Genome Biology | Volume 13 Issue 7

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	Volume 13 Issue 7
	Comment
	Research highlight The greatest catch: big game fishing for mRNA-bound proteins Christopher R Sibley, Jan Attig, Jernej Ule Genome Biology 2012, 13:163 (17 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Jernej Ule and colleagues highlight two recent studies that have identified many novel RNA-binding proteins
	Research highlight piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense Allison C Billi, Mallory A Freeberg, John K Kim Genome Biology 2012, 13:164 (20 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary John Kim and colleagues discuss transgenerational genome surveillance and the recognition of non-self by the worm piRNA system
	Research highlight The aging epigenome: DNA methylation from the cradle to the grave Marc Winnefeld, Frank Lyko Genome Biology 2012, 13:165 (30 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Frank Lyko and Marc Winnefeld highlight a new survey of age-related epigenetic changes in newborn and centenarian methylomes
	Review
	Review Autism genetics: searching for specificity and convergence Jamee M Berg, Daniel H Geschwind Genome Biology 2012, 13:247 (31 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Daniel Geschwind and Jamee Berg review the genes associated with autism spectrum disorders: how might their functions relate to one another?
	Report
	Meeting report Eastern genomics promises Scott C Edmunds Genome Biology 2012, 13:317 (17 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Bio-IT World Asia meeting, Marina Bay Sands, Singapore, 6-8 June 2012.
	Research
	Research Conserved rules govern genetic interaction degree across species Elizabeth N Koch, Michael Costanzo, Jeremy Bellay, Raamesh Deshpande, Kate Chatfield-Reed, Gordon Chua, Gennaro D'Urso, Brenda J Andrews, Charles Boone, Chad L Myers Genome Biology 2012, 13:R57 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genetic interaction degree is conserved between fission and budding yeast, but functional rewiring is also apparent
	Research Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome Atsunori Higashino, Ryuichi Sakate, Yosuke Kameoka, Ichiro Takahashi, Makoto Hirata, Reiko Tanuma, Tohru Masui, Yasuhiro Yasutomi, Naoki Osada Genome Biology 2012, 13:R58 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Malaysian cynomolgus macaque genome sheds light on structural variation between primate species
	Research E2F mediates enhanced alternative polyadenylation in proliferation Ran Elkon, Jarno Drost, Gijs van Haaften, Mathias Jenal, Mariette Schrier, Joachim AF Oude Vrielink, Reuven Agami Genome Biology 2012, 13:R59 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptome sequencing of two cell lines reveals shortened 3' UTRs and use of alternative polyadenylation sites associated with cell proliferation
	Research RNA processing in the minimal organism Nanoarchaeum equitans Lennart Randau Genome Biology 2012, 13:R63 (18 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq in the minimal archaeon Nanoarchaeum equitans reveals details of unusual RNA processing such as trans splicing of tRNA molecules
	Research Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates Sean Conlan, Lilia A Mijares, NISC Comparative Sequencing Program, Jesse Becker, Robert W Blakesley, Gerard G Bouffard, Shelise Brooks, Holly Coleman, Jyoti Gupta, Natalie Gurson, Morgan Park, Brian Schmidt, Pamela J Thomas, Michael Otto, Heidi H Kong, Patrick R Murray, Julia A Segre Genome Biology 2012, 13:R64 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparative genomics of skin commensal and hospital infection-associated isolates uncovers a putative clinical biomarker
	Research Developmental features of DNA methylation during activation of the embryonic zebrafish genome Ingrid S Andersen, Andrew H Reiner, Håvard Aanes, Peter Aleström, Philippe Collas Genome Biology 2012, 13:R65 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA methylation patterning at developmental genes is assayed before, during and after zygotic genome activation
	Research Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation Markus Lommer, Michael Specht, Alexandra-Sophie Roy, Lars Kraemer, Reidar Andreson, Magdalena A Gutowska, Juliane Wolf, Sonja V Bergner, Markus B Schilhabel, Ulrich C Klostermeier, Robert G Beiko, Philip Rosenstiel, Michael Hippler, Julie LaRoche Genome Biology 2012, 13:R66 (26 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptomic and proteomic insights into the low-iron tolerance of Thalassoiosira oceanic, an oceanic diatom
	Method A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples Serena Dollive, Gregory L Peterfreund, Scott Sherrill-Mix, Kyle Bittinger, Rohini Sinha, Christian Hoffmann, Christopher S Nabel, David A Hill, David Artis, Michael A Bachman, Rebecca Custers-Allen, Stephanie Grunberg, Gary D Wu, James D Lewis, Frederic D Bushman Genome Biology 2012, 13:R60 (3 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BROCC, a pipeline for the analysis of eukaryotes of microbiomes using conserved ribosomal rDNA sequences as markers
	Method Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman Genome Biology 2012, 13:R61 (11 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A model-based SNP caller for bisulfite sequencing data improves methylation estimates and imprinting analysis
	Software CIDeR: multifactorial interaction networks in human diseases Martin Lechner, Veit Höhn, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Gabi Kastenmüller, Brigitte Waegele, Andreas Ruepp Genome Biology 2012, 13:R62 (18 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A database of interactions in neurological and metabolic disorders, with a wide range of search options and graphical outputs

