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		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 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 \| Editor’s summary HSF binding to conserved sites in Alu repeats initiates an antisense transcript-mediated response to heat shock
		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 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-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
		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
		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 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
		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
		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
		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 \| Editor’s summary A method that uses both chromatin features and motif identification to predict transcription factor binding sites
		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
		Comment Bailing out Gregory A Petsko Genome Biology 2011, 12:131 (29 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Let us shout to the public and private sectors, this is not the time to be bailing out
		Review Genome-wide association studies in plants: the missing heritability is in the field Benjamin Brachi, Geoffrey P Morris, Justin O Borevitz Genome Biology 2011, 12:232 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Justin Borevitz on how high-power association mapping is going back 'into the field' through the combination of genomics and population biology
		Research highlight 1, 2, 3: Counting the fingers on a chicken wing Martin D Carkett, Malcolm PO Logan Genome Biology 2011, 12:130 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Malcolm Logan on an RNA-seq approach to clarifying a long-standing dispute between paleontologists and embryologists
		Research Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles Maya Botzman, Hanah Margalit Genome Biology 2011, 12:R109 (27 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Application of a new method to prokaryotic genomes reveals an association between lifestyle and codon bias
		Protein family review The rhomboid protease family: a decade of progress on function and mechanism Sinisa Urban, Seth W Dickey Genome Biology 2011, 12:231 (27 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The rhomboid family of membrane-immersed proteases are found in all domains of life and have been implicated in several human diseases.
		Method Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity Markus Rasmussen, Magnus Sundström, Hanna Kultima, Johan Botling, Patrick Micke, Helgi Birgisson, Bengt Glimelius, Anders Isaksson Genome Biology 2011, 12:R108 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TAPS is a method for identifying allele-specific copy number changes in tumor samples
		Research The draft genome of the carcinogenic human liver fluke Clonorchis sinensis Xiaoyun Wang, Wenjun Chen, Yan Huang, Jiufeng Sun, Jingtao Men, Hailiang Liu, Fang Luo, Lei Guo, Xiaoli Lv, Chuanhuan Deng, Chenhui Zhou, Yongxiu Fan, Xuerong Li, Lisi Huang, Yue Hu, Chi Liang, Xuchu Hu, Jin Xu, Xinbing Yu Genome Biology 2011, 12:R107 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A draft genome sequence of the liver fluke Clonorchis sinensis, which is a leading cause of liver cancer in Asia
		Meeting report Moving beyond genome sequencing into personalized genomic medicine: biological and computing challenges David M Kristensen Genome Biology 2011, 12:308 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Beyond the Genome meeting, the Universities at Shady Grove, Rockville, Maryland, USA, 19-22 September 2011
		Review Bacterial epidemiology and biology - lessons from genome sequencing Julian Parkhill, Brendan W Wren Genome Biology 2011, 12:230 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Brendan Wren and Julian Parkhill on how a new era in microbial genomics has solved ancient controversies and promises to revolutionize our understanding of bacterial pathogens
		Research Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics Vinoy K Ramachandran, Alison K East, Ramakrishnan Karunakaran, J Allan Downie, Philip S Poole Genome Biology 2011, 12:R106 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription is measured in Rhizobium leguminosarum grown on roots of a host plant, a non-host legume and a non-leguminous plant
		Method Integrating diverse genomic data using gene sets Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani Genome Biology 2011, 12:R105 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for integrating multiple genomic data types for the identification of enriched gene sets
		Method High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing David Sims, Ana M Mendes-Pereira, Jessica Frankum, Darren Burgess, Maria-Antonietta Cerone, Cristina Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J Lord Genome Biology 2011, 12:R104 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method
		Editorial How hemp got high Naomi Attar Genome Biology 2011, 12:409 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Senior Assistant Editor Naomi Attar discusses the genome sequence of cannabis

	All
		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 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 \| Editor’s summary HSF binding to conserved sites in Alu repeats initiates an antisense transcript-mediated response to heat shock
		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 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-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
		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
		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 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
		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
		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
		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 \| Editor’s summary A method that uses both chromatin features and motif identification to predict transcription factor binding sites
		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
		Comment Bailing out Gregory A Petsko Genome Biology 2011, 12:131 (29 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Let us shout to the public and private sectors, this is not the time to be bailing out
		Review Genome-wide association studies in plants: the missing heritability is in the field Benjamin Brachi, Geoffrey P Morris, Justin O Borevitz Genome Biology 2011, 12:232 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Justin Borevitz on how high-power association mapping is going back 'into the field' through the combination of genomics and population biology
		Research highlight 1, 2, 3: Counting the fingers on a chicken wing Martin D Carkett, Malcolm PO Logan Genome Biology 2011, 12:130 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Malcolm Logan on an RNA-seq approach to clarifying a long-standing dispute between paleontologists and embryologists
		Research Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles Maya Botzman, Hanah Margalit Genome Biology 2011, 12:R109 (27 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Application of a new method to prokaryotic genomes reveals an association between lifestyle and codon bias
		Protein family review The rhomboid protease family: a decade of progress on function and mechanism Sinisa Urban, Seth W Dickey Genome Biology 2011, 12:231 (27 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The rhomboid family of membrane-immersed proteases are found in all domains of life and have been implicated in several human diseases.
		Method Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity Markus Rasmussen, Magnus Sundström, Hanna Kultima, Johan Botling, Patrick Micke, Helgi Birgisson, Bengt Glimelius, Anders Isaksson Genome Biology 2011, 12:R108 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TAPS is a method for identifying allele-specific copy number changes in tumor samples
		Research The draft genome of the carcinogenic human liver fluke Clonorchis sinensis Xiaoyun Wang, Wenjun Chen, Yan Huang, Jiufeng Sun, Jingtao Men, Hailiang Liu, Fang Luo, Lei Guo, Xiaoli Lv, Chuanhuan Deng, Chenhui Zhou, Yongxiu Fan, Xuerong Li, Lisi Huang, Yue Hu, Chi Liang, Xuchu Hu, Jin Xu, Xinbing Yu Genome Biology 2011, 12:R107 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A draft genome sequence of the liver fluke Clonorchis sinensis, which is a leading cause of liver cancer in Asia
		Meeting report Moving beyond genome sequencing into personalized genomic medicine: biological and computing challenges David M Kristensen Genome Biology 2011, 12:308 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Beyond the Genome meeting, the Universities at Shady Grove, Rockville, Maryland, USA, 19-22 September 2011
		Review Bacterial epidemiology and biology - lessons from genome sequencing Julian Parkhill, Brendan W Wren Genome Biology 2011, 12:230 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Brendan Wren and Julian Parkhill on how a new era in microbial genomics has solved ancient controversies and promises to revolutionize our understanding of bacterial pathogens
		Research Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics Vinoy K Ramachandran, Alison K East, Ramakrishnan Karunakaran, J Allan Downie, Philip S Poole Genome Biology 2011, 12:R106 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription is measured in Rhizobium leguminosarum grown on roots of a host plant, a non-host legume and a non-leguminous plant
		Method Integrating diverse genomic data using gene sets Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani Genome Biology 2011, 12:R105 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for integrating multiple genomic data types for the identification of enriched gene sets
		Method High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing David Sims, Ana M Mendes-Pereira, Jessica Frankum, Darren Burgess, Maria-Antonietta Cerone, Cristina Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J Lord Genome Biology 2011, 12:R104 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method
		Editorial How hemp got high Naomi Attar Genome Biology 2011, 12:409 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Senior Assistant Editor Naomi Attar discusses the genome sequence of cannabis