Genome Biology | Volume 7 Issue 4

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 7 Issue 4
	Comment
	Comment Instructions for repair Gregory A Petsko Genome Biology 2006, 7:106 (28 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Peer review is the foundation quality in science, but now, in the US, the system is broken. What's the best way to fix things.
	Review
	Review Plant NBS-LRR proteins: adaptable guards Leah McHale, Xiaoping Tan, Patrice Koehl, Richard W Michelmore Genome Biology 2006, 7:212 (26 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Plant nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins are a large family involved in disease resistance; they may monitor the status of proteins targeted by pathogens.
	Minireview Getting to synaptic complexes through systems biology Bryen A Jordan, Edward B Ziff Genome Biology 2006, 7:214 (27 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A systems biology approach using network maps and annotated functions of synaptic components has identified biologically relevant networks within a synaptic neurotransmitter receptor complex.
	Minireview TANGOing along the protein secretion pathway Catherine Rabouille, Vangelis Kondylis Genome Biology 2006, 7:213 (28 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An RNAi screen in Drosophila cells has identified about 100 TANGO proteins, which may regulate protein exocytosis or secretion.
	Minireview Circadian rhythms lit up in Chlamydomonas Ghislain Breton, Steve A Kay Genome Biology 2006, 7:215 (28 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A high-throughput luciferase-based assay for circadian gene expression gives a boost to the study of circadian rhythms in Chlamydomonas.
	Opinion Metabolic cycle, cell cycle, and the finishing kick to Start Bruce Futcher Genome Biology 2006, 7:107 (26 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two contrasting views of the relation of the metabolic cycle to the cell cycle in budding yeast are compared.
	Report
	Meeting report Shelling out for genomics Timothy S McClintock, Charles D Derby Genome Biology 2006, 7:312 (20 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the symposium 'Genomic and Proteomic Approaches to Crustacean Biology' held as part of the Society for Integrative and Comparative Biology 2006 Annual Meeting, Orlando, USA, 4-8 January 2006.
	Meeting report Signals and systems Nevan J Krogan, Timothy R Hughes Genome Biology 2006, 7:313 (25 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2006 Keystone Conference on Signaling Networks, Vancouver, Canada, 30 January-4 February 2006.
	Meeting report Cancer and kinases: reports from the front line Stephen K Burley Genome Biology 2006, 7:314 (25 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Keystone Symposium 'Cancer and Kinases: Lessons from the Clinic', Santa Fe, USA, 14-19 February 2006.
	Research
	Research RNA editing of human microRNAs Matthew J Blow, Russell J Grocock, Stijn van Dongen, Anton J Enright, Ed Dicks, P Andrew Futreal, Richard Wooster, Michael R Stratton Genome Biology 2006, 7:R27 (4 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of RNA editing of miRNAs from ten human tissues indicates that RNA editing increases the diversity of miRNAs and their targets.
	Research Genes regulated by estrogen in breast tumor cells in vitro are similarly regulated in vivo in tumor xenografts and human breast tumors Chad J Creighton, Kevin E Cordero, Jose M Larios, Rebecca S Miller, Michael D Johnson, Arul M Chinnaiyan, Marc E Lippman, James M Rae Genome Biology 2006, 7:R28 (7 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Estrogen-regulated gene expression profiles of in vivo breast tumor cell lines and in vitro xenografts and breast tumors are remarkably similar.
	Research Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins Jay R Hesselberth, John P Miller, Anna Golob, Jason E Stajich, Gregory A Michaud, Stanley Fields Genome Biology 2006, 7:R30 (10 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A protein interaction map for 12 of the 13 WW domains present in the proteins of S. cerevisiae was generated by using protein microarray data.
	Research Benchmarking ortholog identification methods using functional genomics data Tim Hulsen, Martijn A Huynen, Jacob de Vlieg, Peter MA Groenen Genome Biology 2006, 7:R31 (13 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A benchmarking of the most popular orthologous identification methods using functional genomics data identifies the two best methods.
	Research Mutation patterns of amino acid tandem repeats in the human proteome Loris Mularoni, Roderic Guigó, M Mar Albà Genome Biology 2006, 7:R33 (26 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide report on the types of mutations occurring in amino acid repeats of human proteins shows that the mutational dynamics of different types of repeats are very diverse.
	Research The genome of Rhizobium leguminosarum has recognizable core and accessory components J Peter W Young, Lisa C Crossman, Andrew WB Johnston, Nicholas R Thomson, Zara F Ghazoui, Katherine H Hull, Margaret Wexler, Andrew RJ Curson, Jonathan D Todd, Philip S Poole, Tim H Mauchline, Alison K East, Michael A Quail, Carol Churcher, Claire Arrowsmith, Inna Cherevach, Tracey Chillingworth, Kay Clarke, Ann Cronin, Paul Davis, Audrey Fraser, Zahra Hance, Heidi Hauser, Kay Jagels, Sharon Moule, Karen Mungall, Halina Norbertczak, Ester Rabbinowitsch, Mandy Sanders, Mark Simmonds, Sally Whitehead, Julian Parkhill et al. Genome Biology 2006, 7:R34 (26 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the α-proteobacterial N2-fixing symbiont of legumes, Rhizobium leguminosarum, is described, revealing a 'core' and an 'accessory' component.
	Research Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics Damian Fermin, Baxter B Allen, Thomas W Blackwell, Rajasree Menon, Marcin Adamski, Yin Xu, Peter Ulintz, Gilbert S Omenn, David J States Genome Biology 2006, 7:R35 (28 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-throughput mass spectroscopy data combined with a six-frame translation of the human genome can be used to identify novel protein encoding genes, as demonstrated with a search for plasma proteins.
	Method A classification based framework for quantitative description of large-scale microarray data Dipen P Sangurdekar, Friedrich Srienc, Arkady B Khodursky Genome Biology 2006, 7:R32 (20 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new classification-based framework is presented that allows quantitative description of microarray data in terms of significance of co-expression within any gene group and condition-specific gene class activity.
	Software Reference based annotation with GeneMapper Sourav Chatterji, Lior Pachter Genome Biology 2006, 7:R29 (5 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GeneMapper, a new program for transferring annotations from a well-annotated reference genome to other genomes, is described.

