Genome Biology | Volume 6 Issue 6

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	Volume 6 Issue 6
	Comment
	Comment How may you help me? Gregory A Petsko Genome Biology 2005, 6:111 (27 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Most of us have had so many bad experiences with service personnel over the years that we harbor the illusion that doing things for ourselves is faster and better.
	Opinion Biochip sensors for the rapid and sensitive detection of viral disease Andrew D Livingston, Colin J Campbell, Edward K Wagner, Peter Ghazal Genome Biology 2005, 6:112 (26 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent advances in DNA and protein microarray methodology and the emerging technology of cell-based sensors have massively increased the speed and sensitivity with which we can detect viral infections.
	Opinion Histone modifications: from genome-wide maps to functional insights Fred van Leeuwen, Bas van Steensel Genome Biology 2005, 6:113 (31 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide mapping approaches provide new opportunities to decipher the complex combinatorial regulatory code of histone modifications but they may suffer from systematic biases.
	Review
	Protein family review The B7 family of immune-regulatory ligands Mary Collins, Vincent Ling, Beatriz M Carreno Genome Biology 2005, 6:223 (31 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The B7 family consists of structurally related, cell-surface protein ligands, which bind to the CD28 family of receptors on lymphocytes and regulate immune responses via 'costimulatory' or 'coinhibitory' signals.
	Minireview The Dictyostelium genome: the private life of a social model revealed? Robert Insall Genome Biology 2005, 6:222 (9 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The complete genome sequence of the social amoeba Dictyostelium reveals unexpected complexities in genome structure, and cell motility and signaling.
	Minireview Making sense of nonsense: the evolution of selenocysteine usage in proteins Paul R Copeland Genome Biology 2005, 6:221 (27 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent analysis of sequences derived from organisms in the Sargasso Sea has revealed a surprisingly different set of selenium-containing proteins than that previously found in sequenced genomes.
	Report
	Paper report Articles selected by Faculty of 1000: muscle differentiation regulatory network; the rules of transcriptional regulation; rapid exprimental determination of DNA-binding protein motifs; polymerase poised and ready to go; bacterial tree accounting for lateral transfer Genome Biology 2005, 6:327 (9 May 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a muscle differentiation regulatory network; the rules of transcriptional regulation; rapid exprimental determination of DNA-binding protein motifs; polymerase poised and ready to go; bacterial tree accounting for lateral transfer.
	Paper report Articles selected by Faculty of 1000: the origin of operons; human linkage disequilibrium maps; genomics finds novel secondary metabolites; complex epistasis of fly genes; how did the turtle get its shell? Genome Biology 2005, 6:328 (24 May 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the origin of operons; human linkage disequilibrium maps; genomics finds novel secondary metabolites; complex epistasis of fly genes; how did the turtle get its shell?
	Meeting report Plant and animal genomes achieve functionality Peter M Gresshoff Genome Biology 2005, 6:324 (20 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the conference 'Plant and Animal Genomes XIII', San Diego, USA, 15-19 January 2005.
	Meeting report Biocomputing enters its adolescence Shamil Sunyaev Genome Biology 2005, 6:325 (31 May 2005) Full text \| PDF \| PubMed \| Editor’s summary A report on the tenth Pacific Symposium on Biocomputing, Big Island, Hawaii, USA, 4-8 January 2005.
