Genome Biology | Volume 13 Issue 12

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	Volume 13 Issue 12
	Comment
	Comment How to be wrong but useful Adam Kucharski Genome Biology 2012, 13:180 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Adam Kucharski, 2012's winner of the Wellcome Trust science writing prize, applauds Alan Turing, Nate Silver and the power of models
	Research highlight A new era of human population genetics Alexander Platt, John Novembre Genome Biology 2012, 13:182 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Alexander Platt and John Novembre discuss what the 1000 Genomes Project teaches us about human population genetics
	Research highlight Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone Todd J Treangen, Adam M Phillippy Genome Biology 2012, 13:181 (27 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of methicillin-resistant Staphylococcus aureus reveals its recombination trends, and highlights the challenges of phylogeographic analysis of these pathogens
	Review
	Protein family review The ADAR protein family Yiannis A Savva, Leila E Rieder, Robert A Reenan Genome Biology 2012, 13:252 (28 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ADARs and RNA editing: a Protein Family Review by Robert Reenan and colleagues
	Report
	Meeting report Personal genomes and precision medicine Gareth Highnam, David Mittelman Genome Biology 2012, 13:324 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012
	Research
	Research Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data Matthew Parker, Xiang Chen, Armita Bahrami, James Dalton, Michael Rusch, Gang Wu, John Easton, Nai-Kong Cheung, Michael Dyer, Elaine R Mardis, Richard K Wilson, Charles Mullighan, Richard Gilbertson, Suzanne J Baker, Gerard Zambetti, David W Ellison, James R Downing, Jinghui Zhang, the Pediatric Cancer Genome Project Genome Biology 2012, 13:R113 (11 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive analysis of telomere length changes in a large collection of pediatric tumors
	Research Widespread promoter-mediated coordination of transcription and mRNA degradation Mally Dori-Bachash, Ophir Shalem, Yair S Manor, Yitzhak Pilpel, Itay Tirosh Genome Biology 2012, 13:R114 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription and degradation of mRNA in yeast is commonly coordinated through promoters
	Research Whole-genome reconstruction and mutational signatures in gastric cancer Niranjan Nagarajan, Denis Bertrand, Axel M Hillmer, Zhi Zang, Fei Yao, Pierre-Étienne Jacques, Audrey SM Teo, Ioana Cutcutache, Zhenshui Zhang, Wah Lee, Yee Sia, Song Gao, Pramila N Ariyaratne, Andrea Ho, Xing Woo, Lavanya Veeravali, Choon Ong, Niantao Deng, Kartiki V Desai, Chiea Khor, Martin L Hibberd, Atif Shahab, Jaideepraj Rao, Mengchu Wu, Ming Teh, Feng Zhu, Sze Chin, Brendan Pang, Jimmy BY So, Guillaume Bourque et al. Genome Biology 2012, 13:R115 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study the whole genome sequencing is used to reveal mutational signatures in gastric cancer.
	Research Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements Xue Dong, Julia Reimer, Ulrike Göbel, Julia Engelhorn, Fei He, Heiko Schoof, Franziska Turck Genome Biology 2012, 13:R117 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
	Research Microevolutionary analysis of Clostridium difficile genomes to investigate transmission Xavier Didelot, David W Eyre, Madeleine Cule, Camilla LC Ip, M Ansari, David Griffiths, Alison Vaughan, Lily O'Connor, Tanya Golubchik, Elizabeth M Batty, Paolo Piazza, Daniel J Wilson, Rory Bowden, Peter J Donnelly, Kate E Dingle, Mark Wilcox, A Walker, Derrick W Crook, Tim E A Peto, Rosalind M Harding Genome Biology 2012, 13:R118 (21 December 2012) Abstract \| Full text \| PDF \| PubMed \| f1000 \| Editor’s summary Transmission events of Clostridium difficile are inferred from whole-genome sequencing of isolates and estimating divergence time of bacterial strains
	Research Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing Margarida Cardoso-Moreira, J Arguello, Andrew G Clark Genome Biology 2012, 13:R119 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of breakpoints in Drosophila melanogaster genomes reveals similarities and differences with breakpoint formation in humans
	Research A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts Eric J Suh, Matthew Y Remillard, Aster Legesse-Miller, Elizabeth L Johnson, Johanna MS Lemons, Talia R Chapman, Joshua J Forman, Mina Kojima, Eric S Silberman, Hilary A Coller Genome Biology 2012, 13:R121 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study identifying microRNAs both facilitating and delaying fibroblast cell cycle re-entry from quiescence
	Research Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus Santiago Castillo-Ramírez, Jukka Corander, Pekka Marttinen, Mona Aldeljawi, William P Hanage, Henrik Westh, Kit Boye, Zeynep Gulay, Stephen D Bentley, Julian Parkhill, Matthew T Holden, Edward J Feil Genome Biology 2012, 13:R126 (27 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Different evolution rates of methicillin-resistant Staphylococcus aureus clone ST239 collected in different geographical locations are caused by fast global dissemination
