Genome Biology | Volume 6 Issue 5

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	Volume 6 Issue 5
	Comment
	Comment A matter of life and death Gregory A Petsko Genome Biology 2005, 6:109 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Our ability to sustain some of the outward signs of life has rendered obsolete the legal system's definition of what it means to be alive.
	Opinion Why genes persist in organelle genomes Daniel O Daley, James Whelan Genome Biology 2005, 6:110 (29 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mitochondria and plastids (including chloroplasts) have a small but vital genetic coding capacity, but what are the properties of some genes that dictate that they must remain encoded in organelles?
	Review
	Protein family review The cryptochromes Chentao Lin, Takeshi Todo Genome Biology 2005, 6:220 (29 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cryptochromes are photoreceptors that regulate entrainment of the circadian clock by light in plants and animals. They are related to DNA photolyases and have similar three-dimensional structures, characterized by a α/β domain and a helical domain and including a chromophore, flavin adenine dinucleotide.
	Minireview Marsupials and monotremes sort genome treasures from junk Matthew J Wakefield, Jennifer AM Graves Genome Biology 2005, 6:218 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals and more distant vertebrate species.
	Minireview Circadian clocks are seeing the systems biology light Kevin R Hayes, Julie E Baggs, John B Hogenesch Genome Biology 2005, 6:219 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The generation of a circadian transcriptional network has led to a better understanding of the gene-expression patterns that regulate the precise 24-hour clock.
	Report
	Paper report Articles selected by Faculty of 1000: similar embryos from divergent genomes; gene expression variation in twins; the E. coli stress response network; adaptive immune system evolution; alloployploid tobacco evolution Genome Biology 2005, 6:322 (8 April 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering similar embryos from divergent genomes; gene expression variation in twins; the E. coli stress response network; adaptive immune system evolution; alloployploid tobacco evolution.
	Paper report Articles selected by Faculty of 1000: enhancer evolution in flies; modeling nuclear import; cell-cycle kinase substrates; transgenic plants change little; early embryo epigenetics Genome Biology 2005, 6:323 (22 April 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering enhancer evolution in flies; modeling nuclear import; cell-cycle kinase substrates; transgenic plants change little; early embryo epigenetics.
	Meeting report The diversity of bacterial pathogenicity mechanisms Eugene Rosenberg Genome Biology 2005, 6:320 (8 April 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the international conference 'Molecular basis of bacterial pathogenesis', sponsored by the Federation of European Microbiological Societies (FEMS) and the Israel Center for the Study of Emerging Diseases, Ein Gedi, Israel, 23-27 January 2005.
	Deposited research article All motifs are NOT created equal: structural properties of transcription factor-DNA interactions and the inference of sequence specificity Michael B Eisen Genome Biology 2005, 6:P7 (31 March 2005) Abstract \| Full text \| PDF \| Editor’s summary The identification of transcription factor binding sites in genome sequences is an important problem in contemporary sequence analysis. Our structural and biochemical understanding of the interactions between transcription factors and DNA can be used to guide de novo motif detection methods.
	Deposited research article Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences Yi Xing, Christopher Lee Genome Biology 2005, 6:P8 (11 April 2005) Abstract \| Full text \| PDF \| Editor’s summary We show that alternative splicing relaxes Ka/Ks selection pressure up to seven-fold, but this effect is accompanied by a strong increase in selection pressure against synonymous mutations, which propagates into the adjacent intron, and correlates strongly with the alternative splicing level observed for each exon. Thus alternative splicing apparently can create evolutionary "hotspots" within a protein sequence, and these events have evidently been selected for during mammalian evolution.
