Volume 16, Issue 12 | December 2006

PERSPECTIVE
- - Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed
    Mariano Rocchi
    Nicoletta Archidiacono
    Roscoe Stanyon
    First Published October 19, 2006
REVIEWS
- - Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
    Albertha J.M. Walhout
    First Published October 19, 2006
  - Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
    Laura Elnitski
    Victor X. Jin
    Peggy J. Farnham
    Steven J.M. Jones
    First Published October 19, 2006
LETTERS
- - Novel patterns of genome rearrangement and their association with survival in breast cancer
    James Hicks
    Alexander Krasnitz
    B. Lakshmi
    Nicholas E. Navin
    Michael Riggs
    Evan Leibu Diane Esposito Joan Alexander Jen Troge Vladimir Grubor Seungtai Yoon Michael Wigler Kenny Ye Anne-Lise Børresen-Dale Bjørn Naume Ellen Schlicting Larry Norton Torsten Hägerström Lambert Skoog
    ...[+14 authors]...,
    Gert Auer
    Susanne Månér
    Pär Lundin
    Anders Zetterberg
    First Published December 1, 2006
  - Experimental validation of predicted mammalian erythroid cis-regulatory modules
    Hao Wang
    Ying Zhang
    Yong Cheng
    Yuepin Zhou
    David C. King
    James Taylor Francesca Chiaromonte Jyotsna Kasturi Hanna Petrykowska Brian Gibb Christine Dorman Webb Miller
    ...[+7 authors]...,
    Louis C. Dore
    John Welch
    Mitchell J. Weiss
    Ross C. Hardison
    First Published October 12, 2006
  - Human heterochromatin proteins form large domains containing KRAB-ZNF genes
    Maartje J. Vogel
    Lars Guelen
    Elzo de Wit
    Daniel Peric Hupkes
    Martin Lodén
    Wendy Talhout
    ...[+1 authors]...,
    Marike Feenstra
    Ben Abbas
    Anne-Kathrin Classen
    Bas van Steensel
    First Published October 12, 2006
  - Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin
    Steven M. Johnson
    Frederick J. Tan
    Heather L. McCullough
    Daniel P. Riordan
    Andrew Z. Fire
    First Published October 12, 2006
  - Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
    Xiao Liu
    Cheol-Koo Lee
    Joshua A. Granek
    Neil D. Clarke
    Jason D. Lieb
    First Published October 19, 2006
  - Origins and impact of constraints in evolution of gene families
    Boris E. Shakhnovich
    Eugene V. Koonin
    First Published October 19, 2006
  - Similar compositional biases are caused by very different mutational effects
    Eduardo P.C. Rocha
    Marie Touchon
    Edward J. Feil
    First Published October 26, 2006
  - Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements
    Marie Dewannieux
    Francis Harper
    Aurélien Richaud
    Claire Letzelter
    David Ribet
    First Published October 31, 2006
Methods
- - Reconstructing contiguous regions of an ancestral genome
    Jian Ma
    Louxin Zhang
    Bernard B. Suh
    Brian J. Raney
    Richard C. Burhans
    First Published September 18, 2006
  - Accurate and reliable high-throughput detection of copy number variation in the human genome
    Heike Fiegler
    Richard Redon
    Dan Andrews
    Carol Scott
    Robert Andrews
    Carol Carder Richard Clark Oliver Dovey Peter Ellis Lars Feuk Lisa French Paul Hunt Dimitrios Kalaitzopoulos James Larkin Lyndal Montgomery George H. Perry Bob W. Plumb Keith Porter Rachel E. Rigby Diane Rigler Armand Valsesia Cordelia Langford Sean J. Humphray
    ...[+18 authors]...,
    Stephen W. Scherer
    Charles Lee
    Matthew E. Hurles
    Nigel P. Carter
    First Published November 22, 2006
  - Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
    Daisuke Komura
    Fan Shen
    Shumpei Ishikawa
    Karen R. Fitch
    Wenwei Chen
    Jane Zhang Guoying Liu Sigeo Ihara Hiroshi Nakamura Matthew E. Hurles Charles Lee Stephen W. Scherer
    ...[+7 authors]...,
    Keith W. Jones
    Michael H. Shapero
    Jing Huang
    Hiroyuki Aburatani
    First Published November 22, 2006
  - A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1
    Victor X. Jin
    Alina Rabinovich
    Sharon L. Squazzo
    Roland Green
    Peggy J. Farnham
    First Published October 19, 2006
  - ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
    James Taylor
    Svitlana Tyekucheva
    David C. King
    Ross C. Hardison
    Webb Miller
    First Published October 19, 2006

Table of Contents

Volume 16, Issue 12 | December 2006

PERSPECTIVE

Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed

REVIEWS

Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping

Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques

LETTERS

Novel patterns of genome rearrangement and their association with survival in breast cancer

Experimental validation of predicted mammalian erythroid cis-regulatory modules

Human heterochromatin proteins form large domains containing KRAB-ZNF genes

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection

Origins and impact of constraints in evolution of gene families

Similar compositional biases are caused by very different mutational effects

Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements

Methods

Reconstructing contiguous regions of an ancestral genome

Accurate and reliable high-throughput detection of copy number variation in the human genome

Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays

A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1

ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements

Table of Contents

Volume 16, Issue 12 | December 2006

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