Genome Biology | Volume 4 Issue 8

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	Volume 4 Issue 8
	Comment
	Comment Galileo's stepchildren Gregory A Petsko Genome Biology 2003, 4:114 (24 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Every enlightened society has held the view that science and the arts are not intrinsically incompatible. Which raises the question: what does that make us?
	Review
	Protein family review Angiotensin-I-converting enzyme and its relatives James F Riordan Genome Biology 2003, 4:225 (25 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Angiotensin-I-converting enzyme (ACE) is a monomeric, membrane-bound, zinc- and chloride-dependent protein that catalyzes the conversion of the decapeptide angiotensin I to the octapeptide angiotensin II. ACE is a key part of the system that regulates blood pressure, and recent X-ray structures may help design improved ACE inhibitors.
	Minireview Untangling genetic networks of panic, phobia, fear and anxiety Sandra Villafuerte, Margit Burmeister Genome Biology 2003, 4:224 (28 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As is the case for normal individual variation in anxiety levels, the conditions panic disorder, agoraphobia and other phobias have a significant genetic basis. Recent reports have started to untangle the genetic relationships between predispositions to anxiety and anxiety disorders.
	Opinion Comparative genomics of archaea: how much have we learned in six years, and what's next? Kira S Makarova, Eugene V Koonin Genome Biology 2003, 4:115 (16 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes that are represented in all sequenced archaeal genomes, plus a variable 'shell' that is prone to lineage-specific gene loss and horizontal gene exchange.
	Report
	Paper report Articles selected by Faculty of 1000: yeast metabolomics; genome-wide threading-based predictions; dissecting C. albicans growth pathways; knockout rats; ENU mutagenesis and humoral immunity Genome Biology 2003, 4:333 (7 July 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering yeast metabolomics, genome-wide threading-based predictions of protein-protein interactions, genetic analysis of filamentous growth in C. albicans, the production of knockout rats and genome-wide mutagenesis of humoral immune responses.
	Paper report Articles selected by Faculty of 1000: single-cell neuronal expression analysis; array analysis of chick hair cells; coiled-coil protein arrays; high-throughput identification of plasmodesmata-interacting proteins; multicompenent therapeutics Genome Biology 2003, 4:334 (18 July 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering single-cell neuronal expression analysis, array analysis of chick hair cells, coiled-coil protein arrays, high-throughput identification of plasmodesmata-interacting proteins and multicompenent therapeutics.
	Meeting report Getting positive about selection Eugene V Koonin, Igor B Rogozin Genome Biology 2003, 4:331 (23 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 68th Symposium on Quantitative Biology, 'The Genome of Homo Sapiens', Cold Spring Harbor, USA, 28 May-2 June 2003.
	Meeting report From microarrays to genome duplications Christian Roth, Timothy Hughes Genome Biology 2003, 4:332 (23 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the fifth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), 'Bioinformatics 2003', Helsinki, Finland, 22-24 May 2003.
	Research news Malaria in profile Cathy Holding Genome Biology 2003, 4:spotlight-20030801-01 (1 August 2003) Abstract \| Full text \| Editor’s summary A high-density microarray reveals the gene expression pattern of the Plasmodium life cycle
	Research news Arabidopsis insertional mutant database C L Bishop Genome Biology 2003, 4:spotlight-20030801-02 (1 August 2003) Abstract \| Full text \| Editor’s summary Analysis of a genome-wide mutant collection reveals a novel ethylene pathway protein family
	Research news Tony Hyman wins EMBO Gold Medal Martina Habeck Genome Biology 2003, 4:spotlight-20030805-01 (5 August 2003) Abstract \| Full text \| Editor’s summary EMBO award goes to cell biologist for work on cell division mechanisms
	Research news Alien genes in bacteria Cathy Holding Genome Biology 2003, 4:spotlight-20030808-01 (8 August 2003) Abstract \| Full text \| Editor’s summary Lateral gene transfer can cause phylogenetic conflict but may not be the only mechanism
	Research news Controlling origins of replication Cathy Holding Genome Biology 2003, 4:spotlight-20030812-01 (12 August 2003) Abstract \| Full text \| Editor’s summary Nucleotide pools are implicated in modulating the speed of cell division
