Genome Biology | Volume 4 Issue 12

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	Volume 4 Issue 12
	Comment
	Comment For the good of the state Gregory A Petsko Genome Biology 2003, 4:121 (27 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent advances in biology and medicine, from the sequence of the human genome to the cloning of mammals have made many lay people profoundly uneasy about the future of humanity.
	Opinion Multi-species sequence comparison: the next frontier in genome annotation Inna Dubchak, Kelly Frazer Genome Biology 2003, 4:122 (27 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most current computational tools have been designed for pairwise comparisons of DNA sequences, and efficient extension of these tools to multiple species will require knowledge of the ideal evolutionary distance to choose and the development of new algorithms for alignment, analysis of conservation, and visualization of results.
	Review
	Review Toward an understanding of the structural basis of translation Joachim Frank Genome Biology 2003, 4:237 (19 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recently solved X-ray crystal structures of the ribosome have provided opportunities for studying the molecular basis of translation with a variety of methods including cryo-electron microscopy.
	Minireview The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans Bhagwati P Gupta, Paul W Sternberg Genome Biology 2003, 4:238 (18 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The publication of the draft genome sequence of Caenorhabditis briggsae improves the annotation of the genome of C. elegans and will facilitate comparative genomics and the study of the evolutionary changes during development.
	Minireview Localizing the proteome Jeremy C Simpson, Rainer Pepperkok Genome Biology 2003, 4:240 (18 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The subcellular localization of the entire proteome of the yeast Saccharomyces cerevisiae, and comparison with less comprehensive studies of mammalian cells, provides insights into the localization of the mammalian proteome.
	Minireview Signaling advances from immunogenetics to immunogenomics Mark Boothby Genome Biology 2003, 4:239 (19 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies describe new genome-wide mutagenesis strategies, coupled with phenotypic screening, and demonstrate the power of such approaches to provide new insights into the genetics of the immune response.
	Minireview Genetics and functional genomics of type 2 diabetes mellitus Ayo Toye, Dominique Gauguier Genome Biology 2003, 4:241 (24 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide studies of transcription in the skeletal muscle of type 2 diabetic patients have identified coordinated changes in the expression of genes involved in oxidative phosphorylation, and have underlined the central role of the oxidative-phosphorylation regulator, PCG1α.
	Report
	Paper report Articles selected by Faculty of 1000: profiling human and chimpanzee brains; genome-wide search for cellular systems; crossover control in C. elegans; RNA role in prion disease; self-assembly of protein arrays Genome Biology 2003, 4:353 (5 November 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the profiling of human and chimpanzee brains, a genome-wide search for cellular systems, crossover control in C. elegans, a role for RNA molecules in prion disease and self-assembly of protein arrays.
	Paper report Articles selected by Faculty of 1000: CNS gene-expression atlas; finding Cdk1 targets; metabolic labeling C. elegans and Drosophila; allele-specific silencing by RNAi; identifying long-range enhancers Genome Biology 2003, 4:354 (18 November 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a gene expression atlas of the central nervous system, the identification of Cdk1 targets, metabolic labeling C. elegans and Drosophila, allele-specific silencing by RNAi and identifying human long-range enhancers.
	Meeting report Finding the functional gems in plant genomes Alexandra M Jones, Murray Grant Genome Biology 2003, 4:350 (5 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint second Plant Genomics European Meeting (Plant GEMs) and fourth Genomic Arabidopsis Resource Network (GARNet) meeting, York, UK, 3-6 September 2003.
	Meeting report MGED comes of age Helen C Causton, Laurence Game Genome Biology 2003, 4:351 (13 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Sixth International Meeting of the Microarray Gene Expression Data Society ('MGED6'), Aix-en-Provence, France, 6-8 September 2003.
	Meeting report Yeast functional genomics and cell biology: no longer in the dark Helena Friesen, Jonathan S Millman, Brenda J Andrews Genome Biology 2003, 4:352 (24 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Yeast Cell Biology', Cold Spring Harbor, USA, 12-17 August 2003.