	Volume 7 Issue 4
	Comment
	Comment Instructions for repair Gregory A Petsko Genome Biology 2006, 7:106 (28 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Peer review is the foundation quality in science, but now, in the US, the system is broken. What's the best way to fix things.
	Review
	Review Plant NBS-LRR proteins: adaptable guards Leah McHale, Xiaoping Tan, Patrice Koehl, Richard W Michelmore Genome Biology 2006, 7:212 (26 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Plant nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins are a large family involved in disease resistance; they may monitor the status of proteins targeted by pathogens.
	Minireview Getting to synaptic complexes through systems biology Bryen A Jordan, Edward B Ziff Genome Biology 2006, 7:214 (27 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A systems biology approach using network maps and annotated functions of synaptic components has identified biologically relevant networks within a synaptic neurotransmitter receptor complex.
	Minireview TANGOing along the protein secretion pathway Catherine Rabouille, Vangelis Kondylis Genome Biology 2006, 7:213 (28 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An RNAi screen in Drosophila cells has identified about 100 TANGO proteins, which may regulate protein exocytosis or secretion.
	Minireview Circadian rhythms lit up in Chlamydomonas Ghislain Breton, Steve A Kay Genome Biology 2006, 7:215 (28 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A high-throughput luciferase-based assay for circadian gene expression gives a boost to the study of circadian rhythms in Chlamydomonas.
	Opinion Metabolic cycle, cell cycle, and the finishing kick to Start Bruce Futcher Genome Biology 2006, 7:107 (26 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two contrasting views of the relation of the metabolic cycle to the cell cycle in budding yeast are compared.
	Report
	Meeting report Shelling out for genomics Timothy S McClintock, Charles D Derby Genome Biology 2006, 7:312 (20 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the symposium 'Genomic and Proteomic Approaches to Crustacean Biology' held as part of the Society for Integrative and Comparative Biology 2006 Annual Meeting, Orlando, USA, 4-8 January 2006.
	Meeting report Signals and systems Nevan J Krogan, Timothy R Hughes Genome Biology 2006, 7:313 (25 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2006 Keystone Conference on Signaling Networks, Vancouver, Canada, 30 January-4 February 2006.
	Meeting report Cancer and kinases: reports from the front line Stephen K Burley Genome Biology 2006, 7:314 (25 April 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Keystone Symposium 'Cancer and Kinases: Lessons from the Clinic', Santa Fe, USA, 14-19 February 2006.
	Research
	Research RNA editing of human microRNAs Matthew J Blow, Russell J Grocock, Stijn van Dongen, Anton J Enright, Ed Dicks, P Andrew Futreal, Richard Wooster, Michael R Stratton Genome Biology 2006, 7:R27 (4 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of RNA editing of miRNAs from ten human tissues indicates that RNA editing increases the diversity of miRNAs and their targets.
	Research Genes regulated by estrogen in breast tumor cells in vitro are similarly regulated in vivo in tumor xenografts and human breast tumors Chad J Creighton, Kevin E Cordero, Jose M Larios, Rebecca S Miller, Michael D Johnson, Arul M Chinnaiyan, Marc E Lippman, James M Rae Genome Biology 2006, 7:R28 (7 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Estrogen-regulated gene expression profiles of in vivo breast tumor cell lines and in vitro xenografts and breast tumors are remarkably similar.
