Genome Biology | Volume 11 Issue 11

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	Volume 11 Issue 11
	Comment
	Comment Every dog has his day in court Gregory A Petsko Genome Biology 2010, 11:139 (30 November 2010) Full text \| PDF \| PubMed \| Editor’s summary The dog days of stem cell funding.
	Research highlight Metastasis suppression: a role of the Dice(r) Scott Valastyan, Robert A Weinberg Genome Biology 2010, 11:141 (30 November 2010) Abstract \| Full text \| PDF \| PubMed
	Research highlight Somatic signals counteract reproductive aging in females Ronald E Ellis, Qing Wei Genome Biology 2010, 11:142 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The signaling pathways involved in the decline in oocyte quality with age in nematodes are also conserved in humans.
	Review
	Opinion Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology Noam Kaplan, Timothy R Hughes, Jason D Lieb, Jonathan Widom, Eran Segal Genome Biology 2010, 11:140 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary There is less controversy over whether the preferences of histones for particular sequences determine nucleosome position than has been thought.
	Report
	Meeting report Beyond the Genome: genomics research ten years after the human genome sequence Amanda M Casto, Clara Amid Genome Biology 2010, 11:309 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Beyond the Genome', Boston, USA, 11-13 October 2010.
	Research
	Research A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Simon R Ellwood, Zhaohui Liu, Rob A Syme, Zhibing Lai, James K Hane, Felicity Keiper, Caroline S Moffat, Richard P Oliver, Timothy L Friesen Genome Biology 2010, 11:R109 (10 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Characterization of barley filamentous fungal pathogen genome by paired-end Solexa sequencing, genome assembly and karyotyping, with insights into pathogenicity.
	Research Immunostaining of modified histones defines high-level features of the human metaphase epigenome Edith Terrenoire, Fiona McRonald, John A Halsall, Paula Page, Robert S Illingworth, A Malcolm R Taylor, Val Davison, Laura P O'Neill, Bryan M Turner Genome Biology 2010, 11:R110 (15 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Immunofluorescent mapping of histone modifications in single cells at metaphase demonstrates both stable and altered patterns through mitosis
	Research Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise Nadia C Whitelaw, Suyinn Chong, Daniel K Morgan, Colm Nestor, Timothy J Bruxner, Alyson Ashe, Eleanore Lambley, Richard Meehan, Emma Whitelaw Genome Biology 2010, 11:R111 (19 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mutants for two epigenetic modifiers are found to be associated with increased intangible variation in phenotypes and in gene expression levels.
	Research Genetic diversity in India and the inference of Eurasian population expansion Jinchuan Xing, W Scott Watkins, Ya Hu, Chad D Huff, Aniko Sabo, Donna M Muzny, Michael J Bamshad, Richard A Gibbs, Lynn B Jorde, Fuli Yu Genome Biology 2010, 11:R113 (24 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SNP study demonstrates a high degree of Indian genetic diversity and suggests a significant isolation period between Out-of-Africa and Eurasian expansion.
	Research Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing Qi Zhao, Ewen F Kirkness, Otavia L Caballero, Pedro A Galante, Raphael B Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R Vasconcelos, Bing Ren, Sandro J de Souza, Anamaria A Camargo, Andrew JG Simpson, Robert L Strausberg Genome Biology 2010, 11:R114 (25 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Sequencing of the exome and transcriptome of a breast cancer cell line allows discovery of potentially tumorigenic loss of heterozygosity events.
	Research Comparative genomics reveals birth and death of fragile regions in mammalian evolution Max A Alekseyev, Pavel A Pevzner Genome Biology 2010, 11:R117 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new model explains the frequencies of breakpoints at genomic rearrangement hotspots by demonstrating that fragile sites undergo birth and death.
	Research Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level Olivier Harismendy, Vikas Bansal, Gaurav Bhatia, Masakazu Nakano, Michael Scott, Xiaoyun Wang, Colette Dib, Edouard Turlotte, Jack C Sipe, Sarah S Murray, Jean Deleuze, Vineet Bafna, Eric J Topol, Kelly A Frazer Genome Biology 2010, 11:R118 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Re-sequencing of human endocannabinoid metabolic genes from a large population reveals rare variants associated with extreme obesity.
	Method Patient-oriented gene set analysis for cancer mutation data Simina M Boca, Kenneth W Kinzler, Victor E Velculescu, Bert Vogelstein, Giovanni Parmigiani Genome Biology 2010, 11:R112 (23 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel patient-orientated gene set analysis method is presented and applied to a glioblastoma multiforme dataset
	Software Constructing a fish metabolic network model Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer Genome Biology 2010, 11:R115 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide fish metabolic model, MetaFishNet, is presented.
	Software Quake: quality-aware detection and correction of sequencing errors David R Kelley, Michael C Schatz, Steven L Salzberg Genome Biology 2010, 11:R116 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Quake employs a sophisticated approach to error identification and correction in next generation sequencing data.

