Genome Biology | Volume 14 Issue 7

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	Volume 14 Issue 7
	Comment
	Comment So, you want to sequence a genome... Derek L Stemple Genome Biology 2013, 14:128 (30 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Derek Stemple discusses lessons learned from the zebrafish genome project
	Research highlight MicroRNAs circulate around Alzheimer's disease Thalyana Smith-Vikos, Frank J Slack Genome Biology 2013, 14:125 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Frank Slack and Thalyana Smith-Vikos discuss the blood miRNA signature for Alzheimer's disease reported in this issue of Genome Biology
	Research highlight DNA methylation, genotype and gene expression: who is driving and who is along for the ride? Meaghan J Jones, Anthony P Fejes, Michael S Kobor Genome Biology 2013, 14:126 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Michael Kobor and colleagues discuss regulatory interactions between DNA methylation, genotype and gene expression
	Research highlight Microbiota's 'little helpers': bacteriophages and antibiotic-associated responses in the gut microbiome Christine L Sun, David A Relman Genome Biology 2013, 14:127 (30 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Relman and Christine Sun discuss recent research into how bacteriophage mediate the impact of antibiotics on the gut microbiome
	Review
	Review Ant genomics sheds light on the molecular regulation of social organization Romain Libbrecht, Peter R Oxley, Daniel JC Kronauer, Laurent Keller Genome Biology 2013, 14:212 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Laurent Keller and colleagues review new insights into insect social organization that have arisen from ant genome sequences and epigenomics research
	Report
	Meeting report Next-generation sequencing for identifying new genes in rare genetic diseases: many challenges and a pinch of luck Amélie Bonnefond, Philippe Froguel Genome Biology 2013, 14:309 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the European Society of Human Genetics conference, held in Paris, France, June 8-11, 2013
	Research
	Research Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene Mar Gonzàlez-Porta, Adam Frankish, Johan Rung, Jennifer Harrow, Alvis Brazma Genome Biology 2013, 14:R70 (1 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of RNA-seq data across different tissues and cell lines reveals that the majority of genes have a single dominant transcript
	Research Variants in exons and in transcription factors affect gene expression in trans Anat Kreimer, Itsik Pe'er Genome Biology 2013, 14:R71 (11 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Mapping of eSNPs onto a protein-protein interaction network reveals that SNPs in transcription factors can have a trans effect
	Research A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design Robin P Smith, Samantha J Riesenfeld, Alisha K Holloway, Qiang Li, Karl K Murphy, Natalie M Feliciano, Lorenzo Orecchia, Nir Oksenberg, Katherine S Pollard, Nadav Ahituv Genome Biology 2013, 14:R72 (18 July 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary All possible 6-mers are incorporated into a compact set of 15-mer synthetic enhancer sequences, which are then screened in zebrafish embryos
	Research VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer Georges St Laurent, Dmitry Shtokalo, Biao Dong, Michael R Tackett, Xiaoxuan Fan, Sandra Lazorthes, Estelle Nicolas, Nianli Sang, Timothy J Triche, Timothy A McCaffrey, Weidong Xiao, Philipp Kapranov Genome Biology 2013, 14:R73 (22 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The expression of vlincRNAs from retroviral promoters is correlated with pluripotency and malignancy
	Research Gene expression changes with age in skin, adipose tissue, blood and brain Daniel Glass, Ana Viñuela, Matthew N Davies, Adaikalavan Ramasamy, Leopold Parts, David Knowles, Andrew A Brown, Åsa K Hedman, Kerrin S Small, Alfonso Buil, Elin Grundberg, Alexandra C Nica, PaolaDi Meglio, Frank O Nestle, Mina Ryten, the UK Brain Expression consortium, the MuTHER consortium, Richard Durbin, Mark I McCarthy, Panagiotis Deloukas, Emmanouil T Dermitzakis, Michael E Weale, Veronique Bataille, Tim D Spector Genome Biology 2013, 14:R75 (26 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of microarray experiments in subjects of varying age shows that gene expression in four different tissues changes with time
