Genome Biology | Volume 5 Issue 11

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	Volume 5 Issue 11
	Comment
	Comment The emperor's new shibboleth Gregory A Petsko Genome Biology 2004, 5:118 (29 October 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If an idea or result can't be conveyed in plain language, how important can it really be?
	Review
	Protein family review The 3-hydroxy-3-methylglutaryl coenzyme-A (HMG-CoA) reductases Jon A Friesen, Victor W Rodwell Genome Biology 2004, 5:248 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase catalyzes the conversion of HMG-CoA to mevalonate and is a target for anti-hypercholesterolemic drugs (statins).
	Minireview Integrating transcriptional controls for plant cell expansion Keithanne Mockaitis, Mark Estelle Genome Biology 2004, 5:245 (28 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In addition to independent transcriptional responses generated by auxin and brassinosteroid, recent microarray analyses indicate that these two plant hormones also coordinate the expression of a set of shared target genes.
	Minireview Human molecular chronotyping in sight? Urs Albrecht Genome Biology 2004, 5:246 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent research on mouse models has taken us closer to deciphering the molecular clock mechanism that defines an individual's 'body time'.
	Minireview Uncovering the complexities of Kaposi's sarcoma through genome-wide expression analysis Daniel Di Bartolo, Ethel Cesarman Genome Biology 2004, 5:247 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene-expression profiling of endothelial cells infected with Kaposi's sarcoma-associated herpesvirus has led to a greater understanding of the histogenesis and pathogenesis of Kaposi's sarcoma.
	Report
	Paper report Articles selected by Faculty of 1000: Xenopus embryo gene expression patterns; detecting SNPs; Arabidopsis circadian clock mutations; Deinococcus radiation resistant genes; Mycobacterium drug resistance Genome Biology 2004, 5:355 (11 October 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering gene expression patterns in the Xenopus embryo; detecting SNPs; circadian clock mutations in Arabidopsis; radiation resistant genes in Deinococcus; Mycobacterium drug resistance.
	Paper report Articles selected by Faculty of 1000: comparative genomics of fruit ripening; gene co-regulation during evolution; histone acetylation during plant development; microRNA gene identification; ChIP-on-chip analysis in E. coli Genome Biology 2004, 5:356 (22 October 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering fruit ripening comparative genomics; gene co-regulation during evolution; histone acetylation during plant development; microRNA gene identification; ChIP-on-chip analysis in E. coli.
	Meeting report The dosage-compensation complex in flies and humans Karim Bouazoune, Michael Korenjak, Alexander Brehm Genome Biology 2004, 5:352 (26 October 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 6th EMBL Transcription Meeting, Heidelberg, Germany, 28 August-1 September 2004.
	Meeting report High society (of nematologists) David Bird Genome Biology 2004, 5:353 (28 October 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 43rd annual meeting of the Society of Nematologists (SON), Estes Park, USA, 7-11 August 2004.
	Meeting report From genomes to systems David I Ellis, Steve O'Hagan, Warwick B Dunn, Marie Brown, Seetharaman Vaidyanathan Genome Biology 2004, 5:354 (28 October 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2nd Conference of the Consortium for Post-Genome Science (CPGS) 'Genomes to Systems', Manchester, UK, 1-3 September 2004.
	Deposited research article ResurfP: a response surface aided parametric test for identifying differentials in GeneChip based oligonucleotide array experiments Suresh Gopalan Genome Biology 2004, 5:P14 (28 September 2004) Abstract \| Full text \| PDF \| Editor’s summary A response surface assisted approach (termed ResurfP) is proposed for the analysis of probe-level microarray data. The approach will be effective in determining the optimal combination of data-specific thresholds for the number of probe-pairs and of the t-statistic.