	Research news Alternate cell-death program identified Melissa Phillips Genome Biology 2005, 6:spotlight-20050603-01 (3 June 2005) Abstract \| Full text \| Editor’s summary Researchers find chemical inhibitor of nonapoptotic programmed cell-death process called 'necroptosis'
	Research news EU science budget threatened Jane Burgermeister Genome Biology 2005, 6:spotlight-20050609-01 (9 June 2005) Abstract \| Full text \| Editor’s summary Scientists called to mobilize as plan to double EU research funds faces severe blow
	Research news MicroRNAs linked to cancer Graciela Flores Genome Biology 2005, 6:spotlight-20050610-01 (10 June 2005) Abstract \| Full text \| Editor’s summary Trio of Nature papers describes elevated miRNAs in various human tumors and models
	Research news Circadian regulation of reward Melissa Phillips Genome Biology 2005, 6:gb-spotlight-20050614-01 (14 June 2005) Abstract \| Full text \| Editor’s summary Mice lacking Clock gene have elevated dopamine transmission in brain's reward pathway
	Research news Jumping genes in the brain Charles Q Choi Genome Biology 2005, 6:gb-spotlight-20050616-01 (16 June 2005) Abstract \| Full text \| Editor’s summary Retrotransposons in neurons could lead to brain differences between individuals
	Research news Science retracts highly cited paper Graciela Flores Genome Biology 2005, 6:gb-spotlight-20050617-01 (17 June 2005) Abstract \| Full text \| Editor’s summary Study on the causes of childhood illness retracted after author found guilty of falsifying data
	Research news Primate-specific microRNAs found Charles Q Choi Genome Biology 2005, 6:spotlight-20050620-01 (20 June 2005) Abstract \| Full text \| Editor’s summary Identification of 89 new genes doubles the number of sequenced human microRNAs
	Research news Transcription factors link rhizobia, legumes Ishani Ganguli Genome Biology 2005, 6:spotlight-20050621-01 (21 June 2005) Abstract \| Full text \| Editor’s summary GRAS family proteins found to regulate nodules where nitrogen-fixing bacteria live
	Research news RCUK draft mandates open access Stephen Pincock Genome Biology 2005, 6:spotlight-20050624-01 (24 June 2005) Abstract \| Full text \| Editor’s summary Policy, which will now be debated, requires deposition in a repository 'at the earliest opportunity'
	Research news Little fire ant males are clones Nick Atkinson Genome Biology 2005, 6:spotlight-20050630-01 (30 June 2005) Abstract \| Full text \| Editor’s summary Researchers identify first ant species in which both males and females have reverted to asexuality
	Research
	Research The rarity of gene shuffling in conserved genes Gavin C Conant, Andreas Wagner Genome Biology 2005, 6:R50 (9 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The incidence of gene shuffling is estimated in conserved genes in 10 organisms from the three domains of life. Successful gene shuffling is found to be very rare among such conserved genes. This suggests that gene shuffling may not be a major force in reshaping the core genomes of eukaryotes.
	Research Large-scale ¹³C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast Lars M Blank, Lars Kuepfer, Uwe Sauer Genome Biology 2005, 6:R49 (17 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-scale 13^C-flux analysis in Saccharomyces cerevisiae revealed that the apparent dispensability of knockout mutants with metabolic function can be explained by gene inactivity under a particular condition, by network redundancy through duplicated genes or by alternative pathways.
	Research Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture Lei Li, Xiangfeng Wang, Mian Xia, Viktor Stolc, Ning Su, Zhiyu Peng, Songgang Li, Jun Wang, Xiping Wang, Xing Deng Genome Biology 2005, 6:R52 (27 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptome analysis of chromosome 10 of 2 rice subspecies identifies 549 new gene models and gives experimental evidence for around 75% of the previously unsupported predicted genes.
	Research Mechanisms of aging in senescence-accelerated mice Todd A Carter, Jennifer A Greenhall, Shigeo Yoshida, Sebastian Fuchs, Robert Helton, Anand Swaroop, David J Lockhart, Carrolee Barlow Genome Biology 2005, 6:R48 (1 June 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene-expression analysis and polymorphism screening to study molecular senescence of the retina and hippocampus in two rare inbred mouse models of accelerated neurological senescence as well as a related and an unrelated normal strain showed that most age-related gene expression changes were strain-specific.
	Research Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation Chih-Hung Jen, Ioannis Michalopoulos, David R Westhead, Peter Meyer Genome Biology 2005, 6:R51 (1 June 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription data analysis of overlapping gene pairs in Arabidopsis thaliana argues against a predominant RNA degradation effect induced by dsRNA formation. Instead, it suggests alternative roles for dsRNAs such as regulation of alternative splicing in polyadenylation.
	Method Single-feature polymorphism discovery in the barley transcriptome Nils Rostoks, Justin O Borevitz, Peter E Hedley, Joanne Russell, Sharon Mudie, Jenny Morris, Linda Cardle, David F Marshall, Robbie Waugh Genome Biology 2005, 6:R54 (11 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A probe level model for analysis of GeneChip gene expression data is presented which identified more than 10,000 single-feature polymorphisms between two barley genotypes, with a high sensitivity. This method is applicable to all oligonucleotide microarray data.
	Method Identification of co-regulated transcripts affecting male body size in Drosophila Cynthia J Coffman, Marta L Wayne, Sergey V Nuzhdin, Laura A Higgins, Lauren M McIntyre Genome Biology 2005, 6:R53 (1 June 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Factor analysis is applied to microarray data in order to relate gene networks to complex traits and identifies a factor associated with body size in Drosophila simulans.
	Software Refinement and prediction of protein prenylation motifs Sebastian Maurer-Stroh, Frank Eisenhaber Genome Biology 2005, 6:R55 (27 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three prenylation motif predictors are presented that allow discrimination between proteins that are unique substrates of farnesyltransferase (FT) and those that can be alternatively processed by geranylgeranyltransferase I (GGT1).