	Research The strength of genetic interactions scales weakly with mutational effects Andrea Velenich, Jeff Gore Genome Biology 2013, 14:R76 (26 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A simple and surprisingly weak scaling law for epistasis is revealed in the DRYGIN large-scale yeast genetic interaction dataset
	Research The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation Gretchen M Ehrenkaufer, Gareth D Weedall, Daryl Williams, Hernan A Lorenzi, Elisabet Caler, Neil Hall, Upinder Singh Genome Biology 2013, 14:R77 (26 July 2013) Abstract \| Full text \| PDF \| PubMed \| f1000 \| Editor’s summary Genome and transcriptome analyses of Entamoeba invadens reveal insights into the process of encystation and its role in pathogenicity
	Research A blood based 12-miRNA signature of Alzheimer disease patients Petra Leidinger, Christina Backes, Stephanie Deutscher, Katja Schmitt, Sabine C Mueller, Karen Frese, Jan Haas, Klemens Ruprecht, Friedemann Paul, Cord Stähler, Christoph JG Lang, Benjamin Meder, Tamas Bartfai, Eckart Meese, Andreas Keller Genome Biology 2013, 14:R78 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A 12-miRNA signature in blood samples can be used to detect Alzheimer’s disease and other neurological disorders
	Research Experimental characterization of the human non-sequence-specific nucleic acid interactome Gerhard Dürnberger, Tilmann Bürckstümmer, Kilian Huber, Roberto Giambruno, Tobias Doerks, Evren Karayel, Thomas R Burkard, Ines Kaupe, André C Müller, Andreas Schönegger, Gerhard F Ecker, Hans Lohninger, Peer Bork, Keiryn L Bennett, Giulio Superti-Furga, Jacques Colinge Genome Biology 2013, 14:R81 (31 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mass spectrometry and bioinformatics approach identifies human proteins that bind nucleic acids in a non-sequence-specific manner
	Research A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains Michelle M Simon, Simon Greenaway, Jacqueline K White, Helmut Fuchs, Valérie Gailus-Durner, Sara Wells, Tania Sorg, Kim Wong, Elodie Bedu, Elizabeth J Cartwright, Romain Dacquin, Sophia Djebali, Jeanne Estabel, Jochen Graw, Neil J Ingham, Ian J Jackson, Andreas Lengeling, Silvia Mandillo, Jacqueline Marvel, Hamid Meziane, Frédéric Preitner, Oliver Puk, Michel Roux, David J Adams, Sarah Atkins, Abdel Ayadi, Lore Becker, Andrew Blake, Debra Brooker, Heather Cater, Marie-France Champy, Roy Combe, Petr Danecek, Armida di Fenza, Hilary Gates, Anna-Karin Gerdin, Elisabetta Golini, John M Hancock et al. Genome Biology 2013, 14:R82 (31 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A comprehensive genomic and phenotypic analysis identifies significant differences between the widely used C57BL/6J and C57BL/6N mouse strains
	Method A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of targeting nucleases Shimin Lim, Yin Wang, Xueyao Yu, Yian Huang, Mark S Featherstone, Karuna Sampath Genome Biology 2013, 14:R69 (1 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for engineering large-scale deletions enables heritable, specific removal of loci, transcripts or regulatory elements from the zebrafish genome
	Method GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-seq data Keyan Zhao, Zhi-xiang Lu, Juw Park, Qing Zhou, Yi Xing Genome Biology 2013, 14:R74 (22 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary GLiMMPS is a method for detecting QTLs associated with alternative splicing
	Method THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data Layla Oesper, Ahmad Mahmoody, Benjamin J Raphael Genome Biology 2013, 14:R80 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for determining tumor heterogeneity from high-throughput DNA sequencing data
	Software PARma: identification of microRNA target sites in AGO-PAR-CLIP data Florian Erhard, Lars Dölken, Lukasz Jaskiewicz, Ralf Zimmer Genome Biology 2013, 14:R79 (29 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new software tool for the identification of microRNA target sites in AGO-PAR-CLIP data

	Volume 14 Issue 7
