Genome Biology | Volume 5 Issue 6

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	Volume 5 Issue 6
	Comment
	Comment Pharmacogenomics arrives Gregory A Petsko Genome Biology 2004, 5:108 (28 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We've had the human genome sequence for a little while now, and it looks as though we're still some way off being able to exclude from most clinical trials those people who will probably suffer side effects.
	Review
	Review The diversity of LTR retrotransposons Ericka R Havecker, Xiang Gao, Daniel F Voytas Genome Biology 2004, 5:225 (18 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Although most long terminal repeat retrotransposons have common structural features and encode similar genes, there is nonetheless considerable diversity.
	Review An overview of the basic helix-loop-helix proteins Susan Jones Genome Biology 2004, 5:226 (28 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The basic helix-loop-helix proteins, dimeric transcription factors, are found in almost all eukaryotes and in animals are important regulators of embryonic development.
	Minireview Common ground in the transcriptional profiles of wounds and tumors Richard Grose Genome Biology 2004, 5:228 (26 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent microarray studies comparing wounds and tumors have identified characteristic similarities in gene expression that may prove to be useful for assessing cancer prognosis and for choosing subsequent treatment.
	Minireview Root genomics: towards digital in situ hybridization Ben Scheres, Henk van den Toorn, Renze Heidstra Genome Biology 2004, 5:227 (27 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Separation of cell types and developmental stages in the Arabidopsis root has enabled generation of global gene-expression map.
	Opinion Metabolite profiling in plant biology: platforms and destinations Joachim Kopka, Alisdair Fernie, Wolfram Weckwerth, Yves Gibon, Mark Stitt Genome Biology 2004, 5:109 (18 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The most used technologies for metabolite profiling, including mass spectral, nuclear magnetic resonance and enzyme based approaches, have various advantages and disadvantages.
	Report
	Paper report Articles selected by Faculty of 1000: fluorescent tagging of Arabidopsis proteins; chromosome-wide transcription-factor binding scan; Wolbachia genome; HNF 1β transcriptional network; the proteome of the last universal common ancester Genome Biology 2004, 5:329 (12 May 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the fluorescent tagging of proteins in Arabidopsis; a chromosome-wide transcription-factor binding scan; the Wolbachia genome; the HNF 1β transcriptional network; the proteome of the last universal common ancester.
	Paper report Articles selected by Faculty of 1000: profiling biofilms and antibiotic responses; seleno proteomics; nitrilases from uncloned genomes; fish comparative morphology and genetics; comparing mass spectrometry algorithms Genome Biology 2004, 5:330 (25 May 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the profiling of biofilms and antibiotic responses; seleno proteomics; the identification of nitrilases from uncloned genomes; fish comparative morphology and genetics; the comparison of mass spectrometry algorithms.
	Meeting report A burst of energy in metabolic disease research Jaswinder K Sethi Genome Biology 2004, 5:327 (27 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Diabetes Mellitus' and 'Adipogenesis and Obesity' joint Keystone Symposia, Banff, Canada, 4-10 March 2004.
	Meeting report Genomic, chromosomal and allelic assessment of the amazing diversity of maize Virginia Walbot Genome Biology 2004, 5:328 (28 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 46th Annual Maize Genetics Conference, Mexico City, Mexico, 11-14 March 2004.
	Deposited research article Negative selection pressure against premature protein truncation is reduced by both alternative splicing and diploidy Yi Xing, Christopher Lee Genome Biology 2004, 5:P12 (29 April 2004) Abstract \| Full text \| PDF \| Editor’s summary Analysis of 13,384 full-length transcript isoforms from human and 2,227 isoforms from mouse shows that alternatively spliced isoforms have a much higher frequency of premature termination codons compared with the major transcript form of each gene. This effect was strongly influenced by the chromosomal location of the gene, being much lower on the X chromosome.
	Research news Messages from intergenic space David Secko Genome Biology 2004, 5:spotlight-20040603-01 (3 June 2004) Abstract \| Full text \| Editor’s summary A non-protein-coding RNA regulates a neighboring gene by simply being turned on