	Research news How ubiquitin silences genes Cathy Holding Genome Biology 2004, 5:spotlight-20041109-01 (9 November 2004) Abstract \| Full text \| Editor’s summary A study uncovers the mechanism of histone monoubiquitylation and gene silencing
	Research news Gene manipulation for variola? Robert Walgate Genome Biology 2004, 5:spotlight-20041109-01 (15 November 2004) Abstract \| Full text \| Editor’s summary WHO asked to approve genetic engineering of smallpox virus for drug development
	Research news Google Scholar welcomed Doug Payne Genome Biology 2004, 5:spotlight-20041123-01 (23 November 2004) Abstract \| Full text \| Editor’s summary New academic search service is applauded but librarians, academics have some reservations
	Research news Mice tolerate siRNAs Charles Q Choi Genome Biology 2004, 5:spotlight-20041125-01 (25 November 2004) Abstract \| Full text \| Editor’s summary Studies show small interfering RNAs can be used without triggering immune response
	Research news Gene fusion identified in prostate cancer Ishani Ganguli Genome Biology 2004, 5:spotlight-20051102-01 (2 November 2005) Abstract \| Full text \| Editor’s summary Find is unusual in solid tumors, typically characterized solely by random genetic changes
	Research news Seeing traits, close-up Nicole Johnston Genome Biology 2004, 5:spotlight-20051107-01 (7 November 2005) Abstract \| Full text \| Editor’s summary Researchers dissect a quantitative trait to the single nucleotide level
	Research news For RNA polymerase, it's one base at a time Don Monroe Genome Biology 2004, 5:spotlight-20051118-01 (18 November 2005) Abstract \| Full text \| Editor’s summary Researchers track functioning enzyme with atomic resolution
	Research
	Research Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum Jinling Huang, Nandita Mullapudi, Cheryl A Lancto, Marla Scott, Mitchell S Abrahamsen, Jessica C Kissinger Genome Biology 2004, 5:R88 (19 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An analysis of Cryptosporidium parvum genes of likely endosymbiont or prokaryotic origin supports the hypothesis that C. arvum evolved from a plastid-containing lineage.
	Research Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria Dmitry A Rodionov, Inna Dubchak, Adam Arkin, Eric Alm, Mikhail S Gelfand Genome Biology 2004, 5:R90 (22 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of the genetic and regulatory factors in several biosynthesis, metal ion homeostasis, stress response, and energy metabolism pathways suggests that phylogenetically diverse δ-proteobacteria have homologous regulatory components.
	Research Transcriptome analysis of haploid male gametophyte development in Arabidopsis David Honys, David Twell Genome Biology 2004, 5:R85 (27 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptome analysis of male gametophyte development in Arabidopsis uncovers distinct temporal classes of gene expression and opens the door to detailed studies of the regulatory pathways involved.
	Research Spatial patterns of transcriptional activity in the chromosome of Escherichia coli Kyeong Jeong, Jaeyong Ahn, Arkady B Khodursky Genome Biology 2004, 5:R86 (27 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the transcriptional activity in Escherichia coli K12 revealed an asymmetry in the distribution of transcriptional patterns along the bacterial chromosome and showed that spatial patterns of transcription could be modulated pharmacologically and genetically.
	Research Assembly and characterization of heterochromatin and euchromatin on human artificial chromosomes Brenda R Grimes, Jennifer Babcock, M Katharine Rudd, Brian Chadwick, Huntington F Willard Genome Biology 2004, 5:R89 (27 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An assay of the formation of heterochromatin and euchromatin on de novo human artificial chromosomes containing alpha satellite DNA revealed that only a small amount of heterochromatin may be required for centromere function and that replication late in S phase is not a requirement for centromere function.
	Research Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants Peter M Palenchar, Andrei Kouranov, Laurence V Lejay, Gloria M Coruzzi Genome Biology 2004, 5:R91 (29 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis and the 'InterAct class' method were used to study interactions between carbon and nitrogen signaling in Arabidopsis.
	Research Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli Brian J Peter, Javier Arsuaga, Adam M Breier, Arkady B Khodursky, Patrick O Brown, Nicholas R Cozzarelli Genome Biology 2004, 5:R87 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Microarray analysis shows that transcription of 306 E. Coli genes is affected by changes in the level of chromosome supercoiling, suggesting that supercoiling transmits regulatory signals from the environment to many cellular pathways.
	Method Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana Anja Wille, Philip Zimmermann, Eva Vranová, Andreas Fürholz, Oliver Laule, Stefan Bleuler, Lars Hennig, Amela Prelić, Peter von Rohr, Lothar Thiele, Eckart Zitzler, Wilhelm Gruissem, Peter Bühlmann Genome Biology 2004, 5:R92 (25 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel approach for modeling gene-regulatory networks, based on graphical Gaussian modeling, is used to create a network for the isoprenoid biosynthesis pathway in Arabidopsis.
	Method How biologically relevant are interaction-based modules in protein networks? Juan F Poyatos, Laurence D Hurst Genome Biology 2004, 5:R93 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The authors present a method to identify modules within protein-interaction networks. Phylogenetic profiles are used to determine the biological relevance of the modules.
	Method Consensus clustering and functional interpretation of gene-expression data Stephen Swift, Allan Tucker, Veronica Vinciotti, Nigel Martin, Christine Orengo, Xiaohui Liu, Paul Kellam Genome Biology 2004, 5:R94 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Consensus clustering, a new method for analyzing microarray data that takes a consensus set of clusters from various algorithms, is shown to perform better than individual methods alone.