	Research news Survival of the not-so-fit Cathy Holding Genome Biology 2003, 4:spotlight-20030814-01 (14 August 2003) Abstract \| Full text \| Editor’s summary Whooping cough bacteria may only have survived by evolving coincidentally with the human population explosion
	Research news Adding insult to injury Cathy Holding Genome Biology 2003, 4:spotlight-20030815-01 (15 August 2003) Abstract \| Full text \| Editor’s summary A putative splicing factor mutation causes phenotypic variation of an inherited disease
	Research news A large look at lipids Diane Martindale Genome Biology 2003, 4:spotlight-20030818-01 (18 August 2003) Abstract \| Full text \| Editor’s summary Major grant will fund team effort to characterize human lipidome
	Research news NIH to build zebrafish lab Ted Agres Genome Biology 2003, 4:spotlight-20030820-02 (20 August 2003) Abstract \| Full text \| Editor’s summary Genomic utility spawns demand by researchers
	Research news Martha Chase dies Milly Dawson Genome Biology 2003, 4:spotlight-20030820-01 (20 August 2003) Abstract \| Full text \| Editor’s summary With Alfred D. Hershey, she established DNA as the genetic material
	Research news JAW miRNAs regulate plant development C L Bishop Genome Biology 2003, 4:spotlight-20030820-02 (21 August 2003) Abstract \| Full text \| Editor’s summary Identification of a conserved miRNA-producing locus in Arabidopsis
	Research news Highlighting hotspots Joe Bateman Genome Biology 2003, 4:spotlight-20030821-01 (21 August 2003) Abstract \| Full text \| Editor’s summary Two studies emphasize that all genes are not equal targets for evolutionary variation
	Research news Sex and the honeybee Cathy Holding Genome Biology 2003, 4:spotlight-20030827-01 (27 August 2003) Abstract \| Full text \| Editor’s summary Identifying the primary sex-determining signal reveals the mechanisms behind complementary sex determination
	Research news Old genes, new tricks Stuart Blackman Genome Biology 2003, 4:spotlight-20030828-01 (28 August 2003) Abstract \| Full text \| Editor’s summary A role for highly conserved Hox genes has been revealed in the evolution of novel molluscan structures
	Research news Nanos keeps its job David Secko Genome Biology 2003, 4:spotlight-20030829-01 (29 August 2003) Abstract \| Full text \| Editor’s summary Analysis of two mouse Nanos proteins reveals their conserved role in germ cell development
	Research
	Research Recent segmental and gene duplications in the mouse genome Joseph Cheung, Michael D Wilson, Junjun Zhang, Razi Khaja, Jeffrey R MacDonald, Henry HQ Heng, Ben F Koop, Stephen W Scherer Genome Biology 2003, 4:R47 (9 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BLAST-based computational heuristics were used to identify large and recent segmental duplications in the mouse genome sequence. Here a database of recently duplicated regions of the mouse genome is presented.
	Research Duplication is more common among laterally transferred genes than among indigenous genes Sean D Hooper, Otto G Berg Genome Biology 2003, 4:R48 (11 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using both a compositional method and a gene-tree approach, a number of proposed laterally transferred genes have been identified and their nucleotide composition and frequency of duplication studied.
	Research Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster Devin P Locke, Nicoletta Archidiacono, Doriana Misceo, Maria Cardone, Stephane Deschamps, Bruce Roe, Mariano Rocchi, Evan E Eichler Genome Biology 2003, 4:R50 (15 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative fluorescence in situ hybridization approach, using probes selected from a combination of physical mapping, genomic sequence, and segmental duplication analyses has been employed to narrow the breakpoint interval of a pericentric inversion in chimpanzee involving the orthologous human 15q11-q13 region.
	Software THoR: a tool for domain discovery and curation of multiple alignments Nicholas J Dickens, Chris P Ponting Genome Biology 2003, 4:R52 (23 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A tool, THoR, has been described that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an accurate and comprehensive alignment for any domain family.
	Software A comparative proteomics resource: proteins of Arabidopsis thaliana Wilfred W Li, Greg B Quinn, Nickolai N Alexandrov, Philip E Bourne, Ilya N Shindyalov Genome Biology 2003, 4:R51 (28 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using an integrative genome annotation pipeline (iGAP) for proteome-wide protein structure and functional domain assignment, all the proteins of Arabidopsis thaliana have been analyzed.

