REVIEW:

Karen Usdin

The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases
Genome Res. 2008 18: 1011-1019. [Abstract] [Full Text] [PDF]  

LETTERS:

Ines Hellmann, Yuan Mang, Zhiping Gu, Peter Li, Francisco M. de la Vega, Andrew G. Clark, and Rasmus Nielsen

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
Genome Res. 2008 18: 1020-1029. Published in Advance April 14, 2008, 10.1101/gr.074187.107 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Stefan Kirsch, Claudia Münch, Zhaoshi Jiang, Ze Cheng, Lin Chen, Christiane Batz, Evan E. Eichler, and Werner Schempp

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
Genome Res. 2008 18: 1030-1042. Published in Advance April 29, 2008, 10.1101/gr.076711.108 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Elizabeth A. Grice, Heidi H. Kong, Gabriel Renaud, Alice C. Young, NISC Comparative Sequencing Program, Gerard G. Bouffard, Robert W. Blakesley, Tyra G. Wolfsberg, Maria L. Turner, and Julia A. Segre

A diversity profile of the human skin microbiota
Genome Res. 2008 18: 1043-1050. Published in Advance May 23, 2008, 10.1101/gr.075549.107 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Anton Valouev, Jeffrey Ichikawa, Thaisan Tonthat, Jeremy Stuart, Swati Ranade, Heather Peckham, Kathy Zeng, Joel A. Malek, Gina Costa, Kevin McKernan, Arend Sidow, Andrew Fire, and Steven M. Johnson

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
Genome Res. 2008 18: 1051-1063. Published in Advance May 13, 2008, 10.1101/gr.076463.108 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Jun S. Song, Xingkun Liu, X. Shirley Liu, and Xiangwei He

A high-resolution map of nucleosome positioning on a fission yeast centromere
Genome Res. 2008 18: 1064-1072. Published in Advance April 14, 2008, 10.1101/gr.075374.107 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Travis N. Mavrich, Ilya P. Ioshikhes, Bryan J. Venters, Cizhong Jiang, Lynn P. Tomsho, Ji Qi, Stephan C. Schuster, Istvan Albert, and B. Franklin Pugh

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
Genome Res. 2008 18: 1073-1083. Published in Advance June 12, 2008, 10.1101/gr.078261.108 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Itay Tirosh and Naama Barkai

Two strategies for gene regulation by promoter nucleosomes
Genome Res. 2008 18: 1084-1091. Published in Advance April 30, 2008, 10.1101/gr.076059.108 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Gabriel Musso, Michael Costanzo, ManQin Huangfu, Andrew M. Smith, Jadine Paw, Bryan-Joseph San Luis, Charles Boone, Guri Giaever, Corey Nislow, Andrew Emili, and Zhaolei Zhang

The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast
Genome Res. 2008 18: 1092-1099. Published in Advance May 7, 2008, 10.1101/gr.076174.108 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Linda Z. Holland, Ricard Albalat, Kaoru Azumi, Èlia Benito-Gutiérrez, Matthew J. Blow, Marianne Bronner-Fraser, Frederic Brunet, Thomas Butts, Simona Candiani, Larry J. Dishaw, David E.K. Ferrier, Jordi Garcia-Fernàndez, Jeremy J. Gibson-Brown, Carmela Gissi, Adam Godzik, Finn Hallböök, Dan Hirose, Kazuyoshi Hosomichi, Tetsuro Ikuta, Hidetoshi Inoko, Masanori Kasahara, Jun Kasamatsu, Takeshi Kawashima, Ayuko Kimura, Masaaki Kobayashi, Zbynek Kozmik, Kaoru Kubokawa, Vincent Laudet, Gary W. Litman, Alice C. McHardy, Daniel Meulemans, Masaru Nonaka, Robert P. Olinski, Zeev Pancer, Len A. Pennacchio, Mario Pestarino, Jonathan P. Rast, Isidore Rigoutsos, Marc Robinson-Rechavi, Graeme Roch, Hidetoshi Saiga, Yasunori Sasakura, Masanobu Satake, Yutaka Satou, Michael Schubert, Nancy Sherwood, Takashi Shiina, Naohito Takatori, Javier Tello, Pavel Vopalensky, Shuichi Wada, Anlong Xu, Yuzhen Ye, Keita Yoshida, Fumiko Yoshizaki, Jr-Kai Yu, Qing Zhang, Christian M. Zmasek, Pieter J. de Jong, Kazutoyo Osoegawa, Nicholas H. Putnam, Daniel S. Rokhsar, Noriyuki Satoh, and Peter W.H. Holland

