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Volume 12 Issue 8
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Comment |
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Nothing to do and all day to do it in
Gregory A Petsko Genome Biology 2011, 12:126 (31 August 2011)
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Editor’s summary
The perfect end to a perfect vacation day
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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)
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Editor’s summary
The Sanger Institute's David Adams finds our kangaroo genome sequence article to be a fascinating window on mammalian evolution
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Repeated phenotypic changes highlight molecular targets of convergent evolution
Maggie R Wagner, Thomas Mitchell-Olds Genome Biology 2011, 12:124 (23 August 2011)
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Editor’s summary
Maggie Wagner and Thomas Mitchell-Olds discuss how selection might preferentially target certain genes that have a strong phenotypic effect
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Review |
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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)
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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
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Report |
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Computational biology: plus c'est la même chose, plus ça change
Curtis Huttenhower Genome Biology 2011, 12:307 (23 August 2011)
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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
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Research |
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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)
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Editor’s summary
A specific agonist demonstrates the contrast between PPAR-delta and PPAR-gamma function in lipid metabolism
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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)
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Editor’s summary
Treating cultured cells from Hutchinson-Gilford progeria patients with farnesyltransferase inhibitors restores wildtype chromosome dynamics
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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)
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Editor’s summary
Next generation sequencing was used to investigate the transcriptome of head regeneration in the planarian Schmidtea mediterranea
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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)
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Editor’s summary
Expression profiling in mouse models of mammary tumors identifies miRNA signatures particular to lineages or driver oncogenes
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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)
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Editor’s summary
A phospho-proteomics screen identifies many novel Chk1 substrates and a target site consensus motif
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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)
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Editor’s summary
The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
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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)
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Editor’s summary
A study of marks associated with introns in S. pombe finds distinct patterns of histones, open chromatin and PolII enrichment
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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)
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Editor’s summary
A method for single cell transcriptomics is developed and is demonstrated on single hyphae of Aspergillus niger
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TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
Daehwan Kim, Steven L Salzberg Genome Biology 2011, 12:R72 (11 August 2011)
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Editor’s summary
A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm
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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)
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Editor’s summary
Baits generated from Plasmodium DNA are used in solution hybridization to enrich parasite DNA from clinical samples to facilitate sequencing
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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)
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Editor’s summary
A method for identifying RNA binding sites and miRNA target motifs from PAR-CLIP data
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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)
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Editor’s summary
A method is presented for detecting copy number variations from array CGH data specifically optimized for use with single cells
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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)
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Editor’s summary
A Galaxy-based web application for integrative analysis of ChIP data
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