Genome Biology | Volume 9 Issue 11

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 9 Issue 11
	Comment
	Comment The wisdom, and madness, of crowds Gregory A Petsko Genome Biology 2008, 9:112 (1 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A 19th-century Scottish poet has a message for our times.
	Review
	Protein family review The Hedgehog protein family Thomas R Bürglin Genome Biology 2008, 9:241 (19 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hedgehog proteins, which are important in developmental signaling, have been joined by other newly discovered proteins from throughout the eukaryotes in the Hint-domain-containing group of proteins.
	Minireview Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis Robert P Zinzen, Eileen EM Furlong Genome Biology 2008, 9:240 (4 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Significant differences between species in genomic occupancy of conserved transcription factors are mostly due to species-specificity of cis-regulatory sequences.
	Minireview Network-based approaches for linking metabolism with environment Sarath Janga, M Madan Babu Genome Biology 2008, 9:239 (24 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide metabolic maps allow the development of network-based computational approaches for linking an organism with its biochemical habitat.
	Report
	Meeting report A new era for proteomics research? Mathias Uhlen Genome Biology 2008, 9:325 (4 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 7th Annual Human Proteome Organization (HUPO) Conference, Amsterdam, the Netherlands, 16-20 August 2008.
	Meeting report From sequence to structure to networks Nir Yosef, Lukas Käll Genome Biology 2008, 9:326 (4 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 7th European Conference on Computational Biology (ECCB), Cagliari, Italy, 22-26 September 2008.
	Meeting report Bacterial networking Kathleen Marchal, Sigrid CJ De Keersmaecker Genome Biology 2008, 9:327 (12 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the ESF-EMBO Symposium Bacterial Networks (BacNet08), Sant Feliu de Guixols, Spain, 13-18 September 2008.
	Research
	Research A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans Mircea Podar, Iain Anderson, Kira S Makarova, James G Elkins, Natalia Ivanova, Mark A Wall, Athanasios Lykidis, Kostantinos Mavromatis, Hui Sun, Matthew E Hudson, Wenqiong Chen, Cosmin Deciu, Don Hutchison, Jonathan R Eads, Abraham Anderson, Fillipe Fernandes, Ernest Szeto, Alla Lapidus, Nikos C Kyrpides, Milton H Saier, Paul M Richardson, Reinhard Rachel, Harald Huber, Jonathan A Eisen, Eugene V Koonin, Martin Keller, Karl O Stetter Genome Biology 2008, 9:R158 (10 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of the complete genome of Ignicoccus hospitalis gives insight into its association with another species of Archaea, Nanoarchaeum equitans.
	Research Characterization of the differentially methylated region of the Impact gene that exhibits Glires-specific imprinting Kohji Okamura, Richard F Wintle, Stephen W Scherer Genome Biology 2008, 9:R160 (13 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomic analysis of the Impact locus, which is imprinted in Glires but not in other mammals, reveals features required for genomic imprinting.
	Research Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1 Jimmy H Saw, Bruce W Mountain, Lu Feng, Marina V Omelchenko, Shaobin Hou, Jennifer A Saito, Matthew B Stott, Dan Li, Guang Zhao, Junli Wu, Michael Y Galperin, Eugene V Koonin, Kira S Makarova, Yuri I Wolf, Daniel J Rigden, Peter F Dunfield, Lei Wang, Maqsudul Alam Genome Biology 2008, 9:R161 (17 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation.
	Research Proteomics studies confirm the presence of alternative protein isoforms on a large scale Michael L Tress, Bernd Bodenmiller, Ruedi Aebersold, Alfonso Valencia Genome Biology 2008, 9:R162 (18 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Stably expressed alternatively-spliced protein isoforms are produced on a genome-wide scale in Drosophila.
	Research Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases Eri Fukuda, Katarzyna H Kaminska, Janusz M Bujnicki, Ichizo Kobayashi Genome Biology 2008, 9:R163 (21 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The McrBC methyl-specific deoxyribonuclease from Escherichia coli can respond to genome methylation by host killing.
	Research Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata Gaëlle Lelandais, Véronique Tanty, Colette Geneix, Catherine Etchebest, Claude Jacq, Frédéric Devaux Genome Biology 2008, 9:R164 (24 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative transcriptomics of Saccharomyces cerevisiae and Candida glabrata revealed a remarkable conservation of response to drug-induced stress, despite underlying differences in the regulatory networks.
	Research Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip Shilpi Arora, Yipeng Wang, Zhenyu Jia, Saynur Vardar-Sengul, Ayla Munawar, Kutbuddin S Doctor, Michael Birrer, Michael McClelland, Eileen Adamson, Dan Mercola Genome Biology 2008, 9:R166 (25 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary UV stimulation of prostate cells causes an apoptotic response that is dependent on the zinc finger transcription factor Egr1; downstream targets of Egr1 in this response were identified.
	Research Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment Anna Shevchenko, Assen Roguev, Daniel Schaft, Luke Buchanan, Bianca Habermann, Cagri Sakalar, Henrik Thomas, Nevan J Krogan, Andrej Shevchenko, A Francis Stewart Genome Biology 2008, 9:R167 (28 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High resolution mapping of the proteomic environment and proteomic hyperlinks in fission and budding yeast reveals that divergent hyperlinks are due to gene duplications.
	Method Whole genome transcriptome polymorphisms in Arabidopsis thaliana Xu Zhang, Jake K Byrnes, Thomas S Gal, Wen-Hsiung Li, Justin O Borevitz Genome Biology 2008, 9:R165 (24 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New methods for detecting global patterns of gene expression and splicing variation in natural Arabidopsis thaliana populations.
	Software ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets Patrick J Killion, Vishwanath R Iyer Genome Biology 2008, 9:R159 (12 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics.
	Correspondence
	Correspondence Do we use the appropriate controls for the identification of informative methylation markers for early cancer detection? Yasser Riazalhosseini, Jörg D Hoheisel Genome Biology 2008, 9:405 (26 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary It is possible to miss potential DNA methylation markers of tumorigenesis because profiling results are initially filtered on the basis of inappropriate controls.

