Genome Biology | Volume 5 Issue 7

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	Volume 5 Issue 7
	Comment
	Comment Powerless to stop myself Gregory A Petsko Genome Biology 2004, 5:110 (23 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary With PowerPoint someone with a machine can accomplish in a week what it used to take a human laborer a day to do.
	Review
	Review The uses of genome-wide yeast mutant collections Bart Scherens, Andre Goffeau Genome Biology 2004, 5:229 (25 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary We assess five years of usage of the major genome-wide collections of mutants from Saccharomyces cerevisiae.
	Protein family review The Frizzled family: receptors for multiple signal transduction pathways Hui-Chuan Huang, Peter S Klein Genome Biology 2004, 5:234 (14 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Frizzled genes encode integral membrane proteins that function in multiple signal transduction pathways in animals. They are receptors for secreted Wnt proteins, as well as other ligands, and are essential for many processes in developing and adult organisms.
	Minireview Candida albicans genome sequence: a platform for genomics in the absence of genetics Frank C Odds, Alistair JP Brown, Neil AR Gow Genome Biology 2004, 5:230 (11 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparative genomic analysis highlights genes that may contribute to Candida albicans survival and its fitness as a human commensal and pathogen.
	Minireview Unfashionable crop species flourish in the 21st century Wayne Powell, Peter Langridge Genome Biology 2004, 5:233 (14 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In wheat, there are now more than 500,000 expressed sequence tags, and these are being used in conjunction with specially designed deletion stocks to unravel patterns of genome evolution, recombination and polyploid genome behavior.
	Minireview Analysis of alternative splicing with microarrays: successes and challenges Christopher Lee, Meenakshi Roy Genome Biology 2004, 5:231 (21 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This article reviews the latest results from the analysis of alternative splicing using DNA microarrays and highlights the current challenges that they have revealed.
	Minireview Cross-species comparison of genome-wide expression patterns Xianghong Zhou, Greg Gibson Genome Biology 2004, 5:232 (21 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent studies have used cross-species comparisons of expression profiles to annotate gene functions, to draw evolutionary inferences concerning specific biological processes and to study the global properties of expression networks.
	Opinion After 'completion': the changing face of human chromosomes 21 and 22 Todd Taylor Genome Biology 2004, 5:111 (30 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In the four years since the publication of the first two 'complete' human chromosome sequences the type of research being done on each has shifted subtly, reflecting the impact of genomic data on biological science in general.
	Report
	Paper report Articles selected by Faculty of 1000: profiling flowers; targeted transgenesis in Drosophila; aging and oxidation in plants; membrane protein localization in E. coli; immune response to siRNAs Genome Biology 2004, 5:335 (9 June 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the profiling of flowers; targeted transgenesis in Drosophila; the aging and oxidation in plants; membrane protein localization in E. coli; immune responses to siRNAs.
	Paper report Articles selected by Faculty of 1000: bacterial ORFans: ORFs with no known homologs; fluorescent marker of histone phosphorylation; genome-wide chromatin analysis; protein macroarrays; clinically relevant Trichomonas variation Genome Biology 2004, 5:336 (18 June 2004) Abstract \| Full text \| Editor’s summary Bacterial ORFans: identifying ORFs with no known homologs; a fluorescent marker of histone phosphorylation; genome-wide chromatin analysis; protein macroarrays; studying clinically relevant Trichomonas variation.
	Meeting report Integrative functional genomics Martha L Bulyk Genome Biology 2004, 5:331 (24 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Keystone Symposium 'Biological Discovery Using Diverse High-Throughput Data', Steamboat Springs, USA, 30 March-4 April 2004.
	Meeting report Cancer, oncogenes and signal transduction Edward J McManus, Dario R Alessi Genome Biology 2004, 5:332 (24 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the European Molecular Biology Laboratory (EMBL) 'Oncogenes and Growth Control' meeting, Heidelberg, Germany, 17-20 April 2004.
