Genome Biology | Volume 14 Issue 5

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	Volume 14 Issue 5
	Comment
	Comment After the gold rush Neil Hall Genome Biology 2013, 14:115 (7 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Neil Hall wonders whether genomics is ready for a plateau in sequencing costs
	Research highlight New gene expression pipelines gush lncRNAs Jiashi Wang, Bronwyn A Lucas, Lynne E Maquat Genome Biology 2013, 14:117 (24 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The characterization of lncRNA expression during neuronal development is a useful resource for elucidating the functions of non-coding transcripts
	Research highlight Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine Sean M Cullen, Margaret A Goodell Genome Biology 2013, 14:116 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight examines why differentiation in the small intestine crypt bypasses the DNA methylation changes observed in other lineage progressions
	Research highlight Deep C diving: mapping the low-abundance modifications of the DNA demethylation pathway John P Thomson, Jennifer M Hunter, Richard R Meehan Genome Biology 2013, 14:118 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Richard Meehan and colleagues highlight recent insights into the 5th, 6th, 7th and 8th DNA bases: 5mC, 5hmC, 5fC and 5caC
	Review
	Review Machine learning and genome annotation: a match meant to be? Kevin Y Yip, Chao Cheng, Mark Gerstein Genome Biology 2013, 14:205 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mark Gerstein, Kevin Yip and Chao Cheng present a beginner's guide to machine learning for genome annotation
	Report
	Meeting report Epigenetics and transgenerational inheritance Emilie Brasset, Séverine Chambeyron Genome Biology 2013, 14:306 (24 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Non-coding RNA, epigenetics and transgenerational inheritance' meeting, held at Churchill College, Cambridge, UK, April 11-12, 2013.
	Meeting report Genomic triumph meets clinical reality Qasim Ayub, Yali Xue, Chris Tyler-Smith Genome Biology 2013, 14:307 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Genomic Disorders 2013 - from 60 years of DNA to human genomes in the clinic' meeting, held at Homerton College, Hills Road, Cambridge, UK, April 10-12, 2013.
	Research
	Research Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
	Research Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance David Martino, Yuk Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
	Research Inactive or moderately active human promoters are enriched for inter-individual epialleles Carolina Gemma, Sreeram V Ramagopalan, Thomas A Down, Huriya Beyan, Mohammed I Hawa, Michelle L Holland, Paul J Hurd, Gavin Giovannoni, R David Leslie, George C Ebers, Vardhman K Rakyan Genome Biology 2013, 14:R43 (25 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Epialleles between monozygotic twins are temporally stable, associated with chromatin changes and enriched in transcriptionally inactive regions
	Research Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles Nicole YP Souren, Pavlo Lutsik, Gilles Gasparoni, Sascha Tierling, Jasmin Gries, Matthias Riemenschneider, Jean-Pierre Fryns, Catherine Derom, Maurice P Zeegers, Jörn Walter Genome Biology 2013, 14:R44 (26 May 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Monozygotic twins discordant for birth weight have very similar DNA methylation profiles
	Research Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing Shivendra Kishore, Andreas R Gruber, Dominik J Jedlinski, Afzal P Syed, Hadi Jorjani, Mihaela Zavolan Genome Biology 2013, 14:R45 (26 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary PAR-CLIP of snoRNA-associated proteins reveals the existence of extensive human loci that are processed into snoRNAs
	Research 5-Hydroxymethylcytosine is an essential intermediate of active DNA demethylation processes in primary human monocytes Maja Klug, Sandra Schmidhofer, Claudia Gebhard, Reinhard Andreesen, Michael Rehli Genome Biology 2013, 14:R46 (26 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary TET2-mediated conversion of 5mC to 5hmC initiates active demethylation of the genome during monocyte differentiation
	Research Genome-wide analysis of functional sirtuin chromatin targets in yeast Mingguang Li, Veena Valsakumar, Kunal Poorey, Stefan Bekiranov, Jeffrey S Smith Genome Biology 2013, 14:R48 (27 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sirtuins regulate both glycolytic gene expression and condensin/cohesin deposition, suggesting a mechanistic link between metabolism and chromatin architecture
	Research Mutations within lncRNAs are effectively selected against in fruitfly but not in human Wilfried Haerty, Chris P Ponting Genome Biology 2013, 14:R49 (27 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of lncRNA conservation in fruitfly and humans shows that these elements are well conserved in insects, but not in mammals
	Research DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus Lucas TJ Kaaij, Marc van de Wetering, Fang Fang, Benjamin Decato, Antoine Molaro, Harmen JG van de Werken, Johan H van Es, Jurian Schuijers, Elzo de Wit, Wouter de Laat, Gregory J Hannon, Hans C Clevers, Andrew D Smith, René F Ketting Genome Biology 2013, 14:R50 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Intriguingly, DNA methylation in mouse intestinal cells does not change much during differentiation
	Research Characterizing and measuring bias in sequence data Michael G Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J Lennon, Ryan Hegarty, Chad Nusbaum, David B Jaffe Genome Biology 2013, 14:R51 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A comparison of the bias in sequencing data from four different platforms reveals that some human promoters are completelymissed
	Method Integrated analysis of recurrent properties of cancer genes to identify novel drivers Matteo D'Antonio, Francesca D Ciccarelli Genome Biology 2013, 14:R52 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to detect rare driver genes through integrated analysis of expression profiles, mutation effects and properties of known cancer genes
	Software REAPR: a universal tool for genome assembly evaluation Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman, Thomas D Otto Genome Biology 2013, 14:R47 (27 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new user-friendly software tool for genome assembly evaluation

