Genome Biology | Volume 12 Issue 11

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	Volume 12 Issue 11
	Comment
	Comment Dominoes Gregory A Petsko Genome Biology 2011, 12:134 (30 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If we fund the next big science program, how many smaller research programs will receive no funding as a consequence?
	Research highlight Wrangling for microRNAs provokes much crosstalk Ana C Marques, Jennifer Tan, Chris P Ponting Genome Biology 2011, 12:132 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chris Ponting highlights recent articles on competitive endogenous RNAs that illustrate how miRNA response elements enable crosstalk between transcripts
	Research highlight BRD4 jump-starts transcription after mitotic silencing Philipp Voigt, Danny Reinberg Genome Biology 2011, 12:133 (29 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Philipp Voigt and Danny Reinberg highlight BRD4's role in gene bookmarking during mitosis, and how this might be exploited in chemotherapy
	Review
	Review A world in a grain of sand: human history from genetic data Vincenza Colonna, Luca Pagani, Yali Xue, Chris Tyler-Smith Genome Biology 2011, 12:234 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome-wide genotypes and sequences are enriching our understanding of the past 50,000 years of human history, according to Chris Tyler-Smith
	Protein family review Tissue inhibitors of metalloproteinases Gillian Murphy Genome Biology 2011, 12:233 (11 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As metalloproteinase-independent functions are discovered for TIMPs, future work will focus on identifying receptors and downstream signaling mechanisms
	Report
	Meeting report Human genetics in full resolution Alicia Schiavi, Nicholas Light, Veronique Adoue, Stephan Busche, Tomi Pastinen Genome Biology 2011, 12:309 (24 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 12th International Congress of Human Genetics, and the annual American Society of Human Genetics conference, October 2011
	Research
	Research Composite effects of gene determinants on the translation speed and density of ribosomes Tamir Tuller, Isana Veksler-Lublinsky, Nir Gazit, Martin Kupiec, Eytan Ruppin, Michal Ziv-Ukelson Genome Biology 2011, 12:R110 (3 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Codon usage, amino acid charge and mRNA folding energy all correlate with translation speed and ribosome density
	Research Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems André E Minoche, Juliane C Dohm, Heinz Himmelbauer Genome Biology 2011, 12:R112 (8 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Error rates are compared in data from Illumina's HiSeq and GAIIx systems
	Research Discovery of active enhancers through bidirectional expression of short transcripts Michael F Melgar, Francis S Collins, Praveen Sethupathy Genome Biology 2011, 12:R113 (14 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Regions showing bidirectional expression of short transcripts can be used to identify active enhancers
	Research Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor) Lei-Ying Zheng, Xiao-Sen Guo, Bing He, Lian-Jun Sun, Yao Peng, Shan-Shan Dong, Teng-Fei Liu, Shuye Jiang, Srinivasan Ramachandran, Chun-Ming Liu, Hai-Chun Jing Genome Biology 2011, 12:R114 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomes from three strains of Sorghum bicolor (one grain and two sweet) have been sequenced and compared with the reference genome
	Research Whole genome sequencing of penicillin-resistant Streptococcus pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease Fereshteh Fani, Philippe Leprohon, Danielle Légaré, Marc Ouellette Genome Biology 2011, 12:R115 (22 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of antibiotic resistant Streptococcus pneumoniae reveals an initial mutation in an iron permease conferring tolerance to antibiotic-induced accumulation of oxidants
	Research Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional chinese medicine Peng Zheng, Yongliang Xia, Guohua Xiao, Chenghui Xiong, Xiao Hu, Siwei Zhang, Huajun Zheng, Yin Huang, Yan Zhou, Shengyue Wang, Guo-Ping Zhao, Xingzhong Liu, Raymond J St Leger, Chengshu Wang Genome Biology 2011, 12:R116 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome and transcriptome sequences of Cordyceps militaris, a fungal pathogen of insects that is used in traditional Chinese medicine
	Research Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism Rajesh Pandey, Amit K Mandal, Vineet Jha, Mitali Mukerji Genome Biology 2011, 12:R117 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary HSF binding to conserved sites in Alu repeats initiates an antisense transcript-mediated response to heat shock
	Research Hundreds of putatively functional small open reading frames in Drosophila Emmanuel Ladoukakis, Vini Pereira, Emile G Magny, Adam Eyre-Walker, Juan Pablo Couso Genome Biology 2011, 12:R118 (25 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Drosophila genome contains hundreds of small open reading frames with putative functionality
	Method Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors Chao Cheng, Chong Shou, Kevin Y Yip, Mark B Gerstein Genome Biology 2011, 12:R111 (7 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method that uses both chromatin features and motif identification to predict transcription factor binding sites
	Correspondence
	Correction Correction: Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes Carolina Bartolomé, Xabier Bello, Xulio Maside Genome Biology 2011, 12:411 (15 January 2012) Abstract \| Full text \| PDF
	Correction Correction: Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases Eri Fukuda, Katarzyna H Kaminska, Janusz M Bujnicki, Ichizo Kobayashi Genome Biology 2011, 12:412 (15 January 2012) Abstract \| Full text \| PDF