	Meeting report Developmental biology reaches new lineages Carolina Minguillon, Malcolm Logan Genome Biology 2004, 5:333 (24 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Developmental Biology Annual Symposium and GENETICS 2004, Warwick, UK, 14-16 March 2004.
	Research news How yeasts evolve Cathy Holding Genome Biology 2004, 5:spotlight-20040702-01 (2 July 2004) Abstract \| Full text \| Editor’s summary The publication of four more genomes confirms the disputed whole genome duplication theory
	Research news New plans for NIMR Pat Hagan Genome Biology 2004, 5:spotlight-20040707-02 (7 July 2004) Abstract \| Full text \| Editor’s summary Task force recommends UK institute join forces with a major London university
	Research news MICER resource saves time Cathy Holding Genome Biology 2004, 5:spotlight-20040707-03 (7 July 2004) Abstract \| Full text \| Editor’s summary Online supply of vector sequences adds to resources available for annotating mouse genome
	Research news Mattaj outlines EMBL goals Ned Stafford Genome Biology 2004, 5:spotlight-20040707-01 (7 July 2004) Abstract \| Full text \| Editor’s summary Director general designate of EMBL says a priority is incorporating computational methods
	Research news Evolution of innate immunity Cathy Holding Genome Biology 2004, 5:spotlight-20040709-01 (9 July 2004) Abstract \| Full text \| Editor’s summary Lamprey study shows distinct mechanisms of lymphocyte receptor diversity among vertebrates
	Research news Good news on rotavirus vaccine? Sam Jaffe Genome Biology 2004, 5:spotlight-20040713-01 (13 July 2004) Abstract \| Full text \| Editor’s summary Reanalysis of data shows that many cases of intussusception were unrelated to vaccine
	Research news Ploidy predicts lifestyle Cathy Holding Genome Biology 2004, 5:spotlight-20040714-01 (14 July 2004) Abstract \| Full text \| Editor’s summary A study explores how host-parasite interactions select for genome number
	Research news How worms tackle stress David Secko Genome Biology 2004, 5:spotlight-20040715-01 (15 July 2004) Abstract \| Full text \| Editor’s summary JNK and p38 pathways are used and integrated in response to pathogen stress in C. elegans
	Research news Mutations go tick, tock Cathy Holding Genome Biology 2004, 5:spotlight-20040721-02 (21 July 2004) Abstract \| Full text \| Editor’s summary Statistical analysis reveals evidence for molecular clock in neutral DNA substitutions
	Research news UK committee backs open access Stephen Pincock Genome Biology 2004, 5:spotlight-20040721-01 (21 July 2004) Abstract \| Full text \| Editor’s summary Politicians urge the government to insist on free archiving of scientific papers
	Research news Open access to US government work urged Alison McCook Genome Biology 2004, 5:spotlight-20040722-01 (22 July 2004) Abstract \| Full text \| Editor’s summary Publishers argue change could undermine the industry and limit authors' options
	Research news Chagas parasite invades genome David Secko Genome Biology 2004, 5:spotlight-20040726-01 (26 July 2004) Abstract \| Full text \| Editor’s summary Typanosoma cruzi kinetoplast DNA found in the genomes of infected patients and animals
	Research news Epigenetic switch for Igf2 Cathy Holding Genome Biology 2004, 5:spotlight-20040728-01 (28 July 2004) Abstract \| Full text \| Editor’s summary Data supports model for looping mechanism governing long-distance interactions
	Research news Francis Crick dies Pete Moore Genome Biology 2004, 5:spotlight-20040730-01 (30 July 2004) Abstract \| Full text \| Editor’s summary The master of science and arguably the founder of molecular biology was 88
	Research news Bacterial proteins on the move Charles Q Choi Genome Biology 2004, 5:spotlight-20050705-01 (5 July 2005) Abstract \| Full text \| Editor’s summary Cell surface materials passed via direct contact can restart the engines of stalled myxococci
	Research news How epigenetics affects twins Charles Q Choi Genome Biology 2004, 5:spotlight-20050708-02 (8 July 2005) Abstract \| Full text \| Editor’s summary In genetically identical siblings, DNA methylation and histone acetylation correlate with age and lifestyle
