Genome Biology | Volume 4 Issue 9

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 4 Issue 9
	Comment
	Comment The road worrier Gregory A Petsko Genome Biology 2003, 4:116 (28 August 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scientists travel a lot on business, for young scientists, travel is essential as a means of getting one's work and oneself known in the community at large.
	Review
	Minireview The organization and evolution of the human Y chromosome Brian Charlesworth Genome Biology 2003, 4:226 (14 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The recent sequencing of a large chunk of euchromatin from the human Y chromosome is a technical tour de force. It answers some evolutionary questions about this unusual chromosome while raising others.
	Minireview The fitness costs to plants of resistance to pathogens Jeremy J Burdon, Peter H Thrall Genome Biology 2003, 4:227 (14 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new study has shown that a gene giving resistance to pathogens imposes a cost on the fitness in Arabidopsis. This raises questions about how generally the results apply and how such costs are controlled in plants carrying resistance genes to several different pathogens.
	Minireview Towards a complete description of the microRNA complement of animal genomes Julius Brennecke, Stephen M Cohen Genome Biology 2003, 4:228 (21 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent cloning and computational studies have sought to catalog all the microRNA genes encoded in animal genomes. Here, we highlight recent advances in identifying Caenorhabditis elegans and Drosophila melanogaster microRNAs.
	Opinion Comparing protein abundance and mRNA expression levels on a genomic scale Dov Greenbaum, Christopher Colangelo, Kenneth Williams, Mark Gerstein Genome Biology 2003, 4:117 (29 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary We review the results of attempts to correlate protein abundance with mRNA expression levels, focusing on yeast.
	Report
	Paper report Articles selected by Faculty of 1000: archaeal adaptation to cold; human chromosome 7 sequence; comparative protein-structure modeling; new algorithm for sequence alignment; expression profiling human mast cells Genome Biology 2003, 4:338 (7 August 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering genomic analysis of cold-adapted methanogenic archaea, the sequence of human chromosome 7, comparative protein-structure modeling, a new algorithm for multiple sequence alignment and expression profiling human mast cells.
	Paper report Articles selected by Faculty of 1000: linkage disequilibrium across the human genome; identifying low abundance proteins; bacterial phylogenetics; trans-acting regulatory variation in yeast; promoter detection in Arabidopsis Genome Biology 2003, 4:339 (26 August 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the distribution of linkage disequilibrium across the human genome, identifying low abundance and membrane proteins, bacterial phylogenetics, trans-acting regulatory variation in yeast and promoter detection in Arabidopsis.
	Meeting report An international showcase of bioinformatics research Todd Vision Genome Biology 2003, 4:337 (28 August 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 11th International Conference on Intelligent Systems for Molecular Biology, Brisbane, Queensland, Australia, 29 June - 3 July 2003.
	Meeting report A window on the world of plants Clare Lister, Cathie Martin Genome Biology 2003, 4:335 (1 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the seventh meeting of the International Society for Plant Molecular Biology (ISPMB), Barcelona, Spain, 23-28 June 2003.
	Meeting report Open-source software accelerates bioinformatics John Quackenbush Genome Biology 2003, 4:336 (1 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003.
	Deposited research article Short segmental duplication: parsimony in growth of microbial genomes Li-Ching Hsieh, Liaofu Luo, Hoong-Chien Lee Genome Biology 2003, 4:P7 (4 August 2003) Abstract \| Full text \| PDF \| Editor’s summary We compare the distributions of occurrence frequencies of oligonucleotides two to ten bases long in microbial complete genomes with corresponding distributions obtained from random sequences and find that the genomic distributions are uniformly many times wider in a universal manner, that is, the same for all microbial complete genomes.
	Research news Serine protease Jurassic Park Cathy Holding Genome Biology 2003, 4:spotlight-20030903-01 (3 September 2003) Abstract \| Full text \| Editor’s summary A functional ancestral protein created from its predicted structure shows 'evolution in action'
	Research news Balancing act Cathy Holding Genome Biology 2003, 4:spotlight-20030904-01 (4 September 2003) Abstract \| Full text \| Editor’s summary A balancer chromosome has been used to maintain otherwise lethal mutant mouse stocks for gene function analysis
	Research news Sequence of the color purple Cathy Holding Genome Biology 2003, 4:spotlight-20030909-01 (9 September 2003) Abstract \| Full text \| Editor’s summary Knowledge of biotechnologically important bacteria could save the Brazilian rain forests
	Research news A new umbrella body for British biology Anna Fazackerley Genome Biology 2003, 4:spotlight-20030911-01 (11 September 2003) Abstract \| Full text \| Editor’s summary The UK Biosciences Federation, to be inaugurated next week, will represent 61,000 life scientists
	Research news Schistosomiasis under scrutiny Cathy Holding Genome Biology 2003, 4:spotlight-20030915-01 (15 September 2003) Abstract \| Full text \| Editor’s summary Schistosome transcriptome analysis identifies novel genes that could form basis for a vaccine
	Research news Comprehensive interference David Secko Genome Biology 2003, 4:spotlight-20030915-01 (18 September 2003) Abstract \| Full text \| Editor’s summary RNAi-sensitive Drosophila cells provide insights into lamella formation and motor protein specificity
