Genome Biology | Volume 9 Issue 7

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	Volume 9 Issue 7
	Comment
	Comment Having an impact (factor) Gregory A Petsko Genome Biology 2008, 9:107 (29 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recently departed genome biologist discusses the impact factor of his life with St Peter at the Pearly Gates.
	Review
	Review New clues to organ size control in plants László Bögre, Zoltán Magyar, Enrique López-Juez Genome Biology 2008, 9:226 (29 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the mechanisms that control organ size in plants.
	Protein family review The tektin family of microtubule-stabilizing proteins Linda A Amos Genome Biology 2008, 9:229 (29 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tektins are insoluble a-helical proteins essential for the construction of cilia and flagella and are found throughout the eukaryotes apart from higher plants.
	Minireview Engineering a DNA damage response without DNA damage ManTek Yeung, Daniel Durocher Genome Biology 2008, 9:227 (28 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA damage response signaling has been achieved experimentally in the absence of double-strand DNA breaks.
	Report
	Meeting report Integrating systems biology with clinical research Rainer Pepperkok, Stefan Wiemann Genome Biology 2008, 9:314 (1 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the conference 'Systems Genomics 2008', Heidelberg, Germany, 2-3 May 2008.
	Meeting report Gene regulation and signal transduction in the immune system Tiffany Horng, Shalini Oberdoerffer, Anjana Rao Genome Biology 2008, 9:315 (10 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'Gene Expression and Signaling in the Immune System', Cold Spring Harbor, USA, 22-26 April 2008.
	Meeting report Mathematical models in mammalian cell biology Hanspeter Herzel, Nils Blüthgen Genome Biology 2008, 9:316 (15 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Conference on Systems Biology of Mammalian Cells, Dresden, Germany, 22-24 May 2008.
	Research
	Research Asymmetric histone modifications between the original and derived loci of human segmental duplications Deyou Zheng Genome Biology 2008, 9:R105 (3 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of histone modifications between human segmental duplications shows that two seemingly identical genomic copies have distinct epigenomic properties.
	Research Taxonomic distribution of large DNA viruses in the sea Adam Monier, Jean-Michel Claverie, Hiroyuki Ogata Genome Biology 2008, 9:R106 (3 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic mapping of metagenomics data reveals the taxonomic distribution of large DNA viruses in the sea, including giant viruses of the Mimiviridae family.
	Research Protein structure protection commits gene expression patterns Jianping Chen, Han Liang, Ariel Fernández Genome Biology 2008, 9:R107 (7 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A proteomic association study between protein three-dimensional structure and transcriptional and post-transcriptional regulation in yeast and human.
	Research Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers Kamila Naxerova, Carol J Bult, Anne Peaston, Karen Fancher, Barbara B Knowles, Simon Kasif, Isaac S Kohane Genome Biology 2008, 9:R108 (8 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of the relationship between the neoplastic and developmental transcriptome provides an outline of global trends in cancer gene expression.
	Research Concerted gene recruitment in early plant evolution Jinling Huang, J Peter Gogarten Genome Biology 2008, 9:R109 (8 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analyses of the red algal Cyanidioschyzon genome identified 37 genes that were acquired from non-organellar sources prior to the split of red algae and green plants.
	Research Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF Agathe Bourgogne, Danielle A Garsin, Xiang Qin, Kavindra V Singh, Jouko Sillanpaa, Shailaja Yerrapragada, Yan Ding, Shannon Dugan-Rocha, Christian Buhay, Hua Shen, Guan Chen, Gabrielle Williams, Donna Muzny, Arash Maadani, Kristina A Fox, Jason Gioia, Lei Chen, Yue Shang, Cesar A Arias, Sreedhar R Nallapareddy, Meng Zhao, Vittal P Prakash, Shahreen Chowdhury, Huaiyang Jiang, Richard A Gibbs, Barbara E Murray, Sarah K Highlander, George M Weinstock Genome Biology 2008, 9:R110 (8 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of two strains of the hospital pathogen Enterococcus faecalis suggests that mediators of virulence differ between strains and that virulence does not depend on mobile gene elements
	Research Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors Thomas J Lukas, Haixi Miao, Lin Chen, Sean M Riordan, Wenjun Li, Andrea M Crabb, Alexandria Wise, Pan Du, Simon M Lin, M Rosario Hernandez Genome Biology 2008, 9:R111 (9 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of gene expression in normal and glaucomatous eyes from Caucasian American and African American donors reveals differences that might reflect different susceptibility to glaucoma.
