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PERSPECTIVE

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Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed
- Mariano Rocchi,
- Nicoletta Archidiacono,
- and Roscoe Stanyon
Genome Res. December 2006 16: 1441-1444; Published in Advance October 19, 2006, doi:10.1101/gr.5687906

REVIEWS

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Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
- Albertha J.M. Walhout
Genome Res. December 2006 16: 1445-1454; Published in Advance October 19, 2006, doi:10.1101/gr.5321506
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Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
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LETTERS

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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,
- Gert Auer,
- Susanne Månér,
- Pär Lundin,
- and Anders Zetterberg
Genome Res. December 2006 16: 1465-1479; doi:10.1101/gr.5460106
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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,
- Louis C. Dore,
- John Welch,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2006 16: 1480-1492; Published in Advance October 12, 2006, doi:10.1101/gr.5353806
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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,
- Marike Feenstra,
- Ben Abbas,
- Anne-Kathrin Classen,
- and Bas van Steensel
Genome Res. December 2006 16: 1493-1504; Published in Advance October 12, 2006, doi:10.1101/gr.5391806
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Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin
- Steven M. Johnson,
- Frederick J. Tan,
- Heather L. McCullough,
- Daniel P. Riordan,
- and Andrew Z. Fire
Genome Res. December 2006 16: 1505-1516; Published in Advance October 12, 2006, doi:10.1101/gr.5560806
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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,
- and Jason D. Lieb
Genome Res. December 2006 16: 1517-1528; Published in Advance October 19, 2006, doi:10.1101/gr.5655606
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Origins and impact of constraints in evolution of gene families
- Boris E. Shakhnovich and
- Eugene V. Koonin
Genome Res. December 2006 16: 1529-1536; Published in Advance October 19, 2006, doi:10.1101/gr.5346206
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Similar compositional biases are caused by very different mutational effects
- Eduardo P.C. Rocha,
- Marie Touchon,
- and Edward J. Feil
Genome Res. December 2006 16: 1537-1547; Published in Advance October 26, 2006, doi:10.1101/gr.5525106
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Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements
- Marie Dewannieux,
- Francis Harper,
- Aurélien Richaud,
- Claire Letzelter,
- David Ribet,
- Gérard Pierron,
- and Thierry Heidmann
Genome Res. December 2006 16: 1548-1556; Published in Advance October 31, 2006, doi:10.1101/gr.5565706

Methods

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Reconstructing contiguous regions of an ancestral genome
- Jian Ma,
- Louxin Zhang,
- Bernard B. Suh,
- Brian J. Raney,
- Richard C. Burhans,
- W. James Kent,
- Mathieu Blanchette,
- David Haussler,
- and Webb Miller
Genome Res. December 2006 16: 1557-1565; Published in Advance September 18, 2006, doi:10.1101/gr.5383506
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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,
- Stephen W. Scherer,
- Charles Lee,
- Matthew E. Hurles,
- and Nigel P. Carter
Genome Res. December 2006 16: 1566-1574; Published in Advance November 22, 2006, doi:10.1101/gr.5630906
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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,
- Keith W. Jones,
- Michael H. Shapero,
- Jing Huang,
- and Hiroyuki Aburatani
Genome Res. December 2006 16: 1575-1584; Published in Advance November 22, 2006, doi:10.1101/gr.5629106
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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,
- and Peggy J. Farnham
Genome Res. December 2006 16: 1585-1595; Published in Advance October 19, 2006, doi:10.1101/gr.5520206
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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,
- and Francesca Chiaromonte
Genome Res. December 2006 16: 1596-1604; Published in Advance October 19, 2006, doi:10.1101/gr.4537706
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Table of Contents

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

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