	Volume 11 Issue 11
	Comment
	Comment Every dog has his day in court Gregory A Petsko Genome Biology 2010, 11:139 (30 November 2010) Full text \| PDF \| PubMed \| Editor’s summary The dog days of stem cell funding.
	Research highlight Metastasis suppression: a role of the Dice(r) Scott Valastyan, Robert A Weinberg Genome Biology 2010, 11:141 (30 November 2010) Abstract \| Full text \| PDF \| PubMed
	Research highlight Somatic signals counteract reproductive aging in females Ronald E Ellis, Qing Wei Genome Biology 2010, 11:142 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The signaling pathways involved in the decline in oocyte quality with age in nematodes are also conserved in humans.
	Review
	Opinion Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology Noam Kaplan, Timothy R Hughes, Jason D Lieb, Jonathan Widom, Eran Segal Genome Biology 2010, 11:140 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary There is less controversy over whether the preferences of histones for particular sequences determine nucleosome position than has been thought.
	Report
	Meeting report Beyond the Genome: genomics research ten years after the human genome sequence Amanda M Casto, Clara Amid Genome Biology 2010, 11:309 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Beyond the Genome', Boston, USA, 11-13 October 2010.
	Research
	Research A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres Simon R Ellwood, Zhaohui Liu, Rob A Syme, Zhibing Lai, James K Hane, Felicity Keiper, Caroline S Moffat, Richard P Oliver, Timothy L Friesen Genome Biology 2010, 11:R109 (10 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Characterization of barley filamentous fungal pathogen genome by paired-end Solexa sequencing, genome assembly and karyotyping, with insights into pathogenicity.
	Research Immunostaining of modified histones defines high-level features of the human metaphase epigenome Edith Terrenoire, Fiona McRonald, John A Halsall, Paula Page, Robert S Illingworth, A Malcolm R Taylor, Val Davison, Laura P O'Neill, Bryan M Turner Genome Biology 2010, 11:R110 (15 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Immunofluorescent mapping of histone modifications in single cells at metaphase demonstrates both stable and altered patterns through mitosis
	Research Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise Nadia C Whitelaw, Suyinn Chong, Daniel K Morgan, Colm Nestor, Timothy J Bruxner, Alyson Ashe, Eleanore Lambley, Richard Meehan, Emma Whitelaw Genome Biology 2010, 11:R111 (19 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mutants for two epigenetic modifiers are found to be associated with increased intangible variation in phenotypes and in gene expression levels.
	Research Genetic diversity in India and the inference of Eurasian population expansion Jinchuan Xing, W Scott Watkins, Ya Hu, Chad D Huff, Aniko Sabo, Donna M Muzny, Michael J Bamshad, Richard A Gibbs, Lynn B Jorde, Fuli Yu Genome Biology 2010, 11:R113 (24 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SNP study demonstrates a high degree of Indian genetic diversity and suggests a significant isolation period between Out-of-Africa and Eurasian expansion.
	Research Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing Qi Zhao, Ewen F Kirkness, Otavia L Caballero, Pedro A Galante, Raphael B Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R Vasconcelos, Bing Ren, Sandro J de Souza, Anamaria A Camargo, Andrew JG Simpson, Robert L Strausberg Genome Biology 2010, 11:R114 (25 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Sequencing of the exome and transcriptome of a breast cancer cell line allows discovery of potentially tumorigenic loss of heterozygosity events.
	Research Comparative genomics reveals birth and death of fragile regions in mammalian evolution Max A Alekseyev, Pavel A Pevzner Genome Biology 2010, 11:R117 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new model explains the frequencies of breakpoints at genomic rearrangement hotspots by demonstrating that fragile sites undergo birth and death.
	Research Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level Olivier Harismendy, Vikas Bansal, Gaurav Bhatia, Masakazu Nakano, Michael Scott, Xiaoyun Wang, Colette Dib, Edouard Turlotte, Jack C Sipe, Sarah S Murray, Jean Deleuze, Vineet Bafna, Eric J Topol, Kelly A Frazer Genome Biology 2010, 11:R118 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Re-sequencing of human endocannabinoid metabolic genes from a large population reveals rare variants associated with extreme obesity.
	Method Patient-oriented gene set analysis for cancer mutation data Simina M Boca, Kenneth W Kinzler, Victor E Velculescu, Bert Vogelstein, Giovanni Parmigiani Genome Biology 2010, 11:R112 (23 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel patient-orientated gene set analysis method is presented and applied to a glioblastoma multiforme dataset
	Software Constructing a fish metabolic network model Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer Genome Biology 2010, 11:R115 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide fish metabolic model, MetaFishNet, is presented.
	Software Quake: quality-aware detection and correction of sequencing errors David R Kelley, Michael C Schatz, Steven L Salzberg Genome Biology 2010, 11:R116 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Quake employs a sophisticated approach to error identification and correction in next generation sequencing data.

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Volume 11 Issue 11

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