	Research Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids Yong-Hwee E Loh, Lee S Katz, Meryl C Mims, Thomas D Kocher, Soojin V Yi, J Todd Streelman Genome Biology 2008, 9:R113 (10 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Low coverage survey sequencing shows that although Lake Malawi cichlids are phenotypically and behaviorally diverse, they appear genetically like a subdivided population.
	Research The transcriptional program underlying the physiology of clostridial sporulation Shawn W Jones, Carlos J Paredes, Bryan Tracy, Nathan Cheng, Ryan Sillers, Ryan S Senger, Eleftherios T Papoutsakis Genome Biology 2008, 9:R114 (16 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A detailed microarray analysis of transcription during sporulation of the strict anaerobe and endospore former Clostridium acetobutylicum is presented.
	Research Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy Jean-Michel Ubeda, Danielle Légaré, Frédéric Raymond, Amin Ouameur, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Michel J Tremblay, Martin Olivier, Barbara Papadopoulou, Marc Ouellette Genome Biology 2008, 9:R115 (18 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene expression and DNA copy number analyses using full genome oligonucleotide microarrays of Leishmania reveal molecular mechanisms of methotrexate resistance.
	Research The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation Dong Xia, Sanya J Sanderson, Andrew R Jones, Judith H Prieto, John R Yates, Elizabeth Bromley, Fiona M Tomley, Kalpana Lal, Robert E Sinden, Brian P Brunk, David S Roos, Jonathan M Wastling Genome Biology 2008, 9:R116 (21 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A proteomics analysis identifies one third of the predicted Toxoplasma gondii proteins and integrates proteomics and genomics data to refine genome annotation.
	Research Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants Sophie Gaudriault, Sylvie Pages, Anne Lanois, Christine Laroui, Corinne Teyssier, Estelle Jumas-Bilak, Alain Givaudan Genome Biology 2008, 9:R117 (22 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative genomic study of Photorhabdus variants sheds light into bacterial genome architecture and the role of clonal genomic variation in bacterial genome evolution.
	Research The IL-10 and IFN-γ pathways are essential to the potent immunosuppressive activity of cultured CD8⁺NKT-like cells Li Zhou, Hongjie Wang, Xing Zhong, Yulan Jin, Qing-Sheng Mi, Ashok Sharma, Richard A McIndoe, Nikhil Garge, Robert Podolsky, Jin-Xiong She Genome Biology 2008, 9:R119 (29 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Global gene expression profiling of in vitro cultured CD8⁺T cells that express natural killer cell markers revealed differential expression of about 3,000 genes between these cells and naïve CD8⁺T cells.
	Research Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling Timothy E Gookin, Junhyong Kim, Sarah M Assmann Genome Biology 2008, 9:R120 (31 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Computational prediction and in vivo protein coupling experiments identify candidate plant G-protein coupled receptors in Arabidopsis, rice and poplar.
	Method At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana Sascha Laubinger, Georg Zeller, Stefan R Henz, Timo Sachsenberg, Christian K Widmer, Naïra Naouar, Marnik Vuylsteke, Bernhard Schölkopf, Gunnar Rätsch, Detlef Weigel Genome Biology 2008, 9:R112 (9 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A developmental expression atlas, At-TAX, based on whole-genome tiling arrays, is presented along with associated analysis methods.
	Software MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis Vu T Chu, Raphael Gottardo, Adrian E Raftery, Roger E Bumgarner, Ka Yeung Genome Biology 2008, 9:R118 (24 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MeV+R provides users with point-and-click access to traditionally command-line-driven tools written in R.
	Correspondence
	Open letter The ethics of characterizing difference: guiding principles on using racial categories in human genetics Sandra Lee, Joanna Mountain, Barbara Koenig, Russ Altman, Melissa Brown, Albert Camarillo, Luca Cavalli-Sforza, Mildred Cho, Jennifer Eberhardt, Marcus Feldman, Richard Ford, Henry Greely, Roy King, Hazel Markus, Debra Satz, Matthew Snipp, Claude Steele, Peter Underhill Genome Biology 2008, 9:404 (15 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary We are a multidisciplinary group of Stanford faculty who propose ten principles to guide the use of racial and ethnic categories when characterizing group differences in research into human genetic variation.