	Research news Rat olfaction molded early Graciela Flores Genome Biology 2004, 5:spotlight-20050708-01 (8 July 2005) Abstract \| Full text \| Editor’s summary Study in newborn rodents shows how first exposure to smells alters synaptic development
	Research news How mtDNA mutations cause aging Charles Q Choi Genome Biology 2004, 5:spotlight-20050718-01 (18 July 2005) Abstract \| Full text \| Editor’s summary Apoptosis, not oxidative damage from free radicals, drives process, according to Science study
	Research news Did bitter tasters do better? Ishani Ganguli Genome Biology 2004, 5:spotlight-20050727-01 (27 July 2005) Abstract \| Full text \| Editor’s summary Genetic clues suggest distinguishing bitter natural toxins was advantageous in human evolution
	Research
	Research Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana G Marais, B Charlesworth, S I Wright Genome Biology 2004, 5:R45 (14 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The effects of recombination and self-fertilization on base composition were investigated both theoretically and experimentally in the Arabidopsis genome. Levels of inbreeding modulate the effect of recombination on base composition.
	Research Tissue-specific spatial organization of genomes Luis A Parada, Philip G McQueen, Tom Misteli Genome Biology 2004, 5:R44 (21 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of the spatial positioning of a subset of mouse chromosomes reveals that chromosomes exhibit tissue-specific organization in the nucleus.
	Research Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes Hui Huang, Eitan E Winter, Huajun Wang, Keith G Weinstock, Heming Xing, Leo Goodstadt, Peter D Stenson, David N Cooper, Douglas Smith, M Mar Albà, Chris P Ponting, Kim Fechtel Genome Biology 2004, 5:R47 (28 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change. Rodent orthologs of human trinucleotide repeat-expansion disease genes were also found to contain substantially fewer such repeats.
	Research From co-expression to co-regulation: how many microarray experiments do we need? Ka Yeung, Mario Medvedovic, Roger E Bumgarner Genome Biology 2004, 5:R48 (28 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The ability to identify co-regulated genes from microarray clustering results is strongly dependent on the number of microarray experiments used in cluster analysis and the accuracy of these associations plateaus at between 50 and 100 experiments on yeast data. Even with large numbers of experiments, the false positive rate may exceed the true positive rate.
	Research Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica Cizhong Jiang, Xun Gu, Thomas Peterson Genome Biology 2004, 5:R46 (29 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Myb genes from Arabidopsis and rice were clustered into subgroups. The distribution of introns in the phylogenetic tree suggests that introns were inserted during evolution.
	Method Detecting DNA regulatory motifs by incorporating positional trends in information content Katherina J Kechris, Erik van Zwet, Peter J Bickel, Michael B Eisen Genome Biology 2004, 5:R50 (24 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, a simple extension to the model-based motif discovery method is proposed. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.
	Method Systematic quantification of gene interactions by phenotypic array analysis John L Hartman, Nicholas P Tippery Genome Biology 2004, 5:R49 (29 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A phenotypic array method, developed for quantifying cell growth, was applied to the haploid and homozygous diploid yeast deletion strain sets. A growth index was developed to screen for non-additive interacting effects between gene deletion and induced perturbations.
	Method Clustering analysis of SAGE data using a Poisson approach Li Cai, Haiyan Huang, Seth Blackshaw, Jun S Liu, Connie Cepko, Wing H Wong Genome Biology 2004, 5:R51 (29 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two Poisson-based distances were developed for SAGE data; their application to simulated and experimental mouse retina data show that they are more appropriate and reliable for analyzing SAGE data than other commonly used distances or similarity measures.

