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Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest
Christopher I Keeling, Macaire MS Yuen, Nancy Y Liao, T Roderick Docking, Simon K Chan, Greg A Taylor, Diana L Palmquist, Shaun D Jackman, Anh Nguyen, Maria Li, Hannah Henderson, Jasmine K Janes, Yongjun Zhao, Pawan Pandoh, Richard Moore, Felix AH Sperling, Dezene PW Huber, Inanc Birol, Stephen JM Jones, Joerg Bohlmann Genome Biology 2013, 14:R27 (27 March 2013)
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Editor’s summary
The genome sequence of the mountain pine beetle, only the second beetle genome to be sequenced |
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Pushing the (nuclear) envelope into meiosis
Abby F Dernburg Genome Biology 2013, 14:110 (27 March 2013)
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Abby Dernburg discusses recent research linking nuclear lamins to chromosome pairing in meiosis |
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Sequestration: inadvertently killing biomedical research to score political points
Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013)
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Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction |
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RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken embryos and allows comprehensive annotation of W-chromosome genes
Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grutzner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013)
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A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation |
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Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb-target genes
James P Reddington, Sara M Perricone, Colm E Nestor, Judith Reichmann, Neil A Youngson, Masako Suzuki, Diana Reinhardt, Donncha S Dunican, James G Prendegast, Heidi Mjoseng, Bernard H Ramsahoye, Emma Whitelaw, John M Greally, Ian R Adams, Wendy A Bickmore, Richard R Meehan Genome Biology 2013, 14:R25 (25 March 2013)
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An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells |
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Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue
Markus Mayrhofer, Sebastian DiLorenzo, Anders Isaksson Genome Biology 2013, 14:R24 (25 March 2013)
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Patchwork is a method for determining allele-specific copy number variation in sequenced tumor samples |
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Go retro and get a GRIP
Kim Wong, David J Adams, Thomas M Keane Genome Biology 2013, 14:108 (19 March 2013)
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David Adams and colleagues grapple with the GRIPs (gene retrocopy insertion polymorphisms) identified by Ewing et al in this month's issue |
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DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels
Huiying Zhao, Yuedong Yang, Hai Lin, Xinjun Zhang, Matthew Mort, David N Copper, Yunlong Liu, Yaoqi Zhou Genome Biology 2013, 14:R23 (13 March 2013)
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DDIG-in is a method for predicting the deleterious effects of short indels |
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Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
Adam D Ewing, Tracy J Ballinger, Dent Earl, Broad Institute Genome Sequencing and Analysis Program and Platform, Christopher C Harris, Li Ding, Richard K Wilson, David Haussler Genome Biology 2013, 14:R22 (13 March 2013)
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An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues |
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DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes
Dvir Aran, Sivan Sabato, Asaf Hellman Genome Biology 2013, 14:R21 (12 March 2013)
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A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers |
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Studying the microbiology of the indoor environment
Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013)
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Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study |
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Food for thought from plant and animal genomes
Emily Abrash Genome Biology 2013, 14:302 (27 February 2013)
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A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013. |
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Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes
Pedro G Ferreira, Solenn Patalano, Ritika Chauhan, Richard Ffrench-Constant, Toni Gabaldon, Roderic Guigo, Seirian Sumner Genome Biology 2013, 14:R20 (26 February 2013)
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An RNA-seq analysis of the genetic mechanisms controlling alternative phenotypes in the primitive eusocial wasp Polistes canadensis |
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A CRISPR way to engineer the human genome
Sivaprakash Ramalingam, Narayana Annaluru, Srinivasan Chandrasegaran Genome Biology 2013, 14:107 (26 February 2013)
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Srinivasan Chandrasegaran and colleagues explain how recent advances in mammalian genome engineering exploit the natural properties of the bacterial CRISPR system |
