Genome Biology | Volume 11 Issue 7

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	Volume 11 Issue 7
	Comment
	Comment When the pie is too small Gregory A Petsko Genome Biology 2010, 11:127 (30 July 2010) Full text \| PDF \| PubMed \| Editor’s summary The NIH science funding pie has many mouths to feed; can a little go a long way?
	Research highlight How do proteins gain new domains? Joseph A Marsh, Sarah A Teichmann Genome Biology 2010, 11:126 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Research highlight Annotating conserved and novel features of primate transcriptomes using sequencing Philipp Khaitovich Genome Biology 2010, 11:125 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of chimpanzee and human transcripts reveals transcripts lost in humans and highlights the incompleteness of non-human primate genome annotations.
	Review
	Review Nuclear transcription factors in mammalian mitochondria Sarah Leigh-Brown, José Enriquez, Duncan T Odom Genome Biology 2010, 11:215 (29 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Some nuclear-encoded transcription factors also act within mitochondria to regulate mitochondrial function.
	Research
	Research Contrasting chromatin organization of CpG islands and exons in the human genome Jung Kyoon Choi Genome Biology 2010, 11:R70 (5 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of CpG methylation and histone positioning finds that these both help to define exons.
	Research Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays Adnane Sellam, Hervé Hogues, Christopher Askew, Faiza Tebbji, Marco van het Hoog, Hugo Lavoie, Carol A Kumamoto, Malcolm Whiteway, André Nantel Genome Biology 2010, 11:R71 (9 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Candida albicans transcriptional landscape reveals antisense transcription, novel open reading frames and non-coding RNAs, whose expression is correlated with RNA polymerase occupancy.
	Research Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes Rebecca A Chodroff, Leo Goodstadt, Tamara M Sirey, Peter L Oliver, Kay E Davies, Eric D Green, Zoltán Molnár, Chris P Ponting Genome Biology 2010, 11:R72 (12 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Long non-coding RNAs are shown to have conserved sequence and expression in brain tissue across amniotes, suggesting a conserved functional role.
	Research Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris et al. Genome Biology 2010, 11:R73 (13 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the plant pathogenic oomycete, Pythium ultimum and a comparison with the related potato blight pathogen genome reveals differences in pathogenicity.
	Research Quantifying the mechanisms of domain gain in animal proteins Marija Buljan, Adam Frankish, Alex Bateman Genome Biology 2010, 11:R74 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The main mechanism of domain gain in metazoan proteins is shown to be the joining of exons from adjacent genes.
	Research RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, Oliver J Rando Genome Biology 2010, 11:R75 (16 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-chip for RNA PolII occupancy and transcription analysis reveals that mRNA levels in yeast do not correlate with PolII abundance on genes.
	Research Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering Dwight Kuo, Kai Tan, Guy Zinman, Timothy Ravasi, Ziv Bar-Joseph, Trey Ideker Genome Biology 2010, 11:R77 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three yeast species respond to azole drugs in different ways and show different sensitivities to fluconazole
	Research Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing Anna Wetterbom, Adam Ameur, Lars Feuk, Ulf Gyllensten, Lucia Cavelier Genome Biology 2010, 11:R78 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of chimpanzee transcriptomes from different tissues and individuals using RNA-seq reveals novel transcribed regions.
	Research Paternally biased X inactivation in mouse neonatal brain Xu Wang, Paul D Soloway, Andrew G Clark Genome Biology 2010, 11:R79 (27 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pyrosequencing of X-linked genes in embryonic mouse brains reveals a small but statistically significant preference for inactivating the paternal X chromosome.
	Method Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis Eric Letouzé, Yves Allory, Marc A Bollet, François Radvanyi, Frédéric Guyon Genome Biology 2010, 11:R76 (22 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TuMult is a method for reconstructing the history of cancer progression from copy number variations in several samples from a patient
	Correspondence
	Correspondence Genomic information infrastructure after the deluge Julian Parkhill, Ewan Birney, Paul Kersey Genome Biology 2010, 11:402 (26 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands.