	Volume 12 Issue 11
	Comment
	Comment Dominoes Gregory A Petsko Genome Biology 2011, 12:134 (30 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If we fund the next big science program, how many smaller research programs will receive no funding as a consequence?
	Research highlight Wrangling for microRNAs provokes much crosstalk Ana C Marques, Jennifer Tan, Chris P Ponting Genome Biology 2011, 12:132 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chris Ponting highlights recent articles on competitive endogenous RNAs that illustrate how miRNA response elements enable crosstalk between transcripts
	Research highlight BRD4 jump-starts transcription after mitotic silencing Philipp Voigt, Danny Reinberg Genome Biology 2011, 12:133 (29 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Philipp Voigt and Danny Reinberg highlight BRD4's role in gene bookmarking during mitosis, and how this might be exploited in chemotherapy
	Review
	Review A world in a grain of sand: human history from genetic data Vincenza Colonna, Luca Pagani, Yali Xue, Chris Tyler-Smith Genome Biology 2011, 12:234 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome-wide genotypes and sequences are enriching our understanding of the past 50,000 years of human history, according to Chris Tyler-Smith
	Protein family review Tissue inhibitors of metalloproteinases Gillian Murphy Genome Biology 2011, 12:233 (11 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As metalloproteinase-independent functions are discovered for TIMPs, future work will focus on identifying receptors and downstream signaling mechanisms
	Report
	Meeting report Human genetics in full resolution Alicia Schiavi, Nicholas Light, Veronique Adoue, Stephan Busche, Tomi Pastinen Genome Biology 2011, 12:309 (24 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 12th International Congress of Human Genetics, and the annual American Society of Human Genetics conference, October 2011
	Research
	Research Composite effects of gene determinants on the translation speed and density of ribosomes Tamir Tuller, Isana Veksler-Lublinsky, Nir Gazit, Martin Kupiec, Eytan Ruppin, Michal Ziv-Ukelson Genome Biology 2011, 12:R110 (3 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Codon usage, amino acid charge and mRNA folding energy all correlate with translation speed and ribosome density
	Research Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems André E Minoche, Juliane C Dohm, Heinz Himmelbauer Genome Biology 2011, 12:R112 (8 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Error rates are compared in data from Illumina's HiSeq and GAIIx systems
	Research Discovery of active enhancers through bidirectional expression of short transcripts Michael F Melgar, Francis S Collins, Praveen Sethupathy Genome Biology 2011, 12:R113 (14 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Regions showing bidirectional expression of short transcripts can be used to identify active enhancers
	Research Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor) Lei-Ying Zheng, Xiao-Sen Guo, Bing He, Lian-Jun Sun, Yao Peng, Shan-Shan Dong, Teng-Fei Liu, Shuye Jiang, Srinivasan Ramachandran, Chun-Ming Liu, Hai-Chun Jing Genome Biology 2011, 12:R114 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomes from three strains of Sorghum bicolor (one grain and two sweet) have been sequenced and compared with the reference genome
	Research Whole genome sequencing of penicillin-resistant Streptococcus pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease Fereshteh Fani, Philippe Leprohon, Danielle Légaré, Marc Ouellette Genome Biology 2011, 12:R115 (22 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of antibiotic resistant Streptococcus pneumoniae reveals an initial mutation in an iron permease conferring tolerance to antibiotic-induced accumulation of oxidants
	Research Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional chinese medicine Peng Zheng, Yongliang Xia, Guohua Xiao, Chenghui Xiong, Xiao Hu, Siwei Zhang, Huajun Zheng, Yin Huang, Yan Zhou, Shengyue Wang, Guo-Ping Zhao, Xingzhong Liu, Raymond J St Leger, Chengshu Wang Genome Biology 2011, 12:R116 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome and transcriptome sequences of Cordyceps militaris, a fungal pathogen of insects that is used in traditional Chinese medicine
	Research Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism Rajesh Pandey, Amit K Mandal, Vineet Jha, Mitali Mukerji Genome Biology 2011, 12:R117 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary HSF binding to conserved sites in Alu repeats initiates an antisense transcript-mediated response to heat shock
	Research Hundreds of putatively functional small open reading frames in Drosophila Emmanuel Ladoukakis, Vini Pereira, Emile G Magny, Adam Eyre-Walker, Juan Pablo Couso Genome Biology 2011, 12:R118 (25 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Drosophila genome contains hundreds of small open reading frames with putative functionality
	Method Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors Chao Cheng, Chong Shou, Kevin Y Yip, Mark B Gerstein Genome Biology 2011, 12:R111 (7 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method that uses both chromatin features and motif identification to predict transcription factor binding sites
	Correspondence
	Correction Correction: Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes Carolina Bartolomé, Xabier Bello, Xulio Maside Genome Biology 2011, 12:411 (15 January 2012) Abstract \| Full text \| PDF
	Correction Correction: Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases Eri Fukuda, Katarzyna H Kaminska, Janusz M Bujnicki, Ichizo Kobayashi Genome Biology 2011, 12:412 (15 January 2012) Abstract \| Full text \| PDF

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Volume 12 Issue 11

Comment

Review

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Research

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