	Volume 9 Issue 7
	Comment
	Comment Having an impact (factor) Gregory A Petsko Genome Biology 2008, 9:107 (29 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recently departed genome biologist discusses the impact factor of his life with St Peter at the Pearly Gates.
	Review
	Review New clues to organ size control in plants László Bögre, Zoltán Magyar, Enrique López-Juez Genome Biology 2008, 9:226 (29 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the mechanisms that control organ size in plants.
	Protein family review The tektin family of microtubule-stabilizing proteins Linda A Amos Genome Biology 2008, 9:229 (29 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tektins are insoluble a-helical proteins essential for the construction of cilia and flagella and are found throughout the eukaryotes apart from higher plants.
	Minireview Engineering a DNA damage response without DNA damage ManTek Yeung, Daniel Durocher Genome Biology 2008, 9:227 (28 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA damage response signaling has been achieved experimentally in the absence of double-strand DNA breaks.
	Report
	Meeting report Integrating systems biology with clinical research Rainer Pepperkok, Stefan Wiemann Genome Biology 2008, 9:314 (1 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the conference 'Systems Genomics 2008', Heidelberg, Germany, 2-3 May 2008.
	Meeting report Gene regulation and signal transduction in the immune system Tiffany Horng, Shalini Oberdoerffer, Anjana Rao Genome Biology 2008, 9:315 (10 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'Gene Expression and Signaling in the Immune System', Cold Spring Harbor, USA, 22-26 April 2008.
	Meeting report Mathematical models in mammalian cell biology Hanspeter Herzel, Nils Blüthgen Genome Biology 2008, 9:316 (15 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Conference on Systems Biology of Mammalian Cells, Dresden, Germany, 22-24 May 2008.
	Research
	Research Asymmetric histone modifications between the original and derived loci of human segmental duplications Deyou Zheng Genome Biology 2008, 9:R105 (3 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of histone modifications between human segmental duplications shows that two seemingly identical genomic copies have distinct epigenomic properties.
	Research Taxonomic distribution of large DNA viruses in the sea Adam Monier, Jean-Michel Claverie, Hiroyuki Ogata Genome Biology 2008, 9:R106 (3 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic mapping of metagenomics data reveals the taxonomic distribution of large DNA viruses in the sea, including giant viruses of the Mimiviridae family.
	Research Protein structure protection commits gene expression patterns Jianping Chen, Han Liang, Ariel Fernández Genome Biology 2008, 9:R107 (7 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A proteomic association study between protein three-dimensional structure and transcriptional and post-transcriptional regulation in yeast and human.
	Research Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers Kamila Naxerova, Carol J Bult, Anne Peaston, Karen Fancher, Barbara B Knowles, Simon Kasif, Isaac S Kohane Genome Biology 2008, 9:R108 (8 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of the relationship between the neoplastic and developmental transcriptome provides an outline of global trends in cancer gene expression.
	Research Concerted gene recruitment in early plant evolution Jinling Huang, J Peter Gogarten Genome Biology 2008, 9:R109 (8 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analyses of the red algal Cyanidioschyzon genome identified 37 genes that were acquired from non-organellar sources prior to the split of red algae and green plants.
	Research Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF Agathe Bourgogne, Danielle A Garsin, Xiang Qin, Kavindra V Singh, Jouko Sillanpaa, Shailaja Yerrapragada, Yan Ding, Shannon Dugan-Rocha, Christian Buhay, Hua Shen, Guan Chen, Gabrielle Williams, Donna Muzny, Arash Maadani, Kristina A Fox, Jason Gioia, Lei Chen, Yue Shang, Cesar A Arias, Sreedhar R Nallapareddy, Meng Zhao, Vittal P Prakash, Shahreen Chowdhury, Huaiyang Jiang, Richard A Gibbs, Barbara E Murray, Sarah K Highlander, George M Weinstock Genome Biology 2008, 9:R110 (8 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of two strains of the hospital pathogen Enterococcus faecalis suggests that mediators of virulence differ between strains and that virulence does not depend on mobile gene elements
	Research Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors Thomas J Lukas, Haixi Miao, Lin Chen, Sean M Riordan, Wenjun Li, Andrea M Crabb, Alexandria Wise, Pan Du, Simon M Lin, M Rosario Hernandez Genome Biology 2008, 9:R111 (9 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of gene expression in normal and glaucomatous eyes from Caucasian American and African American donors reveals differences that might reflect different susceptibility to glaucoma.