	Comment
	Comment So, you want to sequence a genome... Derek L Stemple Genome Biology 2013, 14:128 (30 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Derek Stemple discusses lessons learned from the zebrafish genome project
	Research highlight MicroRNAs circulate around Alzheimer's disease Thalyana Smith-Vikos, Frank J Slack Genome Biology 2013, 14:125 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Frank Slack and Thalyana Smith-Vikos discuss the blood miRNA signature for Alzheimer's disease reported in this issue of Genome Biology
	Research highlight DNA methylation, genotype and gene expression: who is driving and who is along for the ride? Meaghan J Jones, Anthony P Fejes, Michael S Kobor Genome Biology 2013, 14:126 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Michael Kobor and colleagues discuss regulatory interactions between DNA methylation, genotype and gene expression
	Research highlight Microbiota's 'little helpers': bacteriophages and antibiotic-associated responses in the gut microbiome Christine L Sun, David A Relman Genome Biology 2013, 14:127 (30 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Relman and Christine Sun discuss recent research into how bacteriophage mediate the impact of antibiotics on the gut microbiome
	Review
	Review Ant genomics sheds light on the molecular regulation of social organization Romain Libbrecht, Peter R Oxley, Daniel JC Kronauer, Laurent Keller Genome Biology 2013, 14:212 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Laurent Keller and colleagues review new insights into insect social organization that have arisen from ant genome sequences and epigenomics research
	Report
	Meeting report Next-generation sequencing for identifying new genes in rare genetic diseases: many challenges and a pinch of luck Amélie Bonnefond, Philippe Froguel Genome Biology 2013, 14:309 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the European Society of Human Genetics conference, held in Paris, France, June 8-11, 2013
	Research
	Research Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene Mar Gonzàlez-Porta, Adam Frankish, Johan Rung, Jennifer Harrow, Alvis Brazma Genome Biology 2013, 14:R70 (1 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of RNA-seq data across different tissues and cell lines reveals that the majority of genes have a single dominant transcript
	Research Variants in exons and in transcription factors affect gene expression in trans Anat Kreimer, Itsik Pe'er Genome Biology 2013, 14:R71 (11 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Mapping of eSNPs onto a protein-protein interaction network reveals that SNPs in transcription factors can have a trans effect
	Research A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design Robin P Smith, Samantha J Riesenfeld, Alisha K Holloway, Qiang Li, Karl K Murphy, Natalie M Feliciano, Lorenzo Orecchia, Nir Oksenberg, Katherine S Pollard, Nadav Ahituv Genome Biology 2013, 14:R72 (18 July 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary All possible 6-mers are incorporated into a compact set of 15-mer synthetic enhancer sequences, which are then screened in zebrafish embryos
	Research VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer Georges St Laurent, Dmitry Shtokalo, Biao Dong, Michael R Tackett, Xiaoxuan Fan, Sandra Lazorthes, Estelle Nicolas, Nianli Sang, Timothy J Triche, Timothy A McCaffrey, Weidong Xiao, Philipp Kapranov Genome Biology 2013, 14:R73 (22 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The expression of vlincRNAs from retroviral promoters is correlated with pluripotency and malignancy
	Research Gene expression changes with age in skin, adipose tissue, blood and brain Daniel Glass, Ana Viñuela, Matthew N Davies, Adaikalavan Ramasamy, Leopold Parts, David Knowles, Andrew A Brown, Åsa K Hedman, Kerrin S Small, Alfonso Buil, Elin Grundberg, Alexandra C Nica, PaolaDi Meglio, Frank O Nestle, Mina Ryten, the UK Brain Expression consortium, the MuTHER consortium, Richard Durbin, Mark I McCarthy, Panagiotis Deloukas, Emmanouil T Dermitzakis, Michael E Weale, Veronique Bataille, Tim D Spector Genome Biology 2013, 14:R75 (26 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of microarray experiments in subjects of varying age shows that gene expression in four different tissues changes with time