	Volume 13 Issue 7
	Comment
	Research highlight The greatest catch: big game fishing for mRNA-bound proteins Christopher R Sibley, Jan Attig, Jernej Ule Genome Biology 2012, 13:163 (17 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Jernej Ule and colleagues highlight two recent studies that have identified many novel RNA-binding proteins
	Research highlight piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense Allison C Billi, Mallory A Freeberg, John K Kim Genome Biology 2012, 13:164 (20 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary John Kim and colleagues discuss transgenerational genome surveillance and the recognition of non-self by the worm piRNA system
	Research highlight The aging epigenome: DNA methylation from the cradle to the grave Marc Winnefeld, Frank Lyko Genome Biology 2012, 13:165 (30 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Frank Lyko and Marc Winnefeld highlight a new survey of age-related epigenetic changes in newborn and centenarian methylomes
	Review
	Review Autism genetics: searching for specificity and convergence Jamee M Berg, Daniel H Geschwind Genome Biology 2012, 13:247 (31 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Daniel Geschwind and Jamee Berg review the genes associated with autism spectrum disorders: how might their functions relate to one another?
	Report
	Meeting report Eastern genomics promises Scott C Edmunds Genome Biology 2012, 13:317 (17 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Bio-IT World Asia meeting, Marina Bay Sands, Singapore, 6-8 June 2012.
	Research
	Research Conserved rules govern genetic interaction degree across species Elizabeth N Koch, Michael Costanzo, Jeremy Bellay, Raamesh Deshpande, Kate Chatfield-Reed, Gordon Chua, Gennaro D'Urso, Brenda J Andrews, Charles Boone, Chad L Myers Genome Biology 2012, 13:R57 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genetic interaction degree is conserved between fission and budding yeast, but functional rewiring is also apparent
	Research Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome Atsunori Higashino, Ryuichi Sakate, Yosuke Kameoka, Ichiro Takahashi, Makoto Hirata, Reiko Tanuma, Tohru Masui, Yasuhiro Yasutomi, Naoki Osada Genome Biology 2012, 13:R58 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Malaysian cynomolgus macaque genome sheds light on structural variation between primate species
	Research E2F mediates enhanced alternative polyadenylation in proliferation Ran Elkon, Jarno Drost, Gijs van Haaften, Mathias Jenal, Mariette Schrier, Joachim AF Oude Vrielink, Reuven Agami Genome Biology 2012, 13:R59 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptome sequencing of two cell lines reveals shortened 3' UTRs and use of alternative polyadenylation sites associated with cell proliferation
	Research RNA processing in the minimal organism Nanoarchaeum equitans Lennart Randau Genome Biology 2012, 13:R63 (18 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq in the minimal archaeon Nanoarchaeum equitans reveals details of unusual RNA processing such as trans splicing of tRNA molecules
	Research Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates Sean Conlan, Lilia A Mijares, NISC Comparative Sequencing Program, Jesse Becker, Robert W Blakesley, Gerard G Bouffard, Shelise Brooks, Holly Coleman, Jyoti Gupta, Natalie Gurson, Morgan Park, Brian Schmidt, Pamela J Thomas, Michael Otto, Heidi H Kong, Patrick R Murray, Julia A Segre Genome Biology 2012, 13:R64 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparative genomics of skin commensal and hospital infection-associated isolates uncovers a putative clinical biomarker
	Research Developmental features of DNA methylation during activation of the embryonic zebrafish genome Ingrid S Andersen, Andrew H Reiner, Håvard Aanes, Peter Aleström, Philippe Collas Genome Biology 2012, 13:R65 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA methylation patterning at developmental genes is assayed before, during and after zygotic genome activation
	Research Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation Markus Lommer, Michael Specht, Alexandra-Sophie Roy, Lars Kraemer, Reidar Andreson, Magdalena A Gutowska, Juliane Wolf, Sonja V Bergner, Markus B Schilhabel, Ulrich C Klostermeier, Robert G Beiko, Philip Rosenstiel, Michael Hippler, Julie LaRoche Genome Biology 2012, 13:R66 (26 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptomic and proteomic insights into the low-iron tolerance of Thalassoiosira oceanic, an oceanic diatom
	Method A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples Serena Dollive, Gregory L Peterfreund, Scott Sherrill-Mix, Kyle Bittinger, Rohini Sinha, Christian Hoffmann, Christopher S Nabel, David A Hill, David Artis, Michael A Bachman, Rebecca Custers-Allen, Stephanie Grunberg, Gary D Wu, James D Lewis, Frederic D Bushman Genome Biology 2012, 13:R60 (3 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BROCC, a pipeline for the analysis of eukaryotes of microbiomes using conserved ribosomal rDNA sequences as markers
	Method Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman Genome Biology 2012, 13:R61 (11 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A model-based SNP caller for bisulfite sequencing data improves methylation estimates and imprinting analysis
	Software CIDeR: multifactorial interaction networks in human diseases Martin Lechner, Veit Höhn, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Gabi Kastenmüller, Brigitte Waegele, Andreas Ruepp Genome Biology 2012, 13:R62 (18 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A database of interactions in neurological and metabolic disorders, with a wide range of search options and graphical outputs

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Volume 13 Issue 7

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