Genome Biology | Volume 11 Issue 12

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	Volume 11 Issue 12
	Comment
	Comment The long and the short of it Gregory A Petsko Genome Biology 2010, 11:145 (23 December 2010) Full text \| PDF \| PubMed \| Editor’s summary An end of year assessment of potential scientific investments.
	Research highlight Creating a blood line from human skin Michael H Sieweke Genome Biology 2010, 11:143 (20 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Blood cell progenitors with therapeutic potential have been produced directly from human fibroblasts without intermediate pluripotent stem cells.
	Research highlight Whole-exome sequencing for finding de novo mutations in sporadic mental retardation Peter N Robinson Genome Biology 2010, 11:144 (21 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work has used a family-based approach and whole-exome sequencing to identify de novo mutations in sporadic cases of mental retardation.
	Review
	Review From RNA-seq reads to differential expression results Alicia Oshlack, Mark D Robinson, Matthew D Young Genome Biology 2010, 11:220 (22 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
	Research
	Research Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2 Kohta Ikegami, Thea A Egelhofer, Susan Strome, Jason D Lieb Genome Biology 2010, 11:R120 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A modENCODE survey of chromosome interactions with the inner nuclear membrane finds interacting regions are distal and gene sparse
	Research Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic Shafagh Al Nadaf, Paul D Waters, Edda Koina, Janine E Deakin, Kristen S Jordan, Jennifer AM Graves Genome Biology 2010, 11:R122 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Incomplete escape from X inactivation in marsupials is revealed by a map of gene expression from the tammar wallaby X chromosome.
	Research Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate Gabriel Krouk, Piotr Mirowski, Yann LeCun, Dennis E Shasha, Gloria M Coruzzi Genome Biology 2010, 11:R123 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene networks downstream of nitrate signaling are characterized with temporal resolution in a transcriptome analysis, including an early response SPL9 hub
	Research Large scale comparison of global gene expression patterns in human and mouse Xiangqun Zheng-Bradley, Johan Rung, Helen Parkinson, Alvis Brazma Genome Biology 2010, 11:R124 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of all human and mouse arrays deposited in ArrayExpress reveals broadly similar transcription of orthologous genes between species
	Research Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners Peter L Chang, Brian P Dilkes, Michelle McMahon, Luca Comai, Sergey V Nuzhdin Genome Biology 2010, 11:R125 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Arabidopsis suecica homoeolog-specific gene expression has a parent of origin preference
	Research Novel genes exhibit distinct patterns of function acquisition and network integration John A Capra, Katherine S Pollard, Mona Singh Genome Biology 2010, 11:R127 (27 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genes arising de novo from non-coding sequence in yeast have different functions and network properties from those arising from duplication.
	Method Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition Andrew Adey, Hilary G Morrison, Asan, Xu Xun, Jacob O Kitzman, Emily H Turner, Bethany Stackhouse, Alexandra P MacKenzie, Nicholas C Caruccio, Xiuqing Zhang, Jay Shendure Genome Biology 2010, 11:R119 (8 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protocols for rapid, low-input sequencing library construction without clean up.
	Software The Genomic HyperBrowser: inferential genomics at the sequence level Geir K Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi, Eivind Hovig Genome Biology 2010, 11:R121 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel platform for the statistical analysis of sequence-level genomic information.
	Software ArchAlign: coordinate-free chromatin alignment reveals novel architectures William KM Lai, Michael J Buck Genome Biology 2010, 11:R126 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An algorithm for discovery of chromatin architectures
	Software Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly Kim Wong, Thomas M Keane, James Stalker, David J Adams Genome Biology 2010, 11:R128 (31 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SVMerge is a pipeline combining the outputs of several structural variation detection programs to improve structural variation detection