Genome Biology | Volume 10 Issue 6

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	Volume 10 Issue 6
	Comment
	Comment What my genome told me - and what it didn't Gregory A Petsko Genome Biology 2009, 10:108 (29 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Lessons in personal genome analysis, social networking or health information?
	Review
	Review Translational disease interpretation with molecular networks Anaïs Baudot, Gonzalo Gómez-López, Alfonso Valencia Genome Biology 2009, 10:221 (29 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The integration of medical information into gene and protein networks could lead to a better understanding of complex diseases.
	Protein family review The WASP and WAVE family proteins Shusaku Kurisu, Tadaomi Takenawa Genome Biology 2009, 10:226 (15 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the cytoskeleton-organizing WASP and WAVE family proteins.
	Minireview Sequence patches on MAPK surfaces define protein-protein interactions Gary L Johnson, Shawn M Gomez Genome Biology 2009, 10:222 (5 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Redesigning ‘surface patches’ on a mitogen-activated protein kinase can change its interactions with other proteins.
	Minireview DNA breaks as triggers for antigenic variation in African trypanosomes Sam Alsford, David Horn, Lucy Glover Genome Biology 2009, 10:223 (8 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Double-strand breaks initiate coat protein switching in African trypanosomes.
	Minireview Transposons that clean up after themselves Douglas L Chalker Genome Biology 2009, 10:224 (15 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transposon in the germline genome of the ciliate Oxytricha removes itself from the differentiating somatic genome during development.
	Minireview Genetics and genomics converge on the human blood fluke Andy Tait Genome Biology 2009, 10:225 (30 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genetic map of the human infective blood fluke Schistosoma mansoni offers new approaches for research on this important parasitic worm.
	Report
	Meeting report Interfacing systems biology and synthetic biology Allyson Lister, Varodom Charoensawan, Subhajyoti De, Katherine James, Sarath Chandra Janga, Julian Huppert Genome Biology 2009, 10:309 (26 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of BioSysBio 2009, the IET conference on Synthetic Biology, Systems Biology and Bioinformatics, Cambridge, UK, 23-25 March 2009.
	Research
	Research Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins Michelle Simon, John M Hancock Genome Biology 2009, 10:R59 (1 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of amino acid repeats in four mammalian and one bird genome shows that many are associated preferentially with intrinsically unstructured regions.
	Research Metabolic-network-driven analysis of bacterial ecological strategies Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Nir Yosef, Roded Sharan, Uri Gophna, Eytan Ruppin Genome Biology 2009, 10:R61 (5 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bacterial ecological strategies revealed by metabolic network analysis show that ecological diversity correlates with metabolic flexibility, faster growth rate and intense co-habitation.
	Research Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana Xiaoyu Zhang, Yana V Bernatavichute, Shawn Cokus, Matteo Pellegrini, Steven E Jacobsen Genome Biology 2009, 10:R62 (9 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the genome-wide distribution patterns of histone H3 lysine4 methylation in Arabidopsis thaliana seedlings shows that it has widespread roles in regulating gene expression.
	Research The conservation and evolutionary modularity of metabolism José M Peregrín-Alvarez, Chris Sanford, John Parkinson Genome Biology 2009, 10:R63 (12 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel evolutionary analysis of metabolic networks across 26 taxa reveals a highly-conserved but flexible core of metabolic enzymes.
	Research A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes Diego Cortez, Patrick Forterre, Simonetta Gribaldo Genome Biology 2009, 10:R65 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale survey of potential recently acquired integrative elements in 119 archaeal and bacterial genomes reveals that many recently acquired genes have originated from integrative elements
	Research Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress Simon M Dittami, Delphine Scornet, Jean-Louis Petit, Béatrice Ségurens, Corinne Da Silva, Erwan Corre, Michael Dondrup, Karl-Heinz Glatting, Rainer König, Lieven Sterck, Pierre Rouzé, Yves Van de Peer, J Mark Cock, Catherine Boyen, Thierry Tonon Genome Biology 2009, 10:R66 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The brown alga Ectocarpus siliculosus, unlike terrestrial plants, undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress.
