Genome Biology | Volume 9 Issue 12

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	Volume 9 Issue 12
	Comment
	Comment A seat at the table Gregory A Petsko Genome Biology 2008, 9:113 (31 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The appointment of two life scientists, including a genome biologist, to the President-elect Obama's President's Council of Advisors on Science and Technology is encouraging.
	Review
	Review Next-generation biomass feedstocks for biofuel production Blake A Simmons, Dominique Loque, Harvey W Blanch Genome Biology 2008, 9:242 (29 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the potential for biofuel production in the United States from timber and non-grain crops.
	Minireview Lymphatic endothelial differentiation: start out with Sox - carry on with Prox Friedemann Kiefer, Ralf H Adams Genome Biology 2008, 9:243 (29 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Lymphatic system development comes into sharper focus.
	Minireview Replication forks, chromatin loops and dormant replication origins J Julian Blow, Xin Ge Genome Biology 2008, 9:244 (30 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The plasticity of replication origin usage during mitosis is associated with longer-term changes to chromatin loop organization.
	Minireview Diatom genomes come of age Assaf Vardi, Kimberlee Thamatrakoln, Kay D Bidle, Paul G Falkowski Genome Biology 2008, 9:245 (9 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two genome sequences of diatoms, marine single-celled photosynthetic eukaryotes that often have ornate cell walls, give insights into their metabolic and signaling systems.
	Opinion Bioinformatics: alive and kicking Lincoln D Stein Genome Biology 2008, 9:114 (17 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bioinformatics is alive and well in 2008 concludes Lincoln Stein, despite his earlier prediction of its imminent demise.
	Report
	Meeting report Computational models in systems biology Laurence Loewe, Jane Hillston Genome Biology 2008, 9:328 (10 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report of the 6th International Conference on Computational Methods in Systems Biology, Rostock, Germany, 12-15 October 2008.
	Research
	Research Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells Catia Attanasio, Alexandre Reymond, Richard Humbert, Robert Lyle, Michael S Kuehn, Shane Neph, Peter J Sabo, Jeff Goldy, Molly Weaver, Andrew Haydock, Kristin Lee, Michael Dorschner, Emmanouil T Dermitzakis, Stylianos E Antonarakis, John A Stamatoyannopoulos Genome Biology 2008, 9:R168 (2 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The fraction of experimentally active conserved non-coding sequences within any given cell type is low, so classical assays are unlikely to expose their potential.
	Research Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes Ping Wang, Shanye Yin, Zhenguo Zhang, Dedong Xin, Landian Hu, Xiangyin Kong, Laurence D Hurst Genome Biology 2008, 9:R169 (2 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational prediction of human coding RNA trans short sense-antisense pairs suggests that mRNA regulation by other coding transcripts might be a common occurrence.
	Research FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease Rong Chen, Alex A Morgan, Joel Dudley, Tarangini Deshpande, Li Li, Keiichi Kodama, Annie P Chiang, Atul J Butte Genome Biology 2008, 9:R170 (5 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Differential expressed genes are more likely to have variants associated with disease. A new tool, fitSNP, prioritizes candidate SNPs from association studies.
	Research Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence Daniel E Neafsey, Stephen F Schaffner, Sarah K Volkman, Daniel Park, Philip Montgomery, Danny A Milner, Amanda Lukens, David Rosen, Rachel Daniels, Nathan Houde, Joseph F Cortese, Erin Tyndall, Casey Gates, Nicole Stange-Thomann, Ousmane Sarr, Daouda Ndiaye, Omar Ndir, Soulyemane Mboup, Marcelo U Ferreira, Sandra Moraes, Aditya P Dash, Chetan E Chitnis, Roger C Wiegand, Daniel L Hartl, Bruce W Birren, Eric S Lander, Pardis C Sabeti, Dyann F Wirth Genome Biology 2008, 9:R171 (15 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An array-based SNP genotyping platform for Plasmodium falciparum is reported together with an analysis of SNP diversity in global population samples.