	Volume 5 Issue 7
	Comment
	Comment Powerless to stop myself Gregory A Petsko Genome Biology 2004, 5:110 (23 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary With PowerPoint someone with a machine can accomplish in a week what it used to take a human laborer a day to do.
	Review
	Review The uses of genome-wide yeast mutant collections Bart Scherens, Andre Goffeau Genome Biology 2004, 5:229 (25 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary We assess five years of usage of the major genome-wide collections of mutants from Saccharomyces cerevisiae.
	Protein family review The Frizzled family: receptors for multiple signal transduction pathways Hui-Chuan Huang, Peter S Klein Genome Biology 2004, 5:234 (14 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Frizzled genes encode integral membrane proteins that function in multiple signal transduction pathways in animals. They are receptors for secreted Wnt proteins, as well as other ligands, and are essential for many processes in developing and adult organisms.
	Minireview Candida albicans genome sequence: a platform for genomics in the absence of genetics Frank C Odds, Alistair JP Brown, Neil AR Gow Genome Biology 2004, 5:230 (11 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparative genomic analysis highlights genes that may contribute to Candida albicans survival and its fitness as a human commensal and pathogen.
	Minireview Unfashionable crop species flourish in the 21st century Wayne Powell, Peter Langridge Genome Biology 2004, 5:233 (14 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In wheat, there are now more than 500,000 expressed sequence tags, and these are being used in conjunction with specially designed deletion stocks to unravel patterns of genome evolution, recombination and polyploid genome behavior.
	Minireview Analysis of alternative splicing with microarrays: successes and challenges Christopher Lee, Meenakshi Roy Genome Biology 2004, 5:231 (21 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This article reviews the latest results from the analysis of alternative splicing using DNA microarrays and highlights the current challenges that they have revealed.
	Minireview Cross-species comparison of genome-wide expression patterns Xianghong Zhou, Greg Gibson Genome Biology 2004, 5:232 (21 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent studies have used cross-species comparisons of expression profiles to annotate gene functions, to draw evolutionary inferences concerning specific biological processes and to study the global properties of expression networks.
	Opinion After 'completion': the changing face of human chromosomes 21 and 22 Todd Taylor Genome Biology 2004, 5:111 (30 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In the four years since the publication of the first two 'complete' human chromosome sequences the type of research being done on each has shifted subtly, reflecting the impact of genomic data on biological science in general.
	Report
	Paper report Articles selected by Faculty of 1000: profiling flowers; targeted transgenesis in Drosophila; aging and oxidation in plants; membrane protein localization in E. coli; immune response to siRNAs Genome Biology 2004, 5:335 (9 June 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the profiling of flowers; targeted transgenesis in Drosophila; the aging and oxidation in plants; membrane protein localization in E. coli; immune responses to siRNAs.
	Paper report Articles selected by Faculty of 1000: bacterial ORFans: ORFs with no known homologs; fluorescent marker of histone phosphorylation; genome-wide chromatin analysis; protein macroarrays; clinically relevant Trichomonas variation Genome Biology 2004, 5:336 (18 June 2004) Abstract \| Full text \| Editor’s summary Bacterial ORFans: identifying ORFs with no known homologs; a fluorescent marker of histone phosphorylation; genome-wide chromatin analysis; protein macroarrays; studying clinically relevant Trichomonas variation.
	Meeting report Integrative functional genomics Martha L Bulyk Genome Biology 2004, 5:331 (24 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Keystone Symposium 'Biological Discovery Using Diverse High-Throughput Data', Steamboat Springs, USA, 30 March-4 April 2004.
	Meeting report Cancer, oncogenes and signal transduction Edward J McManus, Dario R Alessi Genome Biology 2004, 5:332 (24 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the European Molecular Biology Laboratory (EMBL) 'Oncogenes and Growth Control' meeting, Heidelberg, Germany, 17-20 April 2004.
