Genome Biology | Volume 13 Issue 8

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	Volume 13 Issue 8
	Comment
	Comment A modest proposal for an outreach section in scientific publications Chris Gunter, Anne Osterrieder Genome Biology 2012, 13:168 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary By Chris Gunter and Anne Osterrieder
	Research highlight Genomes of extremophile crucifers: new platforms for comparative genomics and beyond Simon M Dittami, Thierry Tonon Genome Biology 2012, 13:166 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research Highlight: the genome sequences of extremophile crucifers provide valuable insights into the underlying mechanisms of stress tolerance in plants
	Review
	Opinion The tomato genome: implications for plant breeding, genomics and evolution Aashish Ranjan, Yasunori Ichihashi, Neelima R Sinha Genome Biology 2012, 13:167 (30 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The importance of the tomato genome for plant breeding and the future of crop research
	Report
	Meeting report Turning pipe dreams into reality Peter Li, Jeremy Goecks, Tin-Lap Lee Genome Biology 2012, 13:318 (30 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The 2012 Galaxy meeting shows how the bioinformatic tools within Galaxy are developing and automating data analysis in the life sciences
	Meeting report The rise of translational bioinformatics Yves A Lussier, Haiquan Li Genome Biology 2012, 13:319 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 20th International Conference On Intelligent Systems For Molecular Biology (ISMB), held at Long Beach, California, USA, July 15-17, 2012.
	Research
	Research Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins Gary LeRoy, Iouri Chepelev, Peter A DiMaggio, Mario A Blanco, Barry M Zee, Keji Zhao, Benjamin A Garcia Genome Biology 2012, 13:R68 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel proteogenomic strategy links the histone reader proteins Brd3 and Brd4 to HOX gene regulation
	Research Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase Eun-Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E Burgess, Miguel R Branco, Pierre Murat, David Oxley, Michael J Booth, Wolf Reik, Shankar Balasubramanian Genome Biology 2012, 13:R69 (17 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide mapping of 5-formylcytosine in ES cells reveals an enrichment in promoter and exon CpG islands, and an association with transcription
	Research The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite Andrea H Horakova, J Mauro Calabrese, Christine R McLaughlin, Deanna C Tremblay, Terry Magnuson, Brian P Chadwick Genome Biology 2012, 13:R70 (20 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A characterization of the X-linked homogenous tandem repeat DXZ4 in mouse, and a subsequent analysis of conservation across mammals
	Research A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers Nathan P Palmer, Patrick R Schmid, Bonnie Berger, Isaac S Kohane Genome Biology 2012, 13:R71 (21 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive in silico analysis of mRNA expression profiles in human stem cells, cancers and normal tissues
	Research Sequencing and characterization of the FVB/NJ mouse genome Kim Wong, Suzannah Bumpstead, Louise Van Der Weyden, Laura G Reinholdt, Laurens G Wilming, David J Adams, Thomas M Keane Genome Biology 2012, 13:R72 (23 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the FVB/NJ mouse is sequenced, revealing variants specific to this strain
	Research Novel origins of copy number variation in the dog genome Jonas Berglund, Elisa M Nevalainen, Anna-Maja Molin, Michele Perloski, The LUPA Consortium, Catherine André, Michael C Zody, Ted Sharpe, Christophe Hitte, Kerstin Lindblad-Toh, Hannes Lohi, Matthew T Webster Genome Biology 2012, 13:R73 (23 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CNVs were analyzed in dogs from 17 breeds, and were found to be associated with different features compared to other mammals
	Research Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage Hervé Moreau, Bram Verhelst, Arnaud Couloux, Evelyne Derelle, Stephane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F Hohmann-Marriott, Gwenael Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele Genome Biology 2012, 13:R74 (24 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome sequence of the marine green alga Bathycoccus prasinos, and a phylogenomic comparison with other Mammiellales species
	Research Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers Alayne L Brunner, Andrew H Beck, Badreddin Edris, Robert T Sweeney, Shirley X Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W Foley, Daniela M Witten, Craig P Giacomini, Ryan A Flynn, Jonathan R Pollack, Robert Tibshirani, Howard Y Chang, Matt van de Rijn, Robert B West Genome Biology 2012, 13:R75 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs
	Method Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule Genome Biology 2012, 13:R67 (3 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The CLIP and iCLIP methods are compared for their utility in determining RNA binding protein binding sites
	Method A computational framework for boosting confidence in high-throughput protein-protein interaction datasets Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska, Bonnie Berger Genome Biology 2012, 13:R76 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Coev2Net is a method for assigning confidence to high-throughput protein-protein interaction predictions
	Software ggbio: an R package for extending the grammar of graphics for genomic data Tengfei Yin, Dianne Cook, Michael Lawrence Genome Biology 2012, 13:R77 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent, robust and versatile software tool for visualizing genomic data
	Correspondence
	Open letter An encyclopedia of mouse DNA elements (Mouse ENCODE) Mouse ENCODE Consortium, John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J Sabo, Richard Sandstrom, A Sandra Stehling, Robert E Thurman, Sherman M Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G Landt, Zhihai Ma, Barbara J Wold, Job Dekker et al. Genome Biology 2012, 13:418 (13 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome

	Volume 13 Issue 8
	Comment
	Comment A modest proposal for an outreach section in scientific publications Chris Gunter, Anne Osterrieder Genome Biology 2012, 13:168 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary By Chris Gunter and Anne Osterrieder
	Research highlight Genomes of extremophile crucifers: new platforms for comparative genomics and beyond Simon M Dittami, Thierry Tonon Genome Biology 2012, 13:166 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research Highlight: the genome sequences of extremophile crucifers provide valuable insights into the underlying mechanisms of stress tolerance in plants
	Review
	Opinion The tomato genome: implications for plant breeding, genomics and evolution Aashish Ranjan, Yasunori Ichihashi, Neelima R Sinha Genome Biology 2012, 13:167 (30 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The importance of the tomato genome for plant breeding and the future of crop research
	Report
	Meeting report Turning pipe dreams into reality Peter Li, Jeremy Goecks, Tin-Lap Lee Genome Biology 2012, 13:318 (30 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The 2012 Galaxy meeting shows how the bioinformatic tools within Galaxy are developing and automating data analysis in the life sciences
	Meeting report The rise of translational bioinformatics Yves A Lussier, Haiquan Li Genome Biology 2012, 13:319 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 20th International Conference On Intelligent Systems For Molecular Biology (ISMB), held at Long Beach, California, USA, July 15-17, 2012.
	Research
	Research Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins Gary LeRoy, Iouri Chepelev, Peter A DiMaggio, Mario A Blanco, Barry M Zee, Keji Zhao, Benjamin A Garcia Genome Biology 2012, 13:R68 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A novel proteogenomic strategy links the histone reader proteins Brd3 and Brd4 to HOX gene regulation
	Research Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase Eun-Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E Burgess, Miguel R Branco, Pierre Murat, David Oxley, Michael J Booth, Wolf Reik, Shankar Balasubramanian Genome Biology 2012, 13:R69 (17 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide mapping of 5-formylcytosine in ES cells reveals an enrichment in promoter and exon CpG islands, and an association with transcription
	Research The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite Andrea H Horakova, J Mauro Calabrese, Christine R McLaughlin, Deanna C Tremblay, Terry Magnuson, Brian P Chadwick Genome Biology 2012, 13:R70 (20 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A characterization of the X-linked homogenous tandem repeat DXZ4 in mouse, and a subsequent analysis of conservation across mammals
	Research A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers Nathan P Palmer, Patrick R Schmid, Bonnie Berger, Isaac S Kohane Genome Biology 2012, 13:R71 (21 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive in silico analysis of mRNA expression profiles in human stem cells, cancers and normal tissues
	Research Sequencing and characterization of the FVB/NJ mouse genome Kim Wong, Suzannah Bumpstead, Louise Van Der Weyden, Laura G Reinholdt, Laurens G Wilming, David J Adams, Thomas M Keane Genome Biology 2012, 13:R72 (23 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the FVB/NJ mouse is sequenced, revealing variants specific to this strain
	Research Novel origins of copy number variation in the dog genome Jonas Berglund, Elisa M Nevalainen, Anna-Maja Molin, Michele Perloski, The LUPA Consortium, Catherine André, Michael C Zody, Ted Sharpe, Christophe Hitte, Kerstin Lindblad-Toh, Hannes Lohi, Matthew T Webster Genome Biology 2012, 13:R73 (23 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CNVs were analyzed in dogs from 17 breeds, and were found to be associated with different features compared to other mammals
	Research Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage Hervé Moreau, Bram Verhelst, Arnaud Couloux, Evelyne Derelle, Stephane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F Hohmann-Marriott, Gwenael Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele Genome Biology 2012, 13:R74 (24 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome sequence of the marine green alga Bathycoccus prasinos, and a phylogenomic comparison with other Mammiellales species
	Research Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers Alayne L Brunner, Andrew H Beck, Badreddin Edris, Robert T Sweeney, Shirley X Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W Foley, Daniela M Witten, Craig P Giacomini, Ryan A Flynn, Jonathan R Pollack, Robert Tibshirani, Howard Y Chang, Matt van de Rijn, Robert B West Genome Biology 2012, 13:R75 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs
	Method Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule Genome Biology 2012, 13:R67 (3 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The CLIP and iCLIP methods are compared for their utility in determining RNA binding protein binding sites
	Method A computational framework for boosting confidence in high-throughput protein-protein interaction datasets Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska, Bonnie Berger Genome Biology 2012, 13:R76 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Coev2Net is a method for assigning confidence to high-throughput protein-protein interaction predictions
	Software ggbio: an R package for extending the grammar of graphics for genomic data Tengfei Yin, Dianne Cook, Michael Lawrence Genome Biology 2012, 13:R77 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A consistent, robust and versatile software tool for visualizing genomic data
	Correspondence
	Open letter An encyclopedia of mouse DNA elements (Mouse ENCODE) Mouse ENCODE Consortium, John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J Sabo, Richard Sandstrom, A Sandra Stehling, Robert E Thurman, Sherman M Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G Landt, Zhihai Ma, Barbara J Wold, Job Dekker et al. Genome Biology 2012, 13:418 (13 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome

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Volume 13 Issue 8

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