	Research Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences Laurence Ettwiller, Aidan Budd, François Spitz, Joachim Wittbrodt Genome Biology 2008, 9:R172 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the evolutionary dynamics of target gene batteries controlled by 16 different transcription factors reveals stable ancestral cores and highly dynamic regulatory sequences
	Research Evolutionary-new centromeres preferentially emerge within gene deserts Mariana Lomiento, Zhaoshi Jiang, Pietro D'Addabbo, Evan E Eichler, Mariano Rocchi Genome Biology 2008, 9:R173 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study identifying genomic restructuring and the absence of genes as conditions permissive for the seeding of new centromeres in primates
	Research Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution Carlos Quijano, Pavel Tomancak, Jesus Lopez-Marti, Mikita Suyama, Peer Bork, Marco Milan, David Torrents, Miguel Manzanares Genome Biology 2008, 9:R176 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genes occurring in conserved, tandemly-arrayed clusters in Drosophila melanogaster are co-expressed to a much higher extent than other duplicated genes.
	Research Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites Bernardo J Foth, Neng Zhang, Sachel Mok, Peter R Preiser, Zbynek Bozdech Genome Biology 2008, 9:R177 (17 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A quantitative time-course analysis of protein abundance for Plasmodium falciparum schizonts using two-dimensional differential gel electrophoresis reveals significant post-transcriptional regulation.
	Research Male reproductive development: gene expression profiling of maize anther and pollen ontogeny Jiong Ma, David S Skibbe, John Fernandes, Virginia Walbot Genome Biology 2008, 9:R181 (19 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of global gene expression profiles of seven stages of maize anther development reveals expression of many genes
	Research A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development Alyson Ashe, Daniel K Morgan, Nadia C Whitelaw, Timothy J Bruxner, Nicola K Vickaryous, Liza L Cox, Natalie C Butterfield, Carol Wicking, Marnie E Blewitt, Sarah J Wilkins, Gregory J Anderson, Timothy C Cox, Emma Whitelaw Genome Biology 2008, 9:R182 (19 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extended ENU screen for modifiers of transgene variegation identified four new modifiers, MommeD7-D10.
	Research Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps Christopher A Desjardins, Dawn E Gundersen-Rindal, Jessica B Hostetler, Luke J Tallon, Douglas W Fadrosh, Roger W Fuester, Monica J Pedroni, Brian J Haas, Michael C Schatz, Kristine M Jones, Jonathan Crabtree, Heather Forberger, Vishvanath Nene Genome Biology 2008, 9:R183 (30 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genome analysis of two endosymbiotic polydnaviruses from Glyptapanteles parasitic wasps reveals new insights into the evolutionary arms race between host and parasite.
	Method Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy Li Wang, Fengzhu Sun, Ting Chen Genome Biology 2008, 9:R174 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A strategy is presented to prioritize the functional modules that mediate genetic perturbations and their phenotypic effects among candidate modules.
	Method Annotating genomes with massive-scale RNA sequencing France Denoeud, Jean-Marc Aury, Corinne Da Silva, Benjamin Noel, Odile Rogier, Massimo Delledonne, Michele Morgante, Giorgio Valle, Patrick Wincker, Claude Scarpelli, Olivier Jaillon, François Artiguenave Genome Biology 2008, 9:R175 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for de novo genome annotation using high-throughput cDNA sequencing data.
	Method Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum Kevin Brick, Junichi Watanabe, Elisabetta Pizzi Genome Biology 2008, 9:R178 (18 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented to computationally identify core promoters in the Plasmodium falciparum genome using only DNA physicochemical properties.
	Method KEGG spider: interpretation of genomics data in the context of the global gene metabolic network Alexey V Antonov, Sabine Dietmann, Hans W Mewes Genome Biology 2008, 9:R179 (18 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A web-based tool for interpretation of experimentally-derived gene lists that provides global models uniting genes from different metabolic pathways.
	Method Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo Zhandong Liu, Min Wang, James V Alvarez, Megan E Bonney, Chien-chung Chen, Celina D'Cruz, Tien-chi Pan, Mahlet G Tadesse, Lewis A Chodosh Genome Biology 2008, 9:R180 (18 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Singular value decomposition regression can detect the activation of endogenous signaling pathways, allowing the identification of pathway cross-talk.