	Research news Histone released on cell death charges David Secko Genome Biology 2003, 4:spotlight-20030922-01 (22 September 2003) Abstract \| Full text \| Editor’s summary DNA damage-induced apoptosis relies on histone H1.2 release into the cytosol
	Research news Modeling miRNA mechanisms Cathy Holding Genome Biology 2003, 4:spotlight-20030925-02 (25 September 2003) Abstract \| Full text \| Editor’s summary Two more key players in the microRNA regulatory system have been identified
	Research news Discovering the secrets of Hsp90 binding David Secko Genome Biology 2003, 4:spotlight-20030925-01 (25 September 2003) Abstract \| Full text \| Editor’s summary A ubiquitous antitumor drug target preferentially kills tumor cells due to target conformation
	Research news Barking up the right tree Cathy Holding Genome Biology 2003, 4:spotlight-20030926-01 (26 September 2003) Abstract \| Full text \| Editor’s summary Sample sequencing of the dog genome yields good news for genomics in developing countries
	Research news Genomic instability switch identified David Secko Genome Biology 2003, 4:spotlight-20030926-02 (26 September 2003) Abstract \| Full text \| Editor’s summary An age-dependent switch causes old yeast cells to show increased genomic instability
	Research news Exploring the alternatives Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030930-01 (30 September 2003) Abstract \| Full text \| Editor’s summary Splicing investigators see medical applications and a possible new role in gene expression
	Research news Scleroderma exposed Cathy Holding Genome Biology 2003, 4:spotlight-20030930-02 (30 September 2003) Abstract \| Full text \| Editor’s summary Systematic analysis provides means for early detection of systemic scleroderma
	Research
	Research CpG content affects gene silencing in mice: evidence from novel transgenes Christine Chevalier-Mariette, Isabelle Henry, Lucile Montfort, Suzanne Capgras, Sylvie Forlani, John Muschler, Jean-François Nicolas Genome Biology 2003, 4:R53 (14 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary It has been demonstrated that the density of CpG sequences in the transcribed regions of transgenes can have a causal role in repression of transcription. These results show that the mechanism by which CpG islands escape de novo methylation is sensitive to CpG density of adjacent sequences.
	Research Comparison of K⁺-channel genes within the genomes of Anopheles gambiae and Drosophila melanogaster Thomas J McCormack Genome Biology 2003, 4:R58 (20 August 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The completion of the sequencing of the genomes of Drosophila melanogaster and Anopheles gambiae, which belong to the same order, the Diptera, allows us to compare and contrast K+-channel genes and gene families present within the genomes of two dipterans.
	Research The source of laterally transferred genes in bacterial genomes Vincent Daubin, Emmanuelle Lerat, Guy Perrière Genome Biology 2003, 4:R57 (21 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Contrary to previous hypotheses that methods for identifying laterally transferred genes cannot detect genes with similar base composition to that of the donor organism, it is suggested that the number of laterally transferred genes has not been underestimated and that laterally transferred genes fit the description of lambdoid phage genes called 'morons'.
	Research An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Jennifer L Reed, Thuy D Vo, Christophe H Schilling, Bernhard O Palsson Genome Biology 2003, 4:R54 (28 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-scale metabolic model of E. coli has been reconstructed, including 904 genes and 931 unique biochemical reactions, which gives a more complete and chemically accurate description of E. coli metabolism than previous models.
	Research Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ Marina V Omelchenko, Kira S Makarova, Yuri I Wolf, Igor B Rogozin, Eugene V Koonin Genome Biology 2003, 4:R55 (29 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and phylogenetic analysis have been used to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired orthologs and independent assembly of the same or similar operons from genes with different phylogenetic affinities.
	Research Different evolutionary patterns between young duplicate genes in the human genome Peng Zhang, Zhenglong Gu, Wen-Hsiung Li Genome Biology 2003, 4:R56 (1 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Duplicate genes tend to evolve in different patterns following the duplication event. One copy evolves faster than the other and accumulates amino-acid substitutions evenly across the sequence, whereas the other copy evolves more slowly and accumulates amino-acid substitutions unevenly across the sequence.
	Method Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach Michael Strong, Parag Mallick, Matteo Pellegrini, Michael J Thompson, David Eisenberg Genome Biology 2003, 4:R59 (29 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of Mycobacterium tuberculosis was used to evaluate and employ a method to infer genes likely to belong to the same operon, as judged by the nucleotide distance between genes in the same genomic orientation, and this method was combined with those of the Rosetta Stone, Phylogenetic Profile and conserved Gene Neighbor computational methods for the inference of protein function.
	Software DAVID: Database for Annotation, Visualization, and Integrated Discovery Glynn Dennis, Brad T Sherman, Douglas A Hosack, Jun Yang, Wei Gao, H Lane, Richard A Lempicki Genome Biology 2003, 4:R60 (14 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DAVID, a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries, has been described and will assist in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.