	Method A network module-based method for identifying cancer prognostic signatures Guanming Wu, Lincoln Stein Genome Biology 2012, 13:R112 (10 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for identifying prognostic biomarkers from cancer gene expression datasets using gene functional network analysis
	Method FOCAL: an experimental design tool for systematizing metabolic discoveries and model development Christopher J Tervo, Jennifer L Reed Genome Biology 2012, 13:R116 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method that identifies media and knock-out conditions where a given reaction is essential for a measurable phenotype
	Method cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data Evangelos Bellos, Michael R Johnson, Lachlan J M Coin Genome Biology 2012, 13:R120 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrative, probabilistic method for CNV discovery and genotyping
	Method Ray Meta: scalable de novo metagenome assembly and profiling Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil Genome Biology 2012, 13:R122 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
	Method DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer Ali Bashashati, Gholamreza Haffari, Jiarui Ding, Gavin Ha, Kenneth Lui, Jamie Rosner, David G Huntsman, Carlos Caldas, Samuel A Aparicio, Sohrab P Shah Genome Biology 2012, 13:R124 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary DriverNet is a method for identifying driver mutations in cancer samples based on their effects on the transcriptional network
	Method Differential analysis of high-throughput quantitative genetic interaction data Gordon J Bean, Trey Ideker Genome Biology 2012, 13:R123 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method for the differential analysis of genetic interactions
	Method RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network Peggy I Wang, Sohyun Hwang, Rodney P Kincaid, Christopher S Sullivan, Insuk Lee, Edward M Marcotte Genome Biology 2012, 13:R125 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method using guilt-by-association principles to identify associations of unannotated gene sets

	Volume 13 Issue 12
	Comment
	Comment How to be wrong but useful Adam Kucharski Genome Biology 2012, 13:180 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Adam Kucharski, 2012's winner of the Wellcome Trust science writing prize, applauds Alan Turing, Nate Silver and the power of models
	Research highlight A new era of human population genetics Alexander Platt, John Novembre Genome Biology 2012, 13:182 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Alexander Platt and John Novembre discuss what the 1000 Genomes Project teaches us about human population genetics
	Research highlight Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone Todd J Treangen, Adam M Phillippy Genome Biology 2012, 13:181 (27 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of methicillin-resistant Staphylococcus aureus reveals its recombination trends, and highlights the challenges of phylogeographic analysis of these pathogens
	Review
	Protein family review The ADAR protein family Yiannis A Savva, Leila E Rieder, Robert A Reenan Genome Biology 2012, 13:252 (28 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ADARs and RNA editing: a Protein Family Review by Robert Reenan and colleagues
	Report
	Meeting report Personal genomes and precision medicine Gareth Highnam, David Mittelman Genome Biology 2012, 13:324 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012
	Research
	Research Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data Matthew Parker, Xiang Chen, Armita Bahrami, James Dalton, Michael Rusch, Gang Wu, John Easton, Nai-Kong Cheung, Michael Dyer, Elaine R Mardis, Richard K Wilson, Charles Mullighan, Richard Gilbertson, Suzanne J Baker, Gerard Zambetti, David W Ellison, James R Downing, Jinghui Zhang, the Pediatric Cancer Genome Project Genome Biology 2012, 13:R113 (11 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive analysis of telomere length changes in a large collection of pediatric tumors
	Research Widespread promoter-mediated coordination of transcription and mRNA degradation Mally Dori-Bachash, Ophir Shalem, Yair S Manor, Yitzhak Pilpel, Itay Tirosh Genome Biology 2012, 13:R114 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription and degradation of mRNA in yeast is commonly coordinated through promoters
	Research Whole-genome reconstruction and mutational signatures in gastric cancer Niranjan Nagarajan, Denis Bertrand, Axel M Hillmer, Zhi Zang, Fei Yao, Pierre-Étienne Jacques, Audrey SM Teo, Ioana Cutcutache, Zhenshui Zhang, Wah Lee, Yee Sia, Song Gao, Pramila N Ariyaratne, Andrea Ho, Xing Woo, Lavanya Veeravali, Choon Ong, Niantao Deng, Kartiki V Desai, Chiea Khor, Martin L Hibberd, Atif Shahab, Jaideepraj Rao, Mengchu Wu, Ming Teh, Feng Zhu, Sze Chin, Brendan Pang, Jimmy BY So, Guillaume Bourque et al. Genome Biology 2012, 13:R115 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study the whole genome sequencing is used to reveal mutational signatures in gastric cancer.
