Genome Biology | Volume 7 Issue 12

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	Volume 7 Issue 12
	Comment
	Comment A model worth considering? Gregory A Petsko Genome Biology 2006, 7:121 (29 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A business-science hybrid model for medical research that focuses on collaboration rather than competition seems worth exploring.
	Review
	Review The chemokine and chemokine receptor superfamilies and their molecular evolution Albert Zlotnik, Osamu Yoshie, Hisayuki Nomiyama Genome Biology 2006, 7:243 (29 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tandem gene duplication has taken place independently in the mouse and human lineages of some chemokine families, so care needs to be taken when extrapolating experimental results on chemokines from mouse to human
	Minireview Taking care of Dad's DNA Rika Maruyama, Andrew Singson Genome Biology 2006, 7:244 (1 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Proteomic analysis in C. elegans has uncovered sperm chromatin-packaging factors necessary for male fertility.
	Minireview Photosynthesis: what color was its origin? Jin Xiong Genome Biology 2006, 7:245 (3 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent studies suggest several alternative evolutionary scenarios for the origin of photosynthesis.
	Report
	Meeting report The many routes to regulating mRNA translation Kristian E Baker, Jeff Coller Genome Biology 2006, 7:332 (15 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Translational Control' at Cold Spring Harbor, New York, 6-10 September 2006.
	Meeting report Harry Potter and the structural biologist's (Key)stone Damien Devos, Olga V Kalinina, Robert B Russell Genome Biology 2006, 7:333 (29 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the first European Keystone symposium 'Multi-protein complexes involved in cell regulation', Cambridge, UK, 18-23 August 2006.
	Meeting report Moonlight in Vermont illuminates plant development Olivier Voinnet, Kim Baumann Genome Biology 2006, 7:334 (29 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB summer research conference 'Mechanisms in plant development', Saxtons River, USA, 5-9 August 2006.
	Research
	Research An environmental signature for 323 microbial genomes based on codon adaptation indices Hanni Willenbrock, Carsten Friis, Agnieszka S Juncker, David W Ussery Genome Biology 2006, 7:R114 (7 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The correlation of two methods for estimating codon adaptation indices applied to more than 300 bacterial species shows that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle
	Research Is mammalian chromosomal evolution driven by regions of genome fragility? Aurora Ruiz-Herrera, Jose Castresana, Terence J Robinson Genome Biology 2006, 7:R115 (8 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the distribution of evolutionary breakpoints in eight species suggests that certain human chromosomal regions are repeatedly used during the evolutionary process, are associated with fragile sites, and show an enrichment of tandem repeats.
	Research Dissection of a metastatic gene expression signature into distinct components Paul Roepman, Erica de Koning, Dik van Leenen, Roel A de Weger, J Alain Kummer, Piet J Slootweg, Frank CP Holstege Genome Biology 2006, 7:R117 (11 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The dissection of predictive expression signatures into different components based on tumor versus stroma expression shows a strikingly skewed distribution of metastasis associated genes.
	Research Dynamic usage of transcription start sites within core promoters Hideya Kawaji, Martin C Frith, Shintaro Katayama, Albin Sandelin, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki Genome Biology 2006, 7:R118 (12 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An exploration of the internal dynamics of mammalian promoters demonstrates that start site selection within mouse core promoters varies amongst tissues.
	Research Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples Jessica C Mar, Renee Rubio, John Quackenbush Genome Biology 2006, 7:R119 (14 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A simple model for assessing transcript levels based on Poisson statistics is proposed and validated by estimating the variance on gene expression levels as a function of the number of cells surveyed.
	Research Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns Manuela Sironi, Giorgia Menozzi, Giacomo P Comi, Matteo Cereda, Rachele Cagliani, Nereo Bresolin, Uberto Pozzoli Genome Biology 2006, 7:R120 (20 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of humans and mouse genomes indicates that gene function, expression level, and sequence conservation influence transposable elements insertion/fixation in mammalian introns.
	Research Multiple independent evolutionary solutions to core histone gene regulation Leonardo Mariño-Ramírez, I King Jordan, David Landsman Genome Biology 2006, 7:R122 (21 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the evolutionary dynamics of the regulatory mechanisms that give rise to the conserved histone regulatory phenotype indicates a substantial evolutionary turnover of cis-regulatory sequence motifs along with the transcription factors that bind them
	Research Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline Cris L Luengo Hendriks, Soile VE Keränen, Charless C Fowlkes, Lisa Simirenko, Gunther H Weber, Angela H DePace, Clara Henriquez, David W Kaszuba, Bernd Hamann, Michael B Eisen, Jitendra Malik, Damir Sudar, Mark D Biggin, David W Knowles Genome Biology 2006, 7:R123 (21 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A suite of methods that provide the first quantitative three-dimensional description of gene expression and morphology with cellular resolution in whole Drosophila embryos is described.
	Research Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics Soile VE Keränen, Charless C Fowlkes, Cris L Luengo Hendriks, Damir Sudar, David W Knowles, Jitendra Malik, Mark D Biggin Genome Biology 2006, 7:R124 (21 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new spatio-temporal coordinate framework for studying three-dimensional patterns of gene expression in the Drosophila blastoderm is presented that takes account of previously undetected morphological movements.
	Research Evolutionary conservation of domain-domain interactions Zohar Itzhaki, Eyal Akiva, Yael Altuvia, Hanah Margalit Genome Biology 2006, 7:R125 (21 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Mapping of domain-domain interactions onto the cellular protein-protein interaction networks of different organisms demonstrates that there is a catalogue of domain pairs that is used for mediating various interactions in the cell
	Research Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics Nansheng Chen, Allan Mah, Oliver E Blacque, Jeffrey Chu, Kiran Phgora, Mathieu W Bakhoum, C Rebecca Hunt Newbury, Jaswinder Khattra, Susanna Chan, Anne Go, Evgeni Efimenko, Robert Johnsen, Prasad Phirke, Peter Swoboda, Marco Marra, Donald G Moerman, Michel R Leroux, David L Baillie, Lincoln D Stein Genome Biology 2006, 7:R126 (22 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomic analysis of three nematode species identifies 93 genes that encode putative components of the ciliated neurons in C. elegans and are subject to the same regulatory control.
	Method Generation of medaka gene knockout models by target-selected mutagenesis Yoshihito Taniguchi, Shunichi Takeda, Makoto Furutani-Seiki, Yasuhiro Kamei, Takeshi Todo, Takao Sasado, Tomonori Deguchi, Hisato Kondoh, Josine Mudde, Mitsuyoshi Yamazoe, Masayuki Hidaka, Hiroshi Mitani, Atsushi Toyoda, Yoshiyuki Sakaki, Ronald HA Plasterk, Edwin Cuppen Genome Biology 2006, 7:R116 (8 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A reverse genetics approach for the routine generation of medaka (Oryzias latipes) gene knockouts is described and applied to create a cryopreserved resource containing knockouts for most medaka genes.
	Method Classification methods for the development of genomic signatures from high-dimensional data Hojin Moon, Hongshik Ahn, Ralph L Kodell, Chien-Ju Lin, Songjoon Baek, James J Chen Genome Biology 2006, 7:R121 (20 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several classification algorithms for class prediction using high-dimensional biomedical data are presented and applied to data from leukaemia and breast cancer patients

