Man-Hung Eric Tang Xiaobei Zhao Anders Krogh Ole Winther Takahiro Arakawa Jun Kawai Christine Wells Carsten Daub Matthias Harbers
    ...[+15 authors]...,
    Yoshihide Hayashizaki
    Stefano Gustincich
    Albin Sandelin
    Piero Carninci
    First Published December 11, 2008
  - High-resolution human core-promoter prediction with CoreBoost_HM
    Xiaowo Wang
    Zhenyu Xuan
    Xiaoyue Zhao
    Yanda Li
    Michael Q. Zhang
    First Published November 7, 2008
  - 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 January 13, 2009
  - A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements
    Gerhard Mittler
    Falk Butter
    Matthias Mann
    First Published November 17, 2008
  - De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
    Josephine A. Reinhardt
    David A. Baltrus
    Marc T. Nishimura
    William R. Jeck
    Corbin D. Jones
    First Published November 17, 2008
  - Inferring genomic flux in bacteria
    Xavier Didelot
    Aaron Darling
    Daniel Falush
    First Published November 17, 2008
RESOURCES
- - Whole population, genome-wide mapping of hidden relatedness
    Alexander Gusev
    Jennifer K. Lowe
    Markus Stoffel
    Mark J. Daly
    David Altshuler
    First Published October 29, 2008
  - EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    Albert J. Vilella
    Jessica Severin
    Abel Ureta-Vidal
    Li Heng
    Richard Durbin
    First Published November 24, 2008
  - De novo fragment assembly with short mate-paired reads: Does the read length matter?
    Mark J. Chaisson
    Dumitru Brinza
    Pavel A. Pevzner
    First Published December 3, 2008

Table of Contents

Volume 19, Issue 2 | February 2009

LETTERS

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

Chromosomal instability mediated by non-B DNA: Cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans

Widespread balancing selection and pathogen-driven selection at blood group antigen genes

The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome

Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

Methods

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

High-resolution human core-promoter prediction with CoreBoost_HM

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

A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements

De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae

Inferring genomic flux in bacteria

RESOURCES

Whole population, genome-wide mapping of hidden relatedness

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Table of Contents

Volume 19, Issue 2 | February 2009

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LETTERS

Methods

RESOURCES