	Research news A new tool allows open-access search Stephen Pincock Genome Biology 2004, 5:spotlight-20040608-01 (8 June 2004) Abstract \| Full text \| Editor’s summary A new directory lets users search and retrieve articles from about 270 open-access journals
	Research news Integrating plant 'omics' David Secko Genome Biology 2004, 5:spotlight-20040616-01 (16 June 2004) Abstract \| Full text \| Editor’s summary A combination of approaches allows the study of gene-to-metabolite networks in Arabidopsis
	Research news Structural proteomics boost Genome Biology Editorial Staff Genome Biology 2004, 5:spotlight-20040618-01 (18 June 2004) Abstract \| Full text \| Editor’s summary New research programmes in structural proteomics in the UK have been announced
	Research news Plug-n-play in Staph adaptation Cathy Holding Genome Biology 2004, 5:spotlight-20040623-02 (23 June 2004) Abstract \| Full text \| Editor’s summary Mobile antibiotic resistance elements hold implications for spread of MRSA
	Research news Lab mouse genome isn't simple Cathy Holding Genome Biology 2004, 5:spotlight-20040623-01 (23 June 2004) Abstract \| Full text \| Editor’s summary A high-resolution study shows that complex structure is bad news for QTL mapping
	Research news RNAi dissects signal pathway Cathy Holding Genome Biology 2004, 5:spotlight-20040624-01 (24 June 2004) Abstract \| Full text \| Editor’s summary The most comprehensive use yet of high-throughput RNAi screening in a lab setting reveals novel components
	Research news Making enzymes from proteins Charles Q Choi Genome Biology 2004, 5:spotlight-20040629-02 (29 June 2004) Abstract \| Full text \| Editor’s summary Computational design transforms a protein without catalytic properties into an active enzyme
	Research news Bioinformatics awarded Ned Stafford Genome Biology 2004, 5:spotlight-20040629-01 (29 June 2004) Abstract \| Full text \| Editor’s summary Max Planck Institute's prize reflects widespread acceptance of the field, winner says
	Research news Worms reveal intron insights Nicole Johnston Genome Biology 2004, 5:spotlight-20040630-01 (30 June 2004) Abstract \| Full text \| Editor’s summary A team finds 'newborn' introns by comparing the C. elegans and C. briggsae genomes
	Research
	Research Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites Yvonne M Harcus, John Parkinson, Cecilia Fernández, Jennifer Daub, Murray E Selkirk, Mark L Blaxter, Rick M Maizels Genome Biology 2004, 5:R39 (18 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of secreted proteins indicate that they may be undergoing accelerated evolution, either because of relaxed functional constraints, or in response to stronger selective pressure from host immunity.
	Research Bacterial α₂-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome? Aidan Budd, Stephanie Blandin, Elena A Levashina, Toby J Gibson Genome Biology 2004, 5:R38 (26 May 2004) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Homologs of metazoan α₂-macroglobulins have been found in bacteria. The distribution of these genes in diverse bacterial clades suggests they have been acquired by multiple horizontal transfers.
	Research START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors Kathrin Schrick, Diana Nguyen, Wojciech M Karlowski, Klaus FX Mayer Genome Biology 2004, 5:R41 (27 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of proteins containing lipid/sterol-binding StAR-related lipid transfer (START) domains shows that they are amplified in plants and are primarily found within homeodomain (HD) transcription factors.
	Research A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults Michael Parisi, Rachel Nuttall, Pamela Edwards, James Minor, Daniel Naiman, Jining Lü, Michael Doctolero, Marina Vainer, Cathy Chan, James Malley, Scott Eastman, Brian Oliver Genome Biology 2004, 5:R40 (1 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A global analysis of sex-biased transcription in Drosophila shows extensive differential expression between the sexes. Most sex-differential expression is due to germ cells and nearly all genes with germline expression show sex-bias.
	Method Microarray-based genomic surveying of gene polymorphisms in Chlamydia trachomatis Brian W Brunelle, Tracy L Nicholson, Richard S Stephens Genome Biology 2004, 5:R42 (18 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of two genomes of Chlamydia trachomatis using competitive hybridization on DNA microarrays revealed a logarithmic correlation between the signal ratio of the arrays and the 75-99% range of nucleotide identities of the genes.
	Software TXTGate: profiling gene groups with text-based information Patrick Glenisson, Bert Coessens, Steven Van Vooren, Janick Mathys, Yves Moreau, Bart De Moor Genome Biology 2004, 5:R43 (28 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This study implemented a framework called TXTGate that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes.