	Volume 14 Issue 5
	Comment
	Comment After the gold rush Neil Hall Genome Biology 2013, 14:115 (7 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Neil Hall wonders whether genomics is ready for a plateau in sequencing costs
	Research highlight New gene expression pipelines gush lncRNAs Jiashi Wang, Bronwyn A Lucas, Lynne E Maquat Genome Biology 2013, 14:117 (24 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The characterization of lncRNA expression during neuronal development is a useful resource for elucidating the functions of non-coding transcripts
	Research highlight Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine Sean M Cullen, Margaret A Goodell Genome Biology 2013, 14:116 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight examines why differentiation in the small intestine crypt bypasses the DNA methylation changes observed in other lineage progressions
	Research highlight Deep C diving: mapping the low-abundance modifications of the DNA demethylation pathway John P Thomson, Jennifer M Hunter, Richard R Meehan Genome Biology 2013, 14:118 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Richard Meehan and colleagues highlight recent insights into the 5th, 6th, 7th and 8th DNA bases: 5mC, 5hmC, 5fC and 5caC
	Review
	Review Machine learning and genome annotation: a match meant to be? Kevin Y Yip, Chao Cheng, Mark Gerstein Genome Biology 2013, 14:205 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mark Gerstein, Kevin Yip and Chao Cheng present a beginner's guide to machine learning for genome annotation
	Report
	Meeting report Epigenetics and transgenerational inheritance Emilie Brasset, Séverine Chambeyron Genome Biology 2013, 14:306 (24 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Non-coding RNA, epigenetics and transgenerational inheritance' meeting, held at Churchill College, Cambridge, UK, April 11-12, 2013.
	Meeting report Genomic triumph meets clinical reality Qasim Ayub, Yali Xue, Chris Tyler-Smith Genome Biology 2013, 14:307 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Genomic Disorders 2013 - from 60 years of DNA to human genomes in the clinic' meeting, held at Homerton College, Hills Road, Cambridge, UK, April 10-12, 2013.
	Research
	Research Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
	Research Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance David Martino, Yuk Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
	Research Inactive or moderately active human promoters are enriched for inter-individual epialleles Carolina Gemma, Sreeram V Ramagopalan, Thomas A Down, Huriya Beyan, Mohammed I Hawa, Michelle L Holland, Paul J Hurd, Gavin Giovannoni, R David Leslie, George C Ebers, Vardhman K Rakyan Genome Biology 2013, 14:R43 (25 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Epialleles between monozygotic twins are temporally stable, associated with chromatin changes and enriched in transcriptionally inactive regions
	Research Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles Nicole YP Souren, Pavlo Lutsik, Gilles Gasparoni, Sascha Tierling, Jasmin Gries, Matthias Riemenschneider, Jean-Pierre Fryns, Catherine Derom, Maurice P Zeegers, Jörn Walter Genome Biology 2013, 14:R44 (26 May 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Monozygotic twins discordant for birth weight have very similar DNA methylation profiles
	Research Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing Shivendra Kishore, Andreas R Gruber, Dominik J Jedlinski, Afzal P Syed, Hadi Jorjani, Mihaela Zavolan Genome Biology 2013, 14:R45 (26 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary PAR-CLIP of snoRNA-associated proteins reveals the existence of extensive human loci that are processed into snoRNAs
	Research 5-Hydroxymethylcytosine is an essential intermediate of active DNA demethylation processes in primary human monocytes Maja Klug, Sandra Schmidhofer, Claudia Gebhard, Reinhard Andreesen, Michael Rehli Genome Biology 2013, 14:R46 (26 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary TET2-mediated conversion of 5mC to 5hmC initiates active demethylation of the genome during monocyte differentiation
	Research Genome-wide analysis of functional sirtuin chromatin targets in yeast Mingguang Li, Veena Valsakumar, Kunal Poorey, Stefan Bekiranov, Jeffrey S Smith Genome Biology 2013, 14:R48 (27 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sirtuins regulate both glycolytic gene expression and condensin/cohesin deposition, suggesting a mechanistic link between metabolism and chromatin architecture
	Research Mutations within lncRNAs are effectively selected against in fruitfly but not in human Wilfried Haerty, Chris P Ponting Genome Biology 2013, 14:R49 (27 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of lncRNA conservation in fruitfly and humans shows that these elements are well conserved in insects, but not in mammals
	Research DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus Lucas TJ Kaaij, Marc van de Wetering, Fang Fang, Benjamin Decato, Antoine Molaro, Harmen JG van de Werken, Johan H van Es, Jurian Schuijers, Elzo de Wit, Wouter de Laat, Gregory J Hannon, Hans C Clevers, Andrew D Smith, René F Ketting Genome Biology 2013, 14:R50 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Intriguingly, DNA methylation in mouse intestinal cells does not change much during differentiation
	Research Characterizing and measuring bias in sequence data Michael G Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J Lennon, Ryan Hegarty, Chad Nusbaum, David B Jaffe Genome Biology 2013, 14:R51 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A comparison of the bias in sequencing data from four different platforms reveals that some human promoters are completelymissed
	Method Integrated analysis of recurrent properties of cancer genes to identify novel drivers Matteo D'Antonio, Francesca D Ciccarelli Genome Biology 2013, 14:R52 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to detect rare driver genes through integrated analysis of expression profiles, mutation effects and properties of known cancer genes
	Software REAPR: a universal tool for genome assembly evaluation Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman, Thomas D Otto Genome Biology 2013, 14:R47 (27 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new user-friendly software tool for genome assembly evaluation

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Volume 14 Issue 5

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