IN THIS ISSUE:

Hillary E. Sussman

Open Forum
Genome Res. 2006 16: 305. [Full Text] [PDF]  

FORUM:

Lutz Froenicke, Montserrat Garcia Caldés, Alexander Graphodatsky, Stefan Müller, Leslie A. Lyons, Terence J. Robinson, Marianne Volleth, Fengtang Yang, and Johannes Wienberg

Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?
Genome Res. 2006 16: 306-310. [Full Text] [PDF] [Supplemental Research Data]  

Guillaume Bourque, Glenn Tesler, and Pavel A. Pevzner

The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
Genome Res. 2006 16: 311-313. [Full Text] [PDF]  

COMMENTARY:

Richelle Sopko and Brenda Andrews

Small open reading frames: Not so small anymore
Genome Res. 2006 16: 314-315. [Full Text] [PDF]  

PERSPECTIVES:

Li Weng, Edward M. Rubin, and James Bristow

Application of sequence-based methods in human microbial ecology
Genome Res. 2006 16: 316-322. Published in Advance February 6, 2006, 10.1101/gr.3676406 [Abstract] [Full Text] [PDF]  

LETTERS:

Anna González-Neira, Xiayi Ke, Oscar Lao, Francesc Calafell, Arcadi Navarro, David Comas, Howard Cann, Suzannah Bumpstead, Jilur Ghori, Sarah Hunt, Panos Deloukas, Ian Dunham, Lon R. Cardon, and Jaume Bertranpetit

The portability of tagSNPs across populations: A worldwide survey
Genome Res. 2006 16: 323-330. Published in Advance February 8, 2006, 10.1101/gr.4138406 [Abstract] [Full Text] [PDF] [Supplementary Research Data]  

P.V. Krishna Pant, Heng Tao, Erica J. Beilharz, Dennis G. Ballinger, David R. Cox, and Kelly A. Frazer

Analysis of allelic differential expression in human white blood cells
Genome Res. 2006 16: 331-339. Published in Advance February 8, 2006, 10.1101/gr.4559106 [Abstract] [Full Text] [PDF] [SupplementalResearch Data]  

Susan K. Murphy, Catherine M. Nolan, Zhiqing Huang, Katerina S. Kucera, Brad A. Freking, Timothy P.L. Smith, Kreg A. Leymaster, Jennifer R. Weidman, and Randy L. Jirtle

Callipyge mutation affects gene expression in cis: A potential role for chromatin structure
Genome Res. 2006 16: 340-346. Published in Advance January 13, 2006, 10.1101/gr.4389306 [Abstract] [Full Text] [PDF]  

Alexander E. Vinogradov

"Genome design" model: Evidence from conserved intronic sequence in human–mouse comparison
Genome Res. 2006 16: 347-354. Published in Advance February 3, 2006, 10.1101/gr.4318206 [Abstract] [Full Text] [PDF] [Supplementary Research Data]  

Anne E. Hall, Gregory C. Kettler, and Daphne Preuss

Dynamic evolution at pericentromeres
Genome Res. 2006 16: 355-364. Published in Advance February 6, 2006, 10.1101/gr.4399206 [Abstract] [Full Text] [PDF] [Supplementary Research Data]  

James P. Kastenmayer, Li Ni, Angela Chu, Lauren E. Kitchen, Wei-Chun Au, Hui Yang, Carole D. Carter, David Wheeler, Ronald W. Davis, Jef D. Boeke, Michael A. Snyder, and Munira A. Basrai

Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
Genome Res. 2006 16: 365-373. [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Mónica Campillos, Christian von Mering, Lars Juhl Jensen, and Peer Bork

Identification and analysis of evolutionarily cohesive functional modules in protein networks
Genome Res. 2006 16: 374-382. Published in Advance January 31, 2006, 10.1101/gr.4336406 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

METHODS:

Marina Bibikova, Zhenwu Lin, Lixin Zhou, Eugene Chudin, Eliza Wickham Garcia, Bonnie Wu, Dennis Doucet, Neal J. Thomas, Yunhua Wang, Ekkehard Vollmer, Torsten Goldmann, Carola Seifart, Wei Jiang, David L. Barker, Mark S. Chee, Joanna Floros, and Jian-Bing Fan

High-throughput DNA methylation profiling using universal bead arrays
Genome Res. 2006 16: 383-393. Published in Advance January 31, 2006, 10.1101/gr.4410706 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Stanislav Volik, Benjamin J. Raphael, Guiqing Huang, Michael R. Stratton, Graham Bignel, John Murnane, John H. Brebner, Krystyna Bajsarowicz, Pamela L. Paris, Quanzhou Tao, David Kowbel, Anna Lapuk, Dmitri A. Shagin, Irina A. Shagina, Joe W. Gray, Jan-Fang Cheng, Pieter J. de Jong, Pavel Pevzner, and Colin Collins

Decoding the fine-scale structure of a breast cancer genome and transcriptome
Genome Res. 2006 16: 394-404. Published in Advance February 3, 2006, 10.1101/gr.4247306 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Li-Wei Chang, Rakesh Nagarajan, Jeffrey A. Magee, Jeffrey Milbrandt, and Gary D. Stormo

A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles
Genome Res. 2006 16: 405-413. Published in Advance January 31, 2006, 10.1101/gr.4303406 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Yunhai Li, Kee Khoon Lee, Sean Walsh, Caroline Smith, Sophie Hadingham, Karim Sorefan, Gavin Cawley, and Michael W. Bevan

Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine
Genome Res. 2006 16: 414-427. Published in Advance January 19, 2006, 10.1101/gr.4237406 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Sourav Bandyopadhyay, Roded Sharan, and Trey Ideker

Systematic identification of functional orthologs based on protein network comparison
Genome Res. 2006 16: 428-435. Published in Advance January 27, 2006, 10.1101/gr.4526006 [Abstract] [Full Text] [PDF]  

RESOURCES:

Jennifer L. Moran, Andrew D. Bolton, Pamela V. Tran, Alison Brown, Noelle D. Dwyer, Danielle K. Manning, Bryan C. Bjork, Cheng Li, Kate Montgomery, Sandra M. Siepka, Martha Hotz Vitaterna, Joseph S. Takahashi, Tim Wiltshire, David J. Kwiatkowski, Raju Kucherlapati, and David R. Beier

Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse
Genome Res. 2006 16: 436-440. Published in Advance February 3, 2006, 10.1101/gr.4563306 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Joshua A. Udall, Jordan M. Swanson, Karl Haller, Ryan A. Rapp, Michael E. Sparks, Jamie Hatfield, Yeisoo Yu, Yingru Wu, Caitriona Dowd, Aladdin B. Arpat, Brad A. Sickler, Thea A. Wilkins, Jin Ying Guo, Xiao Ya Chen, Jodi Scheffler, Earl Taliercio, Ricky Turley, Helen McFadden, Paxton Payton, Natalya Klueva, Randell Allen, Deshui Zhang, Candace Haigler, Curtis Wilkerson, Jinfeng Suo, Stefan R. Schulze, Margaret L. Pierce, Margaret Essenberg, HyeRan Kim, Danny J. Llewellyn, Elizabeth S. Dennis, David Kudrna, Rod Wing, Andrew H. Paterson, Cari Soderlund, and Jonathan F. Wendel

A global assembly of cotton ESTs
Genome Res. 2006 16: 441-450. Published in Advance February 14, 2006, 10.1101/gr.4602906 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

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