Molecular Systems Biology - New articles published 11 October 2011

Latest Articles 11 October 2011   Featured Article Reports Correspondence   Web feeds About Open access Advertisement Cell Research - Submit today! Cell Research publishes articles, research and reviews covering all disciplines within cell biology and molecular biology. With an international authorship and circulation CR is a great outlet for your research. Submit your paper today at: http://mts-cr.nature.com/cgi-bin/main.plex.   Featured Article Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics This study provides a dynamic view of retinoic acid signalling during cell differentiation, reveals RAR/RXR heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs. Marco A Mendoza-Parra, Mannu Walia, Martial Sankar & Hinrich Gronemeyer Molecular Systems Biology 7:538; doi:10.1038/msb.2011.73; published 11 October 2011 Synopsis | Full Text | PDF | Supp. Inf. | Review Process Reports Toward an understanding of the protein interaction network of the human liver An extensive interaction network of human liver-expressed proteins is described, composed of 3484 interactions among 2582 proteins. Proteins associated with liver disease tend to be central and highly connected in the network. Jian Wang, Keke Huo, Lixin Ma, Liujun Tang, Dong Li, Xiaobi Huang, Yanzhi Yuan, Chunhua Li, Wei Wang, Wei Guan, Hui Chen, Chaozhi Jin, Junchen Wei, Wanqiao Zhang, Yongsheng Yang, Qiongming Liu, Ying Zhou, Cuili Zhang, Zhihao Wu, Wangxiang Xu, Ying Zhang, Tao Liu, Donghui Yu, Yaping Zhang, Liang Chen, Dewu Zhu, Xing Zhong, Lixin Kang, Xiang Gan, Xiaolan Yu, Qi Ma, Jing Yan, Li Zhou, Zhongyang Liu, Yunping Zhu, Tao Zhou, Fuchu He & Xiaoming Yang Molecular Systems Biology 7:536; doi:10.1038/msb.2011.67; published 11 October 2011 Full Text | PDF | Supp. Inf. | Review Process A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 The genome-scale metabolic network reconstruction of Escherichia coli, in use since 2000, is thoroughly updated based on the recent findings in the literature and new experiments. The improved reconstruction accounts for 1366 genes and can be used for constraint-based modeling of metabolic phenotypes. Jeffrey D Orth, Tom M Conrad, Jessica Na, Joshua A Lerman, Hojung Nam, Adam M Feist & Bernhard Ø Palsson Molecular Systems Biology 7:535; doi:10.1038/msb.2011.65; published 11 October 2011 Full Text | PDF | Supp. Inf. | Review Process Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Multiple sequence alignments are fundamental to many sequence analysis methods. The new program Clustal Omega can align virtually any number of protein sequences quickly and has powerful features for adding sequences to existing precomputed alignments. Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson & Desmond G Higgins Molecular Systems Biology 7:539; doi:10.1038/msb.2011.75; published 11 October 2011 Full Text | PDF | Supp. Inf. | Review Process Correspondence   The self-assessment trap: can we all be better than average? Raquel Norel, John Jeremy Rice & Gustavo Stolovitzky Molecular Systems Biology 7:537; doi:10.1038/msb.2011.70; published 11 October 2011 Full Text | PDF | Supp. Inf.

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