	Research Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids Yong-Hwee E Loh, Lee S Katz, Meryl C Mims, Thomas D Kocher, Soojin V Yi, J Todd Streelman Genome Biology 2008, 9:R113 (10 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Low coverage survey sequencing shows that although Lake Malawi cichlids are phenotypically and behaviorally diverse, they appear genetically like a subdivided population.
	Research The transcriptional program underlying the physiology of clostridial sporulation Shawn W Jones, Carlos J Paredes, Bryan Tracy, Nathan Cheng, Ryan Sillers, Ryan S Senger, Eleftherios T Papoutsakis Genome Biology 2008, 9:R114 (16 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A detailed microarray analysis of transcription during sporulation of the strict anaerobe and endospore former Clostridium acetobutylicum is presented.
	Research Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy Jean-Michel Ubeda, Danielle Légaré, Frédéric Raymond, Amin Ouameur, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Michel J Tremblay, Martin Olivier, Barbara Papadopoulou, Marc Ouellette Genome Biology 2008, 9:R115 (18 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene expression and DNA copy number analyses using full genome oligonucleotide microarrays of Leishmania reveal molecular mechanisms of methotrexate resistance.
	Research The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation Dong Xia, Sanya J Sanderson, Andrew R Jones, Judith H Prieto, John R Yates, Elizabeth Bromley, Fiona M Tomley, Kalpana Lal, Robert E Sinden, Brian P Brunk, David S Roos, Jonathan M Wastling Genome Biology 2008, 9:R116 (21 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A proteomics analysis identifies one third of the predicted Toxoplasma gondii proteins and integrates proteomics and genomics data to refine genome annotation.
	Research Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants Sophie Gaudriault, Sylvie Pages, Anne Lanois, Christine Laroui, Corinne Teyssier, Estelle Jumas-Bilak, Alain Givaudan Genome Biology 2008, 9:R117 (22 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative genomic study of Photorhabdus variants sheds light into bacterial genome architecture and the role of clonal genomic variation in bacterial genome evolution.
	Research The IL-10 and IFN-γ pathways are essential to the potent immunosuppressive activity of cultured CD8⁺NKT-like cells Li Zhou, Hongjie Wang, Xing Zhong, Yulan Jin, Qing-Sheng Mi, Ashok Sharma, Richard A McIndoe, Nikhil Garge, Robert Podolsky, Jin-Xiong She Genome Biology 2008, 9:R119 (29 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Global gene expression profiling of in vitro cultured CD8⁺T cells that express natural killer cell markers revealed differential expression of about 3,000 genes between these cells and naïve CD8⁺T cells.
	Research Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling Timothy E Gookin, Junhyong Kim, Sarah M Assmann Genome Biology 2008, 9:R120 (31 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Computational prediction and in vivo protein coupling experiments identify candidate plant G-protein coupled receptors in Arabidopsis, rice and poplar.
	Method At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana Sascha Laubinger, Georg Zeller, Stefan R Henz, Timo Sachsenberg, Christian K Widmer, Naïra Naouar, Marnik Vuylsteke, Bernhard Schölkopf, Gunnar Rätsch, Detlef Weigel Genome Biology 2008, 9:R112 (9 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A developmental expression atlas, At-TAX, based on whole-genome tiling arrays, is presented along with associated analysis methods.
	Software MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis Vu T Chu, Raphael Gottardo, Adrian E Raftery, Roger E Bumgarner, Ka Yeung Genome Biology 2008, 9:R118 (24 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MeV+R provides users with point-and-click access to traditionally command-line-driven tools written in R.
	Correspondence
	Open letter The ethics of characterizing difference: guiding principles on using racial categories in human genetics Sandra Lee, Joanna Mountain, Barbara Koenig, Russ Altman, Melissa Brown, Albert Camarillo, Luca Cavalli-Sforza, Mildred Cho, Jennifer Eberhardt, Marcus Feldman, Richard Ford, Henry Greely, Roy King, Hazel Markus, Debra Satz, Matthew Snipp, Claude Steele, Peter Underhill Genome Biology 2008, 9:404 (15 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary We are a multidisciplinary group of Stanford faculty who propose ten principles to guide the use of racial and ethnic categories when characterizing group differences in research into human genetic variation.

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Volume 9 Issue 7

Comment

Review

Report

Research

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