	Meeting report Developmental biology reaches new lineages Carolina Minguillon, Malcolm Logan Genome Biology 2004, 5:333 (24 June 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Developmental Biology Annual Symposium and GENETICS 2004, Warwick, UK, 14-16 March 2004.
	Research news How yeasts evolve Cathy Holding Genome Biology 2004, 5:spotlight-20040702-01 (2 July 2004) Abstract \| Full text \| Editor’s summary The publication of four more genomes confirms the disputed whole genome duplication theory
	Research news New plans for NIMR Pat Hagan Genome Biology 2004, 5:spotlight-20040707-02 (7 July 2004) Abstract \| Full text \| Editor’s summary Task force recommends UK institute join forces with a major London university
	Research news MICER resource saves time Cathy Holding Genome Biology 2004, 5:spotlight-20040707-03 (7 July 2004) Abstract \| Full text \| Editor’s summary Online supply of vector sequences adds to resources available for annotating mouse genome
	Research news Mattaj outlines EMBL goals Ned Stafford Genome Biology 2004, 5:spotlight-20040707-01 (7 July 2004) Abstract \| Full text \| Editor’s summary Director general designate of EMBL says a priority is incorporating computational methods
	Research news Evolution of innate immunity Cathy Holding Genome Biology 2004, 5:spotlight-20040709-01 (9 July 2004) Abstract \| Full text \| Editor’s summary Lamprey study shows distinct mechanisms of lymphocyte receptor diversity among vertebrates
	Research news Good news on rotavirus vaccine? Sam Jaffe Genome Biology 2004, 5:spotlight-20040713-01 (13 July 2004) Abstract \| Full text \| Editor’s summary Reanalysis of data shows that many cases of intussusception were unrelated to vaccine
	Research news Ploidy predicts lifestyle Cathy Holding Genome Biology 2004, 5:spotlight-20040714-01 (14 July 2004) Abstract \| Full text \| Editor’s summary A study explores how host-parasite interactions select for genome number
	Research news How worms tackle stress David Secko Genome Biology 2004, 5:spotlight-20040715-01 (15 July 2004) Abstract \| Full text \| Editor’s summary JNK and p38 pathways are used and integrated in response to pathogen stress in C. elegans
	Research news Mutations go tick, tock Cathy Holding Genome Biology 2004, 5:spotlight-20040721-02 (21 July 2004) Abstract \| Full text \| Editor’s summary Statistical analysis reveals evidence for molecular clock in neutral DNA substitutions
	Research news UK committee backs open access Stephen Pincock Genome Biology 2004, 5:spotlight-20040721-01 (21 July 2004) Abstract \| Full text \| Editor’s summary Politicians urge the government to insist on free archiving of scientific papers
	Research news Open access to US government work urged Alison McCook Genome Biology 2004, 5:spotlight-20040722-01 (22 July 2004) Abstract \| Full text \| Editor’s summary Publishers argue change could undermine the industry and limit authors' options
	Research news Chagas parasite invades genome David Secko Genome Biology 2004, 5:spotlight-20040726-01 (26 July 2004) Abstract \| Full text \| Editor’s summary Typanosoma cruzi kinetoplast DNA found in the genomes of infected patients and animals
	Research news Epigenetic switch for Igf2 Cathy Holding Genome Biology 2004, 5:spotlight-20040728-01 (28 July 2004) Abstract \| Full text \| Editor’s summary Data supports model for looping mechanism governing long-distance interactions
	Research news Francis Crick dies Pete Moore Genome Biology 2004, 5:spotlight-20040730-01 (30 July 2004) Abstract \| Full text \| Editor’s summary The master of science and arguably the founder of molecular biology was 88
	Research news Bacterial proteins on the move Charles Q Choi Genome Biology 2004, 5:spotlight-20050705-01 (5 July 2005) Abstract \| Full text \| Editor’s summary Cell surface materials passed via direct contact can restart the engines of stalled myxococci
	Research news How epigenetics affects twins Charles Q Choi Genome Biology 2004, 5:spotlight-20050708-02 (8 July 2005) Abstract \| Full text \| Editor’s summary In genetically identical siblings, DNA methylation and histone acetylation correlate with age and lifestyle
