Genome Biology | Volume 7 Issue 9

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	Volume 7 Issue 9
	Comment
	Comment Fly's time Gregory A Petsko Genome Biology 2006, 7:115 (29 September 2006) Abstract \| Full text \| PDF \| Editor’s summary The struggle between public and private efforts to sequence the fly genome is the subject of Michael Ashburner's new book, Won for All: How the Drosophila Genome Was Sequenced
	Opinion Genomics and the bacterial species problem W Ford Doolittle, R Thane Papke Genome Biology 2006, 7:116 (29 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Do we need to describe bacteria as species, and if so, can we?
	Review
	Protein family review Arrestins: ubiquitous regulators of cellular signaling pathways Eugenia V Gurevich, Vsevolod V Gurevich Genome Biology 2006, 7:236 (2 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The arrestins are a small family of proteins that regulate the signaling and trafficking of G-protein-coupled receptors and also serve as ubiquitous signaling regulators in the cytoplasm and nucleus.
	Minireview Functional genomics of the yeast DNA-damage response Gerard Cagney, David Alvaro, Robert JD Reid, Peter H Thorpe, Rodney Rothstein, Nevan J Krogan Genome Biology 2006, 7:233 (7 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two high-throughput studies of the DNA-damage response in yeast reveal new regulatory pathways and genes involved.
	Minireview Molecular orchestration of the hepatic circadian symphony Urs Albrecht Genome Biology 2006, 7:234 (28 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study reveals multiple levels of regulation of the circadian expression of liver proteins.
	Report
	Meeting report A bright future for Chlamydomonas Andrea L Manuell, Stephen P Mayfield Genome Biology 2006, 7:327 (12 September 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 12th International Conference on the Cell and Molecular Biology of Chlamydomonas, Portland, USA, 9-14 May 2006.
	Meeting report Regulatory RNAs and the demise of 'junk' DNA Frank J Slack Genome Biology 2006, 7:328 (28 September 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'Regulatory RNAs', the 71st Cold Spring Harbor Symposium on Quantitative Biology, Cold Spring Harbor, USA, 31 May-5 July 2006.
	Research
	Research The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins Jun Adachi, Chanchal Kumar, Yanling Zhang, Jesper V Olsen, Matthias Mann Genome Biology 2006, 7:R80 (1 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high confidence set of proteins in urine from healthy donors is described as a reference urinary proteome.
	Research Genomic features of Bordetella parapertussis clades with distinct host species specificity Mary M Brinig, Karen B Register, Mark R Ackermann, David A Relman Genome Biology 2006, 7:R81 (6 September 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genomic analysis of human and ovine Bordetella parapertussis strains reveals differences distinguishing the host-restricted subgroups.
	Research Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites Vinsensius B Vega, Chin-Yo Lin, Koon Lai, Say Li Kong, Min Xie, Xiaodi Su, Huey Teh, Jane S Thomsen, Ai Li Yeo, Wing Sung, Guillaume Bourque, Edison T Liu Genome Biology 2006, 7:R82 (9 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Refinement of the functional human estrogen receptor binding site model using a multi-platform genome-wide approach reveals extended binding specificity signal.
	Research Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes Katleen De Preter, Jo Vandesompele, Pierre Heimann, Nurten Yigit, Siv Beckman, Alexander Schramm, Angelika Eggert, Raymond L Stallings, Yves Benoit, Marleen Renard, Anne Paepe, Geneviève Laureys, Sven Påhlman, Frank Speleman Genome Biology 2006, 7:R84 (21 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptome profiling of neuroblasts and neuroblastoma tumor cells provides strong support for a neuroblast origin of neuroblastoma and highlights new candidate neuroblastoma genes
	Research Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression Jie Wu, Xiaohui Xie Genome Biology 2006, 7:R85 (26 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using comparative sequence analysis, a network among REST, CREB and brain-related miRNAs is propsed to mediate neuronal gene expression.
	Research Multiple effects govern endogenous retrovirus survival patterns in human gene introns Louie N van de Lagemaat, Patrik Medstrand, Dixie L Mager Genome Biology 2006, 7:R86 (27 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of human endogenous retrovirus families suggests suppression of splicing among young intronic retroviruses oriented antisense to gene transcription.
	Research Patterns of expansion and expression divergence in the plant polygalacturonase gene family Joonyup Kim, Shin-Han Shiu, Sharon Thoma, Wen-Hsiung Li, Sara E Patterson Genome Biology 2006, 7:R87 (29 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of Arabidopsis and rice polygalacturonases suggests that polygalacturonases duplicates underwent rapid expression divergence and that the mechanisms of duplication affect the divergence rate.
	Software PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification Nandini Krishnamurthy, Duncan P Brown, Dan Kirshner, Kimmen Sjölander Genome Biology 2006, 7:R83 (14 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary PhyloFacts, a structural phylogenomic database for protein functional and structural classification, is described.