	Research news Planarians enter the genomic era Sarah Rothman Genome Biology 2005, 6:spotlight-20050503-01 (3 May 2005) Abstract \| Full text \| Editor’s summary Study in Developmental Cell uses RNAi to probe Schmidtea mediterranea genome
	Research news Signs of selection in our genes Nick Atkinson Genome Biology 2005, 6:spotlight-20050506-01 (6 May 2005) Abstract \| Full text \| Editor’s summary In chimp and human genomes, team finds surprising evidence of selection in apoptosis genes
	Research news Molecular pathway for Monarchs Clementine Wallace Genome Biology 2005, 6:spotlight-20050506-02 (6 May 2005) Abstract \| Full text \| Editor’s summary System links the migratory butterflies' circadian clock and sun compass
	Research news Catalase extends mouse lifespan Don Monroe Genome Biology 2005, 6:spotlight-20050506-03 (6 May 2005) Abstract \| Full text \| Editor’s summary Targeting the antioxidant enzyme to mitochondria supports the free-radical theory of aging
	Research news HIV-1 induces RNA silencing Graciela Flores Genome Biology 2005, 6:spotlight-20050518-01 (17 May 2005) Abstract \| Full text \| Editor’s summary Report in Immunity is first of natural siRNAs triggered by the virus
	Research news Wellcome insists on open access Stephen Pincock Genome Biology 2005, 6:spotlight-20050523-01 (23 May 2005) Abstract \| Full text \| Editor’s summary As of October, all new grant recipients will be required to deposit papers with PubMed Central
	Research news Transcription factor moonlights Graciela Flores Genome Biology 2005, 6:spotlight-20050527-01 (27 May 2005) Abstract \| Full text \| Editor’s summary ATF2, which functions in gene regulation, has another job working in DNA damage response
	Research
	Research Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis Ran Elkon, Sharon Rashi-Elkeles, Yaniv Lerenthal, Chaim Linhart, Tamar Tenne, Ninette Amariglio, Gideon Rechavi, Ron Shamir, Yosef Shiloh Genome Biology 2005, 6:R43 (13 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray and RNAi technologies were applied to dissect a transcriptional network induced by DNA damage in human cells, revealing that two pivotal stress-induced transcription factors (NFκB and p53) mediated most of the damage-induced gene activation while a major transducer of the cellular responses to double strand breaks (ATM) was required for the activation of both pathways.
	Research Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Celine Brochier, Simonetta Gribaldo, Yvan Zivanovic, Fabrice Confalonieri, Patrick Forterre Genome Biology 2005, 6:R42 (14 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An analysis of the position of Nanoarcheum equitans in the archaeal phylogeny using a large dataset of concatenated ribosomal proteins from 25 archaeal genomes suggests that N. equitans is likely to be the representative of a fast-evolving euryarchaeal lineage.
	Research Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome Arun K Ramani, Razvan C Bunescu, Raymond J Mooney, Edward M Marcotte Genome Biology 2005, 6:R40 (15 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In order to consolidate the known human proteins interactions two tests were developed to measure the relative accuracy of the available interaction data. In addition, 6,580 interactions among 3,737 human proteins were recovered from Medline abstracts and combined with existing interaction data to obtain a network of 31,609 interactions among 7,748 human proteins, accurate to the same degree as the existing data sets.
	Research Genome-scale evidence of the nematode-arthropod clade Hernán Dopazo, Joaquín Dopazo Genome Biology 2005, 6:R41 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The most extensive phylogenetic analysis carried out to date, including 11 complete genomes, is shown to support the Ecdysozoa hypothesis in the open-ended debate of the Coelomata-Ecdysozoa evolutionary problem.
	Method Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions L Ryan Baugh, Joanne C Wen, Andrew A Hill, Donna K Slonim, Eugene L Brown, Craig P Hunter Genome Biology 2005, 6:R45 (11 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To identify interactions among genes implicated in posterior patterning of the C. elegans embryo, synthetic lethality following RNA interference of 22 genes was measured in 15 mutant strains. A pair of homologous T-Box transcription factors was found to interact in both C. elegans and C. briggsae, indicating that their compensatory function is conserved.
	Method Relations in biomedical ontologies Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector, Cornelius Rosse Genome Biology 2005, 6:R46 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation.
	Method The Sequence Ontology: a tool for the unification of genome annotations Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin, Michael Ashburner Genome Biology 2005, 6:R44 (29 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The goal of the Sequence Ontology (SO) project is to produce a structured controlled vocabulary with a common set of terms and definitions for parts of a genomic annotation, and to describe the relationships among them. Details of SO construction, design and use, particularly with regard to part-whole relationships are discussed and the practical utility of SO is demonstrated for a set of genome annotations from Drosophila melanogaster.
	Software The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging Ilya G Goldberg, Chris Allan, Jean-Marie Burel, Doug Creager, Andrea Falconi, Harry Hochheiser, Josiah Johnston, Jeff Mellen, Peter K Sorger, Jason R Swedlow Genome Biology 2005, 6:R47 (3 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Open Microscopy Environment (OME) defines a data model and software implementation to serve as an informatics framework for imaging in biological microscopy experiments.

