Genome Biology | Volume 5 Issue 1

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	Volume 5 Issue 1
	Comment
	Comment Live and let diet Gregory A Petsko Genome Biology 2003, 5:101 (22 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary It used to be that one's generation could be defined simply by the war one fought in. Since the middle of the last century, equally defining are the diets that each generation has been swept up in.
	Review
	Review Computational prediction of transcription-factor binding site locations Martha L Bulyk Genome Biology 2003, 5:201 (23 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Various experimental and computational approaches have been used to identify genomic locations of transcription-factor binding sites; methods involving computational comparisons of related genomes have been particularly successful.
	Minireview Scratching the (T cell) surface Joerg Ermann, Chan D Chung, C Garrison Fathman Genome Biology 2003, 5:202 (11 December 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using a genome-scale approach to study transcription levels in a human CD8⁺T-cell clone, a recent study has suggested that the repertoire of molecules on the surface of T cells is close to being completely characterized.
	Minireview How many genes in a genome? Brian Oliver, Benoit Leblanc Genome Biology 2003, 5:204 (22 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study of the Drosophila genome has added perhaps 2,000 genes to the predicted total, and raises a number of questions about how genome annotation data should be stored and presented.
	Minireview Characterization of the Schistosoma transcriptome opens up the world of helminth genomics Karl F Hoffmann, David W Dunne Genome Biology 2003, 5:203 (24 December 2003) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Among the metazoan parasites that cause debilitating disease in man, schistosomes are the first group for which near-complete transcriptome complements have been described. This new genomic information will have an enormous impact on all future investigations into the biology, pathogenesis and control of schistosomiasis.
	Minireview Unveiling the gene-expression profile of pollen José da Costa-Nunes, Ueli Grossniklaus Genome Biology 2003, 5:205 (24 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Four recent papers have characterized the transcription profile of pollen grains, showing striking differences between gene expression in pollen and other plant tissues. These studies increase the number of known pollen-expressed genes by as much as 50-fold and have identified many novel genes that are potentially pollen-specific.
	Report
	Paper report Articles selected by Faculty of 1000: Arabidopsis transcription activity analysis; yeast mitochondial proteome; metabolomic survey in Bacillus subtilis; Nanoarchaeum equitans genome sequence; screen for metastatic behvavior in Drosophila Genome Biology 2003, 5:305 (5 December 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering an analysis of transcription activity in Arabidopsis, identification of proteins associated with Saccharomyces cerevisiae mitochondia, a metabolomic survey in Bacillus subtilis, the genome sequence of Nanoarchaeum equitans and a screen for metastatic behvavior in Drosophila.
	Paper report Articles selected by Faculty of 1000: Drosophila protein interaction map; profiling the mammalian AP-1 pathway; chromophore-assisted light inactivation of proteins in vivo; protein design; nucleolar associations Genome Biology 2003, 5:306 (16 December 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a Drosophila protein interaction map, profiling the mammalian AP-1 pathway, chromophore-assisted light inactivation of proteins in vivo, design of a novel protein fold and nucleolar clustering of tRNA genes.
	Meeting report The not-so-humble worm Catriona Crombie, Ariel Junio, Andrew Fraser Genome Biology 2003, 5:301 (15 December 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Wellcome Trust meeting "Caenorhabditis elegans past, present and future: The not-so-humble worm", Hinxton, UK, 10 September 2003.
	Meeting report Frontiers in plant genetics Sarah Hake Genome Biology 2003, 5:302 (19 December 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the American Society for Plant Biologists' meeting 'Plant Genetics 2003: Mechanisms of Genetic Variation', Snowbird, Utah, USA, 22-24 October 2003.
	Meeting report Spiralians in the limelight Detlev Arendt Genome Biology 2003, 5:303 (19 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the meeting 'Developmental Basis of Evolutionary Change', University of Chicago, USA, 16-18 October 2003.
	Deposited research article Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences Ryan J Taft, John S Mattick Genome Biology 2003, 5:P1 (1 December 2003) Abstract \| Full text \| PDF \| Editor’s summary The ratio of noncoding to total genomic DNA (ncDNA/tgDNA) for 85 sequenced species was analyzed and and it was found that this ratio correlates well with increasing biological complexity.
	Deposited research article Is prokaryotic complexity limited by accelerated growth in regulatory overhead? Larry J Croft, Martin J Lercher, Michael J Gagen, John S Mattick Genome Biology 2003, 5:P2 (15 December 2003) Abstract \| Full text \| PDF \| Editor’s summary Two models for the growth of regulatory networks are presented. Both predict that the number of transcriptional regulators will scale quadratically with total gene number.