	Research news Iron overload lifted Cathy Holding Genome Biology 2003, 4:spotlight-20031201-01 (1 December 2003) Abstract \| Full text \| Editor’s summary A single piece in the genomic puzzle answers questions of juvenile hemochromatosis
	Research news Harvard plans new 'science hub' Lynne Lederman Genome Biology 2003, 4:spotlight-20031201-02 (1 December 2003) Abstract \| Full text \| Editor’s summary Local residents find little to object to, but many faculty criticize proposal and process
	Research news EU researches superbugs Rossella Lorenzi Genome Biology 2003, 4:spotlight-20031202-01 (2 December 2003) Abstract \| Full text \| Editor’s summary The mechanisms of antibiotic resistance receive support from FP6
	Research news German-Austrian genome deal Jane Burgermeister Genome Biology 2003, 4:spotlight-20031205-01 (5 December 2003) Abstract \| Full text \| Editor’s summary Austrian genome researchers get access to resources from a German center
	Research news Clustering round the links Cathy Holding Genome Biology 2003, 4:spotlight-20031201-08 (8 December 2003) Abstract \| Full text \| Editor’s summary Hierarchical clustering of functional linkage maps reveals protein networks
	Research news NIH to launch ethics review Ted Agres Genome Biology 2003, 4:spotlight-20031210-01 (10 December 2003) Abstract \| Full text \| Editor’s summary Zerhouni promises a comprehensive look at the lucrative consulting payments to top officials
	Research news UK probes scientific publications Pat Hagan Genome Biology 2003, 4:spotlight-20031212-01 (12 December 2003) Abstract \| Full text \| Editor’s summary Science and Technology Committee to investigate issues around access to information
	Research news Perfidious proteobacterium Cathy Holding Genome Biology 2003, 4:spotlight-20031212-02 (12 December 2003) Abstract \| Full text \| Editor’s summary Analysis of Geobacter genome unearths many previously unrecognized capabilities
	Research news Repeats revisited Cathy Holding Genome Biology 2003, 4:spotlight-20031212-03 (12 December 2003) Abstract \| Full text \| Editor’s summary Effects of triplet repeat expansion in myotonic dystrophy explained
	Research news Chimp genome released Eugene Russo Genome Biology 2003, 4:spotlight-20031215-01 (15 December 2003) Abstract \| Full text \| Editor’s summary A NHGRI-led project aligns sequence with the human genome to make comparisons easier
	Research news HapMap Project launched Cathy Holding Genome Biology 2003, 4:spotlight-20031219-01 (19 December 2003) Abstract \| Full text \| Editor’s summary International effort seeks to generate a haplotype map of the entire human genome
	Research news Sorting the maize Tudor Toma Genome Biology 2003, 4:spotlight-20031222-01 (22 December 2003) Abstract \| Full text \| Editor’s summary Methylation filtration and High C₀t are efficient strategies for sequencing repetitive genomes
	Research news Variations on a splice theme Cathy Holding Genome Biology 2003, 4:spotlight-20031223-01 (23 December 2003) Abstract \| Full text \| Editor’s summary Systematic analysis of exon-exon junctions reveals many novel splice variants
	Research
	Research Expressed sequence tag analysis in Cycas, the most primitive living seed plant Eric D Brenner, Dennis W Stevenson, Richard W McCombie, Manpreet S Katari, Stephen A Rudd, Klaus FX Mayer, Peter M Palenchar, Suzan J Runko, Richard W Twigg, Guangwei Dai, Rob A Martienssen, Phillip N Benfey, Gloria M Coruzzi Genome Biology 2003, 4:R78 (18 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of cycad ESTs has uncovered conserved and potentially novel genes. The presence of a glutamate receptor agonist, as well as a glutamate receptor-like gene in cycads, supports the hypothesis that such neuroactive plant products are not merely herbivore deterrents but may also serve a role in plant signaling.
	Research New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system Vivek Anantharaman, L Aravind Genome Biology 2003, 4:R81 (26 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequence profile analysis of the RelE- and ParE-type post-segregational cell killing (PSK) toxins from diverse bacteria and archaea has unified these proteins into a single superfamily. Further comparative analysis suggests that the core of the eukaryotic nonsense-mediated RNA decay system has probably evolved from a PSK-related system.