	Volume 9 Issue 11
	Comment
	Comment The wisdom, and madness, of crowds Gregory A Petsko Genome Biology 2008, 9:112 (1 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A 19th-century Scottish poet has a message for our times.
	Review
	Protein family review The Hedgehog protein family Thomas R Bürglin Genome Biology 2008, 9:241 (19 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hedgehog proteins, which are important in developmental signaling, have been joined by other newly discovered proteins from throughout the eukaryotes in the Hint-domain-containing group of proteins.
	Minireview Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis Robert P Zinzen, Eileen EM Furlong Genome Biology 2008, 9:240 (4 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Significant differences between species in genomic occupancy of conserved transcription factors are mostly due to species-specificity of cis-regulatory sequences.
	Minireview Network-based approaches for linking metabolism with environment Sarath Janga, M Madan Babu Genome Biology 2008, 9:239 (24 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide metabolic maps allow the development of network-based computational approaches for linking an organism with its biochemical habitat.
	Report
	Meeting report A new era for proteomics research? Mathias Uhlen Genome Biology 2008, 9:325 (4 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 7th Annual Human Proteome Organization (HUPO) Conference, Amsterdam, the Netherlands, 16-20 August 2008.
	Meeting report From sequence to structure to networks Nir Yosef, Lukas Käll Genome Biology 2008, 9:326 (4 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 7th European Conference on Computational Biology (ECCB), Cagliari, Italy, 22-26 September 2008.
	Meeting report Bacterial networking Kathleen Marchal, Sigrid CJ De Keersmaecker Genome Biology 2008, 9:327 (12 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the ESF-EMBO Symposium Bacterial Networks (BacNet08), Sant Feliu de Guixols, Spain, 13-18 September 2008.
	Research
	Research A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans Mircea Podar, Iain Anderson, Kira S Makarova, James G Elkins, Natalia Ivanova, Mark A Wall, Athanasios Lykidis, Kostantinos Mavromatis, Hui Sun, Matthew E Hudson, Wenqiong Chen, Cosmin Deciu, Don Hutchison, Jonathan R Eads, Abraham Anderson, Fillipe Fernandes, Ernest Szeto, Alla Lapidus, Nikos C Kyrpides, Milton H Saier, Paul M Richardson, Reinhard Rachel, Harald Huber, Jonathan A Eisen, Eugene V Koonin, Martin Keller, Karl O Stetter Genome Biology 2008, 9:R158 (10 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of the complete genome of Ignicoccus hospitalis gives insight into its association with another species of Archaea, Nanoarchaeum equitans.
	Research Characterization of the differentially methylated region of the Impact gene that exhibits Glires-specific imprinting Kohji Okamura, Richard F Wintle, Stephen W Scherer Genome Biology 2008, 9:R160 (13 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomic analysis of the Impact locus, which is imprinted in Glires but not in other mammals, reveals features required for genomic imprinting.
	Research Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1 Jimmy H Saw, Bruce W Mountain, Lu Feng, Marina V Omelchenko, Shaobin Hou, Jennifer A Saito, Matthew B Stott, Dan Li, Guang Zhao, Junli Wu, Michael Y Galperin, Eugene V Koonin, Kira S Makarova, Yuri I Wolf, Daniel J Rigden, Peter F Dunfield, Lei Wang, Maqsudul Alam Genome Biology 2008, 9:R161 (17 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation.
