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Molecular Systems Biology

Cover image for Vol. 10 Issue 7

July 2014

Volume 10, Issue 7

  1. Articles

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    2. Articles
    3. News & Views
    4. Articles
    5. News & Views
    1. You have full text access to this OnlineOpen article
      Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

      Traver Hart, Kevin R Brown, Fabrice Sircoulomb, Robert Rottapel and Jason Moffat

      Version of Record online: 1 JUL 2014 | DOI: 10.15252/msb.20145216

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      This study provides a gold-standard set for essential and nonessential human genes in cancer cell lines. The ‘Daisy model’ for core versus context-specific essentiality provides a method to evaluate data quality in genome-scale RNAi and CRISPR screens.

    2. You have full text access to this OnlineOpen article
      Minimal metabolic pathway structure is consistent with associated biomolecular interactions

      Aarash Bordbar, Harish Nagarajan, Nathan E Lewis, Haythem Latif, Ali Ebrahim, Stephen Federowicz, Jan Schellenberger and Bernhard O Palsson

      Version of Record online: 1 JUL 2014 | DOI: 10.15252/msb.20145243

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      The MinSpan algorithm is presented that defines the shortest functional metabolic pathways at the genome scale, based on whole network function and parsimonious use of cellular components. The pathways are biologically supported by biomolecular interaction networks.

  2. News & Views

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      The Good, the Bad, and the Ugly: in search of gold standards for assessing functional genetic screen quality

      Bastiaan Evers, Rene Bernards and Roderick L Beijersbergen

      Version of Record online: 1 JUL 2014 | DOI: 10.15252/msb.20145372

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      Variable screen quality, off-target effects and unclear false discovery rates often hamper large-scale functional genomic screens. Hart et al (2014) introduce gold standard reference sets of essential and non-essential genes, aiming at standardizing the analysis of genome-wide screens.

  3. Articles

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    1. You have full text access to this OnlineOpen article
      An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

      Javier Carrera, Raissa Estrela, Jing Luo, Navneet Rai, Athanasios Tsoukalas and Ilias Tagkopoulos

      Version of Record online: 1 JUL 2014 | DOI: 10.15252/msb.20145108

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      A data-driven, integrative modeling methodology is presented that unifies signal transduction, gene expression, and metabolic processes under a common framework. Training on an aggregated dataset results in improved prediction of regulatory connections and measured phenotypes.

    2. You have full text access to this OnlineOpen article
      Phenotypic bistability in Escherichia coli's central carbon metabolism

      Oliver Kotte, Benjamin Volkmer, Jakub L Radzikowski and Matthias Heinemann

      Version of Record online: 1 JUL 2014 | DOI: 10.15252/msb.20135022

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      Upon nutrient change, a homogeneous E. coli population can split into a growing and a non-growing persister phenotype. Stochastic variation in metabolic flux is responsible for this responsive diversification.

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      Intercellular network structure and regulatory motifs in the human hematopoietic system

      Wenlian Qiao, Weijia Wang, Elisa Laurenti, Andrei L Turinsky, Shoshana J Wodak, Gary D Bader, John E Dick and Peter W Zandstra

      Version of Record online: 15 JUL 2014 | DOI: 10.15252/msb.20145141

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      A directional cell-cell communication network of human hematopoietic cells reveals mechanisms of hematopoietic cell feedback in HSC fate regulation and provides insight into the design principles of the human hematopoietic system.

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      A system-level model for the microbial regulatory genome

      Aaron N Brooks, David J Reiss, Antoine Allard, Wei-Ju Wu, Diego M Salvanha, Christopher L Plaisier, Sriram Chandrasekaran, Min Pan, Amardeep Kaur and Nitin S Baliga

      Version of Record online: 15 JUL 2014 | DOI: 10.15252/msb.20145160

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      Genome-scale reconstruction of microbial gene regulatory networks using genome sequence and transcriptional profiles reveals condition-dependent co-regulated modules (corems) and predicts the underlying cis-regulatory mechanisms.

    5. You have full text access to this OnlineOpen article
      Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells

      Jonathan Bieler, Rosamaria Cannavo, Kyle Gustafson, Cedric Gobet, David Gatfield and Felix Naef

      Version of Record online: 15 JUL 2014 | DOI: 10.15252/msb.20145218

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      Single-cell time-lapse analyses in mouse cells show that circadian and cell cycles are robustly synchronized. This state reflects a predominant unilateral influence of the cell cycle on the circadian oscillator.

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      Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases

      Manikandan Narayanan, Jimmy L Huynh, Kai Wang, Xia Yang, Seungyeul Yoo, Joshua McElwee, Bin Zhang, Chunsheng Zhang, John R Lamb, Tao Xie, Christine Suver, Cliona Molony, Stacey Melquist, Andrew D Johnson, Guoping Fan, David J Stone, Eric E Schadt, Patrizia Casaccia, Valur Emilsson and Jun Zhu

      Version of Record online: 30 JUL 2014 | DOI: 10.15252/msb.20145304

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      Network analysis of changes in gene co-regulation, between large sets of Alzheimer's (AD) or Huntington's (HD) disease versus control brains, reveals that opposing dysregulation of two interacting processes, chromatin organization and neural differentiation, underlies both AD and HD.

    7. You have full text access to this OnlineOpen article
      A ‘resource allocator’ for transcription based on a highly fragmented T7 RNA polymerase

      Thomas H Segall-Shapiro, Adam J Meyer, Andrew D Ellington, Eduardo D Sontag and Christopher A Voigt

      Version of Record online: 30 JUL 2014 | DOI: 10.15252/msb.20145299

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      The T7 RNA polymerase is split into two to four fragments that retain activity when co-expressed. These parts provide a toolbox to allocate resources to a genetic system, set its transcriptional activity and partition it between multiple orthogonal promoters.

  4. News & Views

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      Synthetic biology: the many facets of T7 RNA polymerase

      David L Shis and Matthew R Bennett

      Version of Record online: 30 JUL 2014 | DOI: 10.15252/msb.20145492

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      How many times can T7 RNA polymerase be split, yet retain function? A tripartite T7 RNAP presented by Voigt and colleagues, expands the utility of the enzyme in orthogonal gene circuits that are decoupled from host regulatory processes.

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