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Commentary Every genome sequence needs a good map Harris A. Lewin, Denis M. Larkin, Joan Pontius, and Stephen J. O'Brien Genome Res. 2009 November; 19(11): 1925–1928. doi: 10.1101/gr.094557.109.PMCID: PMC2775595 | Free in PMC on 2010/05/01 | Perspective Phylogenomics of primates and their ancestral populations Adam Siepel Genome Res. 2009 November; 19(11): 1929–1941. doi: 10.1101/gr.084228.108.PMCID: PMC2775601 | Free in PMC on 2010/05/01 | Letters Population genomics in a disease targeted primary cell model Elin Grundberg, Tony Kwan, Bing Ge, Kevin C.L. Lam, Vonda Koka, Andreas Kindmark, Hans Mallmin, Joana Dias, Dominique J. Verlaan, Manon Ouimet, Daniel Sinnett, Fernando Rivadeneira, Karol Estrada, Albert Hofman, Joyce M. van Meurs, André Uitterlinden, Patrick Beaulieu, Alexandru Graziani, Eef Harmsen, Östen Ljunggren, Claes Ohlsson, Dan Mellström, Magnus K. Karlsson, Olle Nilsson, and Tomi Pastinen Genome Res. 2009 November; 19(11): 1942–1952. doi: 10.1101/gr.095224.109.PMCID: PMC2775606 | Free in PMC on 2010/05/01 | Coexpression network based on natural variation in human gene expression reveals gene interactions and functions Renuka R. Nayak, Michael Kearns, Richard S. Spielman, and Vivian G. Cheung Genome Res. 2009 November; 19(11): 1953–1962. doi: 10.1101/gr.097600.109.PMCID: PMC2775589 | Free in PMC on 2010/05/01 | Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery Joanna Boros, Ian J. Donaldson, Amanda O'Donnell, Zaneta A. Odrowaz, Leo Zeef, Mathieu Lupien, Clifford A. Meyer, X. Shirley Liu, Myles Brown, and Andrew D. Sharrocks Genome Res. 2009 November; 19(11): 1963–1973. doi: 10.1101/gr.093047.109.PMCID: PMC2775591 The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands Hideyuki Takeshima, Satoshi Yamashita, Taichi Shimazu, Tohru Niwa, and Toshikazu Ushijima Genome Res. 2009 November; 19(11): 1974–1982. doi: 10.1101/gr.093310.109.PMCID: PMC2775588 | Free in PMC on 2010/05/01 | Exon-trapping mediated by the human retrotransposon SVA Dustin C. Hancks, Adam D. Ewing, Jesse E. Chen, Katsushi Tokunaga, and Haig H. Kazazian, Jr Genome Res. 2009 November; 19(11): 1983–1991. doi: 10.1101/gr.093153.109.PMCID: PMC2775590 | Free in PMC on 2010/05/01 | 5′-Transducing SVA retrotransposon groups spread efficiently throughout the human genome Annette Damert, Julija Raiz, Axel V. Horn, Johannes Löwer, Hui Wang, Jinchuan Xing, Mark A. Batzer, Roswitha Löwer, and Gerald G. Schumann Genome Res. 2009 November; 19(11): 1992–2008. doi: 10.1101/gr.093435.109.PMCID: PMC2775593 | Free in PMC on 2010/05/01 | Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C–miRNA complexes and the degradation of miRNA targets Jean Hausser, Markus Landthaler, Lukasz Jaskiewicz, Dimos Gaidatzis, and Mihaela Zavolan Genome Res. 2009 November; 19(11): 2009–2020. doi: 10.1101/gr.091181.109.PMCID: PMC2775596 Complex selection on 5′ splice sites in intron-rich organisms Manuel Irimia, Scott William Roy, Daniel E. Neafsey, Josep F. Abril, Jordi Garcia-Fernandez, and Eugene V. Koonin Genome Res. 2009 November; 19(11): 2021–2027. doi: 10.1101/gr.089276.108.PMCID: PMC2775602 Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences Elmar Schilling, Carol El Chartouni, and Michael Rehli Genome Res. 2009 November; 19(11): 2028–2035. doi: 10.1101/gr.095562.109.PMCID: PMC2775599 | Free in PMC on 2010/05/01 | Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention Andrew L. Hufton, Susanne Mathia, Helene Braun, Udo Georgi, Hans Lehrach, Martin Vingron, Albert J. Poustka, and Georgia Panopoulou Genome Res. 2009 November; 19(11): 2036–2051. doi: 10.1101/gr.093237.109.PMCID: PMC2775584 | Free in PMC on 2010/05/01 | Profiling the repertoire of phenotypes influenced by environmental cues that occur during asexual reproduction Aviv Dombrovsky, Laury Arthaud, Terence N. Ledger, Sophie Tares, and Alain Robichon Genome Res. 2009 November; 19(11): 2052–2063. doi: 10.1101/gr.091611.109.PMCID: PMC2775594 | Free in PMC on 2010/05/01 | Repertoire and evolution of miRNA genes in four divergent nematode species Elzo de Wit, Sam E.V. Linsen, Edwin Cuppen, and Eugene Berezikov Genome Res. 2009 November; 19(11): 2064–2074. doi: 10.1101/gr.093781.109.PMCID: PMC2775598 | Free in PMC on 2010/05/01 | Methods Rapid inexpensive genome-wide association using pooled whole blood Jamie E. Craig, Alex W. Hewitt, Amy E. McMellon, Anjali K. Henders, Lingjun Ma, Leanne Wallace, Shiwani Sharma, Kathryn P. Burdon, Peter M. Visscher, Grant W. Montgomery, and Stuart MacGregor Genome Res. 2009 November; 19(11): 2075–2080. doi: 10.1101/gr.094680.109.PMCID: PMC2775600 | Free in PMC on 2010/05/01 | Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS) Zhenyi Liu, Anna C. Obenauf, Michael R. Speicher, and Raphael Kopan Genome Res. 2009 November; 19(11): 2081–2089. doi: 10.1101/gr.093856.109.PMCID: PMC2775603 | Free in PMC on 2010/05/01 | Distinguishing direct versus indirect transcription factor–DNA interactions Raluca Gordân, Alexander J. Hartemink, and Martha L. Bulyk Genome Res. 2009 November; 19(11): 2090–2100. doi: 10.1101/gr.094144.109.PMCID: PMC2775597 An ensemble model of competitive multi-factor binding of the genome Todd Wasson and Alexander J. Hartemink Genome Res. 2009 November; 19(11): 2101–2112. doi: 10.1101/gr.093450.109.PMCID: PMC2775586 | Free in PMC on 2010/05/01 | Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time Nathalie Harder, Felipe Mora-Bermúdez, William J. Godinez, Annelie Wünsche, Roland Eils, Jan Ellenberg, and Karl Rohr Genome Res. 2009 November; 19(11): 2113–2124. doi: 10.1101/gr.092494.109.PMCID: PMC2775592 | Free in PMC on 2010/05/01 | Resources LookSeq: A browser-based viewer for deep sequencing data Heinrich Magnus Manske and Dominic P. Kwiatkowski Genome Res. 2009 November; 19(11): 2125–2132. doi: 10.1101/gr.093443.109.PMCID: PMC2775587 mGene: Accurate SVM-based gene finding with an application to nematode genomes Gabriele Schweikert, Alexander Zien, Georg Zeller, Jonas Behr, Christoph Dieterich, Cheng Soon Ong, Petra Philips, Fabio De Bona, Lisa Hartmann, Anja Bohlen, Nina Krüger, Sören Sonnenburg, and Gunnar Rätsch Genome Res. 2009 November; 19(11): 2133–2143. doi: 10.1101/gr.090597.108.PMCID: PMC2775605 Windshield splatter analysis with the Galaxy metagenomic pipeline Sergei Kosakovsky Pond, Samir Wadhawan, Francesca Chiaromonte, Guruprasad Ananda, Wen-Yu Chung, James Taylor, Anton Nekrutenko, and The Galaxy Team Genome Res. 2009 November; 19(11): 2144–2153. doi: 10.1101/gr.094508.109.PMCID: PMC2775585 Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations Yik-Ying Teo, Xueling Sim, Rick T.H. Ong, Adrian K.S. Tan, Jieming Chen, Erwin Tantoso, Kerrin S. Small, Chee-Seng Ku, Edmund J.D. Lee, Mark Seielstad, and Kee-Seng Chia Genome Res. 2009 November; 19(11): 2154–2162. doi: 10.1101/gr.095000.109.PMCID: PMC2775604
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