	Volume 9 Issue 12
	Comment
	Comment A seat at the table Gregory A Petsko Genome Biology 2008, 9:113 (31 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The appointment of two life scientists, including a genome biologist, to the President-elect Obama's President's Council of Advisors on Science and Technology is encouraging.
	Review
	Review Next-generation biomass feedstocks for biofuel production Blake A Simmons, Dominique Loque, Harvey W Blanch Genome Biology 2008, 9:242 (29 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the potential for biofuel production in the United States from timber and non-grain crops.
	Minireview Lymphatic endothelial differentiation: start out with Sox - carry on with Prox Friedemann Kiefer, Ralf H Adams Genome Biology 2008, 9:243 (29 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Lymphatic system development comes into sharper focus.
	Minireview Replication forks, chromatin loops and dormant replication origins J Julian Blow, Xin Ge Genome Biology 2008, 9:244 (30 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The plasticity of replication origin usage during mitosis is associated with longer-term changes to chromatin loop organization.
	Minireview Diatom genomes come of age Assaf Vardi, Kimberlee Thamatrakoln, Kay D Bidle, Paul G Falkowski Genome Biology 2008, 9:245 (9 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two genome sequences of diatoms, marine single-celled photosynthetic eukaryotes that often have ornate cell walls, give insights into their metabolic and signaling systems.
	Opinion Bioinformatics: alive and kicking Lincoln D Stein Genome Biology 2008, 9:114 (17 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bioinformatics is alive and well in 2008 concludes Lincoln Stein, despite his earlier prediction of its imminent demise.
	Report
	Meeting report Computational models in systems biology Laurence Loewe, Jane Hillston Genome Biology 2008, 9:328 (10 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report of the 6th International Conference on Computational Methods in Systems Biology, Rostock, Germany, 12-15 October 2008.
	Research
	Research Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells Catia Attanasio, Alexandre Reymond, Richard Humbert, Robert Lyle, Michael S Kuehn, Shane Neph, Peter J Sabo, Jeff Goldy, Molly Weaver, Andrew Haydock, Kristin Lee, Michael Dorschner, Emmanouil T Dermitzakis, Stylianos E Antonarakis, John A Stamatoyannopoulos Genome Biology 2008, 9:R168 (2 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The fraction of experimentally active conserved non-coding sequences within any given cell type is low, so classical assays are unlikely to expose their potential.
	Research Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes Ping Wang, Shanye Yin, Zhenguo Zhang, Dedong Xin, Landian Hu, Xiangyin Kong, Laurence D Hurst Genome Biology 2008, 9:R169 (2 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational prediction of human coding RNA trans short sense-antisense pairs suggests that mRNA regulation by other coding transcripts might be a common occurrence.
	Research FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease Rong Chen, Alex A Morgan, Joel Dudley, Tarangini Deshpande, Li Li, Keiichi Kodama, Annie P Chiang, Atul J Butte Genome Biology 2008, 9:R170 (5 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Differential expressed genes are more likely to have variants associated with disease. A new tool, fitSNP, prioritizes candidate SNPs from association studies.
	Research Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence Daniel E Neafsey, Stephen F Schaffner, Sarah K Volkman, Daniel Park, Philip Montgomery, Danny A Milner, Amanda Lukens, David Rosen, Rachel Daniels, Nathan Houde, Joseph F Cortese, Erin Tyndall, Casey Gates, Nicole Stange-Thomann, Ousmane Sarr, Daouda Ndiaye, Omar Ndir, Soulyemane Mboup, Marcelo U Ferreira, Sandra Moraes, Aditya P Dash, Chetan E Chitnis, Roger C Wiegand, Daniel L Hartl, Bruce W Birren, Eric S Lander, Pardis C Sabeti, Dyann F Wirth Genome Biology 2008, 9:R171 (15 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An array-based SNP genotyping platform for Plasmodium falciparum is reported together with an analysis of SNP diversity in global population samples.