	Research
	Research Antisense transcripts with rice full-length cDNAs Naoki Osato, Hitomi Yamada, Kouji Satoh, Hisako Ooka, Makoto Yamamoto, Kohji Suzuki, Jun Kawai, Piero Carninci, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsubara, Shoshi Kikuchi, Yoshihide Hayashizaki Genome Biology 2003, 5:R5 (11 December 2003) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary In this study, 687 sense-antisense transcript pairs from 32,127 full-length rice cDNA sequences were identified by aligning the cDNA sequences with rice genome sequences. The large number of pairs suggests that gene regulation by antisense transcripts occurs in plants and not only in animals.
	Research MicroRNA targets in Drosophila Anton J Enright, Bino John, Ulrike Gaul, Thomas Tuschl, Chris Sander, Debora S Marks Genome Biology 2003, 5:R1 (12 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A computational method for whole-genome prediction of microRNA target genes is presented. Application of this method to the Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known microRNAs.
	Research Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae Evan H Hurowitz, Patrick O Brown Genome Biology 2003, 5:R2 (22 December 2003) Abstract \| Full text \| PDF \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel 'Virtual Northern' method provides a practical and efficient method for genome-scale analysis of mRNA transcript lengths. A study in Saccharomyces cerevisiae has revealed that approximately 12-15% of the yeast genome is represented in untranslated sequences of mRNAs.
	Research An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome M Hild, B Beckmann, SA Haas, B Koch, V Solovyev, C Busold, K Fellenberg, M Boutros, M Vingron, F Sauer, JD Hoheisel, R Paro Genome Biology 2003, 5:R3 (22 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel Drosophila microarray constructed on the basis of an integrated in silico/wet biology approach provides evidence for the transcription of approximately 2,600 additional genes. Validation indicates a lower limit of 2,000 novel annotations, thus raising the number of genes that make a fly.
	Research Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells Michael E Wright, Jimmy Eng, James Sherman, David M Hockenbery, Peter S Nelson, Timothy Galitski, Ruedi Aebersold Genome Biology 2003, 5:R4 (23 December 2003) Abstract \| Full text \| PDF \| Editor’s summary A large-scale proteomic approach has been used to define cellular processes that are responsive to androgen treatment in LNCaP prostate cancer cells. The results provide evidence for the role of androgenic hormones in coordinating the expression of critical components involved in distinct cellular processes
	Method Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network Christine Brun, François Chevenet, David Martin, Jérôme Wojcik, Alain Guénoche, Bernard Jacq Genome Biology 2003, 5:R6 (15 December 2003) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary PRODISTIN, a new computational method allowing the functional clustering of proteins on the basis of protein-protein interaction data. This method was used to classify 11% of the Saccharomyces cerevisiae proteome into several groups.

	Volume 5 Issue 1
	Comment
	Comment Live and let diet Gregory A Petsko Genome Biology 2003, 5:101 (22 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary It used to be that one's generation could be defined simply by the war one fought in. Since the middle of the last century, equally defining are the diets that each generation has been swept up in.
	Review
	Review Computational prediction of transcription-factor binding site locations Martha L Bulyk Genome Biology 2003, 5:201 (23 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Various experimental and computational approaches have been used to identify genomic locations of transcription-factor binding sites; methods involving computational comparisons of related genomes have been particularly successful.
	Minireview Scratching the (T cell) surface Joerg Ermann, Chan D Chung, C Garrison Fathman Genome Biology 2003, 5:202 (11 December 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using a genome-scale approach to study transcription levels in a human CD8⁺T-cell clone, a recent study has suggested that the repertoire of molecules on the surface of T cells is close to being completely characterized.
	Minireview How many genes in a genome? Brian Oliver, Benoit Leblanc Genome Biology 2003, 5:204 (22 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study of the Drosophila genome has added perhaps 2,000 genes to the predicted total, and raises a number of questions about how genome annotation data should be stored and presented.
	Minireview Characterization of the Schistosoma transcriptome opens up the world of helminth genomics Karl F Hoffmann, David W Dunne Genome Biology 2003, 5:203 (24 December 2003) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Among the metazoan parasites that cause debilitating disease in man, schistosomes are the first group for which near-complete transcriptome complements have been described. This new genomic information will have an enormous impact on all future investigations into the biology, pathogenesis and control of schistosomiasis.
	Minireview Unveiling the gene-expression profile of pollen José da Costa-Nunes, Ueli Grossniklaus Genome Biology 2003, 5:205 (24 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Four recent papers have characterized the transcription profile of pollen grains, showing striking differences between gene expression in pollen and other plant tissues. These studies increase the number of known pollen-expressed genes by as much as 50-fold and have identified many novel genes that are potentially pollen-specific.
	Report
	Paper report Articles selected by Faculty of 1000: Arabidopsis transcription activity analysis; yeast mitochondial proteome; metabolomic survey in Bacillus subtilis; Nanoarchaeum equitans genome sequence; screen for metastatic behvavior in Drosophila Genome Biology 2003, 5:305 (5 December 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering an analysis of transcription activity in Arabidopsis, identification of proteins associated with Saccharomyces cerevisiae mitochondia, a metabolomic survey in Bacillus subtilis, the genome sequence of Nanoarchaeum equitans and a screen for metastatic behvavior in Drosophila.
