Computational biology and bioinformatics articles within Nature

Featured

  • Career Brief |

    Pan-European programme seeks bioinformaticians and biocurators.

  • Feature |

    With biological databases growing in size and number, curators are needed to update and correct their contents. For those who prefer computers to pipettes, there are opportunities.

    • Katharine Sanderson

  • News & Views |

    Cellular compartmentalization is an effective way to build gene circuits capable of complex logic operations, in which binary inputs are converted into binary outputs according to user-defined rules. See Letters p.207 & p.212

    • Bochong Li
    •  & Lingchong You

  • News & Views Forum |

    Many scientists now use the power of computer models to advance their subjects. But there is a choice: to simplify complex systems or to include more detail. Modelling the intricate processes of sedimentary geology is a case in point.

    • Chris Paola
    •  & Mike Leeder

  • Letter |

    For synthetic biologists' creativity to be unleashed, basic circuits must become truly interchangeable, that is, modular and scalable. This study, one of two linked papers, has harnessed yeast pheromone communication to achieve complex computation through communication between individual cells performing simple logic functions. Such extracellular 'chemical wiring' is one promising way to get around intracellular noise when building more complex genetic circuitry.

    • Sergi Regot
    • , Javier Macia
    •  & Ricard Solé

  • Letter |

    For synthetic biologists' creativity to be unleashed, basic circuits must become truly interchangeable, that is, modular and scalable. This study, one of two linked papers, has harnessed bacterial 'quorum sensing' to achieve complex computation through communication between individual cells performing simple logic functions. Such extracellular 'chemical wiring' is one promising way to get around intracellular noise when building more complex genetic circuitry.

    • Alvin Tamsir
    • , Jeffrey J. Tabor
    •  & Christopher A. Voigt

  • Article |

    The central amygdala relies on inhibitory circuitry to encode fear memories, but how this information is acquired and expressed in these connections is unknown. Two new papers use a combination of cutting-edge technologies to reveal two distinct microcircuits within the central amygdala, one required for fear acquisition and the other critical for conditioned fear responses. Understanding this architecture provides a strong link between activity in a specific circuit and particular behavioural consequences.

    • Stephane Ciocchi
    • , Cyril Herry
    •  & Andreas Lüthi

  • News Q&A |

    An open-source computer program flouts patents to test for cancer-causing gene mutations.

    • Alla Katsnelson

  • World View |

    Freely provided working code — whatever its quality — improves programming and enables others to engage with your research, says Nick Barnes.

    • Nick Barnes

  • Article |

    Water security affects human wellbeing both directly and indirectly, through its effects on biodiversity. Here, a global map has been generated that shows threats to both direct and indirect water security from a full range of potential stressors. Technological investments have also been incorporated. The map shows that nearly 80% of the world's population is exposed to high levels of threat to water security. Investment enables rich nations to offset high stressor levels, but less wealthy nations remain vulnerable.

    • C. J. Vörösmarty
    • , P. B. McIntyre
    •  & P. M. Davies

  • Opinion |

    Taxonomists should work with specialists in pattern recognition, machine learning and artificial intelligence, say Norman MacLeod, Mark Benfield and Phil Culverhouse — more accuracy and less drudgery will result.

    • Norman MacLeod
    • , Mark Benfield
    •  & Phil Culverhouse

  • Letter |

    Predicting the structure of a folded protein from first principles for any given amino-acid sequence remains a formidable computational challenge. To recruit human abilities to the task, these authors turned their Rosetta structure prediction algorithm into an online multiplayer game in which thousands of non-scientists competed and collaborated to produce new algorithms and search strategies for protein structure refinement. This shows that computationally complex problems can be effectively 'crowd-sourced' through interactive multiplayer games.

    • Seth Cooper
    • , Firas Khatib
    •  & Foldit players

  • News Feature |

    Networks of human minds are taking citizen science to a new level, reports Eric Hand.

    • Eric Hand

  • News |

    The Deepwater Horizon oil spill puts ocean-current modelling to the test.

    • Janet Fang

  • Technology Feature |

    Proteins in cell membranes are notoriously hard to crystallize, but new techniques give scientists the means to map them. Monya Baker scouts out the tools for cracking the structure of membrane proteins.

    • Monya Baker

  • Editorial |

    The successful transplantation of a synthesized genome highlights unresolved ethical and security issues posed by synthetic biology.

  • Letter |

    The need to maintain the structural and functional integrity of an evolving protein limits the range of acceptable amino-acid substitutions — but to what extent does this constrain how far homologous protein sequences can diverge? Here, sequence divergence data are used to explore the limits of protein evolution, and to conclude that ancient proteins are continuing to diverge from one another, indicating that the protein sequence universe is slowly expanding.

    • Inna S. Povolotskaya
    •  & Fyodor A. Kondrashov

  • News |

    Test case for electronic publication of new species names breaks with over 200 years of history.

    • Daniel Cressey

  • Letter |

    Modern networks are rarely independent, instead being coupled together with many others. Thus the failure of a small fraction of nodes in one network may lead to the complete fragmentation of a system of several interdependent networks. Here, a framework is developed for understanding the robustness of interacting networks subject to such 'cascading' failures. Surprisingly, a broader degree distribution increases the vulnerability of interdependent networks to random failure.

    • Sergey V. Buldyrev
    • , Roni Parshani
    •  & Shlomo Havlin

  • Careers and Recruitment |

    Applying systems biology to cancer research has become a growth area for computationally minded scientists. Kelly Rae Chi tallies the possibilities.

    • Kelly Rae Chi

  • News & Views |

    A study of failures in interconnected networks highlights the vulnerability of tightly coupled infrastructures and shows the need to consider mutually dependent network properties in designing resilient systems.

    • Alessandro Vespignani

  • Editorial |

    Britain's Department of Health must respond to concerns about electronic medical records.

  • Letter |

    Genotype and phenotype cannot be connected simply by one-to-one mapping; instead they are linked by the nonlinear process of development. Here, a computational model is described — based on real data about the development of seal teeth — that attempts to combine the three. The results show that a few genetic parameters regulating signalling during cusp development may explain variation among individuals. But a cellular parameter regulating epithelial growth may explain tooth-to-tooth variation along the jaw.

    • Isaac Salazar-Ciudad
    •  & Jukka Jernvall

  • Article |

    Local adaptations are often governed by several interacting genes scattered throughout the genome. Here a novel type of multi–locus genetic variation is described that has been maintained within a species over a vast period of time. A balanced unlinked gene network polymorphism is dissected that involves galactose utilization in a close relative of baker's yeast.

    • Chris Todd Hittinger
    • , Paula Gonçalves
    •  & Antonis Rokas

  • News Feature |

    Scientists are struggling to make sense of the expanding scientific literature. Corie Lok asks whether computational tools can do the hard work for them.

    • Corie Lok

  • Article |

    A defining focus of synthetic biology is the engineering of genetic circuits with predictive functionality in living cells. Here, a decade after the first synthesized genetic toggle switch and oscillator, an engineered gene network with global intercellular coupling is designed that is capable of generating synchronized oscillations in a growing population of cells.

    • Tal Danino
    • , Octavio Mondragón-Palomino
    •  & Jeff Hasty

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