Computational biology and bioinformatics articles within Nature Communications

Featured

  • Article
    | Open Access

    Misfolded protein accumulation is a hallmark of many neurodegenerative diseases. Here Budrikis et al. model protein aggregation in the endoplasmic reticulum and show that it is the result of a non-equilibrium phase transition caused by tipping the balance from the rates of protein production to degradation.

    • Zoe Budrikis
    • , Giulio Costantini
    •  & Stefano Zapperi

  • Article |

    The enzyme butyrylcholinesterase (BChE) can metabolize cocaine, albeit at relatively low speeds. Here the authors use computational methods to define mutations that increase BChE-mediated cocaine hydrolysis, achieving a catalytic activity comparable to that of one of the fastest naturally occurring enzyme.

    • Fang Zheng
    • , Liu Xue
    •  & Chang-Guo Zhan

  • Article
    | Open Access

    Gene expression is highly variable between tissues, and changes during development and with age. Here, the authors provide a comprehensive RNA-Seq analysis of the rat transcriptome, spanning eleven organs, four developmental stages and both sexes.

    • Ying Yu
    • , James C. Fuscoe
    •  & Charles Wang

  • Article
    | Open Access

    mRNA transport contributes to the proper localization of its cognate proteins. Here the authors report a correlation between the physicochemical properties of mRNAs and their cognate proteins, suggesting that these properties of mRNAs can predict the subcellular localization of their cognate proteins.

    • Anton A. Polyansky
    • , Mario Hlevnjak
    •  & Bojan Zagrovic

  • Article |

    Predicting the dynamics and disorder of a protein is a computationally complex task that, until now, has depended on prior knowledge of protein structure. Cilia et al.develop a tool to rapidly predict protein backbone dynamics based on sequence alone.

    • Elisa Cilia
    • , Rita Pancsa
    •  & Wim F. Vranken

  • Article |

    Non-small cell lung cancers (NSCLC) that harbour mutations in KRas can be separated into KRas-dependent and -independent subsets. By analysing transcriptome, proteome and phosphoproteome data from NSCLC cell lines, Balbin et al. show that KRas-dependent cell lines activate the Lck pathway.

    • O. Alejandro Balbin
    • , John R. Prensner
    •  & Arul M. Chinnaiyan

  • Article
    | Open Access

    FGFR2 gene variation is associated with breast cancer risk but the molecular mechanism is unknown. Fletcher et al. provide a link between FGFR2 signalling and breast cancer susceptibility by demonstrating that FGFR2 signalling activates the ERa transcriptional network, which drives transcription of risk genes.

    • Michael N. C. Fletcher
    • , Mauro A. A. Castro
    •  & Kerstin B. Meyer

  • Article |

    Mutually exclusive splicing of genes is a mechanism for generating proteome diversity. Here Kollmar et al. determine the mutually exclusive spliced exome of Drosophila melanogaster and reveal insights into its evolutionary history within the Drosophilagroup.

    • Klas Hatje
    •  & Martin Kollmar

  • Article
    | Open Access

    Dynamic changes in T cell repertoire underlie immune responses during infection, allergy, autoimmunity and cancer. Here, Li et al. present a workflow for high throughput sequencing and analysis of T cell receptor sequences, and use it to monitor the T cell response to influenza vaccination in a human patient.

    • Shuo Li
    • , Marie-Paule Lefranc
    •  & Eric J. Gowans

  • Article |

    Sequencing whole microbial genomes has become standard practice and methods to examine their phylogenetic relationships need to match the increasing demand. Segata et al. present a new computational pipeline that allows fast and accurate taxonomic assignment of microbial species.

    • Nicola Segata
    • , Daniela Börnigen
    •  & Curtis Huttenhower

  • Article
    | Open Access

    Biological network data are often incomplete, which makes it difficult to determine interaction motifs within such data sets. Here Tran et al. present a new method to count motif numbers in large networks from noisy and incomplete biological data.

    • Ngoc Hieu Tran
    • , Kwok Pui Choi
    •  & Louxin Zhang

  • Article
    | Open Access

    Systematic large-scale analysis of embryonic development requires the processing of large amounts of microscopy data. Here Schmid et al.solve this problem by developing a high-speed imaging system that projects zebrafish embryos onto a ‘world map’ in real time, revealing characteristic migration patterns in the early endoderm.

    • Benjamin Schmid
    • , Gopi Shah
    •  & Jan Huisken

  • Article
    | Open Access

    The comprehensive bioanalysis of proteins usually requires multi-step surface and mobile phase measurements. Here, the authors use chips functionalized with dynamically actuated nanolevers—DNA strands that can be switched in an electric field—to obtain motional dynamic measurements of proteins on a chip.

