PERSPECTIVE:

Mariano Rocchi, Nicoletta Archidiacono, and Roscoe Stanyon

Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed
Genome Res. 2006 16: 1441-1444. Published in Advance October 19, 2006, 10.1101/gr.5687906 [Full Text] [PDF] [Supplemental Research Data]  

REVIEW:

Albertha J.M. Walhout

Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
Genome Res. 2006 16: 1445-1454. Published in Advance October 19, 2006, 10.1101/gr.5321506 [Abstract] [Full Text] [PDF]  

Laura Elnitski, Victor X. Jin, Peggy J. Farnham, and Steven J.M. Jones

Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
Genome Res. 2006 16: 1455-1464. Published in Advance October 19, 2006, 10.1101/gr.4140006 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

LETTERS:

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

Novel patterns of genome rearrangement and their association with survival in breast cancer
Genome Res. 2006 16: 1465-1479. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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

Experimental validation of predicted mammalian erythroid cis-regulatory modules
Genome Res. 2006 16: 1480-1492. Published in Advance October 12, 2006, 10.1101/gr.5353806 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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

Human heterochromatin proteins form large domains containing KRAB-ZNF genes
Genome Res. 2006 16: 1493-1504. Published in Advance October 12, 2006, 10.1101/gr.5391806 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Steven M. Johnson, Frederick J. Tan, Heather L. McCullough, Daniel P. Riordan, and Andrew Z. Fire

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin
Genome Res. 2006 16: 1505-1516. Published in Advance October 12, 2006, 10.1101/gr.5560806 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Xiao Liu, Cheol-Koo Lee, Joshua A. Granek, Neil D. Clarke, and Jason D. Lieb

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
Genome Res. 2006 16: 1517-1528. Published in Advance October 19, 2006, 10.1101/gr.5655606 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Boris E. Shakhnovich and Eugene V. Koonin

Origins and impact of constraints in evolution of gene families
Genome Res. 2006 16: 1529-1536. Published in Advance October 19, 2006, 10.1101/gr.5346206 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Eduardo P.C. Rocha, Marie Touchon, and Edward J. Feil

Similar compositional biases are caused by very different mutational effects
Genome Res. 2006 16: 1537-1547. Published in Advance October 26, 2006, 10.1101/gr.5525106 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Marie Dewannieux, Francis Harper, Aurélien Richaud, Claire Letzelter, David Ribet, Gérard Pierron, and Thierry Heidmann

Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements
Genome Res. 2006 16: 1548-1556. Published in Advance October 31, 2006, 10.1101/gr.5565706 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

METHODS:

Jian Ma, Louxin Zhang, Bernard B. Suh, Brian J. Raney, Richard C. Burhans, W. James Kent, Mathieu Blanchette, David Haussler, and Webb Miller

Reconstructing contiguous regions of an ancestral genome
Genome Res. 2006 16: 1557-1565. Published in Advance September 18, 2006, 10.1101/gr.5383506 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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

Accurate and reliable high-throughput detection of copy number variation in the human genome
Genome Res. 2006 16: 1566-1574. Published in Advance November 22, 2006, 10.1101/gr.5630906 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
Genome Res. 2006 16: 1575-1584. Published in Advance November 22, 2006, 10.1101/gr.5629106 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Victor X. Jin, Alina Rabinovich, Sharon L. Squazzo, Roland Green, and Peggy J. Farnham

A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1
Genome Res. 2006 16: 1585-1595. Published in Advance October 19, 2006, 10.1101/gr.5520206 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

James Taylor, Svitlana Tyekucheva, David C. King, Ross C. Hardison, Webb Miller, and Francesca Chiaromonte

ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
Genome Res. 2006 16: 1596-1604. Published in Advance October 19, 2006, 10.1101/gr.4537706 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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