	Volume 4 Issue 9
	Comment
	Comment The road worrier Gregory A Petsko Genome Biology 2003, 4:116 (28 August 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scientists travel a lot on business, for young scientists, travel is essential as a means of getting one's work and oneself known in the community at large.
	Review
	Minireview The organization and evolution of the human Y chromosome Brian Charlesworth Genome Biology 2003, 4:226 (14 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The recent sequencing of a large chunk of euchromatin from the human Y chromosome is a technical tour de force. It answers some evolutionary questions about this unusual chromosome while raising others.
	Minireview The fitness costs to plants of resistance to pathogens Jeremy J Burdon, Peter H Thrall Genome Biology 2003, 4:227 (14 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new study has shown that a gene giving resistance to pathogens imposes a cost on the fitness in Arabidopsis. This raises questions about how generally the results apply and how such costs are controlled in plants carrying resistance genes to several different pathogens.
	Minireview Towards a complete description of the microRNA complement of animal genomes Julius Brennecke, Stephen M Cohen Genome Biology 2003, 4:228 (21 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent cloning and computational studies have sought to catalog all the microRNA genes encoded in animal genomes. Here, we highlight recent advances in identifying Caenorhabditis elegans and Drosophila melanogaster microRNAs.
	Opinion Comparing protein abundance and mRNA expression levels on a genomic scale Dov Greenbaum, Christopher Colangelo, Kenneth Williams, Mark Gerstein Genome Biology 2003, 4:117 (29 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary We review the results of attempts to correlate protein abundance with mRNA expression levels, focusing on yeast.
	Report
	Paper report Articles selected by Faculty of 1000: archaeal adaptation to cold; human chromosome 7 sequence; comparative protein-structure modeling; new algorithm for sequence alignment; expression profiling human mast cells Genome Biology 2003, 4:338 (7 August 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering genomic analysis of cold-adapted methanogenic archaea, the sequence of human chromosome 7, comparative protein-structure modeling, a new algorithm for multiple sequence alignment and expression profiling human mast cells.
	Paper report Articles selected by Faculty of 1000: linkage disequilibrium across the human genome; identifying low abundance proteins; bacterial phylogenetics; trans-acting regulatory variation in yeast; promoter detection in Arabidopsis Genome Biology 2003, 4:339 (26 August 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the distribution of linkage disequilibrium across the human genome, identifying low abundance and membrane proteins, bacterial phylogenetics, trans-acting regulatory variation in yeast and promoter detection in Arabidopsis.
	Meeting report An international showcase of bioinformatics research Todd Vision Genome Biology 2003, 4:337 (28 August 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 11th International Conference on Intelligent Systems for Molecular Biology, Brisbane, Queensland, Australia, 29 June - 3 July 2003.
	Meeting report A window on the world of plants Clare Lister, Cathie Martin Genome Biology 2003, 4:335 (1 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the seventh meeting of the International Society for Plant Molecular Biology (ISPMB), Barcelona, Spain, 23-28 June 2003.
	Meeting report Open-source software accelerates bioinformatics John Quackenbush Genome Biology 2003, 4:336 (1 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003.