	Volume 5 Issue 6
	Comment
	Comment Pharmacogenomics arrives Gregory A Petsko Genome Biology 2004, 5:108 (28 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We've had the human genome sequence for a little while now, and it looks as though we're still some way off being able to exclude from most clinical trials those people who will probably suffer side effects.
	Review
	Review The diversity of LTR retrotransposons Ericka R Havecker, Xiang Gao, Daniel F Voytas Genome Biology 2004, 5:225 (18 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Although most long terminal repeat retrotransposons have common structural features and encode similar genes, there is nonetheless considerable diversity.
	Review An overview of the basic helix-loop-helix proteins Susan Jones Genome Biology 2004, 5:226 (28 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The basic helix-loop-helix proteins, dimeric transcription factors, are found in almost all eukaryotes and in animals are important regulators of embryonic development.
	Minireview Common ground in the transcriptional profiles of wounds and tumors Richard Grose Genome Biology 2004, 5:228 (26 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent microarray studies comparing wounds and tumors have identified characteristic similarities in gene expression that may prove to be useful for assessing cancer prognosis and for choosing subsequent treatment.
	Minireview Root genomics: towards digital in situ hybridization Ben Scheres, Henk van den Toorn, Renze Heidstra Genome Biology 2004, 5:227 (27 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Separation of cell types and developmental stages in the Arabidopsis root has enabled generation of global gene-expression map.
	Opinion Metabolite profiling in plant biology: platforms and destinations Joachim Kopka, Alisdair Fernie, Wolfram Weckwerth, Yves Gibon, Mark Stitt Genome Biology 2004, 5:109 (18 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The most used technologies for metabolite profiling, including mass spectral, nuclear magnetic resonance and enzyme based approaches, have various advantages and disadvantages.
	Report
	Paper report Articles selected by Faculty of 1000: fluorescent tagging of Arabidopsis proteins; chromosome-wide transcription-factor binding scan; Wolbachia genome; HNF 1β transcriptional network; the proteome of the last universal common ancester Genome Biology 2004, 5:329 (12 May 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the fluorescent tagging of proteins in Arabidopsis; a chromosome-wide transcription-factor binding scan; the Wolbachia genome; the HNF 1β transcriptional network; the proteome of the last universal common ancester.
	Paper report Articles selected by Faculty of 1000: profiling biofilms and antibiotic responses; seleno proteomics; nitrilases from uncloned genomes; fish comparative morphology and genetics; comparing mass spectrometry algorithms Genome Biology 2004, 5:330 (25 May 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the profiling of biofilms and antibiotic responses; seleno proteomics; the identification of nitrilases from uncloned genomes; fish comparative morphology and genetics; the comparison of mass spectrometry algorithms.
	Meeting report A burst of energy in metabolic disease research Jaswinder K Sethi Genome Biology 2004, 5:327 (27 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Diabetes Mellitus' and 'Adipogenesis and Obesity' joint Keystone Symposia, Banff, Canada, 4-10 March 2004.
	Meeting report Genomic, chromosomal and allelic assessment of the amazing diversity of maize Virginia Walbot Genome Biology 2004, 5:328 (28 May 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 46th Annual Maize Genetics Conference, Mexico City, Mexico, 11-14 March 2004.
	Deposited research article Negative selection pressure against premature protein truncation is reduced by both alternative splicing and diploidy Yi Xing, Christopher Lee Genome Biology 2004, 5:P12 (29 April 2004) Abstract \| Full text \| PDF \| Editor’s summary Analysis of 13,384 full-length transcript isoforms from human and 2,227 isoforms from mouse shows that alternatively spliced isoforms have a much higher frequency of premature termination codons compared with the major transcript form of each gene. This effect was strongly influenced by the chromosomal location of the gene, being much lower on the X chromosome.
	Research news Messages from intergenic space David Secko Genome Biology 2004, 5:spotlight-20040603-01 (3 June 2004) Abstract \| Full text \| Editor’s summary A non-protein-coding RNA regulates a neighboring gene by simply being turned on
	Research news A new tool allows open-access search Stephen Pincock Genome Biology 2004, 5:spotlight-20040608-01 (8 June 2004) Abstract \| Full text \| Editor’s summary A new directory lets users search and retrieve articles from about 270 open-access journals