	Volume 6 Issue 5
	Comment
	Comment A matter of life and death Gregory A Petsko Genome Biology 2005, 6:109 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Our ability to sustain some of the outward signs of life has rendered obsolete the legal system's definition of what it means to be alive.
	Opinion Why genes persist in organelle genomes Daniel O Daley, James Whelan Genome Biology 2005, 6:110 (29 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mitochondria and plastids (including chloroplasts) have a small but vital genetic coding capacity, but what are the properties of some genes that dictate that they must remain encoded in organelles?
	Review
	Protein family review The cryptochromes Chentao Lin, Takeshi Todo Genome Biology 2005, 6:220 (29 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cryptochromes are photoreceptors that regulate entrainment of the circadian clock by light in plants and animals. They are related to DNA photolyases and have similar three-dimensional structures, characterized by a α/β domain and a helical domain and including a chromophore, flavin adenine dinucleotide.
	Minireview Marsupials and monotremes sort genome treasures from junk Matthew J Wakefield, Jennifer AM Graves Genome Biology 2005, 6:218 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals and more distant vertebrate species.
	Minireview Circadian clocks are seeing the systems biology light Kevin R Hayes, Julie E Baggs, John B Hogenesch Genome Biology 2005, 6:219 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The generation of a circadian transcriptional network has led to a better understanding of the gene-expression patterns that regulate the precise 24-hour clock.
	Report
	Paper report Articles selected by Faculty of 1000: similar embryos from divergent genomes; gene expression variation in twins; the E. coli stress response network; adaptive immune system evolution; alloployploid tobacco evolution Genome Biology 2005, 6:322 (8 April 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering similar embryos from divergent genomes; gene expression variation in twins; the E. coli stress response network; adaptive immune system evolution; alloployploid tobacco evolution.
	Paper report Articles selected by Faculty of 1000: enhancer evolution in flies; modeling nuclear import; cell-cycle kinase substrates; transgenic plants change little; early embryo epigenetics Genome Biology 2005, 6:323 (22 April 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering enhancer evolution in flies; modeling nuclear import; cell-cycle kinase substrates; transgenic plants change little; early embryo epigenetics.
	Meeting report The diversity of bacterial pathogenicity mechanisms Eugene Rosenberg Genome Biology 2005, 6:320 (8 April 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the international conference 'Molecular basis of bacterial pathogenesis', sponsored by the Federation of European Microbiological Societies (FEMS) and the Israel Center for the Study of Emerging Diseases, Ein Gedi, Israel, 23-27 January 2005.
	Deposited research article All motifs are NOT created equal: structural properties of transcription factor-DNA interactions and the inference of sequence specificity Michael B Eisen Genome Biology 2005, 6:P7 (31 March 2005) Abstract \| Full text \| PDF \| Editor’s summary The identification of transcription factor binding sites in genome sequences is an important problem in contemporary sequence analysis. Our structural and biochemical understanding of the interactions between transcription factors and DNA can be used to guide de novo motif detection methods.
	Deposited research article Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences Yi Xing, Christopher Lee Genome Biology 2005, 6:P8 (11 April 2005) Abstract \| Full text \| PDF \| Editor’s summary We show that alternative splicing relaxes Ka/Ks selection pressure up to seven-fold, but this effect is accompanied by a strong increase in selection pressure against synonymous mutations, which propagates into the adjacent intron, and correlates strongly with the alternative splicing level observed for each exon. Thus alternative splicing apparently can create evolutionary "hotspots" within a protein sequence, and these events have evidently been selected for during mammalian evolution.
