Genome Biology | Volume 12 Issue 8

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	Volume 12 Issue 8
	Comment
	Comment Nothing to do and all day to do it in Gregory A Petsko Genome Biology 2011, 12:126 (31 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The perfect end to a perfect vacation day
	Research highlight Sequencing skippy: the genome sequence of an Australian kangaroo, Macropus eugenii Elizabeth P Murchison, David J Adams Genome Biology 2011, 12:123 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sanger Institute's David Adams finds our kangaroo genome sequence article to be a fascinating window on mammalian evolution
	Research highlight Repeated phenotypic changes highlight molecular targets of convergent evolution Maggie R Wagner, Thomas Mitchell-Olds Genome Biology 2011, 12:124 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Maggie Wagner and Thomas Mitchell-Olds discuss how selection might preferentially target certain genes that have a strong phenotypic effect
	Review
	Opinion The real cost of sequencing: higher than you think! Andrea Sboner, Xinmeng Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein Genome Biology 2011, 12:125 (25 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data
	Report
	Meeting report Computational biology: plus c'est la même chose, plus ça change Curtis Huttenhower Genome Biology 2011, 12:307 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint 19th Annual ISMB/10th Annual ECCB and the 7th ISCB Student Council Symposium, Vienna, Austria, 15-19 July 2011
	Research
	Research The contrasting roles of PPARδ and PPARγ in regulating the metabolic switch between oxidation and storage of fats in white adipose tissue Lee D Roberts, Andrew J Murray, David Menassa, Tom Ashmore, Andrew W Nicholls, Julian L Griffin Genome Biology 2011, 12:R75 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A specific agonist demonstrates the contrast between PPAR-delta and PPAR-gamma function in lipid metabolism
	Research Farnesyltransferase inhibitor treatment restores chromosome territory positions and active chromosome dynamics in Hutchinson-Gilford progeria syndrome cells Ishita S Mehta, Christopher H Eskiw, Halime D Arican, Ian R Kill, Joanna M Bridger Genome Biology 2011, 12:R74 (12 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Treating cultured cells from Hutchinson-Gilford progeria patients with farnesyltransferase inhibitors restores wildtype chromosome dynamics
	Research The head-regeneration transcriptome of the planarian Schmidtea mediterranea Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer Genome Biology 2011, 12:R76 (16 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Next generation sequencing was used to investigate the transcriptome of head regeneration in the planarian Schmidtea mediterranea
	Research Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage Min Zhu, Ming Yi, Chang Hee Kim, Chuxia Deng, Yi Li, Daniel Medina, Robert M Stephens, Jeffrey E Green Genome Biology 2011, 12:R77 (16 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expression profiling in mouse models of mammary tumors identifies miRNA signatures particular to lineages or driver oncogenes
	Research A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1 Melanie Blasius, Josep V Forment, Neha Thakkar, Sebastian A Wagner, Chunaram Choudhary, Stephen P Jackson Genome Biology 2011, 12:R78 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phospho-proteomics screen identifies many novel Chk1 substrates and a target site consensus motif
	Research Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:R81 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
	Research Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast Brian T Wilhelm, Samuel Marguerat, Sofia Aligianni, Sandra Codlin, Stephen Watt, Jürg Bähler Genome Biology 2011, 12:R82 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of marks associated with introns in S. pombe finds distinct patterns of histones, open chromatin and PolII enrichment
	Method Single cell transcriptomics of neighboring hyphae of Aspergillus niger Charissa de Bekker, Oskar Bruning, Martijs J Jonker, Timo M Breit, Han AB Wösten Genome Biology 2011, 12:R71 (4 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for single cell transcriptomics is developed and is demonstrated on single hyphae of Aspergillus niger
	Method TopHat-Fusion: an algorithm for discovery of novel fusion transcripts Daehwan Kim, Steven L Salzberg Genome Biology 2011, 12:R72 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm
	Method Hybrid selection for sequencing pathogen genomes from clinical samples Alexandre Melnikov, Kevin Galinsky, Peter Rogov, Timothy Fennell, Daria Van Tyne, Carsten Russ, Rachel Daniels, Kayla G Barnes, James Bochicchio, Daouda Ndiaye, Papa D Sene, Dyann F Wirth, Chad Nusbaum, Sarah K Volkman, Bruce W Birren, Andreas Gnirke, Daniel E Neafsey Genome Biology 2011, 12:R73 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Baits generated from Plasmodium DNA are used in solution hybridization to enrich parasite DNA from clinical samples to facilitate sequencing
	Method PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data David L Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca L Skalsky, Jack D Keene, Uwe Ohler Genome Biology 2011, 12:R79 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for identifying RNA binding sites and miRNA target motifs from PAR-CLIP data
	Method Single-cell copy number variation detection Jiqiu Cheng, Evelyne Vanneste, Peter Konings, Thierry Voet, Joris R Vermeesch, Yves Moreau Genome Biology 2011, 12:R80 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method is presented for detecting copy number variations from array CGH data specifically optimized for use with single cells
	Software Cistrome: an integrative platform for transcriptional regulation studies Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu Genome Biology 2011, 12:R83 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Galaxy-based web application for integrative analysis of ChIP data