	Volume 7 Issue 12
	Comment
	Comment A model worth considering? Gregory A Petsko Genome Biology 2006, 7:121 (29 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A business-science hybrid model for medical research that focuses on collaboration rather than competition seems worth exploring.
	Review
	Review The chemokine and chemokine receptor superfamilies and their molecular evolution Albert Zlotnik, Osamu Yoshie, Hisayuki Nomiyama Genome Biology 2006, 7:243 (29 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tandem gene duplication has taken place independently in the mouse and human lineages of some chemokine families, so care needs to be taken when extrapolating experimental results on chemokines from mouse to human
	Minireview Taking care of Dad's DNA Rika Maruyama, Andrew Singson Genome Biology 2006, 7:244 (1 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Proteomic analysis in C. elegans has uncovered sperm chromatin-packaging factors necessary for male fertility.
	Minireview Photosynthesis: what color was its origin? Jin Xiong Genome Biology 2006, 7:245 (3 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent studies suggest several alternative evolutionary scenarios for the origin of photosynthesis.
	Report
	Meeting report The many routes to regulating mRNA translation Kristian E Baker, Jeff Coller Genome Biology 2006, 7:332 (15 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Translational Control' at Cold Spring Harbor, New York, 6-10 September 2006.
	Meeting report Harry Potter and the structural biologist's (Key)stone Damien Devos, Olga V Kalinina, Robert B Russell Genome Biology 2006, 7:333 (29 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the first European Keystone symposium 'Multi-protein complexes involved in cell regulation', Cambridge, UK, 18-23 August 2006.
	Meeting report Moonlight in Vermont illuminates plant development Olivier Voinnet, Kim Baumann Genome Biology 2006, 7:334 (29 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB summer research conference 'Mechanisms in plant development', Saxtons River, USA, 5-9 August 2006.
	Research
	Research An environmental signature for 323 microbial genomes based on codon adaptation indices Hanni Willenbrock, Carsten Friis, Agnieszka S Juncker, David W Ussery Genome Biology 2006, 7:R114 (7 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The correlation of two methods for estimating codon adaptation indices applied to more than 300 bacterial species shows that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle
	Research Is mammalian chromosomal evolution driven by regions of genome fragility? Aurora Ruiz-Herrera, Jose Castresana, Terence J Robinson Genome Biology 2006, 7:R115 (8 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the distribution of evolutionary breakpoints in eight species suggests that certain human chromosomal regions are repeatedly used during the evolutionary process, are associated with fragile sites, and show an enrichment of tandem repeats.
	Research Dissection of a metastatic gene expression signature into distinct components Paul Roepman, Erica de Koning, Dik van Leenen, Roel A de Weger, J Alain Kummer, Piet J Slootweg, Frank CP Holstege Genome Biology 2006, 7:R117 (11 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The dissection of predictive expression signatures into different components based on tumor versus stroma expression shows a strikingly skewed distribution of metastasis associated genes.
	Research Dynamic usage of transcription start sites within core promoters Hideya Kawaji, Martin C Frith, Shintaro Katayama, Albin Sandelin, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki Genome Biology 2006, 7:R118 (12 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An exploration of the internal dynamics of mammalian promoters demonstrates that start site selection within mouse core promoters varies amongst tissues.
	Research Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples Jessica C Mar, Renee Rubio, John Quackenbush Genome Biology 2006, 7:R119 (14 December 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A simple model for assessing transcript levels based on Poisson statistics is proposed and validated by estimating the variance on gene expression levels as a function of the number of cells surveyed.
