Genome Biology | Volume 8 Issue 1

Submit a manuscript Register Follow us on

Explore Genome Biology

Articles

	Volume 8 Issue 1
	Comment
	Comment Jumping the shark Gregory A Petsko Genome Biology 2007, 8:101 (31 January 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In popular-culture, 'jumping the shark' refers to an abandoning of core values in an attempt to appeal to dwindling audiences, a metaphor that might be reasonably be applied to some areas of genomics-based research.
	Opinion Genome re-annotation: a wiki solution? Steven L Salzberg Genome Biology 2007, 8:102 (1 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome annotation currently tends to represent a static snapshot. Routine re-annotation, perhaps using wiki software, would help.
	Review
	Minireview Analysis of genetic systems using experimental evolution and whole-genome sequencing Matthew Hegreness, Roy Kishony Genome Biology 2007, 8:201 (1 February 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Whole-genome sequencing of bacteria evolving in the laboratory promises to reveal the complex network of mutations that underlie adaptation.
	Minireview Signaling netwErks get the global treatment Michael B Yaffe, Forest M White Genome Biology 2007, 8:202 (1 February 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two landmark analyses of signaling networks by RNAi and phosphoproteomics provide complementary snapshots of the phosphoproteome.
	Report
	Meeting report The intelligence in developing systems for molecular biology S Cenk Sahinalp Genome Biology 2007, 8:301 (31 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 6-10 August 2006.
	Research
	Research Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons Qian-fei Wang, Shyam Prabhakar, Sumita Chanan, Jan-Fang Cheng, Edward M Rubin, Dario Boffelli Genome Biology 2007, 8:R1 (3 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Intra-primate genome comparisons identify functional modules that are undetected by comparisons with non-mammalian genomes.
	Research Update of the Anopheles gambiae PEST genome assembly Maria V Sharakhova, Martin P Hammond, Neil F Lobo, Jaroslaw Krzywinski, Maria F Unger, Maureen E Hillenmeyer, Robert V Bruggner, Ewan Birney, Frank H Collins Genome Biology 2007, 8:R5 (8 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An update on the Anopheles gambiae PEST genome assembly places about 33% of previously unmapped sequences on the chromosomes.
	Research Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis Rodrigo A Gutiérrez, Laurence V Lejay, Alexis Dean, Francesca Chiaromonte, Dennis E Shasha, Gloria M Coruzzi Genome Biology 2007, 8:R7 (11 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis and indicate that regulation by carbon/nitrogen metabolites occurs at multiple levels.
	Research Sequential gene profiling of basal cell carcinomas treated with imiquimod in a placebo-controlled study defines the requirements for tissue rejection Monica C Panelli, Mitchell E Stashower, Herbert B Slade, Kina Smith, Christopher Norwood, Andrea Abati, Patricia Fetsch, Armando Filie, Shelley-Ann Walters, Calvin Astry, Eleonora Aricó, Yingdong Zhao, Silvia Selleri, Ena Wang, Francesco M Marincola Genome Biology 2007, 8:R8 (15 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of basal cell carcinoma subjected to local application of imiquimod revealed that most transcripts stimulated by imiquimod involve the activation of cellular innate and adaptive immune-effector mechanisms.
	Research Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila Yongsheng Bai, Claudio Casola, Cédric Feschotte, Esther Betrán Genome Biology 2007, 8:R11 (18 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome comparisons between 12 Drosophila species elucidate the origins of retroposition events that have led to the emergence of candidate functional genes.