	Volume 7 Issue 9
	Comment
	Comment Fly's time Gregory A Petsko Genome Biology 2006, 7:115 (29 September 2006) Abstract \| Full text \| PDF \| Editor’s summary The struggle between public and private efforts to sequence the fly genome is the subject of Michael Ashburner's new book, Won for All: How the Drosophila Genome Was Sequenced
	Opinion Genomics and the bacterial species problem W Ford Doolittle, R Thane Papke Genome Biology 2006, 7:116 (29 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Do we need to describe bacteria as species, and if so, can we?
	Review
	Protein family review Arrestins: ubiquitous regulators of cellular signaling pathways Eugenia V Gurevich, Vsevolod V Gurevich Genome Biology 2006, 7:236 (2 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The arrestins are a small family of proteins that regulate the signaling and trafficking of G-protein-coupled receptors and also serve as ubiquitous signaling regulators in the cytoplasm and nucleus.
	Minireview Functional genomics of the yeast DNA-damage response Gerard Cagney, David Alvaro, Robert JD Reid, Peter H Thorpe, Rodney Rothstein, Nevan J Krogan Genome Biology 2006, 7:233 (7 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two high-throughput studies of the DNA-damage response in yeast reveal new regulatory pathways and genes involved.
	Minireview Molecular orchestration of the hepatic circadian symphony Urs Albrecht Genome Biology 2006, 7:234 (28 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study reveals multiple levels of regulation of the circadian expression of liver proteins.
	Report
	Meeting report A bright future for Chlamydomonas Andrea L Manuell, Stephen P Mayfield Genome Biology 2006, 7:327 (12 September 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 12th International Conference on the Cell and Molecular Biology of Chlamydomonas, Portland, USA, 9-14 May 2006.
	Meeting report Regulatory RNAs and the demise of 'junk' DNA Frank J Slack Genome Biology 2006, 7:328 (28 September 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the meeting 'Regulatory RNAs', the 71st Cold Spring Harbor Symposium on Quantitative Biology, Cold Spring Harbor, USA, 31 May-5 July 2006.
	Research
	Research The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins Jun Adachi, Chanchal Kumar, Yanling Zhang, Jesper V Olsen, Matthias Mann Genome Biology 2006, 7:R80 (1 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high confidence set of proteins in urine from healthy donors is described as a reference urinary proteome.
	Research Genomic features of Bordetella parapertussis clades with distinct host species specificity Mary M Brinig, Karen B Register, Mark R Ackermann, David A Relman Genome Biology 2006, 7:R81 (6 September 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genomic analysis of human and ovine Bordetella parapertussis strains reveals differences distinguishing the host-restricted subgroups.
	Research Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites Vinsensius B Vega, Chin-Yo Lin, Koon Lai, Say Li Kong, Min Xie, Xiaodi Su, Huey Teh, Jane S Thomsen, Ai Li Yeo, Wing Sung, Guillaume Bourque, Edison T Liu Genome Biology 2006, 7:R82 (9 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Refinement of the functional human estrogen receptor binding site model using a multi-platform genome-wide approach reveals extended binding specificity signal.
	Research Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes Katleen De Preter, Jo Vandesompele, Pierre Heimann, Nurten Yigit, Siv Beckman, Alexander Schramm, Angelika Eggert, Raymond L Stallings, Yves Benoit, Marleen Renard, Anne Paepe, Geneviève Laureys, Sven Påhlman, Frank Speleman Genome Biology 2006, 7:R84 (21 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptome profiling of neuroblasts and neuroblastoma tumor cells provides strong support for a neuroblast origin of neuroblastoma and highlights new candidate neuroblastoma genes
	Research Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression Jie Wu, Xiaohui Xie Genome Biology 2006, 7:R85 (26 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using comparative sequence analysis, a network among REST, CREB and brain-related miRNAs is propsed to mediate neuronal gene expression.
	Research Multiple effects govern endogenous retrovirus survival patterns in human gene introns Louie N van de Lagemaat, Patrik Medstrand, Dixie L Mager Genome Biology 2006, 7:R86 (27 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of human endogenous retrovirus families suggests suppression of splicing among young intronic retroviruses oriented antisense to gene transcription.
	Research Patterns of expansion and expression divergence in the plant polygalacturonase gene family Joonyup Kim, Shin-Han Shiu, Sharon Thoma, Wen-Hsiung Li, Sara E Patterson Genome Biology 2006, 7:R87 (29 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of Arabidopsis and rice polygalacturonases suggests that polygalacturonases duplicates underwent rapid expression divergence and that the mechanisms of duplication affect the divergence rate.
	Software PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification Nandini Krishnamurthy, Duncan P Brown, Dan Kirshner, Kimmen Sjölander Genome Biology 2006, 7:R83 (14 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary PhyloFacts, a structural phylogenomic database for protein functional and structural classification, is described.

Explore Genome Biology

Articles

Volume 7 Issue 9

Comment

Review

Report

Research