Genome Biology | Volume 14 Issue 3

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	Volume 14 Issue 3
	Comment
	Comment Sequestration: inadvertently killing biomedical research to score political points Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction
	Research highlight Go retro and get a GRIP Kim Wong, David J Adams, Thomas M Keane Genome Biology 2013, 14:108 (19 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Adams and colleagues grapple with the GRIPs (gene retrocopy insertion polymorphisms) identified by Ewing et al in this month's issue
	Research highlight Pushing the (nuclear) envelope into meiosis Abby F Dernburg Genome Biology 2013, 14:110 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Abby Dernburg discusses recent research linking nuclear lamins to chromosome pairing in meiosis
	Review
	Review Recent progress in the use of genetics to understand links between type 2 diabetes and related metabolic traits Hanieh Yaghootkar, Timothy M Frayling Genome Biology 2013, 14:203 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tim Frayling and Hanieh Yaghootkar review how modern genetics is informing our understanding of the mechanisms underlying type 2 diabetes
	Report
	Meeting report The future of genomic medicine is here Konrad J Karczewski Genome Biology 2013, 14:304 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 6th annual Future of Genomic Medicine conference, held at the Scripps Seaside Forum, La Jolla, CA, USA, March 7-8, 2013
	Meeting report Clinical applications of sequencing take center stage Gustavo Glusman Genome Biology 2013, 14:303 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013
	Research
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues
	Research 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 Prendergast, 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells
	Research RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grützner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
	Research 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 P W Huber, Inanc Birol, Steven JM Jones, Joerg Bohlmann Genome Biology 2013, 14:R27 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome sequence of the mountain pine beetle, only the second beetle genome to be sequenced
	Research The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage H Bradley Shaffer, Patrick Minx, Daniel E Warren, Andrew M Shedlock, Robert C Thomson, Nicole Valenzuela, John Abramyan, Chris T Amemiya, Daleen Badenhorst, Kyle K Biggar, Glen M Borchert, Christopher W Botka, Rachel M Bowden, Edward L Braun, Anne M Bronikowski, Benoit G Bruneau, Leslie T Buck, Blanche Capel, Todd A Castoe, Mike Czerwinski, Kim D Delehaunty, Scott V Edwards, Catrina C Fronick, Matthew K Fujita, Lucinda Fulton, Tina A Graves, Richard E Green, Wilfried Haerty, Ramkumar Hariharan, Omar Hernandez et al. Genome Biology 2013, 14:R28 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the western painted turtle, Chrysemys picta bellii, reveals insights into its extreme tolerance to anoxia and freezing
	Research The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude. Qingle Cai, Xiaoju Qian, Yongshan Lang, Yadan Luo, Shengkai Pan, Yuanyuan Hui, Caiyun Gou, Yue Cai, Meirong Hao, Jinyang Zhao, Songbo Wang, Zhaobao Wang, Xinming Zhang, Jinchao Liu, Longhai Luo, Yingrui Li, Jun Wang, Rongjun He, Fumin Lei, Jiaohui Xu Genome Biology 2013, 14:R29 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The ground tit genome, one of the highest quality avian genome assemblies to date, reveals potential mechanisms of high altitude adaptation
	Method DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels Huiying Zhao, Yuedong Yang, Hai Lin, Xinjun Zhang, Matthew Mort, David N Cooper, Yunlong Liu, Yaoqi Zhou Genome Biology 2013, 14:R23 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DDIG-in is a method for predicting the deleterious effects of short indels
	Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Patchwork is a method for determining allele-specific copy number variation in sequenced tumor samples
	Software CRAC: an integrated approach to the analysis of RNA-seq reads Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data

	Volume 14 Issue 3
	Comment
	Comment Sequestration: inadvertently killing biomedical research to score political points Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction
	Research highlight Go retro and get a GRIP Kim Wong, David J Adams, Thomas M Keane Genome Biology 2013, 14:108 (19 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Adams and colleagues grapple with the GRIPs (gene retrocopy insertion polymorphisms) identified by Ewing et al in this month's issue
	Research highlight Pushing the (nuclear) envelope into meiosis Abby F Dernburg Genome Biology 2013, 14:110 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Abby Dernburg discusses recent research linking nuclear lamins to chromosome pairing in meiosis
	Review
	Review Recent progress in the use of genetics to understand links between type 2 diabetes and related metabolic traits Hanieh Yaghootkar, Timothy M Frayling Genome Biology 2013, 14:203 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tim Frayling and Hanieh Yaghootkar review how modern genetics is informing our understanding of the mechanisms underlying type 2 diabetes
	Report
	Meeting report The future of genomic medicine is here Konrad J Karczewski Genome Biology 2013, 14:304 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 6th annual Future of Genomic Medicine conference, held at the Scripps Seaside Forum, La Jolla, CA, USA, March 7-8, 2013
	Meeting report Clinical applications of sequencing take center stage Gustavo Glusman Genome Biology 2013, 14:303 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013
	Research
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues
	Research 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 Prendergast, 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells
	Research RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grützner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
	Research 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 P W Huber, Inanc Birol, Steven JM Jones, Joerg Bohlmann Genome Biology 2013, 14:R27 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome sequence of the mountain pine beetle, only the second beetle genome to be sequenced
	Research The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage H Bradley Shaffer, Patrick Minx, Daniel E Warren, Andrew M Shedlock, Robert C Thomson, Nicole Valenzuela, John Abramyan, Chris T Amemiya, Daleen Badenhorst, Kyle K Biggar, Glen M Borchert, Christopher W Botka, Rachel M Bowden, Edward L Braun, Anne M Bronikowski, Benoit G Bruneau, Leslie T Buck, Blanche Capel, Todd A Castoe, Mike Czerwinski, Kim D Delehaunty, Scott V Edwards, Catrina C Fronick, Matthew K Fujita, Lucinda Fulton, Tina A Graves, Richard E Green, Wilfried Haerty, Ramkumar Hariharan, Omar Hernandez et al. Genome Biology 2013, 14:R28 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the western painted turtle, Chrysemys picta bellii, reveals insights into its extreme tolerance to anoxia and freezing
	Research The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude. Qingle Cai, Xiaoju Qian, Yongshan Lang, Yadan Luo, Shengkai Pan, Yuanyuan Hui, Caiyun Gou, Yue Cai, Meirong Hao, Jinyang Zhao, Songbo Wang, Zhaobao Wang, Xinming Zhang, Jinchao Liu, Longhai Luo, Yingrui Li, Jun Wang, Rongjun He, Fumin Lei, Jiaohui Xu Genome Biology 2013, 14:R29 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The ground tit genome, one of the highest quality avian genome assemblies to date, reveals potential mechanisms of high altitude adaptation
	Method DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels Huiying Zhao, Yuedong Yang, Hai Lin, Xinjun Zhang, Matthew Mort, David N Cooper, Yunlong Liu, Yaoqi Zhou Genome Biology 2013, 14:R23 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DDIG-in is a method for predicting the deleterious effects of short indels
	Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Patchwork is a method for determining allele-specific copy number variation in sequenced tumor samples
	Software CRAC: an integrated approach to the analysis of RNA-seq reads Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data

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Volume 14 Issue 3

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