pmc logo image
Logo of genoresCSHL PressJournal HomeSubscriptionseTOC AlertsBioSupplyNet
Other Issues: Journal List | previous | next | latest | archive
Volume 19(11);  November 2009
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
Other Issues: Journal List | previous | next | latest | archive