    • Andreas Langer
    • , Paul A. Hampel
    •  & Ulrich Rant

  • Article
    | Open Access

    Cell lines are widely used in cancer research to study tumour biology. Here Domcke et al.compare genomic data from ovarian cancer cell lines with those from clinical ovarian tumour samples and identify cell lines that most closely resemble the genomic features of high-grade serous ovarian cancer.

    • Silvia Domcke
    • , Rileen Sinha
    •  & Nikolaus Schultz

  • Article |

    The identification of hosts of blood-sucking insects is important for studying ecological factors that affect pathogen distribution. Önder et al. report a proteomics-based methodology for the analysis of blood remnants in ticks that identifies the host species from which the tick has fed up to 6 months earlier.

    • Özlem Önder
    • , Wenguang Shao
    •  & Dustin Brisson

  • Article
    | Open Access

    The rice sheath blight pathogen, Rhizoctonia solani, is an important fungal pathogen that can devastate rice and maize crops. Zheng and colleagues sequence and assemble the R. solani AG1 IA genome—the first to be sequenced from the Rhizoctoniagenus—using Illumina sequencing technology.

    • Aiping Zheng
    • , Runmao Lin
    •  & Ping Li

  • Article
    | Open Access

    To describe the biochemical composition of an organism multiple data sets must be combined and this information can then be used forin silico analysis. By combining metabolism and transcription data, Lerman et al. discovered new regulons and improved the gene annotation for the simple organism Thermotoga maritima.

    • Joshua A. Lerman
    • , Daniel R. Hyduke
    •  & Bernhard O. Palsson

  • Article |

    Understanding the environmental controls of past wildfires is difficult due to the lack of records of weather or vegetation. This study shows, using cross-scale analysis, how power laws associated with fire-event time series can identify critical thresholds in landscape dynamics in a rapidly changing climate.

    • Donald McKenzie
    •  & Maureen C. Kennedy

  • Article |

    Humans are a network of complex physiological systems, but quantifying these diverse systems is a challenge. This study presents a method to show that each physiological state is characterized by a specific network structure, demonstrating a connection between network topology and function.

    • Amir Bashan
    • , Ronny P. Bartsch
    •  & Plamen Ch. Ivanov

  • Article
    | Open Access

    When two spatially separated parties flip a coin, it is impossible to choose between two alternatives in an unbiased manner. This study presents a quantum coin-flipping protocol that overcomes this problem and ensures a dishonest party cannot bias the outcome completely.

    • Guido Berlín
    • , Gilles Brassard
    •  & Wolfgang Tittel

  • Article |

    Large scale synapse assays can facilitate identification of drug leads. Shiet al. develop a 'synapse microarray' technology that enables sensitive, high-throughput, quantitative screening of synaptogenic events, and use it to identify novel histone deacetylase inhibitors that enhance synaptogenesis.

    • Peng Shi
    • , Mark A. Scott
    •  & Mehmet Fatih Yanik

  • Article
    | Open Access

    The paradigm of reservoir computing shows that, like the human brain, complex networks can perform efficient information processing. Here, a simple delay dynamical system is demonstrated that can efficiently perform computations capable of replacing a complex network in reservoir computing.

    • L. Appeltant
    • , M.C. Soriano
    •  & I. Fischer

  • Article |

    Protein microarrays are useful both in basic research and also in disease monitoring and diagnosis, but their dynamic range is limited. By using plasmonic gold substrates with near-infrared fluorescent enhancement, Tabakman et al. demonstrate a multiplexed protein array with improved detection limits and dynamic range.

    • Scott M. Tabakman
    • , Lana Lau
    •  & Hongjie Dai

  • Article |

    Phylogenetic analysis is used to identify transmission chains, but no software is available for the automated partition of large phylogenies. Prosperiet al. apply a new search algorithm to identify transmission clusters within the phylogeny of HIV-1gene sequences linking molecular and epidemiological data.

    • Mattia C.F. Prosperi
    • , Massimo Ciccozzi
    •  & Andrea De Luca

  • Article
    | Open Access

    Leptosphaeria maculans is a plant pathogen that causes stem canker of oilseed rape. Rouxel et al. sequence and describe the key features of the L. maculansgenome, including partitioning into AT-rich blocks that are enriched in effector genes and transposable elements affected by repeat-induced point mutation.

    • Thierry Rouxel
    • , Jonathan Grandaubert
    •  & Barbara J. Howlett

Browse broader subjects

Browse narrower subjects

Browse Computational biology and bioinformatics across other nature.com journals