	Volume 6 Issue 6
	Comment
	Comment How may you help me? Gregory A Petsko Genome Biology 2005, 6:111 (27 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Most of us have had so many bad experiences with service personnel over the years that we harbor the illusion that doing things for ourselves is faster and better.
	Opinion Biochip sensors for the rapid and sensitive detection of viral disease Andrew D Livingston, Colin J Campbell, Edward K Wagner, Peter Ghazal Genome Biology 2005, 6:112 (26 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent advances in DNA and protein microarray methodology and the emerging technology of cell-based sensors have massively increased the speed and sensitivity with which we can detect viral infections.
	Opinion Histone modifications: from genome-wide maps to functional insights Fred van Leeuwen, Bas van Steensel Genome Biology 2005, 6:113 (31 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide mapping approaches provide new opportunities to decipher the complex combinatorial regulatory code of histone modifications but they may suffer from systematic biases.
	Review
	Protein family review The B7 family of immune-regulatory ligands Mary Collins, Vincent Ling, Beatriz M Carreno Genome Biology 2005, 6:223 (31 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The B7 family consists of structurally related, cell-surface protein ligands, which bind to the CD28 family of receptors on lymphocytes and regulate immune responses via 'costimulatory' or 'coinhibitory' signals.
	Minireview The Dictyostelium genome: the private life of a social model revealed? Robert Insall Genome Biology 2005, 6:222 (9 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The complete genome sequence of the social amoeba Dictyostelium reveals unexpected complexities in genome structure, and cell motility and signaling.
	Minireview Making sense of nonsense: the evolution of selenocysteine usage in proteins Paul R Copeland Genome Biology 2005, 6:221 (27 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent analysis of sequences derived from organisms in the Sargasso Sea has revealed a surprisingly different set of selenium-containing proteins than that previously found in sequenced genomes.
	Report
	Paper report Articles selected by Faculty of 1000: muscle differentiation regulatory network; the rules of transcriptional regulation; rapid exprimental determination of DNA-binding protein motifs; polymerase poised and ready to go; bacterial tree accounting for lateral transfer Genome Biology 2005, 6:327 (9 May 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a muscle differentiation regulatory network; the rules of transcriptional regulation; rapid exprimental determination of DNA-binding protein motifs; polymerase poised and ready to go; bacterial tree accounting for lateral transfer.
	Paper report Articles selected by Faculty of 1000: the origin of operons; human linkage disequilibrium maps; genomics finds novel secondary metabolites; complex epistasis of fly genes; how did the turtle get its shell? Genome Biology 2005, 6:328 (24 May 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the origin of operons; human linkage disequilibrium maps; genomics finds novel secondary metabolites; complex epistasis of fly genes; how did the turtle get its shell?
	Meeting report Plant and animal genomes achieve functionality Peter M Gresshoff Genome Biology 2005, 6:324 (20 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the conference 'Plant and Animal Genomes XIII', San Diego, USA, 15-19 January 2005.
	Meeting report Biocomputing enters its adolescence Shamil Sunyaev Genome Biology 2005, 6:325 (31 May 2005) Full text \| PDF \| PubMed \| Editor’s summary A report on the tenth Pacific Symposium on Biocomputing, Big Island, Hawaii, USA, 4-8 January 2005.
