Genome Biology | Volume 12 Issue 10

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	Volume 12 Issue 10
	Comment
	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
	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
	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
	Review
	Review Revealing the molecular signatures of host-pathogen interactions Chiea-Chuen Khor, Martin L Hibberd Genome Biology 2011, 12:229 (19 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide association studies and pathogen sequencing are revealing unexpected insights into host-pathogen interactions
	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
	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
	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.
	Report
	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
	Research
	Research The transcriptional landscape of Chlamydia pneumoniae Marco Albrecht, Cynthia M Sharma, Marcus T Dittrich, Tobias Müller, Richard Reinhardt, Jörg Vogel, Thomas Rudel Genome Biology 2011, 12:R98 (11 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The life cycle of the obligate intracellular human pathogen C. pneumoniae has a dynamic transcriptional landscape
	Research Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium Lara Rajeev, Eric G Luning, Paramvir S Dehal, Morgan N Price, Adam P Arkin, Aindrila Mukhopadhyay Genome Biology 2011, 12:R99 (12 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary All response regulators in the genome of Desulfovibrius vulgaris are identified, as are all their target genes
	Research Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented
	Research Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer Wigard P Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S Vermaat, Markus J van Roosmalen, Stef van Lieshout, Isaac J Nijman, Wijnand Roessingh, Ruben van 't Slot, José van de Belt, Victor Guryev, Marco Koudijs, Emile Voest, Edwin Cuppen Genome Biology 2011, 12:R103 (19 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromothripsis is found to be a common mechanism driving structural rearrangement in primary colorectal cancer and metastases
	Research The draft genome and transcriptome of Cannabis sativa Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
	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
	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
	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
	Method SpeCond: a method to detect condition-specific gene expression Florence MG Cavalli, Richard Bourgon, Wolfgang Huber, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:R101 (18 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method to detect condition-specific gene expression from microarray data
	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 \| 1 comment \| Editor’s summary The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method
	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 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
	Correspondence
	Correction Correction: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Mogens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2011, 12:140 (20 October 2011) Abstract \| Full text \| PDF

	Volume 12 Issue 10
	Comment
	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
	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
	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
	Review
	Review Revealing the molecular signatures of host-pathogen interactions Chiea-Chuen Khor, Martin L Hibberd Genome Biology 2011, 12:229 (19 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide association studies and pathogen sequencing are revealing unexpected insights into host-pathogen interactions
	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
	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
	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.
	Report
	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
	Research
	Research The transcriptional landscape of Chlamydia pneumoniae Marco Albrecht, Cynthia M Sharma, Marcus T Dittrich, Tobias Müller, Richard Reinhardt, Jörg Vogel, Thomas Rudel Genome Biology 2011, 12:R98 (11 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The life cycle of the obligate intracellular human pathogen C. pneumoniae has a dynamic transcriptional landscape
	Research Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium Lara Rajeev, Eric G Luning, Paramvir S Dehal, Morgan N Price, Adam P Arkin, Aindrila Mukhopadhyay Genome Biology 2011, 12:R99 (12 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary All response regulators in the genome of Desulfovibrius vulgaris are identified, as are all their target genes
	Research Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented
	Research Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer Wigard P Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S Vermaat, Markus J van Roosmalen, Stef van Lieshout, Isaac J Nijman, Wijnand Roessingh, Ruben van 't Slot, José van de Belt, Victor Guryev, Marco Koudijs, Emile Voest, Edwin Cuppen Genome Biology 2011, 12:R103 (19 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromothripsis is found to be a common mechanism driving structural rearrangement in primary colorectal cancer and metastases
	Research The draft genome and transcriptome of Cannabis sativa Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
	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
	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
	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
	Method SpeCond: a method to detect condition-specific gene expression Florence MG Cavalli, Richard Bourgon, Wolfgang Huber, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:R101 (18 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method to detect condition-specific gene expression from microarray data
	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 \| 1 comment \| Editor’s summary The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method
	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 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
	Correspondence
	Correction Correction: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Mogens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2011, 12:140 (20 October 2011) Abstract \| Full text \| PDF

Explore Genome Biology

Articles

Volume 12 Issue 10

Comment

Review

Report

Research

Correspondence