	Research Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns Manuela Sironi, Giorgia Menozzi, Giacomo P Comi, Matteo Cereda, Rachele Cagliani, Nereo Bresolin, Uberto Pozzoli Genome Biology 2006, 7:R120 (20 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of humans and mouse genomes indicates that gene function, expression level, and sequence conservation influence transposable elements insertion/fixation in mammalian introns.
	Research Multiple independent evolutionary solutions to core histone gene regulation Leonardo Mariño-Ramírez, I King Jordan, David Landsman Genome Biology 2006, 7:R122 (21 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the evolutionary dynamics of the regulatory mechanisms that give rise to the conserved histone regulatory phenotype indicates a substantial evolutionary turnover of cis-regulatory sequence motifs along with the transcription factors that bind them
	Research Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline Cris L Luengo Hendriks, Soile VE Keränen, Charless C Fowlkes, Lisa Simirenko, Gunther H Weber, Angela H DePace, Clara Henriquez, David W Kaszuba, Bernd Hamann, Michael B Eisen, Jitendra Malik, Damir Sudar, Mark D Biggin, David W Knowles Genome Biology 2006, 7:R123 (21 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A suite of methods that provide the first quantitative three-dimensional description of gene expression and morphology with cellular resolution in whole Drosophila embryos is described.
	Research Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics Soile VE Keränen, Charless C Fowlkes, Cris L Luengo Hendriks, Damir Sudar, David W Knowles, Jitendra Malik, Mark D Biggin Genome Biology 2006, 7:R124 (21 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new spatio-temporal coordinate framework for studying three-dimensional patterns of gene expression in the Drosophila blastoderm is presented that takes account of previously undetected morphological movements.
	Research Evolutionary conservation of domain-domain interactions Zohar Itzhaki, Eyal Akiva, Yael Altuvia, Hanah Margalit Genome Biology 2006, 7:R125 (21 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Mapping of domain-domain interactions onto the cellular protein-protein interaction networks of different organisms demonstrates that there is a catalogue of domain pairs that is used for mediating various interactions in the cell
	Research Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics Nansheng Chen, Allan Mah, Oliver E Blacque, Jeffrey Chu, Kiran Phgora, Mathieu W Bakhoum, C Rebecca Hunt Newbury, Jaswinder Khattra, Susanna Chan, Anne Go, Evgeni Efimenko, Robert Johnsen, Prasad Phirke, Peter Swoboda, Marco Marra, Donald G Moerman, Michel R Leroux, David L Baillie, Lincoln D Stein Genome Biology 2006, 7:R126 (22 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomic analysis of three nematode species identifies 93 genes that encode putative components of the ciliated neurons in C. elegans and are subject to the same regulatory control.
	Method Generation of medaka gene knockout models by target-selected mutagenesis Yoshihito Taniguchi, Shunichi Takeda, Makoto Furutani-Seiki, Yasuhiro Kamei, Takeshi Todo, Takao Sasado, Tomonori Deguchi, Hisato Kondoh, Josine Mudde, Mitsuyoshi Yamazoe, Masayuki Hidaka, Hiroshi Mitani, Atsushi Toyoda, Yoshiyuki Sakaki, Ronald HA Plasterk, Edwin Cuppen Genome Biology 2006, 7:R116 (8 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A reverse genetics approach for the routine generation of medaka (Oryzias latipes) gene knockouts is described and applied to create a cryopreserved resource containing knockouts for most medaka genes.
	Method Classification methods for the development of genomic signatures from high-dimensional data Hojin Moon, Hongshik Ahn, Ralph L Kodell, Chien-Ju Lin, Songjoon Baek, James J Chen Genome Biology 2006, 7:R121 (20 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several classification algorithms for class prediction using high-dimensional biomedical data are presented and applied to data from leukaemia and breast cancer patients

Explore Genome Biology

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Volume 7 Issue 12

Comment

Review

Report

Research