	Research Expressed sequence tag profiling identifies developmental and anatomic partitioning of gene expression in the mouse prostate Denise E Abbott, Colin Pritchard, Nigel J Clegg, Camari Ferguson, Ruth Dumpit, Robert A Sikes, Peter S Nelson Genome Biology 2003, 4:R79 (28 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary In this article the repertoire of genes expressed in the normal developing mouse prostate is characterized. The identification of several novel genes is reported, including a new member of the β-defensin gene family with prostate-restricted expression
	Research Comparison of the canine and human olfactory receptor gene repertoires Pascale Quignon, Ewen Kirkness, Edouard Cadieu, Nizar Touleimat, Richard Guyon, Corinne Renier, Christophe Hitte, Catherine André, Claire Fraser, Francis Galibert Genome Biology 2003, 4:R80 (28 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In this study, 817 novel canine olfactory receptor (OR) sequences were identified, and 640 have been characterized. Of the 661 characterized OR sequences, representing half of the canine repertoire, 18% are predicted to be pseudogenes, compared with 63% in human and 20% in mouse.
	Method Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells Jae K Lee, Kimberly J Bussey, Fuad G Gwadry, William Reinhold, Gregory Riddick, Sandra L Pelletier, Satoshi Nishizuka, Gergely Szakacs, Jean-Phillipe Annereau, Uma Shankavaram, Samir Lababidi, Lawrence H Smith, Michael M Gottesman, John N Weinstein Genome Biology 2003, 4:R82 (25 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. A different approach is described, based on simultaneous mutual validation of large numbers of genes using two different expression-profiling platforms.
	Software Multiclass classification of microarray data with repeated measurements: application to cancer Ka Yeung, Roger E Bumgarner Genome Biology 2003, 4:R83 (24 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Prediction of the diagnostic category of a tissue sample from its gene-expression profile and selection of relevant genes for class prediction have important applications in cancer research. Uncorrelated shrunken centroid and error-weighted, uncorrelated shrunken centroid algorithms have been developed that are applicable to microarray data with any number of classes.

	Volume 4 Issue 12
	Comment
	Comment For the good of the state Gregory A Petsko Genome Biology 2003, 4:121 (27 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent advances in biology and medicine, from the sequence of the human genome to the cloning of mammals have made many lay people profoundly uneasy about the future of humanity.
	Opinion Multi-species sequence comparison: the next frontier in genome annotation Inna Dubchak, Kelly Frazer Genome Biology 2003, 4:122 (27 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most current computational tools have been designed for pairwise comparisons of DNA sequences, and efficient extension of these tools to multiple species will require knowledge of the ideal evolutionary distance to choose and the development of new algorithms for alignment, analysis of conservation, and visualization of results.
	Review
	Review Toward an understanding of the structural basis of translation Joachim Frank Genome Biology 2003, 4:237 (19 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recently solved X-ray crystal structures of the ribosome have provided opportunities for studying the molecular basis of translation with a variety of methods including cryo-electron microscopy.
	Minireview The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans Bhagwati P Gupta, Paul W Sternberg Genome Biology 2003, 4:238 (18 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The publication of the draft genome sequence of Caenorhabditis briggsae improves the annotation of the genome of C. elegans and will facilitate comparative genomics and the study of the evolutionary changes during development.
	Minireview Localizing the proteome Jeremy C Simpson, Rainer Pepperkok Genome Biology 2003, 4:240 (18 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The subcellular localization of the entire proteome of the yeast Saccharomyces cerevisiae, and comparison with less comprehensive studies of mammalian cells, provides insights into the localization of the mammalian proteome.
	Minireview Signaling advances from immunogenetics to immunogenomics Mark Boothby Genome Biology 2003, 4:239 (19 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies describe new genome-wide mutagenesis strategies, coupled with phenotypic screening, and demonstrate the power of such approaches to provide new insights into the genetics of the immune response.
	Minireview Genetics and functional genomics of type 2 diabetes mellitus Ayo Toye, Dominique Gauguier Genome Biology 2003, 4:241 (24 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide studies of transcription in the skeletal muscle of type 2 diabetic patients have identified coordinated changes in the expression of genes involved in oxidative phosphorylation, and have underlined the central role of the oxidative-phosphorylation regulator, PCG1α.