	Volume 12 Issue 8
	Comment
	Comment Nothing to do and all day to do it in Gregory A Petsko Genome Biology 2011, 12:126 (31 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The perfect end to a perfect vacation day
	Research highlight Sequencing skippy: the genome sequence of an Australian kangaroo, Macropus eugenii Elizabeth P Murchison, David J Adams Genome Biology 2011, 12:123 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sanger Institute's David Adams finds our kangaroo genome sequence article to be a fascinating window on mammalian evolution
	Research highlight Repeated phenotypic changes highlight molecular targets of convergent evolution Maggie R Wagner, Thomas Mitchell-Olds Genome Biology 2011, 12:124 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Maggie Wagner and Thomas Mitchell-Olds discuss how selection might preferentially target certain genes that have a strong phenotypic effect
	Review
	Opinion The real cost of sequencing: higher than you think! Andrea Sboner, Xinmeng Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein Genome Biology 2011, 12:125 (25 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data
	Report
	Meeting report Computational biology: plus c'est la même chose, plus ça change Curtis Huttenhower Genome Biology 2011, 12:307 (23 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint 19th Annual ISMB/10th Annual ECCB and the 7th ISCB Student Council Symposium, Vienna, Austria, 15-19 July 2011
	Research
	Research The contrasting roles of PPARδ and PPARγ in regulating the metabolic switch between oxidation and storage of fats in white adipose tissue Lee D Roberts, Andrew J Murray, David Menassa, Tom Ashmore, Andrew W Nicholls, Julian L Griffin Genome Biology 2011, 12:R75 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A specific agonist demonstrates the contrast between PPAR-delta and PPAR-gamma function in lipid metabolism
	Research Farnesyltransferase inhibitor treatment restores chromosome territory positions and active chromosome dynamics in Hutchinson-Gilford progeria syndrome cells Ishita S Mehta, Christopher H Eskiw, Halime D Arican, Ian R Kill, Joanna M Bridger Genome Biology 2011, 12:R74 (12 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Treating cultured cells from Hutchinson-Gilford progeria patients with farnesyltransferase inhibitors restores wildtype chromosome dynamics
	Research The head-regeneration transcriptome of the planarian Schmidtea mediterranea Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer Genome Biology 2011, 12:R76 (16 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Next generation sequencing was used to investigate the transcriptome of head regeneration in the planarian Schmidtea mediterranea
	Research Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage Min Zhu, Ming Yi, Chang Hee Kim, Chuxia Deng, Yi Li, Daniel Medina, Robert M Stephens, Jeffrey E Green Genome Biology 2011, 12:R77 (16 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expression profiling in mouse models of mammary tumors identifies miRNA signatures particular to lineages or driver oncogenes
	Research A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1 Melanie Blasius, Josep V Forment, Neha Thakkar, Sebastian A Wagner, Chunaram Choudhary, Stephen P Jackson Genome Biology 2011, 12:R78 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phospho-proteomics screen identifies many novel Chk1 substrates and a target site consensus motif
	Research Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:R81 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
	Research Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast Brian T Wilhelm, Samuel Marguerat, Sofia Aligianni, Sandra Codlin, Stephen Watt, Jürg Bähler Genome Biology 2011, 12:R82 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of marks associated with introns in S. pombe finds distinct patterns of histones, open chromatin and PolII enrichment
	Method Single cell transcriptomics of neighboring hyphae of Aspergillus niger Charissa de Bekker, Oskar Bruning, Martijs J Jonker, Timo M Breit, Han AB Wösten Genome Biology 2011, 12:R71 (4 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for single cell transcriptomics is developed and is demonstrated on single hyphae of Aspergillus niger
	Method TopHat-Fusion: an algorithm for discovery of novel fusion transcripts Daehwan Kim, Steven L Salzberg Genome Biology 2011, 12:R72 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm
	Method Hybrid selection for sequencing pathogen genomes from clinical samples Alexandre Melnikov, Kevin Galinsky, Peter Rogov, Timothy Fennell, Daria Van Tyne, Carsten Russ, Rachel Daniels, Kayla G Barnes, James Bochicchio, Daouda Ndiaye, Papa D Sene, Dyann F Wirth, Chad Nusbaum, Sarah K Volkman, Bruce W Birren, Andreas Gnirke, Daniel E Neafsey Genome Biology 2011, 12:R73 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Baits generated from Plasmodium DNA are used in solution hybridization to enrich parasite DNA from clinical samples to facilitate sequencing
	Method PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data David L Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca L Skalsky, Jack D Keene, Uwe Ohler Genome Biology 2011, 12:R79 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for identifying RNA binding sites and miRNA target motifs from PAR-CLIP data
	Method Single-cell copy number variation detection Jiqiu Cheng, Evelyne Vanneste, Peter Konings, Thierry Voet, Joris R Vermeesch, Yves Moreau Genome Biology 2011, 12:R80 (19 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method is presented for detecting copy number variations from array CGH data specifically optimized for use with single cells
	Software Cistrome: an integrative platform for transcriptional regulation studies Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu Genome Biology 2011, 12:R83 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Galaxy-based web application for integrative analysis of ChIP data

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Volume 12 Issue 8

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