	Research Insights into female sperm storage from the spermathecal fluid proteome of the honeybee Apis mellifera Boris Baer, Holger Eubel, Nicolas L Taylor, Nicholas O'Toole, A Harvey Millar Genome Biology 2009, 10:R67 (18 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic and metabolic network analysis of honeybee queen spermathecal fluid provides insights into female long-term sperm storage mechanisms.
	Research Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses Xiyin Wang, Udo Gowik, Haibao Tang, John E Bowers, Peter Westhoff, Andrew H Paterson Genome Biology 2009, 10:R68 (23 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the sorghum, maize and rice genomes shows that gene duplication and functional innovation is common to evolution of most but not all genes in the C4 photosynthetic pathway
	Research iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, Rick L Stevens Genome Biology 2009, 10:R69 (25 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new and validated genome-scale metabolic model of Bacillus subtilis 168, iBsu1103, is presented that has significantly improved completeness and accuracy.
	Research Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea Yvan Zivanovic, Jean Armengaud, Arnaud Lagorce, Christophe Leplat, Philippe Guérin, Murielle Dutertre, Véronique Anthouard, Patrick Forterre, Patrick Wincker, Fabrice Confalonieri Genome Biology 2009, 10:R70 (26 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Thermococcus gammatolerans, a radioresistant archaeon, is described; a proteomic analysis reveals that radioresistance may be due to unknown DNA repair enzymes.
	Research Genomic linkage map of the human blood fluke Schistosoma mansoni Charles D Criscione, Claudia LL Valentim, Hirohisa Hirai, Philip T LoVerde, Timothy JC Anderson Genome Biology 2009, 10:R71 (30 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genetic linkage map of Schistosoma mansoni reveals insights into higher female recombination, confirms ZW inheritance patterns and recombination hotspots.
	Method Closing gaps in the human genome using sequencing by synthesis Manuel Garber, Michael C Zody, Harindra M Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2009, 10:R60 (2 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for closing non-structural gaps in the human genome assembly using 454 sequencing is presented here.
	Method A novel and universal method for microRNA RT-qPCR data normalization Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele Genome Biology 2009, 10:R64 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The mean expression value: a new method for accurate and reliable normalization of microRNA expression data from RT-qPCR experiments.

	Volume 10 Issue 6
	Comment
	Comment What my genome told me - and what it didn't Gregory A Petsko Genome Biology 2009, 10:108 (29 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Lessons in personal genome analysis, social networking or health information?
	Review
	Review Translational disease interpretation with molecular networks Anaïs Baudot, Gonzalo Gómez-López, Alfonso Valencia Genome Biology 2009, 10:221 (29 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The integration of medical information into gene and protein networks could lead to a better understanding of complex diseases.
	Protein family review The WASP and WAVE family proteins Shusaku Kurisu, Tadaomi Takenawa Genome Biology 2009, 10:226 (15 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the cytoskeleton-organizing WASP and WAVE family proteins.
	Minireview Sequence patches on MAPK surfaces define protein-protein interactions Gary L Johnson, Shawn M Gomez Genome Biology 2009, 10:222 (5 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Redesigning ‘surface patches’ on a mitogen-activated protein kinase can change its interactions with other proteins.
	Minireview DNA breaks as triggers for antigenic variation in African trypanosomes Sam Alsford, David Horn, Lucy Glover Genome Biology 2009, 10:223 (8 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Double-strand breaks initiate coat protein switching in African trypanosomes.
	Minireview Transposons that clean up after themselves Douglas L Chalker Genome Biology 2009, 10:224 (15 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transposon in the germline genome of the ciliate Oxytricha removes itself from the differentiating somatic genome during development.
	Minireview Genetics and genomics converge on the human blood fluke Andy Tait Genome Biology 2009, 10:225 (30 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genetic map of the human infective blood fluke Schistosoma mansoni offers new approaches for research on this important parasitic worm.
	Report
	Meeting report Interfacing systems biology and synthetic biology Allyson Lister, Varodom Charoensawan, Subhajyoti De, Katherine James, Sarath Chandra Janga, Julian Huppert Genome Biology 2009, 10:309 (26 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of BioSysBio 2009, the IET conference on Synthetic Biology, Systems Biology and Bioinformatics, Cambridge, UK, 23-25 March 2009.