	Volume 4 Issue 8
	Comment
	Comment Galileo's stepchildren Gregory A Petsko Genome Biology 2003, 4:114 (24 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Every enlightened society has held the view that science and the arts are not intrinsically incompatible. Which raises the question: what does that make us?
	Review
	Protein family review Angiotensin-I-converting enzyme and its relatives James F Riordan Genome Biology 2003, 4:225 (25 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Angiotensin-I-converting enzyme (ACE) is a monomeric, membrane-bound, zinc- and chloride-dependent protein that catalyzes the conversion of the decapeptide angiotensin I to the octapeptide angiotensin II. ACE is a key part of the system that regulates blood pressure, and recent X-ray structures may help design improved ACE inhibitors.
	Minireview Untangling genetic networks of panic, phobia, fear and anxiety Sandra Villafuerte, Margit Burmeister Genome Biology 2003, 4:224 (28 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As is the case for normal individual variation in anxiety levels, the conditions panic disorder, agoraphobia and other phobias have a significant genetic basis. Recent reports have started to untangle the genetic relationships between predispositions to anxiety and anxiety disorders.
	Opinion Comparative genomics of archaea: how much have we learned in six years, and what's next? Kira S Makarova, Eugene V Koonin Genome Biology 2003, 4:115 (16 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes that are represented in all sequenced archaeal genomes, plus a variable 'shell' that is prone to lineage-specific gene loss and horizontal gene exchange.
	Report
	Paper report Articles selected by Faculty of 1000: yeast metabolomics; genome-wide threading-based predictions; dissecting C. albicans growth pathways; knockout rats; ENU mutagenesis and humoral immunity Genome Biology 2003, 4:333 (7 July 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering yeast metabolomics, genome-wide threading-based predictions of protein-protein interactions, genetic analysis of filamentous growth in C. albicans, the production of knockout rats and genome-wide mutagenesis of humoral immune responses.
	Paper report Articles selected by Faculty of 1000: single-cell neuronal expression analysis; array analysis of chick hair cells; coiled-coil protein arrays; high-throughput identification of plasmodesmata-interacting proteins; multicompenent therapeutics Genome Biology 2003, 4:334 (18 July 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering single-cell neuronal expression analysis, array analysis of chick hair cells, coiled-coil protein arrays, high-throughput identification of plasmodesmata-interacting proteins and multicompenent therapeutics.
	Meeting report Getting positive about selection Eugene V Koonin, Igor B Rogozin Genome Biology 2003, 4:331 (23 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 68th Symposium on Quantitative Biology, 'The Genome of Homo Sapiens', Cold Spring Harbor, USA, 28 May-2 June 2003.
	Meeting report From microarrays to genome duplications Christian Roth, Timothy Hughes Genome Biology 2003, 4:332 (23 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the fifth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), 'Bioinformatics 2003', Helsinki, Finland, 22-24 May 2003.
	Research news Malaria in profile Cathy Holding Genome Biology 2003, 4:spotlight-20030801-01 (1 August 2003) Abstract \| Full text \| Editor’s summary A high-density microarray reveals the gene expression pattern of the Plasmodium life cycle
	Research news Arabidopsis insertional mutant database C L Bishop Genome Biology 2003, 4:spotlight-20030801-02 (1 August 2003) Abstract \| Full text \| Editor’s summary Analysis of a genome-wide mutant collection reveals a novel ethylene pathway protein family
	Research news Tony Hyman wins EMBO Gold Medal Martina Habeck Genome Biology 2003, 4:spotlight-20030805-01 (5 August 2003) Abstract \| Full text \| Editor’s summary EMBO award goes to cell biologist for work on cell division mechanisms
	Research news Alien genes in bacteria Cathy Holding Genome Biology 2003, 4:spotlight-20030808-01 (8 August 2003) Abstract \| Full text \| Editor’s summary Lateral gene transfer can cause phylogenetic conflict but may not be the only mechanism
	Research news Controlling origins of replication Cathy Holding Genome Biology 2003, 4:spotlight-20030812-01 (12 August 2003) Abstract \| Full text \| Editor’s summary Nucleotide pools are implicated in modulating the speed of cell division