	Volume 5 Issue 11
	Comment
	Comment The emperor's new shibboleth Gregory A Petsko Genome Biology 2004, 5:118 (29 October 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If an idea or result can't be conveyed in plain language, how important can it really be?
	Review
	Protein family review The 3-hydroxy-3-methylglutaryl coenzyme-A (HMG-CoA) reductases Jon A Friesen, Victor W Rodwell Genome Biology 2004, 5:248 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase catalyzes the conversion of HMG-CoA to mevalonate and is a target for anti-hypercholesterolemic drugs (statins).
	Minireview Integrating transcriptional controls for plant cell expansion Keithanne Mockaitis, Mark Estelle Genome Biology 2004, 5:245 (28 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In addition to independent transcriptional responses generated by auxin and brassinosteroid, recent microarray analyses indicate that these two plant hormones also coordinate the expression of a set of shared target genes.
	Minireview Human molecular chronotyping in sight? Urs Albrecht Genome Biology 2004, 5:246 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent research on mouse models has taken us closer to deciphering the molecular clock mechanism that defines an individual's 'body time'.
	Minireview Uncovering the complexities of Kaposi's sarcoma through genome-wide expression analysis Daniel Di Bartolo, Ethel Cesarman Genome Biology 2004, 5:247 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene-expression profiling of endothelial cells infected with Kaposi's sarcoma-associated herpesvirus has led to a greater understanding of the histogenesis and pathogenesis of Kaposi's sarcoma.
	Report
	Paper report Articles selected by Faculty of 1000: Xenopus embryo gene expression patterns; detecting SNPs; Arabidopsis circadian clock mutations; Deinococcus radiation resistant genes; Mycobacterium drug resistance Genome Biology 2004, 5:355 (11 October 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering gene expression patterns in the Xenopus embryo; detecting SNPs; circadian clock mutations in Arabidopsis; radiation resistant genes in Deinococcus; Mycobacterium drug resistance.
	Paper report Articles selected by Faculty of 1000: comparative genomics of fruit ripening; gene co-regulation during evolution; histone acetylation during plant development; microRNA gene identification; ChIP-on-chip analysis in E. coli Genome Biology 2004, 5:356 (22 October 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering fruit ripening comparative genomics; gene co-regulation during evolution; histone acetylation during plant development; microRNA gene identification; ChIP-on-chip analysis in E. coli.
	Meeting report The dosage-compensation complex in flies and humans Karim Bouazoune, Michael Korenjak, Alexander Brehm Genome Biology 2004, 5:352 (26 October 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 6th EMBL Transcription Meeting, Heidelberg, Germany, 28 August-1 September 2004.
	Meeting report High society (of nematologists) David Bird Genome Biology 2004, 5:353 (28 October 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 43rd annual meeting of the Society of Nematologists (SON), Estes Park, USA, 7-11 August 2004.
	Meeting report From genomes to systems David I Ellis, Steve O'Hagan, Warwick B Dunn, Marie Brown, Seetharaman Vaidyanathan Genome Biology 2004, 5:354 (28 October 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2nd Conference of the Consortium for Post-Genome Science (CPGS) 'Genomes to Systems', Manchester, UK, 1-3 September 2004.
	Deposited research article ResurfP: a response surface aided parametric test for identifying differentials in GeneChip based oligonucleotide array experiments Suresh Gopalan Genome Biology 2004, 5:P14 (28 September 2004) Abstract \| Full text \| PDF \| Editor’s summary A response surface assisted approach (termed ResurfP) is proposed for the analysis of probe-level microarray data. The approach will be effective in determining the optimal combination of data-specific thresholds for the number of probe-pairs and of the t-statistic.