	Research Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins Jay R Hesselberth, John P Miller, Anna Golob, Jason E Stajich, Gregory A Michaud, Stanley Fields Genome Biology 2006, 7:R30 (10 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A protein interaction map for 12 of the 13 WW domains present in the proteins of S. cerevisiae was generated by using protein microarray data.
	Research Benchmarking ortholog identification methods using functional genomics data Tim Hulsen, Martijn A Huynen, Jacob de Vlieg, Peter MA Groenen Genome Biology 2006, 7:R31 (13 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A benchmarking of the most popular orthologous identification methods using functional genomics data identifies the two best methods.
	Research Mutation patterns of amino acid tandem repeats in the human proteome Loris Mularoni, Roderic Guigó, M Mar Albà Genome Biology 2006, 7:R33 (26 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide report on the types of mutations occurring in amino acid repeats of human proteins shows that the mutational dynamics of different types of repeats are very diverse.
	Research The genome of Rhizobium leguminosarum has recognizable core and accessory components J Peter W Young, Lisa C Crossman, Andrew WB Johnston, Nicholas R Thomson, Zara F Ghazoui, Katherine H Hull, Margaret Wexler, Andrew RJ Curson, Jonathan D Todd, Philip S Poole, Tim H Mauchline, Alison K East, Michael A Quail, Carol Churcher, Claire Arrowsmith, Inna Cherevach, Tracey Chillingworth, Kay Clarke, Ann Cronin, Paul Davis, Audrey Fraser, Zahra Hance, Heidi Hauser, Kay Jagels, Sharon Moule, Karen Mungall, Halina Norbertczak, Ester Rabbinowitsch, Mandy Sanders, Mark Simmonds, Sally Whitehead, Julian Parkhill et al. Genome Biology 2006, 7:R34 (26 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the α-proteobacterial N2-fixing symbiont of legumes, Rhizobium leguminosarum, is described, revealing a 'core' and an 'accessory' component.
	Research Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics Damian Fermin, Baxter B Allen, Thomas W Blackwell, Rajasree Menon, Marcin Adamski, Yin Xu, Peter Ulintz, Gilbert S Omenn, David J States Genome Biology 2006, 7:R35 (28 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-throughput mass spectroscopy data combined with a six-frame translation of the human genome can be used to identify novel protein encoding genes, as demonstrated with a search for plasma proteins.
	Method A classification based framework for quantitative description of large-scale microarray data Dipen P Sangurdekar, Friedrich Srienc, Arkady B Khodursky Genome Biology 2006, 7:R32 (20 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new classification-based framework is presented that allows quantitative description of microarray data in terms of significance of co-expression within any gene group and condition-specific gene class activity.
	Software Reference based annotation with GeneMapper Sourav Chatterji, Lior Pachter Genome Biology 2006, 7:R29 (5 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GeneMapper, a new program for transferring annotations from a well-annotated reference genome to other genomes, is described.

Explore Genome Biology

Articles

Volume 7 Issue 4

Comment

Review

Report

Research