	Research news Survival of the not-so-fit Cathy Holding Genome Biology 2003, 4:spotlight-20030814-01 (14 August 2003) Abstract \| Full text \| Editor’s summary Whooping cough bacteria may only have survived by evolving coincidentally with the human population explosion
	Research news Adding insult to injury Cathy Holding Genome Biology 2003, 4:spotlight-20030815-01 (15 August 2003) Abstract \| Full text \| Editor’s summary A putative splicing factor mutation causes phenotypic variation of an inherited disease
	Research news A large look at lipids Diane Martindale Genome Biology 2003, 4:spotlight-20030818-01 (18 August 2003) Abstract \| Full text \| Editor’s summary Major grant will fund team effort to characterize human lipidome
	Research news NIH to build zebrafish lab Ted Agres Genome Biology 2003, 4:spotlight-20030820-02 (20 August 2003) Abstract \| Full text \| Editor’s summary Genomic utility spawns demand by researchers
	Research news Martha Chase dies Milly Dawson Genome Biology 2003, 4:spotlight-20030820-01 (20 August 2003) Abstract \| Full text \| Editor’s summary With Alfred D. Hershey, she established DNA as the genetic material
	Research news JAW miRNAs regulate plant development C L Bishop Genome Biology 2003, 4:spotlight-20030820-02 (21 August 2003) Abstract \| Full text \| Editor’s summary Identification of a conserved miRNA-producing locus in Arabidopsis
	Research news Highlighting hotspots Joe Bateman Genome Biology 2003, 4:spotlight-20030821-01 (21 August 2003) Abstract \| Full text \| Editor’s summary Two studies emphasize that all genes are not equal targets for evolutionary variation
	Research news Sex and the honeybee Cathy Holding Genome Biology 2003, 4:spotlight-20030827-01 (27 August 2003) Abstract \| Full text \| Editor’s summary Identifying the primary sex-determining signal reveals the mechanisms behind complementary sex determination
	Research news Old genes, new tricks Stuart Blackman Genome Biology 2003, 4:spotlight-20030828-01 (28 August 2003) Abstract \| Full text \| Editor’s summary A role for highly conserved Hox genes has been revealed in the evolution of novel molluscan structures
	Research news Nanos keeps its job David Secko Genome Biology 2003, 4:spotlight-20030829-01 (29 August 2003) Abstract \| Full text \| Editor’s summary Analysis of two mouse Nanos proteins reveals their conserved role in germ cell development
	Research
	Research Recent segmental and gene duplications in the mouse genome Joseph Cheung, Michael D Wilson, Junjun Zhang, Razi Khaja, Jeffrey R MacDonald, Henry HQ Heng, Ben F Koop, Stephen W Scherer Genome Biology 2003, 4:R47 (9 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BLAST-based computational heuristics were used to identify large and recent segmental duplications in the mouse genome sequence. Here a database of recently duplicated regions of the mouse genome is presented.
	Research Duplication is more common among laterally transferred genes than among indigenous genes Sean D Hooper, Otto G Berg Genome Biology 2003, 4:R48 (11 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using both a compositional method and a gene-tree approach, a number of proposed laterally transferred genes have been identified and their nucleotide composition and frequency of duplication studied.
	Research Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster Devin P Locke, Nicoletta Archidiacono, Doriana Misceo, Maria Cardone, Stephane Deschamps, Bruce Roe, Mariano Rocchi, Evan E Eichler Genome Biology 2003, 4:R50 (15 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative fluorescence in situ hybridization approach, using probes selected from a combination of physical mapping, genomic sequence, and segmental duplication analyses has been employed to narrow the breakpoint interval of a pericentric inversion in chimpanzee involving the orthologous human 15q11-q13 region.
	Software THoR: a tool for domain discovery and curation of multiple alignments Nicholas J Dickens, Chris P Ponting Genome Biology 2003, 4:R52 (23 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A tool, THoR, has been described that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an accurate and comprehensive alignment for any domain family.
	Software A comparative proteomics resource: proteins of Arabidopsis thaliana Wilfred W Li, Greg B Quinn, Nickolai N Alexandrov, Philip E Bourne, Ilya N Shindyalov Genome Biology 2003, 4:R51 (28 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using an integrative genome annotation pipeline (iGAP) for proteome-wide protein structure and functional domain assignment, all the proteins of Arabidopsis thaliana have been analyzed.

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Volume 4 Issue 8

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