	Research Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences Laurence Ettwiller, Aidan Budd, François Spitz, Joachim Wittbrodt Genome Biology 2008, 9:R172 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the evolutionary dynamics of target gene batteries controlled by 16 different transcription factors reveals stable ancestral cores and highly dynamic regulatory sequences
	Research Evolutionary-new centromeres preferentially emerge within gene deserts Mariana Lomiento, Zhaoshi Jiang, Pietro D'Addabbo, Evan E Eichler, Mariano Rocchi Genome Biology 2008, 9:R173 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study identifying genomic restructuring and the absence of genes as conditions permissive for the seeding of new centromeres in primates
	Research Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution Carlos Quijano, Pavel Tomancak, Jesus Lopez-Marti, Mikita Suyama, Peer Bork, Marco Milan, David Torrents, Miguel Manzanares Genome Biology 2008, 9:R176 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genes occurring in conserved, tandemly-arrayed clusters in Drosophila melanogaster are co-expressed to a much higher extent than other duplicated genes.
	Research Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites Bernardo J Foth, Neng Zhang, Sachel Mok, Peter R Preiser, Zbynek Bozdech Genome Biology 2008, 9:R177 (17 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A quantitative time-course analysis of protein abundance for Plasmodium falciparum schizonts using two-dimensional differential gel electrophoresis reveals significant post-transcriptional regulation.
	Research Male reproductive development: gene expression profiling of maize anther and pollen ontogeny Jiong Ma, David S Skibbe, John Fernandes, Virginia Walbot Genome Biology 2008, 9:R181 (19 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of global gene expression profiles of seven stages of maize anther development reveals expression of many genes
	Research A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development Alyson Ashe, Daniel K Morgan, Nadia C Whitelaw, Timothy J Bruxner, Nicola K Vickaryous, Liza L Cox, Natalie C Butterfield, Carol Wicking, Marnie E Blewitt, Sarah J Wilkins, Gregory J Anderson, Timothy C Cox, Emma Whitelaw Genome Biology 2008, 9:R182 (19 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extended ENU screen for modifiers of transgene variegation identified four new modifiers, MommeD7-D10.
	Research Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps Christopher A Desjardins, Dawn E Gundersen-Rindal, Jessica B Hostetler, Luke J Tallon, Douglas W Fadrosh, Roger W Fuester, Monica J Pedroni, Brian J Haas, Michael C Schatz, Kristine M Jones, Jonathan Crabtree, Heather Forberger, Vishvanath Nene Genome Biology 2008, 9:R183 (30 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genome analysis of two endosymbiotic polydnaviruses from Glyptapanteles parasitic wasps reveals new insights into the evolutionary arms race between host and parasite.
	Method Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy Li Wang, Fengzhu Sun, Ting Chen Genome Biology 2008, 9:R174 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A strategy is presented to prioritize the functional modules that mediate genetic perturbations and their phenotypic effects among candidate modules.
	Method Annotating genomes with massive-scale RNA sequencing France Denoeud, Jean-Marc Aury, Corinne Da Silva, Benjamin Noel, Odile Rogier, Massimo Delledonne, Michele Morgante, Giorgio Valle, Patrick Wincker, Claude Scarpelli, Olivier Jaillon, François Artiguenave Genome Biology 2008, 9:R175 (16 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for de novo genome annotation using high-throughput cDNA sequencing data.
	Method Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum Kevin Brick, Junichi Watanabe, Elisabetta Pizzi Genome Biology 2008, 9:R178 (18 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented to computationally identify core promoters in the Plasmodium falciparum genome using only DNA physicochemical properties.
	Method KEGG spider: interpretation of genomics data in the context of the global gene metabolic network Alexey V Antonov, Sabine Dietmann, Hans W Mewes Genome Biology 2008, 9:R179 (18 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A web-based tool for interpretation of experimentally-derived gene lists that provides global models uniting genes from different metabolic pathways.
	Method Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo Zhandong Liu, Min Wang, James V Alvarez, Megan E Bonney, Chien-chung Chen, Celina D'Cruz, Tien-chi Pan, Mahlet G Tadesse, Lewis A Chodosh Genome Biology 2008, 9:R180 (18 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Singular value decomposition regression can detect the activation of endogenous signaling pathways, allowing the identification of pathway cross-talk.

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Volume 9 Issue 12

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