	Research Proteomics studies confirm the presence of alternative protein isoforms on a large scale Michael L Tress, Bernd Bodenmiller, Ruedi Aebersold, Alfonso Valencia Genome Biology 2008, 9:R162 (18 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Stably expressed alternatively-spliced protein isoforms are produced on a genome-wide scale in Drosophila.
	Research Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases Eri Fukuda, Katarzyna H Kaminska, Janusz M Bujnicki, Ichizo Kobayashi Genome Biology 2008, 9:R163 (21 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The McrBC methyl-specific deoxyribonuclease from Escherichia coli can respond to genome methylation by host killing.
	Research Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata Gaëlle Lelandais, Véronique Tanty, Colette Geneix, Catherine Etchebest, Claude Jacq, Frédéric Devaux Genome Biology 2008, 9:R164 (24 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative transcriptomics of Saccharomyces cerevisiae and Candida glabrata revealed a remarkable conservation of response to drug-induced stress, despite underlying differences in the regulatory networks.
	Research Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip Shilpi Arora, Yipeng Wang, Zhenyu Jia, Saynur Vardar-Sengul, Ayla Munawar, Kutbuddin S Doctor, Michael Birrer, Michael McClelland, Eileen Adamson, Dan Mercola Genome Biology 2008, 9:R166 (25 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary UV stimulation of prostate cells causes an apoptotic response that is dependent on the zinc finger transcription factor Egr1; downstream targets of Egr1 in this response were identified.
	Research Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment Anna Shevchenko, Assen Roguev, Daniel Schaft, Luke Buchanan, Bianca Habermann, Cagri Sakalar, Henrik Thomas, Nevan J Krogan, Andrej Shevchenko, A Francis Stewart Genome Biology 2008, 9:R167 (28 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High resolution mapping of the proteomic environment and proteomic hyperlinks in fission and budding yeast reveals that divergent hyperlinks are due to gene duplications.
	Method Whole genome transcriptome polymorphisms in Arabidopsis thaliana Xu Zhang, Jake K Byrnes, Thomas S Gal, Wen-Hsiung Li, Justin O Borevitz Genome Biology 2008, 9:R165 (24 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New methods for detecting global patterns of gene expression and splicing variation in natural Arabidopsis thaliana populations.
	Software ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets Patrick J Killion, Vishwanath R Iyer Genome Biology 2008, 9:R159 (12 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics.
	Correspondence
	Correspondence Do we use the appropriate controls for the identification of informative methylation markers for early cancer detection? Yasser Riazalhosseini, Jörg D Hoheisel Genome Biology 2008, 9:405 (26 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary It is possible to miss potential DNA methylation markers of tumorigenesis because profiling results are initially filtered on the basis of inappropriate controls.

Explore Genome Biology

Articles

Volume 9 Issue 11

Comment

Review

Report

Research

Correspondence