	Report
	Paper report Articles selected by Faculty of 1000: profiling human and chimpanzee brains; genome-wide search for cellular systems; crossover control in C. elegans; RNA role in prion disease; self-assembly of protein arrays Genome Biology 2003, 4:353 (5 November 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the profiling of human and chimpanzee brains, a genome-wide search for cellular systems, crossover control in C. elegans, a role for RNA molecules in prion disease and self-assembly of protein arrays.
	Paper report Articles selected by Faculty of 1000: CNS gene-expression atlas; finding Cdk1 targets; metabolic labeling C. elegans and Drosophila; allele-specific silencing by RNAi; identifying long-range enhancers Genome Biology 2003, 4:354 (18 November 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a gene expression atlas of the central nervous system, the identification of Cdk1 targets, metabolic labeling C. elegans and Drosophila, allele-specific silencing by RNAi and identifying human long-range enhancers.
	Meeting report Finding the functional gems in plant genomes Alexandra M Jones, Murray Grant Genome Biology 2003, 4:350 (5 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint second Plant Genomics European Meeting (Plant GEMs) and fourth Genomic Arabidopsis Resource Network (GARNet) meeting, York, UK, 3-6 September 2003.
	Meeting report MGED comes of age Helen C Causton, Laurence Game Genome Biology 2003, 4:351 (13 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Sixth International Meeting of the Microarray Gene Expression Data Society ('MGED6'), Aix-en-Provence, France, 6-8 September 2003.
	Meeting report Yeast functional genomics and cell biology: no longer in the dark Helena Friesen, Jonathan S Millman, Brenda J Andrews Genome Biology 2003, 4:352 (24 November 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Yeast Cell Biology', Cold Spring Harbor, USA, 12-17 August 2003.
	Research news Iron overload lifted Cathy Holding Genome Biology 2003, 4:spotlight-20031201-01 (1 December 2003) Abstract \| Full text \| Editor’s summary A single piece in the genomic puzzle answers questions of juvenile hemochromatosis
	Research news Harvard plans new 'science hub' Lynne Lederman Genome Biology 2003, 4:spotlight-20031201-02 (1 December 2003) Abstract \| Full text \| Editor’s summary Local residents find little to object to, but many faculty criticize proposal and process
	Research news EU researches superbugs Rossella Lorenzi Genome Biology 2003, 4:spotlight-20031202-01 (2 December 2003) Abstract \| Full text \| Editor’s summary The mechanisms of antibiotic resistance receive support from FP6
	Research news German-Austrian genome deal Jane Burgermeister Genome Biology 2003, 4:spotlight-20031205-01 (5 December 2003) Abstract \| Full text \| Editor’s summary Austrian genome researchers get access to resources from a German center
	Research news Clustering round the links Cathy Holding Genome Biology 2003, 4:spotlight-20031201-08 (8 December 2003) Abstract \| Full text \| Editor’s summary Hierarchical clustering of functional linkage maps reveals protein networks
	Research news NIH to launch ethics review Ted Agres Genome Biology 2003, 4:spotlight-20031210-01 (10 December 2003) Abstract \| Full text \| Editor’s summary Zerhouni promises a comprehensive look at the lucrative consulting payments to top officials
	Research news UK probes scientific publications Pat Hagan Genome Biology 2003, 4:spotlight-20031212-01 (12 December 2003) Abstract \| Full text \| Editor’s summary Science and Technology Committee to investigate issues around access to information
	Research news Perfidious proteobacterium Cathy Holding Genome Biology 2003, 4:spotlight-20031212-02 (12 December 2003) Abstract \| Full text \| Editor’s summary Analysis of Geobacter genome unearths many previously unrecognized capabilities
	Research news Repeats revisited Cathy Holding Genome Biology 2003, 4:spotlight-20031212-03 (12 December 2003) Abstract \| Full text \| Editor’s summary Effects of triplet repeat expansion in myotonic dystrophy explained
	Research news Chimp genome released Eugene Russo Genome Biology 2003, 4:spotlight-20031215-01 (15 December 2003) Abstract \| Full text \| Editor’s summary A NHGRI-led project aligns sequence with the human genome to make comparisons easier