	Research
	Research Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins Michelle Simon, John M Hancock Genome Biology 2009, 10:R59 (1 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of amino acid repeats in four mammalian and one bird genome shows that many are associated preferentially with intrinsically unstructured regions.
	Research Metabolic-network-driven analysis of bacterial ecological strategies Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Nir Yosef, Roded Sharan, Uri Gophna, Eytan Ruppin Genome Biology 2009, 10:R61 (5 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bacterial ecological strategies revealed by metabolic network analysis show that ecological diversity correlates with metabolic flexibility, faster growth rate and intense co-habitation.
	Research Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana Xiaoyu Zhang, Yana V Bernatavichute, Shawn Cokus, Matteo Pellegrini, Steven E Jacobsen Genome Biology 2009, 10:R62 (9 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the genome-wide distribution patterns of histone H3 lysine4 methylation in Arabidopsis thaliana seedlings shows that it has widespread roles in regulating gene expression.
	Research The conservation and evolutionary modularity of metabolism José M Peregrín-Alvarez, Chris Sanford, John Parkinson Genome Biology 2009, 10:R63 (12 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel evolutionary analysis of metabolic networks across 26 taxa reveals a highly-conserved but flexible core of metabolic enzymes.
	Research A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes Diego Cortez, Patrick Forterre, Simonetta Gribaldo Genome Biology 2009, 10:R65 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale survey of potential recently acquired integrative elements in 119 archaeal and bacterial genomes reveals that many recently acquired genes have originated from integrative elements
	Research Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress Simon M Dittami, Delphine Scornet, Jean-Louis Petit, Béatrice Ségurens, Corinne Da Silva, Erwan Corre, Michael Dondrup, Karl-Heinz Glatting, Rainer König, Lieven Sterck, Pierre Rouzé, Yves Van de Peer, J Mark Cock, Catherine Boyen, Thierry Tonon Genome Biology 2009, 10:R66 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The brown alga Ectocarpus siliculosus, unlike terrestrial plants, undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress.
	Research Insights into female sperm storage from the spermathecal fluid proteome of the honeybee Apis mellifera Boris Baer, Holger Eubel, Nicolas L Taylor, Nicholas O'Toole, A Harvey Millar Genome Biology 2009, 10:R67 (18 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic and metabolic network analysis of honeybee queen spermathecal fluid provides insights into female long-term sperm storage mechanisms.
	Research Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses Xiyin Wang, Udo Gowik, Haibao Tang, John E Bowers, Peter Westhoff, Andrew H Paterson Genome Biology 2009, 10:R68 (23 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the sorghum, maize and rice genomes shows that gene duplication and functional innovation is common to evolution of most but not all genes in the C4 photosynthetic pathway
	Research iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, Rick L Stevens Genome Biology 2009, 10:R69 (25 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new and validated genome-scale metabolic model of Bacillus subtilis 168, iBsu1103, is presented that has significantly improved completeness and accuracy.
	Research Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea Yvan Zivanovic, Jean Armengaud, Arnaud Lagorce, Christophe Leplat, Philippe Guérin, Murielle Dutertre, Véronique Anthouard, Patrick Forterre, Patrick Wincker, Fabrice Confalonieri Genome Biology 2009, 10:R70 (26 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Thermococcus gammatolerans, a radioresistant archaeon, is described; a proteomic analysis reveals that radioresistance may be due to unknown DNA repair enzymes.
	Research Genomic linkage map of the human blood fluke Schistosoma mansoni Charles D Criscione, Claudia LL Valentim, Hirohisa Hirai, Philip T LoVerde, Timothy JC Anderson Genome Biology 2009, 10:R71 (30 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genetic linkage map of Schistosoma mansoni reveals insights into higher female recombination, confirms ZW inheritance patterns and recombination hotspots.
	Method Closing gaps in the human genome using sequencing by synthesis Manuel Garber, Michael C Zody, Harindra M Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2009, 10:R60 (2 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for closing non-structural gaps in the human genome assembly using 454 sequencing is presented here.
	Method A novel and universal method for microRNA RT-qPCR data normalization Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele Genome Biology 2009, 10:R64 (16 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The mean expression value: a new method for accurate and reliable normalization of microRNA expression data from RT-qPCR experiments.

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Volume 10 Issue 6

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