	Research news Planarians enter the genomic era Sarah Rothman Genome Biology 2005, 6:spotlight-20050503-01 (3 May 2005) Abstract \| Full text \| Editor’s summary Study in Developmental Cell uses RNAi to probe Schmidtea mediterranea genome
	Research news Signs of selection in our genes Nick Atkinson Genome Biology 2005, 6:spotlight-20050506-01 (6 May 2005) Abstract \| Full text \| Editor’s summary In chimp and human genomes, team finds surprising evidence of selection in apoptosis genes
	Research news Molecular pathway for Monarchs Clementine Wallace Genome Biology 2005, 6:spotlight-20050506-02 (6 May 2005) Abstract \| Full text \| Editor’s summary System links the migratory butterflies' circadian clock and sun compass
	Research news Catalase extends mouse lifespan Don Monroe Genome Biology 2005, 6:spotlight-20050506-03 (6 May 2005) Abstract \| Full text \| Editor’s summary Targeting the antioxidant enzyme to mitochondria supports the free-radical theory of aging
	Research news HIV-1 induces RNA silencing Graciela Flores Genome Biology 2005, 6:spotlight-20050518-01 (17 May 2005) Abstract \| Full text \| Editor’s summary Report in Immunity is first of natural siRNAs triggered by the virus
	Research news Wellcome insists on open access Stephen Pincock Genome Biology 2005, 6:spotlight-20050523-01 (23 May 2005) Abstract \| Full text \| Editor’s summary As of October, all new grant recipients will be required to deposit papers with PubMed Central
	Research news Transcription factor moonlights Graciela Flores Genome Biology 2005, 6:spotlight-20050527-01 (27 May 2005) Abstract \| Full text \| Editor’s summary ATF2, which functions in gene regulation, has another job working in DNA damage response
	Research
	Research Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis Ran Elkon, Sharon Rashi-Elkeles, Yaniv Lerenthal, Chaim Linhart, Tamar Tenne, Ninette Amariglio, Gideon Rechavi, Ron Shamir, Yosef Shiloh Genome Biology 2005, 6:R43 (13 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray and RNAi technologies were applied to dissect a transcriptional network induced by DNA damage in human cells, revealing that two pivotal stress-induced transcription factors (NFκB and p53) mediated most of the damage-induced gene activation while a major transducer of the cellular responses to double strand breaks (ATM) was required for the activation of both pathways.
	Research Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Celine Brochier, Simonetta Gribaldo, Yvan Zivanovic, Fabrice Confalonieri, Patrick Forterre Genome Biology 2005, 6:R42 (14 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An analysis of the position of Nanoarcheum equitans in the archaeal phylogeny using a large dataset of concatenated ribosomal proteins from 25 archaeal genomes suggests that N. equitans is likely to be the representative of a fast-evolving euryarchaeal lineage.
	Research Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome Arun K Ramani, Razvan C Bunescu, Raymond J Mooney, Edward M Marcotte Genome Biology 2005, 6:R40 (15 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In order to consolidate the known human proteins interactions two tests were developed to measure the relative accuracy of the available interaction data. In addition, 6,580 interactions among 3,737 human proteins were recovered from Medline abstracts and combined with existing interaction data to obtain a network of 31,609 interactions among 7,748 human proteins, accurate to the same degree as the existing data sets.
	Research Genome-scale evidence of the nematode-arthropod clade Hernán Dopazo, Joaquín Dopazo Genome Biology 2005, 6:R41 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The most extensive phylogenetic analysis carried out to date, including 11 complete genomes, is shown to support the Ecdysozoa hypothesis in the open-ended debate of the Coelomata-Ecdysozoa evolutionary problem.
	Method Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions L Ryan Baugh, Joanne C Wen, Andrew A Hill, Donna K Slonim, Eugene L Brown, Craig P Hunter Genome Biology 2005, 6:R45 (11 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To identify interactions among genes implicated in posterior patterning of the C. elegans embryo, synthetic lethality following RNA interference of 22 genes was measured in 15 mutant strains. A pair of homologous T-Box transcription factors was found to interact in both C. elegans and C. briggsae, indicating that their compensatory function is conserved.
	Method Relations in biomedical ontologies Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector, Cornelius Rosse Genome Biology 2005, 6:R46 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation.
	Method The Sequence Ontology: a tool for the unification of genome annotations Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin, Michael Ashburner Genome Biology 2005, 6:R44 (29 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The goal of the Sequence Ontology (SO) project is to produce a structured controlled vocabulary with a common set of terms and definitions for parts of a genomic annotation, and to describe the relationships among them. Details of SO construction, design and use, particularly with regard to part-whole relationships are discussed and the practical utility of SO is demonstrated for a set of genome annotations from Drosophila melanogaster.
	Software The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging Ilya G Goldberg, Chris Allan, Jean-Marie Burel, Doug Creager, Andrea Falconi, Harry Hochheiser, Josiah Johnston, Jeff Mellen, Peter K Sorger, Jason R Swedlow Genome Biology 2005, 6:R47 (3 May 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Open Microscopy Environment (OME) defines a data model and software implementation to serve as an informatics framework for imaging in biological microscopy experiments.

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