The amphioxus genome illuminates vertebrate origins and cephalochordate biology
Genome Res. 2008 18: 1100-1111. Published in Advance June 18, 2008, 10.1101/gr.073676.107 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Shengfeng Huang, Shaochun Yuan, Lei Guo, Yanhong Yu, Jun Li, Tao Wu, Tong Liu, Manyi Yang, Kui Wu, Huiling Liu, Jin Ge, Yingcai Yu, Huiqing Huang, Meiling Dong, Cuiling Yu, Shangwu Chen, and Anlong Xu

Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity
Genome Res. 2008 18: 1112-1126. Published in Advance June 18, 2008, 10.1101/gr.069674.107 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Jr-Kai Yu, Daniel Meulemans, Sonja J. McKeown, and Marianne Bronner-Fraser

Insights from the amphioxus genome on the origin of vertebrate neural crest
Genome Res. 2008 18: 1127-1132. Published in Advance June 18, 2008, 10.1101/gr.076208.108 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

METHODS:

Nitin Gupta, Jamal Benhamida, Vipul Bhargava, Daniel Goodman, Elisabeth Kain, Ian Kerman, Ngan Nguyen, Noah Ollikainen, Jesse Rodriguez, Jian Wang, Mary S. Lipton, Margaret Romine, Vineet Bafna, Richard D. Smith, and Pavel A. Pevzner

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
Genome Res. 2008 18: 1133-1142. Published in Advance April 21, 2008, 10.1101/gr.074344.107 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Wei Chen, Vera Kalscheuer, Andreas Tzschach, Corinna Menzel, Reinhard Ullmann, Marcel Holger Schulz, Fikret Erdogan, Na Li, Zofia Kijas, Ger Arkesteijn, Isidora Lopez Pajares, Margret Goetz-Sothmann, Uwe Heinrich, Imma Rost, Andreas Dufke, Ute Grasshoff, Birgitta Glaeser, Martin Vingron, and H. Hilger Ropers

Mapping translocation breakpoints by next-generation sequencing
Genome Res. 2008 18: 1143-1149. Published in Advance March 7, 2008, 10.1101/gr.076166.108 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Ivan Iossifov, Tian Zheng, Miron Baron, T. Conrad Gilliam, and Andrey Rzhetsky

Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
Genome Res. 2008 18: 1150-1162. Published in Advance April 16, 2008, 10.1101/gr.075622.107 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Yao-Ting Huang, Feng-Chi Chen, Chiuan-Jung Chen, Hsin-Liang Chen, and Trees-Juen Chuang

Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons
Genome Res. 2008 18: 1163-1170. Published in Advance March 27, 2008, 10.1101/gr.075556.107 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Vijay K. Tiwari, Leslie Cope, Kelly M. McGarvey, Joyce E. Ohm, and Stephen B. Baylin

A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations
Genome Res. 2008 18: 1171-1179. Published in Advance May 23, 2008, 10.1101/gr.073452.107 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

RESOURCES:

Chaim Linhart, Yonit Halperin, and Ron Shamir

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
Genome Res. 2008 18: 1180-1189. Published in Advance April 14, 2008, 10.1101/gr.076117.108 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

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