REVIEW:

Sudhir Kumar and Alan Filipski

Multiple sequence alignment: In pursuit of homologous DNA positions
Genome Res. 2007 17: 127-135. [Abstract] [Full Text] [PDF]  

LETTERS:

Sara J. Cooper, Nathan D. Trinklein, Loan Nguyen, and Richard M. Myers

Serum response factor binding sites differ in three human cell types
Genome Res. 2007 17: 136-144. Published in Advance January 2, 2007, 10.1101/gr.5875007 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Daehyun Baek, Colleen Davis, Brent Ewing, David Gordon, and Phil Green

Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters
Genome Res. 2007 17: 145-155. Published in Advance January 8, 2007, 10.1101/gr.5872707 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Bin Tian, Zhenhua Pan, and Ju Youn Lee

Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing
Genome Res. 2007 17: 156-165. Published in Advance January 8, 2007, 10.1101/gr.5532707 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Peng Shi and Jianzhi Zhang

Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land
Genome Res. 2007 17: 166-174. Published in Advance January 8, 2007, 10.1101/gr.6040007 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Takeshi Itoh, Tsuyoshi Tanaka, Roberto A. Barrero, Chisato Yamasaki, Yasuyuki Fujii, Phillip B. Hilton, Baltazar A. Antonio, Hideo Aono, Rolf Apweiler, Richard Bruskiewich, Thomas Bureau, Frances Burr, Antonio Costa de Oliveira, Galina Fuks, Takuya Habara, Georg Haberer, Bin Han, Erimi Harada, Aiko T. Hiraki, Hirohiko Hirochika, Douglas Hoen, Hiroki Hokari, Satomi Hosokawa, Yue Hsing, Hiroshi Ikawa, Kazuho Ikeo, Tadashi Imanishi, Yukiyo Ito, Pankaj Jaiswal, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Hiroaki Kawashima, Jitendra P. Khurana, Shoshi Kikuchi, Setsuko Komatsu, Kanako O. Koyanagi, Hiromi Kubooka, Damien Lieberherr, Yao-Cheng Lin, David Lonsdale, Takashi Matsumoto, Akihiro Matsuya, W. Richard McCombie, Joachim Messing, Akio Miyao, Nicola Mulder, Yoshiaki Nagamura, Jongmin Nam, Nobukazu Namiki, Hisataka Numa, Shin Nurimoto, Claire O’Donovan, Hajime Ohyanagi, Toshihisa Okido, Satoshi OOta, Naoki Osato, Lance E. Palmer, Francis Quetier, Saurabh Raghuvanshi, Naomi Saichi, Hiroaki Sakai, Yasumichi Sakai, Katsumi Sakata, Tetsuya Sakurai, Fumihiko Sato, Yoshiharu Sato, Heiko Schoof, Motoaki Seki, Michie Shibata, Yuji Shimizu, Kazuo Shinozaki, Yuji Shinso, Nagendra K. Singh, Brian Smith-White, Jun-ichi Takeda, Motohiko Tanino, Tatiana Tatusova, Supat Thongjuea, Fusano Todokoro, Mika Tsugane, Akhilesh K. Tyagi, Apichart Vanavichit, Aihui Wang, Rod A. Wing, Kaori Yamaguchi, Mayu Yamamoto, Naoyuki Yamamoto, Yeisoo Yu, Hao Zhang, Qiang Zhao, Kenichi Higo, Benjamin Burr, Takashi Gojobori, Takuji Sasaki, and for the Rice Annotation Project

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
Genome Res. 2007 17: 175-183. Published in Advance January 8, 2007, 10.1101/gr.5509507 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Austen R.D. Ganley and Takehiko Kobayashi

Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data
Genome Res. 2007 17: 184-191. Published in Advance January 2, 2007, 10.1101/gr.5457707 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Timothy P. Stinear, Torsten Seemann, Sacha Pidot, Wafa Frigui, Gilles Reysset, Thierry Garnier, Guillaume Meurice, David Simon, Christiane Bouchier, Laurence Ma, Magali Tichit, Jessica L. Porter, Janine Ryan, Paul D.R. Johnson, John K. Davies, Grant A. Jenkin, Pamela L.C. Small, Louis M. Jones, Fredj Tekaia, Françoise Laval, Mamadou Daffé, Julian Parkhill, and Stewart T. Cole

Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer
Genome Res. 2007 17: 192-200. Published in Advance January 8, 2007, 10.1101/gr.5942807 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

METHODS:

Len A. Pennacchio, Gabriela G. Loots, Marcelo A. Nobrega, and Ivan Ovcharenko

Predicting tissue-specific enhancers in the human genome
Genome Res. 2007 17: 201-211. Published in Advance January 8, 2007, 10.1101/gr.5972507 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Aaron E. Tenney, Jia Qian Wu, Laura Langton, Paul Klueh, Ralph Quatrano, and Michael R. Brent

A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
Genome Res. 2007 17: 212-218. Published in Advance January 8, 2007, 10.1101/gr.5661407 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Vikas Bansal, Ali Bashir, and Vineet Bafna

Evidence for large inversion polymorphisms in the human genome from HapMap data
Genome Res. 2007 17: 219-230. Published in Advance December 21, 2006, 10.1101/gr.5774507 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Stephen Tanner, Zhouxin Shen, Julio Ng, Liliana Florea, Roderic Guigó, Steven P. Briggs, and Vineet Bafna

Improving gene annotation using peptide mass spectrometry
Genome Res. 2007 17: 231-239. Published in Advance December 22, 2006, 10.1101/gr.5646507 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

Michael R. Miller, Joseph P. Dunham, Angel Amores, William A. Cresko, and Eric A. Johnson

Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
Genome Res. 2007 17: 240-248. Published in Advance December 22, 2006, 10.1101/gr.5681207 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

RESOURCES:

Roberta Roberto, Oronzo Capozzi, Richard K. Wilson, Elaine R. Mardis, Mariana Lomiento, Eray Tuzun, Ze Cheng, Alan R. Mootnick, Nicoletta Archidiacono, Mariano Rocchi, and Evan E. Eichler

Molecular refinement of gibbon genome rearrangements
Genome Res. 2007 17: 249-257. Published in Advance December 21, 2006, 10.1101/gr.6052507 [Abstract] [Full Text] [PDF] [Supplemental Research Data]  

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