	Research news Alternate cell-death program identified Melissa Phillips Genome Biology 2005, 6:spotlight-20050603-01 (3 June 2005) Abstract \| Full text \| Editor’s summary Researchers find chemical inhibitor of nonapoptotic programmed cell-death process called 'necroptosis'
	Research news EU science budget threatened Jane Burgermeister Genome Biology 2005, 6:spotlight-20050609-01 (9 June 2005) Abstract \| Full text \| Editor’s summary Scientists called to mobilize as plan to double EU research funds faces severe blow
	Research news MicroRNAs linked to cancer Graciela Flores Genome Biology 2005, 6:spotlight-20050610-01 (10 June 2005) Abstract \| Full text \| Editor’s summary Trio of Nature papers describes elevated miRNAs in various human tumors and models
	Research news Circadian regulation of reward Melissa Phillips Genome Biology 2005, 6:gb-spotlight-20050614-01 (14 June 2005) Abstract \| Full text \| Editor’s summary Mice lacking Clock gene have elevated dopamine transmission in brain's reward pathway
	Research news Jumping genes in the brain Charles Q Choi Genome Biology 2005, 6:gb-spotlight-20050616-01 (16 June 2005) Abstract \| Full text \| Editor’s summary Retrotransposons in neurons could lead to brain differences between individuals
	Research news Science retracts highly cited paper Graciela Flores Genome Biology 2005, 6:gb-spotlight-20050617-01 (17 June 2005) Abstract \| Full text \| Editor’s summary Study on the causes of childhood illness retracted after author found guilty of falsifying data
	Research news Primate-specific microRNAs found Charles Q Choi Genome Biology 2005, 6:spotlight-20050620-01 (20 June 2005) Abstract \| Full text \| Editor’s summary Identification of 89 new genes doubles the number of sequenced human microRNAs
	Research news Transcription factors link rhizobia, legumes Ishani Ganguli Genome Biology 2005, 6:spotlight-20050621-01 (21 June 2005) Abstract \| Full text \| Editor’s summary GRAS family proteins found to regulate nodules where nitrogen-fixing bacteria live
	Research news RCUK draft mandates open access Stephen Pincock Genome Biology 2005, 6:spotlight-20050624-01 (24 June 2005) Abstract \| Full text \| Editor’s summary Policy, which will now be debated, requires deposition in a repository 'at the earliest opportunity'
	Research news Little fire ant males are clones Nick Atkinson Genome Biology 2005, 6:spotlight-20050630-01 (30 June 2005) Abstract \| Full text \| Editor’s summary Researchers identify first ant species in which both males and females have reverted to asexuality
	Research
	Research The rarity of gene shuffling in conserved genes Gavin C Conant, Andreas Wagner Genome Biology 2005, 6:R50 (9 May 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The incidence of gene shuffling is estimated in conserved genes in 10 organisms from the three domains of life. Successful gene shuffling is found to be very rare among such conserved genes. This suggests that gene shuffling may not be a major force in reshaping the core genomes of eukaryotes.
	Research Large-scale ¹³C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast Lars M Blank, Lars Kuepfer, Uwe Sauer Genome Biology 2005, 6:R49 (17 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-scale 13^C-flux analysis in Saccharomyces cerevisiae revealed that the apparent dispensability of knockout mutants with metabolic function can be explained by gene inactivity under a particular condition, by network redundancy through duplicated genes or by alternative pathways.
	Research Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture Lei Li, Xiangfeng Wang, Mian Xia, Viktor Stolc, Ning Su, Zhiyu Peng, Songgang Li, Jun Wang, Xiping Wang, Xing Deng Genome Biology 2005, 6:R52 (27 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptome analysis of chromosome 10 of 2 rice subspecies identifies 549 new gene models and gives experimental evidence for around 75% of the previously unsupported predicted genes.
	Research Mechanisms of aging in senescence-accelerated mice Todd A Carter, Jennifer A Greenhall, Shigeo Yoshida, Sebastian Fuchs, Robert Helton, Anand Swaroop, David J Lockhart, Carrolee Barlow Genome Biology 2005, 6:R48 (1 June 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene-expression analysis and polymorphism screening to study molecular senescence of the retina and hippocampus in two rare inbred mouse models of accelerated neurological senescence as well as a related and an unrelated normal strain showed that most age-related gene expression changes were strain-specific.
	Research Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation Chih-Hung Jen, Ioannis Michalopoulos, David R Westhead, Peter Meyer Genome Biology 2005, 6:R51 (1 June 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription data analysis of overlapping gene pairs in Arabidopsis thaliana argues against a predominant RNA degradation effect induced by dsRNA formation. Instead, it suggests alternative roles for dsRNAs such as regulation of alternative splicing in polyadenylation.
	Method Single-feature polymorphism discovery in the barley transcriptome Nils Rostoks, Justin O Borevitz, Peter E Hedley, Joanne Russell, Sharon Mudie, Jenny Morris, Linda Cardle, David F Marshall, Robbie Waugh Genome Biology 2005, 6:R54 (11 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A probe level model for analysis of GeneChip gene expression data is presented which identified more than 10,000 single-feature polymorphisms between two barley genotypes, with a high sensitivity. This method is applicable to all oligonucleotide microarray data.
	Method Identification of co-regulated transcripts affecting male body size in Drosophila Cynthia J Coffman, Marta L Wayne, Sergey V Nuzhdin, Laura A Higgins, Lauren M McIntyre Genome Biology 2005, 6:R53 (1 June 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Factor analysis is applied to microarray data in order to relate gene networks to complex traits and identifies a factor associated with body size in Drosophila simulans.
	Software Refinement and prediction of protein prenylation motifs Sebastian Maurer-Stroh, Frank Eisenhaber Genome Biology 2005, 6:R55 (27 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three prenylation motif predictors are presented that allow discrimination between proteins that are unique substrates of farnesyltransferase (FT) and those that can be alternatively processed by geranylgeranyltransferase I (GGT1).

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Volume 6 Issue 6

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