	Volume 11 Issue 7
	Comment
	Comment When the pie is too small Gregory A Petsko Genome Biology 2010, 11:127 (30 July 2010) Full text \| PDF \| PubMed \| Editor’s summary The NIH science funding pie has many mouths to feed; can a little go a long way?
	Research highlight How do proteins gain new domains? Joseph A Marsh, Sarah A Teichmann Genome Biology 2010, 11:126 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Research highlight Annotating conserved and novel features of primate transcriptomes using sequencing Philipp Khaitovich Genome Biology 2010, 11:125 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of chimpanzee and human transcripts reveals transcripts lost in humans and highlights the incompleteness of non-human primate genome annotations.
	Review
	Review Nuclear transcription factors in mammalian mitochondria Sarah Leigh-Brown, José Enriquez, Duncan T Odom Genome Biology 2010, 11:215 (29 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Some nuclear-encoded transcription factors also act within mitochondria to regulate mitochondrial function.
	Research
	Research Contrasting chromatin organization of CpG islands and exons in the human genome Jung Kyoon Choi Genome Biology 2010, 11:R70 (5 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of CpG methylation and histone positioning finds that these both help to define exons.
	Research Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays Adnane Sellam, Hervé Hogues, Christopher Askew, Faiza Tebbji, Marco van het Hoog, Hugo Lavoie, Carol A Kumamoto, Malcolm Whiteway, André Nantel Genome Biology 2010, 11:R71 (9 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Candida albicans transcriptional landscape reveals antisense transcription, novel open reading frames and non-coding RNAs, whose expression is correlated with RNA polymerase occupancy.
	Research Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes Rebecca A Chodroff, Leo Goodstadt, Tamara M Sirey, Peter L Oliver, Kay E Davies, Eric D Green, Zoltán Molnár, Chris P Ponting Genome Biology 2010, 11:R72 (12 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Long non-coding RNAs are shown to have conserved sequence and expression in brain tissue across amniotes, suggesting a conserved functional role.
	Research Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris et al. Genome Biology 2010, 11:R73 (13 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the plant pathogenic oomycete, Pythium ultimum and a comparison with the related potato blight pathogen genome reveals differences in pathogenicity.
	Research Quantifying the mechanisms of domain gain in animal proteins Marija Buljan, Adam Frankish, Alex Bateman Genome Biology 2010, 11:R74 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The main mechanism of domain gain in metazoan proteins is shown to be the joining of exons from adjacent genes.
	Research RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, Oliver J Rando Genome Biology 2010, 11:R75 (16 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-chip for RNA PolII occupancy and transcription analysis reveals that mRNA levels in yeast do not correlate with PolII abundance on genes.
	Research Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering Dwight Kuo, Kai Tan, Guy Zinman, Timothy Ravasi, Ziv Bar-Joseph, Trey Ideker Genome Biology 2010, 11:R77 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three yeast species respond to azole drugs in different ways and show different sensitivities to fluconazole
	Research Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing Anna Wetterbom, Adam Ameur, Lars Feuk, Ulf Gyllensten, Lucia Cavelier Genome Biology 2010, 11:R78 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of chimpanzee transcriptomes from different tissues and individuals using RNA-seq reveals novel transcribed regions.
	Research Paternally biased X inactivation in mouse neonatal brain Xu Wang, Paul D Soloway, Andrew G Clark Genome Biology 2010, 11:R79 (27 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pyrosequencing of X-linked genes in embryonic mouse brains reveals a small but statistically significant preference for inactivating the paternal X chromosome.
	Method Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis Eric Letouzé, Yves Allory, Marc A Bollet, François Radvanyi, Frédéric Guyon Genome Biology 2010, 11:R76 (22 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TuMult is a method for reconstructing the history of cancer progression from copy number variations in several samples from a patient
	Correspondence
	Correspondence Genomic information infrastructure after the deluge Julian Parkhill, Ewan Birney, Paul Kersey Genome Biology 2010, 11:402 (26 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands.

Explore Genome Biology

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Volume 11 Issue 7

Comment

Review

Research

Correspondence