	Research news How ubiquitin silences genes Cathy Holding Genome Biology 2004, 5:spotlight-20041109-01 (9 November 2004) Abstract \| Full text \| Editor’s summary A study uncovers the mechanism of histone monoubiquitylation and gene silencing
	Research news Gene manipulation for variola? Robert Walgate Genome Biology 2004, 5:spotlight-20041109-01 (15 November 2004) Abstract \| Full text \| Editor’s summary WHO asked to approve genetic engineering of smallpox virus for drug development
	Research news Google Scholar welcomed Doug Payne Genome Biology 2004, 5:spotlight-20041123-01 (23 November 2004) Abstract \| Full text \| Editor’s summary New academic search service is applauded but librarians, academics have some reservations
	Research news Mice tolerate siRNAs Charles Q Choi Genome Biology 2004, 5:spotlight-20041125-01 (25 November 2004) Abstract \| Full text \| Editor’s summary Studies show small interfering RNAs can be used without triggering immune response
	Research news Gene fusion identified in prostate cancer Ishani Ganguli Genome Biology 2004, 5:spotlight-20051102-01 (2 November 2005) Abstract \| Full text \| Editor’s summary Find is unusual in solid tumors, typically characterized solely by random genetic changes
	Research news Seeing traits, close-up Nicole Johnston Genome Biology 2004, 5:spotlight-20051107-01 (7 November 2005) Abstract \| Full text \| Editor’s summary Researchers dissect a quantitative trait to the single nucleotide level
	Research news For RNA polymerase, it's one base at a time Don Monroe Genome Biology 2004, 5:spotlight-20051118-01 (18 November 2005) Abstract \| Full text \| Editor’s summary Researchers track functioning enzyme with atomic resolution
	Research
	Research Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum Jinling Huang, Nandita Mullapudi, Cheryl A Lancto, Marla Scott, Mitchell S Abrahamsen, Jessica C Kissinger Genome Biology 2004, 5:R88 (19 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An analysis of Cryptosporidium parvum genes of likely endosymbiont or prokaryotic origin supports the hypothesis that C. arvum evolved from a plastid-containing lineage.
	Research Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria Dmitry A Rodionov, Inna Dubchak, Adam Arkin, Eric Alm, Mikhail S Gelfand Genome Biology 2004, 5:R90 (22 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of the genetic and regulatory factors in several biosynthesis, metal ion homeostasis, stress response, and energy metabolism pathways suggests that phylogenetically diverse δ-proteobacteria have homologous regulatory components.
	Research Transcriptome analysis of haploid male gametophyte development in Arabidopsis David Honys, David Twell Genome Biology 2004, 5:R85 (27 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptome analysis of male gametophyte development in Arabidopsis uncovers distinct temporal classes of gene expression and opens the door to detailed studies of the regulatory pathways involved.
	Research Spatial patterns of transcriptional activity in the chromosome of Escherichia coli Kyeong Jeong, Jaeyong Ahn, Arkady B Khodursky Genome Biology 2004, 5:R86 (27 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the transcriptional activity in Escherichia coli K12 revealed an asymmetry in the distribution of transcriptional patterns along the bacterial chromosome and showed that spatial patterns of transcription could be modulated pharmacologically and genetically.
	Research Assembly and characterization of heterochromatin and euchromatin on human artificial chromosomes Brenda R Grimes, Jennifer Babcock, M Katharine Rudd, Brian Chadwick, Huntington F Willard Genome Biology 2004, 5:R89 (27 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An assay of the formation of heterochromatin and euchromatin on de novo human artificial chromosomes containing alpha satellite DNA revealed that only a small amount of heterochromatin may be required for centromere function and that replication late in S phase is not a requirement for centromere function.
	Research Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants Peter M Palenchar, Andrei Kouranov, Laurence V Lejay, Gloria M Coruzzi Genome Biology 2004, 5:R91 (29 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis and the 'InterAct class' method were used to study interactions between carbon and nitrogen signaling in Arabidopsis.
	Research Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli Brian J Peter, Javier Arsuaga, Adam M Breier, Arkady B Khodursky, Patrick O Brown, Nicholas R Cozzarelli Genome Biology 2004, 5:R87 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Microarray analysis shows that transcription of 306 E. Coli genes is affected by changes in the level of chromosome supercoiling, suggesting that supercoiling transmits regulatory signals from the environment to many cellular pathways.
	Method Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana Anja Wille, Philip Zimmermann, Eva Vranová, Andreas Fürholz, Oliver Laule, Stefan Bleuler, Lars Hennig, Amela Prelić, Peter von Rohr, Lothar Thiele, Eckart Zitzler, Wilhelm Gruissem, Peter Bühlmann Genome Biology 2004, 5:R92 (25 October 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel approach for modeling gene-regulatory networks, based on graphical Gaussian modeling, is used to create a network for the isoprenoid biosynthesis pathway in Arabidopsis.
	Method How biologically relevant are interaction-based modules in protein networks? Juan F Poyatos, Laurence D Hurst Genome Biology 2004, 5:R93 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The authors present a method to identify modules within protein-interaction networks. Phylogenetic profiles are used to determine the biological relevance of the modules.
	Method Consensus clustering and functional interpretation of gene-expression data Stephen Swift, Allan Tucker, Veronica Vinciotti, Nigel Martin, Christine Orengo, Xiaohui Liu, Paul Kellam Genome Biology 2004, 5:R94 (1 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Consensus clustering, a new method for analyzing microarray data that takes a consensus set of clusters from various algorithms, is shown to perform better than individual methods alone.

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