	Deposited research article Short segmental duplication: parsimony in growth of microbial genomes Li-Ching Hsieh, Liaofu Luo, Hoong-Chien Lee Genome Biology 2003, 4:P7 (4 August 2003) Abstract \| Full text \| PDF \| Editor’s summary We compare the distributions of occurrence frequencies of oligonucleotides two to ten bases long in microbial complete genomes with corresponding distributions obtained from random sequences and find that the genomic distributions are uniformly many times wider in a universal manner, that is, the same for all microbial complete genomes.
	Research news Serine protease Jurassic Park Cathy Holding Genome Biology 2003, 4:spotlight-20030903-01 (3 September 2003) Abstract \| Full text \| Editor’s summary A functional ancestral protein created from its predicted structure shows 'evolution in action'
	Research news Balancing act Cathy Holding Genome Biology 2003, 4:spotlight-20030904-01 (4 September 2003) Abstract \| Full text \| Editor’s summary A balancer chromosome has been used to maintain otherwise lethal mutant mouse stocks for gene function analysis
	Research news Sequence of the color purple Cathy Holding Genome Biology 2003, 4:spotlight-20030909-01 (9 September 2003) Abstract \| Full text \| Editor’s summary Knowledge of biotechnologically important bacteria could save the Brazilian rain forests
	Research news A new umbrella body for British biology Anna Fazackerley Genome Biology 2003, 4:spotlight-20030911-01 (11 September 2003) Abstract \| Full text \| Editor’s summary The UK Biosciences Federation, to be inaugurated next week, will represent 61,000 life scientists
	Research news Schistosomiasis under scrutiny Cathy Holding Genome Biology 2003, 4:spotlight-20030915-01 (15 September 2003) Abstract \| Full text \| Editor’s summary Schistosome transcriptome analysis identifies novel genes that could form basis for a vaccine
	Research news Comprehensive interference David Secko Genome Biology 2003, 4:spotlight-20030915-01 (18 September 2003) Abstract \| Full text \| Editor’s summary RNAi-sensitive Drosophila cells provide insights into lamella formation and motor protein specificity
	Research news Histone released on cell death charges David Secko Genome Biology 2003, 4:spotlight-20030922-01 (22 September 2003) Abstract \| Full text \| Editor’s summary DNA damage-induced apoptosis relies on histone H1.2 release into the cytosol
	Research news Modeling miRNA mechanisms Cathy Holding Genome Biology 2003, 4:spotlight-20030925-02 (25 September 2003) Abstract \| Full text \| Editor’s summary Two more key players in the microRNA regulatory system have been identified
	Research news Discovering the secrets of Hsp90 binding David Secko Genome Biology 2003, 4:spotlight-20030925-01 (25 September 2003) Abstract \| Full text \| Editor’s summary A ubiquitous antitumor drug target preferentially kills tumor cells due to target conformation
	Research news Barking up the right tree Cathy Holding Genome Biology 2003, 4:spotlight-20030926-01 (26 September 2003) Abstract \| Full text \| Editor’s summary Sample sequencing of the dog genome yields good news for genomics in developing countries
	Research news Genomic instability switch identified David Secko Genome Biology 2003, 4:spotlight-20030926-02 (26 September 2003) Abstract \| Full text \| Editor’s summary An age-dependent switch causes old yeast cells to show increased genomic instability
	Research news Exploring the alternatives Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030930-01 (30 September 2003) Abstract \| Full text \| Editor’s summary Splicing investigators see medical applications and a possible new role in gene expression
	Research news Scleroderma exposed Cathy Holding Genome Biology 2003, 4:spotlight-20030930-02 (30 September 2003) Abstract \| Full text \| Editor’s summary Systematic analysis provides means for early detection of systemic scleroderma
	Research