	Research The strength of genetic interactions scales weakly with mutational effects Andrea Velenich, Jeff Gore Genome Biology 2013, 14:R76 (26 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A simple and surprisingly weak scaling law for epistasis is revealed in the DRYGIN large-scale yeast genetic interaction dataset
	Research The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation Gretchen M Ehrenkaufer, Gareth D Weedall, Daryl Williams, Hernan A Lorenzi, Elisabet Caler, Neil Hall, Upinder Singh Genome Biology 2013, 14:R77 (26 July 2013) Abstract \| Full text \| PDF \| PubMed \| f1000 \| Editor’s summary Genome and transcriptome analyses of Entamoeba invadens reveal insights into the process of encystation and its role in pathogenicity
	Research A blood based 12-miRNA signature of Alzheimer disease patients Petra Leidinger, Christina Backes, Stephanie Deutscher, Katja Schmitt, Sabine C Mueller, Karen Frese, Jan Haas, Klemens Ruprecht, Friedemann Paul, Cord Stähler, Christoph JG Lang, Benjamin Meder, Tamas Bartfai, Eckart Meese, Andreas Keller Genome Biology 2013, 14:R78 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A 12-miRNA signature in blood samples can be used to detect Alzheimer’s disease and other neurological disorders
	Research Experimental characterization of the human non-sequence-specific nucleic acid interactome Gerhard Dürnberger, Tilmann Bürckstümmer, Kilian Huber, Roberto Giambruno, Tobias Doerks, Evren Karayel, Thomas R Burkard, Ines Kaupe, André C Müller, Andreas Schönegger, Gerhard F Ecker, Hans Lohninger, Peer Bork, Keiryn L Bennett, Giulio Superti-Furga, Jacques Colinge Genome Biology 2013, 14:R81 (31 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mass spectrometry and bioinformatics approach identifies human proteins that bind nucleic acids in a non-sequence-specific manner
	Research A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains Michelle M Simon, Simon Greenaway, Jacqueline K White, Helmut Fuchs, Valérie Gailus-Durner, Sara Wells, Tania Sorg, Kim Wong, Elodie Bedu, Elizabeth J Cartwright, Romain Dacquin, Sophia Djebali, Jeanne Estabel, Jochen Graw, Neil J Ingham, Ian J Jackson, Andreas Lengeling, Silvia Mandillo, Jacqueline Marvel, Hamid Meziane, Frédéric Preitner, Oliver Puk, Michel Roux, David J Adams, Sarah Atkins, Abdel Ayadi, Lore Becker, Andrew Blake, Debra Brooker, Heather Cater, Marie-France Champy, Roy Combe, Petr Danecek, Armida di Fenza, Hilary Gates, Anna-Karin Gerdin, Elisabetta Golini, John M Hancock et al. Genome Biology 2013, 14:R82 (31 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A comprehensive genomic and phenotypic analysis identifies significant differences between the widely used C57BL/6J and C57BL/6N mouse strains
	Method A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of targeting nucleases Shimin Lim, Yin Wang, Xueyao Yu, Yian Huang, Mark S Featherstone, Karuna Sampath Genome Biology 2013, 14:R69 (1 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for engineering large-scale deletions enables heritable, specific removal of loci, transcripts or regulatory elements from the zebrafish genome
	Method GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-seq data Keyan Zhao, Zhi-xiang Lu, Juw Park, Qing Zhou, Yi Xing Genome Biology 2013, 14:R74 (22 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary GLiMMPS is a method for detecting QTLs associated with alternative splicing
	Method THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data Layla Oesper, Ahmad Mahmoody, Benjamin J Raphael Genome Biology 2013, 14:R80 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for determining tumor heterogeneity from high-throughput DNA sequencing data
	Software PARma: identification of microRNA target sites in AGO-PAR-CLIP data Florian Erhard, Lars Dölken, Lukasz Jaskiewicz, Ralf Zimmer Genome Biology 2013, 14:R79 (29 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new software tool for the identification of microRNA target sites in AGO-PAR-CLIP data

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Volume 14 Issue 7

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