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Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes
Cecilia Alsmark, Peter G Foster, Thomas Sicheritz-Ponten, Sirintra Nakjang, T Martin Embley, Robert P Hirt Genome Biology 2013, 14:R19 (25 February 2013)
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A survey of the genomes of eukaryotic microbial parasites reveals extensive lateral gene transfer from prokaryotes |
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The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila
Tobias Kockmann, Moritz Gerstung, Tommy Schlumpf, Zhu Xhinzhou, Daniel Hess, Niko Beerenwinkel, Christian Beisel, Renato Paro Genome Biology 2013, 14:R18 (25 February 2013)
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The Trithorax group members ASH1 and FSH act as general coactivators of transcription rather than by blocking Polycomb group repression |
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Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies
Masayuki Sugawara, Brendan Epstein, Brian Badgley, Tatsuya Unno, Lei Xu, Jennifer Reese, Prasad Gyaneshwar, Roxanne Denny, Joann Mudge, Arvind K Bharti, Andrew D Farmer, Gregory D May, Jimmy E Woodward, Claudine Medigue, David Vallenet, Aurelie Lajus, Zoe Rouy, Betsy Martinez-Vaz, Peter Tiffin, Nevin D Young, Michael J Sadowsky Genome Biology 2013, 14:R17 (20 February 2013)
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Sequencing the genomes of 48 strains of Sinorhizobium reveals a large heterogeneity in strategies for colonization in this family |
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A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration
Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Hoeffner, Marcus Krueger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun Genome Biology 2013, 14:R16 (20 February 2013)
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A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration |
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What is it about 'eye of newt'?
Yuliana Mihaylova, A Aziz Aboobaker Genome Biology 2013, 14:106 (20 February 2013)
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Aziz Aboobaker and Yuliana Mihaylova muse on the peculiar powers that led 'eye of newt' to find favor with Macbeth's witches |
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Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta
Stephen R Fairclough, Zehua Chen, Eric Kramer, Qiandong Zeng, Sarah Young, Hugh M Robertson, Emina Begovic, Daniel J Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B Franz Lang, Brian Haas, Chad Nusbaum, Nicole King Genome Biology 2013, 14:R15 (18 February 2013)
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Genome sequencing of Salpingoeca rosetta reveals insights into the genome composition of the metazoan ancestor and the evolution of multicellularity |
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Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery
Nikolaj Zuleger, Shelagh Boyle, David A Kelly, Jose I de las Heras, Vassiliki Lazou, Nadia Korfali, Dzmitry G Batrakou, K Natalie Randles, Glenn E Morris, David J Harrison, Wendy A Bickmore, Eric C Schirmer Genome Biology 2013, 14:R14 (15 February 2013)
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A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner |
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Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae
Mallory A Freeberg, Ting Han, James J Moresco, Andy Kong, Yu-Cheng Yang, Zhi JOHN Lu, John R Yates, John K Kim Genome Biology 2013, 14:R13 (14 February 2013)
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A study of the global binding of RNA binding proteins in yeast in response to stress |
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SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data
Wenlong Jia, Kunlong Qiu, Minghui He, Pengfei Song, Quan Zhou, Feng Zhou, Yuan Yu, Dandan Zhu, Michael L Nickerson, Shengqing Wan, Xiangke Liao, Xiaoqian Zhu, Shaoliang Peng, Yingrui Li, Jun Wang, Guangwu Guo Genome Biology 2013, 14:R12 (14 February 2013)
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SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements |
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Science: it's a role model thing
Chris Gunter Genome Biology 2013, 14:105 (14 February 2013)
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To coincide with International Women's Day on March 8, Chris Gunter ask how important role models are to improving female representation in science |
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Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling
Michael Clarke, Amanda J Lohan, Bernard Liu, Ilias Lagkouvardos, Scott Roy, Nikhat Zafar, Claire Bertelli, Christina Schilde, Arash Kianianmomeni, Thomas R Burglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Soon Heng Tan, Andrew P Hutchins, Thomas Weinmeier, Thomas Rattei, Jeffery SC Chu, Gregory Gimenez, Manuel Irimia, Daniel J Rigden, David A Fitzpatrick, Jacob Lorenzo-Morales, Alex Bateman, Cheng-Hsun Chiu, Petrus Tang et al.
Genome Biology 2013, 14:R11 (1 February 2013)
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Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling |
