Genome Biology | Volume 7 Issue 10

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	Volume 7 Issue 10
	Comment
	Comment Transformation Gregory A Petsko Genome Biology 2006, 7:117 (1 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Nobel process for science are often somewhat controversial for who they omit. A posthumous Nobel honor could help recognize some neglected heroes.
	Review
	Minireview Leaner and meaner genomes in Escherichia coli David W Ussery Genome Biology 2006, 7:237 (24 October 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A streamlined Escherichia coli K-12 has been engineered in which 15% of the genome has been deleted
	Minireview A Melanesian α-thalassemia mutation suggests a novel mechanism for regulating gene expression Qiliang Li Genome Biology 2006, 7:238 (24 October 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mutation that creates a promoter site between the adult α-globin genes and their enhancers causes α-thalassemia, suggesting a new mechanism for disrupting gene epression.
	Minireview Getting a buzz out of the bee genome Michael Ashburner, Charalambos P Kyriacou Genome Biology 2006, 7:239 (26 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the release of the honey-bee genome sequence.
	Opinion The tree of one percent Tal Dagan, William Martin Genome Biology 2006, 7:118 (1 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary As lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes are fundamentally not tree-like in nature, biologists need to depart from the notion that all genomes are related by a single bifurcating tree.
	Report
	Meeting report Developmental genomics reaches new heights Charalampos Rallis Genome Biology 2006, 7:329 (31 October 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the EMBO/SNF symposium 'The Genomics of Development', Arolla, Switzerland, 21-27 August 2006.
	Meeting report Lipids join the post-genomic era Reinhard Bauer, Axel Imhof Genome Biology 2006, 7:330 (31 October 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'From Proteomics to Lipidomics - Basics, Advances and Applications', Bonn, Germany, 30 June-1 July 2006.
	Research
	Research Ancient genomic architecture for mammalian olfactory receptor clusters Ronny Aloni, Tsviya Olender, Doron Lancet Genome Biology 2006, 7:R88 (1 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new tool for genome-wide definition of genomic gene clusters conserved in multiple species was applied to olfactory receptors in five mammals, demonstrating that most mammalian olfactory receptor clusters have a common ancestry.
	Research Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins Shiri Freilich, Tim Massingham, Eric Blanc, Leon Goldovsky, Janet M Thornton Genome Biology 2006, 7:R89 (9 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the relationship between duplication events, the time they took place and the expression breadth of the duplicated genes supports the subfunctionalization model, in which expression divergence following gene duplication promotes the retention of a gene in multicellular species.
	Research Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial Daniel G Lee, Jonathan M Urbach, Gang Wu, Nicole T Liberati, Rhonda L Feinbaum, Sachiko Miyata, Lenard T Diggins, Jianxin He, Maude Saucier, Eric Déziel, Lisa Friedman, Li Li, George Grills, Kate Montgomery, Raju Kucherlapati, Laurence G Rahme, Frederick M Ausubel Genome Biology 2006, 7:R90 (12 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Sequencing of a highly virulent strain of Pseudomonas aeruginosa and comparison to a previously sequenced, less pathogenic, strain, together with experimental testing in a C. elegans model, suggests that Pseudomonas virulence is multifactorial and combinatorial.
	Research Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs Maria Cardone, Alicia Alonso, Michele Pazienza, Mario Ventura, Gabriella Montemurro, Lucia Carbone, Pieter J de Jong, Roscoe Stanyon, Pietro D'Addabbo, Nicoletta Archidiacono, Xinwei She, Evan E Eichler, Peter E Warburton, Mariano Rocchi Genome Biology 2006, 7:R91 (13 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The mammalian evolutionary history of chromosome 13 was characterized and evolutionary-new centromeres compared to two human neocentromeres at 13q21 using chromatin immunoprecipitation and genomic microarrays
	Research Prediction of trans-antisense transcripts in Arabidopsis thaliana Huan Wang, Nam-Hai Chua, Xiu-Jie Wang Genome Biology 2006, 7:R92 (13 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A genome-wide screen for trans-natural antisense transcripts in Arabidopsis thaliana suggests that antisense transcripts could be involved in complex regulatory networks in eukaryotes.
	Research Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways David M Levine, David R Haynor, John C Castle, Sergey B Stepaniants, Matteo Pellegrini, Mao Mao, Jason M Johnson Genome Biology 2006, 7:R93 (17 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of five different measures of pathway expression and a public map of pathway expression in human tissues are presented.
	Research Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues Yan Zhang, Hector Romero, Gustavo Salinas, Vadim N Gladyshev Genome Biology 2006, 7:R94 (20 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and evolutionary analyses to examine the dynamics of selenocysteine utilization in bacteria reveal a dynamic balance between selenoprotein origin and loss.
	Research Transcriptional response to alcohol exposure in Drosophila melanogaster Tatiana V Morozova, Robert RH Anholt, Trudy FC Mackay Genome Biology 2006, 7:R95 (20 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Whole-genome transcriptional analysis following alcohol exposure in flies identifies key enzymes in conserved metabolic pathways that may contribute to human alcohol sensitivity.
	Research An inventory of yeast proteins associated with nucleolar and ribosomal components Eike Staub, Sebastian Mackowiak, Martin Vingron Genome Biology 2006, 7:R98 (26 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic profiling and gene expression analysis of yeast proteins suggests that the nucleolus probably evolved from an archaeal-type ribosome maturation machinery by recruitment of several bacterial-type and mostly eukaryote-specific factors
	Research Global analysis of mRNA stability in the archaeon Sulfolobus Anders F Andersson, Magnus Lundgren, Stefan Eriksson, Magnus Rosenlund, Rolf Bernander, Peter Nilsson Genome Biology 2006, 7:R99 (26 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A microarray-based analysis of mRNA half-lives in two species of Sulfolobus, an hyperthermophilic archaeon, shows that their mRNA half-life distribution is similar to that of much faster growing bacteria
	Research A consensus prognostic gene expression classifier for ER positive breast cancer Andrew E Teschendorff, Ali Naderi, Nuno L Barbosa-Morais, Sarah E Pinder, Ian O Ellis, Sam Aparicio, James D Brenton, Carlos Caldas Genome Biology 2006, 7:R101 (31 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A consensus prognostic classifier for estrogen receptor positive breast tumors has been developed and shown to be valid in nearly 900 samples across different microarray platforms.
	Method Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors Etsuko N Moriyama, Pooja K Strope, Stephen O Opiyo, Zhongying Chen, Alan M Jones Genome Biology 2006, 7:R96 (25 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combination of multiple protein classification methods is described and used to identify a minimum set of 54 candidate seven transmembrane receptors in Arabidopsis thaliana.
	Software Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT Tom Cheung, Yin Kwan, Micah Hamady, Xuedong Liu Genome Biology 2006, 7:R97 (25 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GENEACT, a new software suite for the detection of evolutionarily conserved transcription factor binding sites or microRNAs from differentially expressed genes from DNA microarray data, is described.
	Software CellProfiler: image analysis software for identifying and quantifying cell phenotypes Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Kang, Ola Friman, David A Guertin, Joo Chang, Robert A Lindquist, Jason Moffat, Polina Golland, David M Sabatini Genome Biology 2006, 7:R100 (31 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CellProfiler, the first free, open-source system for flexible and high-throughput cell image analysis is described.

	Volume 7 Issue 10
	Comment
	Comment Transformation Gregory A Petsko Genome Biology 2006, 7:117 (1 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Nobel process for science are often somewhat controversial for who they omit. A posthumous Nobel honor could help recognize some neglected heroes.
	Review
	Minireview Leaner and meaner genomes in Escherichia coli David W Ussery Genome Biology 2006, 7:237 (24 October 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A streamlined Escherichia coli K-12 has been engineered in which 15% of the genome has been deleted
	Minireview A Melanesian α-thalassemia mutation suggests a novel mechanism for regulating gene expression Qiliang Li Genome Biology 2006, 7:238 (24 October 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mutation that creates a promoter site between the adult α-globin genes and their enhancers causes α-thalassemia, suggesting a new mechanism for disrupting gene epression.
	Minireview Getting a buzz out of the bee genome Michael Ashburner, Charalambos P Kyriacou Genome Biology 2006, 7:239 (26 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the release of the honey-bee genome sequence.
	Opinion The tree of one percent Tal Dagan, William Martin Genome Biology 2006, 7:118 (1 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary As lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes are fundamentally not tree-like in nature, biologists need to depart from the notion that all genomes are related by a single bifurcating tree.
	Report
	Meeting report Developmental genomics reaches new heights Charalampos Rallis Genome Biology 2006, 7:329 (31 October 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the EMBO/SNF symposium 'The Genomics of Development', Arolla, Switzerland, 21-27 August 2006.
	Meeting report Lipids join the post-genomic era Reinhard Bauer, Axel Imhof Genome Biology 2006, 7:330 (31 October 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'From Proteomics to Lipidomics - Basics, Advances and Applications', Bonn, Germany, 30 June-1 July 2006.
	Research
	Research Ancient genomic architecture for mammalian olfactory receptor clusters Ronny Aloni, Tsviya Olender, Doron Lancet Genome Biology 2006, 7:R88 (1 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new tool for genome-wide definition of genomic gene clusters conserved in multiple species was applied to olfactory receptors in five mammals, demonstrating that most mammalian olfactory receptor clusters have a common ancestry.
	Research Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins Shiri Freilich, Tim Massingham, Eric Blanc, Leon Goldovsky, Janet M Thornton Genome Biology 2006, 7:R89 (9 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the relationship between duplication events, the time they took place and the expression breadth of the duplicated genes supports the subfunctionalization model, in which expression divergence following gene duplication promotes the retention of a gene in multicellular species.
	Research Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial Daniel G Lee, Jonathan M Urbach, Gang Wu, Nicole T Liberati, Rhonda L Feinbaum, Sachiko Miyata, Lenard T Diggins, Jianxin He, Maude Saucier, Eric Déziel, Lisa Friedman, Li Li, George Grills, Kate Montgomery, Raju Kucherlapati, Laurence G Rahme, Frederick M Ausubel Genome Biology 2006, 7:R90 (12 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Sequencing of a highly virulent strain of Pseudomonas aeruginosa and comparison to a previously sequenced, less pathogenic, strain, together with experimental testing in a C. elegans model, suggests that Pseudomonas virulence is multifactorial and combinatorial.
	Research Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs Maria Cardone, Alicia Alonso, Michele Pazienza, Mario Ventura, Gabriella Montemurro, Lucia Carbone, Pieter J de Jong, Roscoe Stanyon, Pietro D'Addabbo, Nicoletta Archidiacono, Xinwei She, Evan E Eichler, Peter E Warburton, Mariano Rocchi Genome Biology 2006, 7:R91 (13 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The mammalian evolutionary history of chromosome 13 was characterized and evolutionary-new centromeres compared to two human neocentromeres at 13q21 using chromatin immunoprecipitation and genomic microarrays
	Research Prediction of trans-antisense transcripts in Arabidopsis thaliana Huan Wang, Nam-Hai Chua, Xiu-Jie Wang Genome Biology 2006, 7:R92 (13 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A genome-wide screen for trans-natural antisense transcripts in Arabidopsis thaliana suggests that antisense transcripts could be involved in complex regulatory networks in eukaryotes.
	Research Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways David M Levine, David R Haynor, John C Castle, Sergey B Stepaniants, Matteo Pellegrini, Mao Mao, Jason M Johnson Genome Biology 2006, 7:R93 (17 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of five different measures of pathway expression and a public map of pathway expression in human tissues are presented.
	Research Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues Yan Zhang, Hector Romero, Gustavo Salinas, Vadim N Gladyshev Genome Biology 2006, 7:R94 (20 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and evolutionary analyses to examine the dynamics of selenocysteine utilization in bacteria reveal a dynamic balance between selenoprotein origin and loss.
	Research Transcriptional response to alcohol exposure in Drosophila melanogaster Tatiana V Morozova, Robert RH Anholt, Trudy FC Mackay Genome Biology 2006, 7:R95 (20 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Whole-genome transcriptional analysis following alcohol exposure in flies identifies key enzymes in conserved metabolic pathways that may contribute to human alcohol sensitivity.
	Research An inventory of yeast proteins associated with nucleolar and ribosomal components Eike Staub, Sebastian Mackowiak, Martin Vingron Genome Biology 2006, 7:R98 (26 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic profiling and gene expression analysis of yeast proteins suggests that the nucleolus probably evolved from an archaeal-type ribosome maturation machinery by recruitment of several bacterial-type and mostly eukaryote-specific factors
	Research Global analysis of mRNA stability in the archaeon Sulfolobus Anders F Andersson, Magnus Lundgren, Stefan Eriksson, Magnus Rosenlund, Rolf Bernander, Peter Nilsson Genome Biology 2006, 7:R99 (26 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A microarray-based analysis of mRNA half-lives in two species of Sulfolobus, an hyperthermophilic archaeon, shows that their mRNA half-life distribution is similar to that of much faster growing bacteria
	Research A consensus prognostic gene expression classifier for ER positive breast cancer Andrew E Teschendorff, Ali Naderi, Nuno L Barbosa-Morais, Sarah E Pinder, Ian O Ellis, Sam Aparicio, James D Brenton, Carlos Caldas Genome Biology 2006, 7:R101 (31 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A consensus prognostic classifier for estrogen receptor positive breast tumors has been developed and shown to be valid in nearly 900 samples across different microarray platforms.
	Method Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors Etsuko N Moriyama, Pooja K Strope, Stephen O Opiyo, Zhongying Chen, Alan M Jones Genome Biology 2006, 7:R96 (25 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combination of multiple protein classification methods is described and used to identify a minimum set of 54 candidate seven transmembrane receptors in Arabidopsis thaliana.
	Software Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT Tom Cheung, Yin Kwan, Micah Hamady, Xuedong Liu Genome Biology 2006, 7:R97 (25 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GENEACT, a new software suite for the detection of evolutionarily conserved transcription factor binding sites or microRNAs from differentially expressed genes from DNA microarray data, is described.
	Software CellProfiler: image analysis software for identifying and quantifying cell phenotypes Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Kang, Ola Friman, David A Guertin, Joo Chang, Robert A Lindquist, Jason Moffat, Polina Golland, David M Sabatini Genome Biology 2006, 7:R100 (31 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CellProfiler, the first free, open-source system for flexible and high-throughput cell image analysis is described.

Explore Genome Biology

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Volume 7 Issue 10

Comment

Review

Report

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