	Research news HapMap Project launched Cathy Holding Genome Biology 2003, 4:spotlight-20031219-01 (19 December 2003) Abstract \| Full text \| Editor’s summary International effort seeks to generate a haplotype map of the entire human genome
	Research news Sorting the maize Tudor Toma Genome Biology 2003, 4:spotlight-20031222-01 (22 December 2003) Abstract \| Full text \| Editor’s summary Methylation filtration and High C₀t are efficient strategies for sequencing repetitive genomes
	Research news Variations on a splice theme Cathy Holding Genome Biology 2003, 4:spotlight-20031223-01 (23 December 2003) Abstract \| Full text \| Editor’s summary Systematic analysis of exon-exon junctions reveals many novel splice variants
	Research
	Research Expressed sequence tag analysis in Cycas, the most primitive living seed plant Eric D Brenner, Dennis W Stevenson, Richard W McCombie, Manpreet S Katari, Stephen A Rudd, Klaus FX Mayer, Peter M Palenchar, Suzan J Runko, Richard W Twigg, Guangwei Dai, Rob A Martienssen, Phillip N Benfey, Gloria M Coruzzi Genome Biology 2003, 4:R78 (18 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of cycad ESTs has uncovered conserved and potentially novel genes. The presence of a glutamate receptor agonist, as well as a glutamate receptor-like gene in cycads, supports the hypothesis that such neuroactive plant products are not merely herbivore deterrents but may also serve a role in plant signaling.
	Research New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system Vivek Anantharaman, L Aravind Genome Biology 2003, 4:R81 (26 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequence profile analysis of the RelE- and ParE-type post-segregational cell killing (PSK) toxins from diverse bacteria and archaea has unified these proteins into a single superfamily. Further comparative analysis suggests that the core of the eukaryotic nonsense-mediated RNA decay system has probably evolved from a PSK-related system.
	Research Expressed sequence tag profiling identifies developmental and anatomic partitioning of gene expression in the mouse prostate Denise E Abbott, Colin Pritchard, Nigel J Clegg, Camari Ferguson, Ruth Dumpit, Robert A Sikes, Peter S Nelson Genome Biology 2003, 4:R79 (28 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary In this article the repertoire of genes expressed in the normal developing mouse prostate is characterized. The identification of several novel genes is reported, including a new member of the β-defensin gene family with prostate-restricted expression
	Research Comparison of the canine and human olfactory receptor gene repertoires Pascale Quignon, Ewen Kirkness, Edouard Cadieu, Nizar Touleimat, Richard Guyon, Corinne Renier, Christophe Hitte, Catherine André, Claire Fraser, Francis Galibert Genome Biology 2003, 4:R80 (28 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In this study, 817 novel canine olfactory receptor (OR) sequences were identified, and 640 have been characterized. Of the 661 characterized OR sequences, representing half of the canine repertoire, 18% are predicted to be pseudogenes, compared with 63% in human and 20% in mouse.
	Method Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells Jae K Lee, Kimberly J Bussey, Fuad G Gwadry, William Reinhold, Gregory Riddick, Sandra L Pelletier, Satoshi Nishizuka, Gergely Szakacs, Jean-Phillipe Annereau, Uma Shankavaram, Samir Lababidi, Lawrence H Smith, Michael M Gottesman, John N Weinstein Genome Biology 2003, 4:R82 (25 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. A different approach is described, based on simultaneous mutual validation of large numbers of genes using two different expression-profiling platforms.
	Software Multiclass classification of microarray data with repeated measurements: application to cancer Ka Yeung, Roger E Bumgarner Genome Biology 2003, 4:R83 (24 November 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Prediction of the diagnostic category of a tissue sample from its gene-expression profile and selection of relevant genes for class prediction have important applications in cancer research. Uncorrelated shrunken centroid and error-weighted, uncorrelated shrunken centroid algorithms have been developed that are applicable to microarray data with any number of classes.

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Volume 4 Issue 12

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