	Paper report Articles selected by Faculty of 1000: Drosophila protein interaction map; profiling the mammalian AP-1 pathway; chromophore-assisted light inactivation of proteins in vivo; protein design; nucleolar associations Genome Biology 2003, 5:306 (16 December 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a Drosophila protein interaction map, profiling the mammalian AP-1 pathway, chromophore-assisted light inactivation of proteins in vivo, design of a novel protein fold and nucleolar clustering of tRNA genes.
	Meeting report The not-so-humble worm Catriona Crombie, Ariel Junio, Andrew Fraser Genome Biology 2003, 5:301 (15 December 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Wellcome Trust meeting "Caenorhabditis elegans past, present and future: The not-so-humble worm", Hinxton, UK, 10 September 2003.
	Meeting report Frontiers in plant genetics Sarah Hake Genome Biology 2003, 5:302 (19 December 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the American Society for Plant Biologists' meeting 'Plant Genetics 2003: Mechanisms of Genetic Variation', Snowbird, Utah, USA, 22-24 October 2003.
	Meeting report Spiralians in the limelight Detlev Arendt Genome Biology 2003, 5:303 (19 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the meeting 'Developmental Basis of Evolutionary Change', University of Chicago, USA, 16-18 October 2003.
	Deposited research article Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences Ryan J Taft, John S Mattick Genome Biology 2003, 5:P1 (1 December 2003) Abstract \| Full text \| PDF \| Editor’s summary The ratio of noncoding to total genomic DNA (ncDNA/tgDNA) for 85 sequenced species was analyzed and and it was found that this ratio correlates well with increasing biological complexity.
	Deposited research article Is prokaryotic complexity limited by accelerated growth in regulatory overhead? Larry J Croft, Martin J Lercher, Michael J Gagen, John S Mattick Genome Biology 2003, 5:P2 (15 December 2003) Abstract \| Full text \| PDF \| Editor’s summary Two models for the growth of regulatory networks are presented. Both predict that the number of transcriptional regulators will scale quadratically with total gene number.
	Research
	Research Antisense transcripts with rice full-length cDNAs Naoki Osato, Hitomi Yamada, Kouji Satoh, Hisako Ooka, Makoto Yamamoto, Kohji Suzuki, Jun Kawai, Piero Carninci, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsubara, Shoshi Kikuchi, Yoshihide Hayashizaki Genome Biology 2003, 5:R5 (11 December 2003) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary In this study, 687 sense-antisense transcript pairs from 32,127 full-length rice cDNA sequences were identified by aligning the cDNA sequences with rice genome sequences. The large number of pairs suggests that gene regulation by antisense transcripts occurs in plants and not only in animals.
	Research MicroRNA targets in Drosophila Anton J Enright, Bino John, Ulrike Gaul, Thomas Tuschl, Chris Sander, Debora S Marks Genome Biology 2003, 5:R1 (12 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A computational method for whole-genome prediction of microRNA target genes is presented. Application of this method to the Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known microRNAs.
	Research Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae Evan H Hurowitz, Patrick O Brown Genome Biology 2003, 5:R2 (22 December 2003) Abstract \| Full text \| PDF \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel 'Virtual Northern' method provides a practical and efficient method for genome-scale analysis of mRNA transcript lengths. A study in Saccharomyces cerevisiae has revealed that approximately 12-15% of the yeast genome is represented in untranslated sequences of mRNAs.
	Research An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome M Hild, B Beckmann, SA Haas, B Koch, V Solovyev, C Busold, K Fellenberg, M Boutros, M Vingron, F Sauer, JD Hoheisel, R Paro Genome Biology 2003, 5:R3 (22 December 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel Drosophila microarray constructed on the basis of an integrated in silico/wet biology approach provides evidence for the transcription of approximately 2,600 additional genes. Validation indicates a lower limit of 2,000 novel annotations, thus raising the number of genes that make a fly.
	Research Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells Michael E Wright, Jimmy Eng, James Sherman, David M Hockenbery, Peter S Nelson, Timothy Galitski, Ruedi Aebersold Genome Biology 2003, 5:R4 (23 December 2003) Abstract \| Full text \| PDF \| Editor’s summary A large-scale proteomic approach has been used to define cellular processes that are responsive to androgen treatment in LNCaP prostate cancer cells. The results provide evidence for the role of androgenic hormones in coordinating the expression of critical components involved in distinct cellular processes
	Method Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network Christine Brun, François Chevenet, David Martin, Jérôme Wojcik, Alain Guénoche, Bernard Jacq Genome Biology 2003, 5:R6 (15 December 2003) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary PRODISTIN, a new computational method allowing the functional clustering of proteins on the basis of protein-protein interaction data. This method was used to classify 11% of the Saccharomyces cerevisiae proteome into several groups.

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Volume 5 Issue 1

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