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Cell Systems
This journal offers authors two options (open access or subscription) to publish research

Aug 23, 2017

Volume 5Issue 2p87-156
Open Archive
On the cover: Simulated tracks of collective cell migration from Schumacher et al. (pp. 119–127) demonstrate that although all cells are known to be identical, the population can appear to be erroneously heterogeneous under commonly encountered circumstances....
On the cover: Simulated tracks of collective cell migration from Schumacher et al. (pp. 119–127) demonstrate that although all cells are known to be identical, the population can appear to be erroneously heterogeneous under commonly encountered circumstances.

Editorial

  • Considering and Reconsidering Peer Review

    • H. Craig Mak
    The second Monday of September marks the beginning of Peer Review Week 2017. Peer review—and a singular dedication to guiding manuscripts, authors, and reviewers through the review process to the best of our ability—is a pillar on which this and many other journals place their relevance. Yet, for a journal, it is worth examining factors that influence the peer review process and when it breaks down, even if this threatens to undermine our own relevance.

Cell Systems Call

Previews

Perspective

Article

  • Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States

    • Jong Wook Kim,
    • Omar O. Abudayyeh,
    • Huwate Yeerna,
    • Chen-Hsiang Yeang,
    • Michelle Stewart,
    • Russell W. Jenkins,
    • Shunsuke Kitajima,
    • David J. Konieczkowski,
    • Kate Medetgul-Ernar,
    • Taylor Cavazos,
    • Clarence Mah,
    • Stephanie Ting,
    • Eliezer M. Van Allen,
    • Ofir Cohen,
    • John Mcdermott,
    • Emily Damato,
    • Andrew J. Aguirre,
    • Jonathan Liang,
    • Arthur Liberzon,
    • Gabriella Alexe,
    • John Doench,
    • Mahmoud Ghandi,
    • Francisca Vazquez,
    • Barbara A. Weir,
    • Aviad Tsherniak,
    • Aravind Subramanian,
    • Karina Meneses-Cime,
    • Jason Park,
    • Paul Clemons,
    • Levi A. Garraway,
    • David Thomas,
    • Jesse S. Boehm,
    • David A. Barbie,
    • William C. Hahn,
    • Jill P. Mesirov,
    • Pablo Tamayo
    Assessing the functional consequences of oncogene activation is critical for subsequently characterizing disease in a patient and devising effective therapeutic strategies. We describe Onco-GPS, a data-driven analysis framework to summarize, visualize, and discover new associations that may guide therapeutic strategies involving existing or new targets as part of individualized precision medicine paradigms.

Math | Bio

  • Semblance of Heterogeneity in Collective Cell Migration

    • Linus J. Schumacher,
    • Philip K. Maini,
    • Ruth E. Baker
    Schumacher et al. use a mathematical model to show how cell populations can appear heterogeneous in their migratory characteristics, even though they are made up of identically behaving individual cells. This has important consequences for the study of collective cell migration in areas such as embryo development or cancer invasion.

Reports

Tools

  • The GenePattern Notebook Environment

    • Michael Reich,
    • Thorin Tabor,
    • Ted Liefeld,
    • Helga Thorvaldsdóttir,
    • Barbara Hill,
    • Pablo Tamayo,
    • Jill P. Mesirov
    Reich et al. have developed software that integrates the capabilities of electronic analysis notebooks and bioinformatics analysis portals. GenePattern Notebook uses the popular Jupyter Notebook platform that interleaves text, graphics, and code, and brings these tools for reproducible research, as well as access to hundreds of bioinformatics analyses, to non-programmers.
  • Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes

    • Christoph N. Schlaffner,
    • Georg J. Pirklbauer,
    • Andreas Bender,
    • Jyoti S. Choudhary
    We have developed a fast, scalable, and free open-source tool to map peptides identified through mass spectrometry onto reference genomes. It provides extended functionality, supporting representation of single-nucleotide variants, post-translational modifications, and quantitative features. The tool has been integrated in established frameworks and is available as a standalone version with user-friendly graphical interface.
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