	Research news Integrating plant 'omics' David Secko Genome Biology 2004, 5:spotlight-20040616-01 (16 June 2004) Abstract \| Full text \| Editor’s summary A combination of approaches allows the study of gene-to-metabolite networks in Arabidopsis
	Research news Structural proteomics boost Genome Biology Editorial Staff Genome Biology 2004, 5:spotlight-20040618-01 (18 June 2004) Abstract \| Full text \| Editor’s summary New research programmes in structural proteomics in the UK have been announced
	Research news Plug-n-play in Staph adaptation Cathy Holding Genome Biology 2004, 5:spotlight-20040623-02 (23 June 2004) Abstract \| Full text \| Editor’s summary Mobile antibiotic resistance elements hold implications for spread of MRSA
	Research news Lab mouse genome isn't simple Cathy Holding Genome Biology 2004, 5:spotlight-20040623-01 (23 June 2004) Abstract \| Full text \| Editor’s summary A high-resolution study shows that complex structure is bad news for QTL mapping
	Research news RNAi dissects signal pathway Cathy Holding Genome Biology 2004, 5:spotlight-20040624-01 (24 June 2004) Abstract \| Full text \| Editor’s summary The most comprehensive use yet of high-throughput RNAi screening in a lab setting reveals novel components
	Research news Making enzymes from proteins Charles Q Choi Genome Biology 2004, 5:spotlight-20040629-02 (29 June 2004) Abstract \| Full text \| Editor’s summary Computational design transforms a protein without catalytic properties into an active enzyme
	Research news Bioinformatics awarded Ned Stafford Genome Biology 2004, 5:spotlight-20040629-01 (29 June 2004) Abstract \| Full text \| Editor’s summary Max Planck Institute's prize reflects widespread acceptance of the field, winner says
	Research news Worms reveal intron insights Nicole Johnston Genome Biology 2004, 5:spotlight-20040630-01 (30 June 2004) Abstract \| Full text \| Editor’s summary A team finds 'newborn' introns by comparing the C. elegans and C. briggsae genomes
	Research
	Research Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites Yvonne M Harcus, John Parkinson, Cecilia Fernández, Jennifer Daub, Murray E Selkirk, Mark L Blaxter, Rick M Maizels Genome Biology 2004, 5:R39 (18 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of secreted proteins indicate that they may be undergoing accelerated evolution, either because of relaxed functional constraints, or in response to stronger selective pressure from host immunity.
	Research Bacterial α₂-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome? Aidan Budd, Stephanie Blandin, Elena A Levashina, Toby J Gibson Genome Biology 2004, 5:R38 (26 May 2004) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Homologs of metazoan α₂-macroglobulins have been found in bacteria. The distribution of these genes in diverse bacterial clades suggests they have been acquired by multiple horizontal transfers.
	Research START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors Kathrin Schrick, Diana Nguyen, Wojciech M Karlowski, Klaus FX Mayer Genome Biology 2004, 5:R41 (27 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of proteins containing lipid/sterol-binding StAR-related lipid transfer (START) domains shows that they are amplified in plants and are primarily found within homeodomain (HD) transcription factors.
	Research A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults Michael Parisi, Rachel Nuttall, Pamela Edwards, James Minor, Daniel Naiman, Jining Lü, Michael Doctolero, Marina Vainer, Cathy Chan, James Malley, Scott Eastman, Brian Oliver Genome Biology 2004, 5:R40 (1 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A global analysis of sex-biased transcription in Drosophila shows extensive differential expression between the sexes. Most sex-differential expression is due to germ cells and nearly all genes with germline expression show sex-bias.
	Method Microarray-based genomic surveying of gene polymorphisms in Chlamydia trachomatis Brian W Brunelle, Tracy L Nicholson, Richard S Stephens Genome Biology 2004, 5:R42 (18 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of two genomes of Chlamydia trachomatis using competitive hybridization on DNA microarrays revealed a logarithmic correlation between the signal ratio of the arrays and the 75-99% range of nucleotide identities of the genes.
	Software TXTGate: profiling gene groups with text-based information Patrick Glenisson, Bert Coessens, Steven Van Vooren, Janick Mathys, Yves Moreau, Bart De Moor Genome Biology 2004, 5:R43 (28 May 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This study implemented a framework called TXTGate that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes.

Explore Genome Biology

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Volume 5 Issue 6

Comment

Review

Report

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