	Research Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling Adrian Liston, Kristine Hardy, Yvonne Pittelkow, Susan R Wilson, Lydia E Makaroff, Aude M Fahrer, Christopher C Goodnow Genome Biology 2007, 8:R12 (21 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcription profiling study, together with genetic linkage data, provides a molecular map of the T-cell negative selection response in vivo.
	Research Creating a honey bee consensus gene set Christine G Elsik, Aaron J Mackey, Justin T Reese, Natalia V Milshina, David S Roos, George M Weinstock Genome Biology 2007, 8:R13 (22 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-quality consensus gene set for the honey bee (Apis mellifera) created using a new algorithm (GLEAN) is described.
	Research Differential gene expression patterns in cyclooxygenase-1 and cyclooxygenase-2 deficient mouse brain Christopher D Toscano, Vinaykumar V Prabhu, Robert Langenbach, Kevin G Becker, Francesca Bosetti Genome Biology 2007, 8:R14 (31 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis of gene expression in the cerebral cortex and hippocampus of mice deficient in cyclooxygenase-1 or cyclooxygenase-2 reveals that the two enzymes differentially modulate brain gene expression.
	Method Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes Alicia Oshlack, Dianne Emslie, Lynn M Corcoran, Gordon K Smyth Genome Biology 2007, 8:R2 (4 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new normalization method is described for use in specialized boutique arrays which contain a subset of genes selected to test particular biological functions.
	Method Clustering of genes into regulons using integrated modeling-COGRIM Guang Chen, Shane T Jensen, Christian J Stoeckert Genome Biology 2007, 8:R4 (4 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary COGRIM, an implementation that integrates gene expression, ChIP binding and transcription factor motif data, is described and applied to both unicellular and mammalian organisms.
	Method An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invicta John Wang, Stephanie Jemielity, Paolo Uva, Yannick Wurm, Johannes Gräff, Laurent Keller Genome Biology 2007, 8:R9 (15 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An annotated EST resource for the fire ant Solenopsis invicta containing 21,715 ESTs, which represent 11,864 putatively different transcripts, and a corresponding cDNA microarray are described.
	Method Prediction of effective genome size in metagenomic samples Jeroen Raes, Jan O Korbel, Martin J Lercher, Christian von Mering, Peer Bork Genome Biology 2007, 8:R10 (15 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel computational approach shows a link between genome size and habitat from analysis of environmental metagenomic DNA reads.
	Software GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo, Alberto Pascual-Montano Genome Biology 2007, 8:R3 (4 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GENECODIS, a web-based tool for finding annotations that frequently co-occur in a set of genes and ranking them by their statistical significance, is presented.
	Software DiscoverySpace: an interactive data analysis application Neil Robertson, Mehrdad Oveisi-Fordorei, Scott D Zuyderduyn, Richard J Varhol, Christopher Fjell, Marco Marra, Steven Jones, Asim Siddiqui Genome Biology 2007, 8:R6 (8 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DiscoverySpace, a graphical application for bioinformatics data analysis, in particular analysis of SAGE data, is described
	Correspondence
	Correction Correction: 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 De Paepe, Geneviève Laureys, Sven Påhlman, Frank Speleman Genome Biology 2007, 8:401 (31 January 2007) Abstract \| Full text \| PDF

