Networks and systems biology

  • Article
    | Open Access

    Small molecules bioactivity descriptors are enriched representations of compounds, reaching beyond chemical structures and capturing their known biological properties. Here the authors present a collection of deep neural networks able to infer bioactivity signatures for any compound of interest, even when little or no experimental information is available for them.

    • Martino Bertoni
    • , Miquel Duran-Frigola
    •  & Patrick Aloy
  • Article
    | Open Access

    Identifying chemical-genetic interactions in mammalian cells is limited to low-throughput or computational methods. Here, the authors present QMAP-Seq, a broadly accessible and scalable approach that uses NGS for pooled high-throughput chemical-genetic profiling in mammalian cells.

    • Sonia Brockway
    • , Geng Wang
    •  & Marc L. Mendillo
  • Article
    | Open Access

    The secretory pathway is used in the production of most biopharmaceuticals, but the associated biosynthetic costs are little understood. Here, the authors integrate the core secretory pathway into genome-scale metabolic models of human, mouse, and CHO cells, enabling in silico analysis.

    • Jahir M. Gutierrez
    • , Amir Feizi
    •  & Nathan E. Lewis
  • Article
    | Open Access

    Our understanding of the mechanisms of drug interactions remains limited. Here the authors introduce a framework to study how complex cellular perturbations induced by different drugs affect each other in morphological feature space.

    • Michael Caldera
    • , Felix Müller
    •  & Jörg Menche
  • Article
    | Open Access

    Gene expression profiles can classify breast cancer into five clinically relevant subtypes. Here, the authors perform an in-depth quantitative profiling of the proteome of 45 breast tumors, and show they can recapitulate the transcriptome-based classifications and identify many potentially antigenic tumour-specific peptides.

    • Henrik J. Johansson
    • , Fabio Socciarelli
    •  & Janne Lehtiö
  • Article
    | Open Access

    The mechanisms that accommodate variable external dependencies in evolution are not clear. Here, the authors show that switches between external and internal metabolic controls of carotenoid-producing networks in birds are linked to shifts in evolutionary rates, with internalization of control resulting in bursts of evolutionary diversification.

    • Alexander V. Badyaev
    • , Alexander B. Posner
    •  & Dawn M. Higginson
  • Article
    | Open Access

    Combination therapy holds great promise, but discovery remains challenging. Here, the authors propose a method to identify efficacious drug combinations for specific diseases, and find that successful combinations tend to target separate neighbourhoods of the disease module in the human interactome.

    • Feixiong Cheng
    • , István A. Kovács
    •  & Albert-László Barabási
  • Article
    | Open Access

    Multidrug resistance necessitates novel approaches to treating bacterial infections. Here, the authors apply their high-throughput screening and in silico prediction approaches to show that host receptor tyrosine kinases are good targets for host-directed therapies against intracellular bacteria.

    • Cornelis J. Korbee
    • , Matthias T. Heemskerk
    •  & Tom H. M. Ottenhoff
  • Article |

    The spreading dynamics of a contagion depend on the structure of an underlying network, and long-range edges due to airline transportation or media communication can significantly alter such dynamics. Here the authors use contagion dynamics on networks to produce point clouds for this analysis.

    • Dane Taylor
    • , Florian Klimm
    •  & Peter J. Mucha
  • Article
    | Open Access

    Connections in networks are organized to fulfil a function, and a common one is targeted transport or navigation. Here the authors use game theory to show how networks designed to maximize navigation efficiency at minimal cost share basic structural properties, which are also found in real cases.

    • András Gulyás
    • , József J. Bíró
    •  & Dmitri Krioukov
  • Article |

    Multilayer networks have been used to capture the structure of complex systems with different types of interactions, but often contain redundant information. Here, De Domenico et al. present a method based on quantum information, to identify the minimal configuration of layers to retain.

    • Manlio De Domenico
    • , Vincenzo Nicosia
    •  & Vito Latora
  • Article
    | Open Access

    Random walks on a network describe the dynamics of many natural and artificial systems. Here, Perkins et al.study the path distribution—characterizing how the walker moves—and find that it is either finite, stretched exponential or power law for any random walk on a finite network.

    • Theodore J. Perkins
    • , Eric Foxall
    •  & Roderick Edwards
  • Article |

    Unravelling the relationships between disease symptoms and underlying molecular origins is an important task in biomedical research. Here, Zhou et al.link diseases via their symptom overlap, and show that similar phenotypes are mirrored in networks that connect diseases with common genes or protein interactions.

    • XueZhong Zhou
    • , Jörg Menche
    •  & Amitabh Sharma
  • Article |

    Differences in the arrangement of cells is a fundamental precursor to the establishment of different organs. In this study, network theory is applied at the level of individual cells to map patterns in cell-to-cell contacts, creating a new approach to objectively characterise epithelia.

    • Luis M. Escudero
    • , Luciano da F. Costa
    •  & M. Madan Babu