	Research CpG content affects gene silencing in mice: evidence from novel transgenes Christine Chevalier-Mariette, Isabelle Henry, Lucile Montfort, Suzanne Capgras, Sylvie Forlani, John Muschler, Jean-François Nicolas Genome Biology 2003, 4:R53 (14 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary It has been demonstrated that the density of CpG sequences in the transcribed regions of transgenes can have a causal role in repression of transcription. These results show that the mechanism by which CpG islands escape de novo methylation is sensitive to CpG density of adjacent sequences.
	Research Comparison of K⁺-channel genes within the genomes of Anopheles gambiae and Drosophila melanogaster Thomas J McCormack Genome Biology 2003, 4:R58 (20 August 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The completion of the sequencing of the genomes of Drosophila melanogaster and Anopheles gambiae, which belong to the same order, the Diptera, allows us to compare and contrast K+-channel genes and gene families present within the genomes of two dipterans.
	Research The source of laterally transferred genes in bacterial genomes Vincent Daubin, Emmanuelle Lerat, Guy Perrière Genome Biology 2003, 4:R57 (21 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Contrary to previous hypotheses that methods for identifying laterally transferred genes cannot detect genes with similar base composition to that of the donor organism, it is suggested that the number of laterally transferred genes has not been underestimated and that laterally transferred genes fit the description of lambdoid phage genes called 'morons'.
	Research An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Jennifer L Reed, Thuy D Vo, Christophe H Schilling, Bernhard O Palsson Genome Biology 2003, 4:R54 (28 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-scale metabolic model of E. coli has been reconstructed, including 904 genes and 931 unique biochemical reactions, which gives a more complete and chemically accurate description of E. coli metabolism than previous models.
	Research Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ Marina V Omelchenko, Kira S Makarova, Yuri I Wolf, Igor B Rogozin, Eugene V Koonin Genome Biology 2003, 4:R55 (29 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and phylogenetic analysis have been used to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired orthologs and independent assembly of the same or similar operons from genes with different phylogenetic affinities.
	Research Different evolutionary patterns between young duplicate genes in the human genome Peng Zhang, Zhenglong Gu, Wen-Hsiung Li Genome Biology 2003, 4:R56 (1 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Duplicate genes tend to evolve in different patterns following the duplication event. One copy evolves faster than the other and accumulates amino-acid substitutions evenly across the sequence, whereas the other copy evolves more slowly and accumulates amino-acid substitutions unevenly across the sequence.
	Method Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach Michael Strong, Parag Mallick, Matteo Pellegrini, Michael J Thompson, David Eisenberg Genome Biology 2003, 4:R59 (29 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of Mycobacterium tuberculosis was used to evaluate and employ a method to infer genes likely to belong to the same operon, as judged by the nucleotide distance between genes in the same genomic orientation, and this method was combined with those of the Rosetta Stone, Phylogenetic Profile and conserved Gene Neighbor computational methods for the inference of protein function.
	Software DAVID: Database for Annotation, Visualization, and Integrated Discovery Glynn Dennis, Brad T Sherman, Douglas A Hosack, Jun Yang, Wei Gao, H Lane, Richard A Lempicki Genome Biology 2003, 4:R60 (14 August 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DAVID, a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries, has been described and will assist in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.

Explore Genome Biology

Articles

Volume 4 Issue 9

Comment

Review

Report

Research