	Volume 8 Issue 1
	Comment
	Comment Jumping the shark Gregory A Petsko Genome Biology 2007, 8:101 (31 January 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In popular-culture, 'jumping the shark' refers to an abandoning of core values in an attempt to appeal to dwindling audiences, a metaphor that might be reasonably be applied to some areas of genomics-based research.
	Opinion Genome re-annotation: a wiki solution? Steven L Salzberg Genome Biology 2007, 8:102 (1 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome annotation currently tends to represent a static snapshot. Routine re-annotation, perhaps using wiki software, would help.
	Review
	Minireview Analysis of genetic systems using experimental evolution and whole-genome sequencing Matthew Hegreness, Roy Kishony Genome Biology 2007, 8:201 (1 February 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Whole-genome sequencing of bacteria evolving in the laboratory promises to reveal the complex network of mutations that underlie adaptation.
	Minireview Signaling netwErks get the global treatment Michael B Yaffe, Forest M White Genome Biology 2007, 8:202 (1 February 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two landmark analyses of signaling networks by RNAi and phosphoproteomics provide complementary snapshots of the phosphoproteome.
	Report
	Meeting report The intelligence in developing systems for molecular biology S Cenk Sahinalp Genome Biology 2007, 8:301 (31 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 6-10 August 2006.
	Research
	Research Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons Qian-fei Wang, Shyam Prabhakar, Sumita Chanan, Jan-Fang Cheng, Edward M Rubin, Dario Boffelli Genome Biology 2007, 8:R1 (3 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Intra-primate genome comparisons identify functional modules that are undetected by comparisons with non-mammalian genomes.
	Research Update of the Anopheles gambiae PEST genome assembly Maria V Sharakhova, Martin P Hammond, Neil F Lobo, Jaroslaw Krzywinski, Maria F Unger, Maureen E Hillenmeyer, Robert V Bruggner, Ewan Birney, Frank H Collins Genome Biology 2007, 8:R5 (8 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An update on the Anopheles gambiae PEST genome assembly places about 33% of previously unmapped sequences on the chromosomes.
	Research Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis Rodrigo A Gutiérrez, Laurence V Lejay, Alexis Dean, Francesca Chiaromonte, Dennis E Shasha, Gloria M Coruzzi Genome Biology 2007, 8:R7 (11 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis and indicate that regulation by carbon/nitrogen metabolites occurs at multiple levels.
	Research Sequential gene profiling of basal cell carcinomas treated with imiquimod in a placebo-controlled study defines the requirements for tissue rejection Monica C Panelli, Mitchell E Stashower, Herbert B Slade, Kina Smith, Christopher Norwood, Andrea Abati, Patricia Fetsch, Armando Filie, Shelley-Ann Walters, Calvin Astry, Eleonora Aricó, Yingdong Zhao, Silvia Selleri, Ena Wang, Francesco M Marincola Genome Biology 2007, 8:R8 (15 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of basal cell carcinoma subjected to local application of imiquimod revealed that most transcripts stimulated by imiquimod involve the activation of cellular innate and adaptive immune-effector mechanisms.
	Research Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila Yongsheng Bai, Claudio Casola, Cédric Feschotte, Esther Betrán Genome Biology 2007, 8:R11 (18 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome comparisons between 12 Drosophila species elucidate the origins of retroposition events that have led to the emergence of candidate functional genes.
	Research Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling Adrian Liston, Kristine Hardy, Yvonne Pittelkow, Susan R Wilson, Lydia E Makaroff, Aude M Fahrer, Christopher C Goodnow Genome Biology 2007, 8:R12 (21 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcription profiling study, together with genetic linkage data, provides a molecular map of the T-cell negative selection response in vivo.
	Research Creating a honey bee consensus gene set Christine G Elsik, Aaron J Mackey, Justin T Reese, Natalia V Milshina, David S Roos, George M Weinstock Genome Biology 2007, 8:R13 (22 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-quality consensus gene set for the honey bee (Apis mellifera) created using a new algorithm (GLEAN) is described.
	Research Differential gene expression patterns in cyclooxygenase-1 and cyclooxygenase-2 deficient mouse brain Christopher D Toscano, Vinaykumar V Prabhu, Robert Langenbach, Kevin G Becker, Francesca Bosetti Genome Biology 2007, 8:R14 (31 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis of gene expression in the cerebral cortex and hippocampus of mice deficient in cyclooxygenase-1 or cyclooxygenase-2 reveals that the two enzymes differentially modulate brain gene expression.
	Method Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes Alicia Oshlack, Dianne Emslie, Lynn M Corcoran, Gordon K Smyth Genome Biology 2007, 8:R2 (4 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new normalization method is described for use in specialized boutique arrays which contain a subset of genes selected to test particular biological functions.
	Method Clustering of genes into regulons using integrated modeling-COGRIM Guang Chen, Shane T Jensen, Christian J Stoeckert Genome Biology 2007, 8:R4 (4 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary COGRIM, an implementation that integrates gene expression, ChIP binding and transcription factor motif data, is described and applied to both unicellular and mammalian organisms.
	Method An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invicta John Wang, Stephanie Jemielity, Paolo Uva, Yannick Wurm, Johannes Gräff, Laurent Keller Genome Biology 2007, 8:R9 (15 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An annotated EST resource for the fire ant Solenopsis invicta containing 21,715 ESTs, which represent 11,864 putatively different transcripts, and a corresponding cDNA microarray are described.
	Method Prediction of effective genome size in metagenomic samples Jeroen Raes, Jan O Korbel, Martin J Lercher, Christian von Mering, Peer Bork Genome Biology 2007, 8:R10 (15 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel computational approach shows a link between genome size and habitat from analysis of environmental metagenomic DNA reads.
	Software GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo, Alberto Pascual-Montano Genome Biology 2007, 8:R3 (4 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GENECODIS, a web-based tool for finding annotations that frequently co-occur in a set of genes and ranking them by their statistical significance, is presented.
	Software DiscoverySpace: an interactive data analysis application Neil Robertson, Mehrdad Oveisi-Fordorei, Scott D Zuyderduyn, Richard J Varhol, Christopher Fjell, Marco Marra, Steven Jones, Asim Siddiqui Genome Biology 2007, 8:R6 (8 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DiscoverySpace, a graphical application for bioinformatics data analysis, in particular analysis of SAGE data, is described
	Correspondence
	Correction Correction: 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 De Paepe, Geneviève Laureys, Sven Påhlman, Frank Speleman Genome Biology 2007, 8:401 (31 January 2007) Abstract \| Full text \| PDF

Explore Genome Biology

Articles

Volume 8 Issue 1

Comment

Review

Report

Research

Correspondence