	Research news Rat olfaction molded early Graciela Flores Genome Biology 2004, 5:spotlight-20050708-01 (8 July 2005) Abstract \| Full text \| Editor’s summary Study in newborn rodents shows how first exposure to smells alters synaptic development
	Research news How mtDNA mutations cause aging Charles Q Choi Genome Biology 2004, 5:spotlight-20050718-01 (18 July 2005) Abstract \| Full text \| Editor’s summary Apoptosis, not oxidative damage from free radicals, drives process, according to Science study
	Research news Did bitter tasters do better? Ishani Ganguli Genome Biology 2004, 5:spotlight-20050727-01 (27 July 2005) Abstract \| Full text \| Editor’s summary Genetic clues suggest distinguishing bitter natural toxins was advantageous in human evolution
	Research
	Research Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana G Marais, B Charlesworth, S I Wright Genome Biology 2004, 5:R45 (14 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The effects of recombination and self-fertilization on base composition were investigated both theoretically and experimentally in the Arabidopsis genome. Levels of inbreeding modulate the effect of recombination on base composition.
	Research Tissue-specific spatial organization of genomes Luis A Parada, Philip G McQueen, Tom Misteli Genome Biology 2004, 5:R44 (21 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of the spatial positioning of a subset of mouse chromosomes reveals that chromosomes exhibit tissue-specific organization in the nucleus.
	Research Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes Hui Huang, Eitan E Winter, Huajun Wang, Keith G Weinstock, Heming Xing, Leo Goodstadt, Peter D Stenson, David N Cooper, Douglas Smith, M Mar Albà, Chris P Ponting, Kim Fechtel Genome Biology 2004, 5:R47 (28 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change. Rodent orthologs of human trinucleotide repeat-expansion disease genes were also found to contain substantially fewer such repeats.
	Research From co-expression to co-regulation: how many microarray experiments do we need? Ka Yeung, Mario Medvedovic, Roger E Bumgarner Genome Biology 2004, 5:R48 (28 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The ability to identify co-regulated genes from microarray clustering results is strongly dependent on the number of microarray experiments used in cluster analysis and the accuracy of these associations plateaus at between 50 and 100 experiments on yeast data. Even with large numbers of experiments, the false positive rate may exceed the true positive rate.
	Research Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica Cizhong Jiang, Xun Gu, Thomas Peterson Genome Biology 2004, 5:R46 (29 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Myb genes from Arabidopsis and rice were clustered into subgroups. The distribution of introns in the phylogenetic tree suggests that introns were inserted during evolution.
	Method Detecting DNA regulatory motifs by incorporating positional trends in information content Katherina J Kechris, Erik van Zwet, Peter J Bickel, Michael B Eisen Genome Biology 2004, 5:R50 (24 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, a simple extension to the model-based motif discovery method is proposed. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.
	Method Systematic quantification of gene interactions by phenotypic array analysis John L Hartman, Nicholas P Tippery Genome Biology 2004, 5:R49 (29 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A phenotypic array method, developed for quantifying cell growth, was applied to the haploid and homozygous diploid yeast deletion strain sets. A growth index was developed to screen for non-additive interacting effects between gene deletion and induced perturbations.
	Method Clustering analysis of SAGE data using a Poisson approach Li Cai, Haiyan Huang, Seth Blackshaw, Jun S Liu, Connie Cepko, Wing H Wong Genome Biology 2004, 5:R51 (29 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two Poisson-based distances were developed for SAGE data; their application to simulated and experimental mouse retina data show that they are more appropriate and reliable for analyzing SAGE data than other commonly used distances or similarity measures.

Explore Genome Biology

Articles

Volume 5 Issue 7

Comment

Review

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