	Research Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements Xue Dong, Julia Reimer, Ulrike Göbel, Julia Engelhorn, Fei He, Heiko Schoof, Franziska Turck Genome Biology 2012, 13:R117 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
	Research Microevolutionary analysis of Clostridium difficile genomes to investigate transmission Xavier Didelot, David W Eyre, Madeleine Cule, Camilla LC Ip, M Ansari, David Griffiths, Alison Vaughan, Lily O'Connor, Tanya Golubchik, Elizabeth M Batty, Paolo Piazza, Daniel J Wilson, Rory Bowden, Peter J Donnelly, Kate E Dingle, Mark Wilcox, A Walker, Derrick W Crook, Tim E A Peto, Rosalind M Harding Genome Biology 2012, 13:R118 (21 December 2012) Abstract \| Full text \| PDF \| PubMed \| f1000 \| Editor’s summary Transmission events of Clostridium difficile are inferred from whole-genome sequencing of isolates and estimating divergence time of bacterial strains
	Research Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing Margarida Cardoso-Moreira, J Arguello, Andrew G Clark Genome Biology 2012, 13:R119 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of breakpoints in Drosophila melanogaster genomes reveals similarities and differences with breakpoint formation in humans
	Research A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts Eric J Suh, Matthew Y Remillard, Aster Legesse-Miller, Elizabeth L Johnson, Johanna MS Lemons, Talia R Chapman, Joshua J Forman, Mina Kojima, Eric S Silberman, Hilary A Coller Genome Biology 2012, 13:R121 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study identifying microRNAs both facilitating and delaying fibroblast cell cycle re-entry from quiescence
	Research Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus Santiago Castillo-Ramírez, Jukka Corander, Pekka Marttinen, Mona Aldeljawi, William P Hanage, Henrik Westh, Kit Boye, Zeynep Gulay, Stephen D Bentley, Julian Parkhill, Matthew T Holden, Edward J Feil Genome Biology 2012, 13:R126 (27 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Different evolution rates of methicillin-resistant Staphylococcus aureus clone ST239 collected in different geographical locations are caused by fast global dissemination
	Method A network module-based method for identifying cancer prognostic signatures Guanming Wu, Lincoln Stein Genome Biology 2012, 13:R112 (10 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for identifying prognostic biomarkers from cancer gene expression datasets using gene functional network analysis
	Method FOCAL: an experimental design tool for systematizing metabolic discoveries and model development Christopher J Tervo, Jennifer L Reed Genome Biology 2012, 13:R116 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method that identifies media and knock-out conditions where a given reaction is essential for a measurable phenotype
	Method cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data Evangelos Bellos, Michael R Johnson, Lachlan J M Coin Genome Biology 2012, 13:R120 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrative, probabilistic method for CNV discovery and genotyping
	Method Ray Meta: scalable de novo metagenome assembly and profiling Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil Genome Biology 2012, 13:R122 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
	Method DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer Ali Bashashati, Gholamreza Haffari, Jiarui Ding, Gavin Ha, Kenneth Lui, Jamie Rosner, David G Huntsman, Carlos Caldas, Samuel A Aparicio, Sohrab P Shah Genome Biology 2012, 13:R124 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary DriverNet is a method for identifying driver mutations in cancer samples based on their effects on the transcriptional network
	Method Differential analysis of high-throughput quantitative genetic interaction data Gordon J Bean, Trey Ideker Genome Biology 2012, 13:R123 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method for the differential analysis of genetic interactions
	Method RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network Peggy I Wang, Sohyun Hwang, Rodney P Kincaid, Christopher S Sullivan, Insuk Lee, Edward M Marcotte Genome Biology 2012, 13:R125 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method using guilt-by-association principles to identify associations of unannotated gene sets

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Volume 13 Issue 12

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