Bioinformatics articles within Nature Reviews Genetics

Featured

  • Review Article |

    In this Review, the authors summarize and discuss guidelines for omics benchmarking. They highlight common oversights and difficulties, offer guidance for frequently encountered issues and provide a structured form that can be used for comprehensive reporting of benchmarking studies.

    • Thomas G. Brooks
    • , Nicholas F. Lahens
    •  & Gregory R. Grant

  • Review Article |

    In this Review, Zhang et al. discuss how recent advances in computational methods are helping to reveal the multiscale features involved in genome folding within the nucleus and how the resulting 3D genome organization relates to genome function.

    • Yang Zhang
    • , Lorenzo Boninsegna
    •  & Jian Ma

  • Review Article |

    This Review summarizes the genetic and non-genetic factors that impact the transferability of polygenic risk scores (PRSs) across populations, highlighting the technical challenges of existing PRS construction methods for diverse ancestries and the emerging resources for more widespread use of PRSs.

    • Linda Kachuri
    • , Nilanjan Chatterjee
    •  & Tian Ge

  • Research Highlight |

    A study in Nature Biotechnology describes Scriabin, a highly scalable framework for inference of cell–cell communication from scRNA-seq data at the level of individual cells.

    • Dorothy Clyde

  • Review Article |

    Combining single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics can localize transcriptionally characterized single cells within their native tissue context. This Review discusses methodologies and tools to integrate scRNA-seq with spatial transcriptomics approaches, and illustrates the types of insights that can be gained.

    • Sophia K. Longo
    • , Margaret G. Guo
    •  & Paul A. Khavari

  • Review Article |

    Various genomics-related fields are increasingly taking advantage of long-read sequencing and long-range mapping technologies, but making sense of the data requires new analysis strategies. This Review discusses bioinformatics tools that have been devised to handle the numerous characteristic features of these long-range data types, with applications in genome assembly, genetic variant detection, haplotype phasing, transcriptomics and epigenomics.

    • Fritz J. Sedlazeck
    • , Hayan Lee
    •  & Michael C. Schatz

  • Review Article |

    The wealth of DNA methylation data continues to grow rapidly, including from epigenome-wide association studies (EWAS). However, extracting meaningful biological and clinical information requires diverse computational approaches for data analysis. This Review discusses the range of statistical tools available, including for cell-type deconvolution, identification of important methylation data features, causation and system-level integration with other types of omic data.

    • Andrew E. Teschendorff
    •  & Caroline L. Relton

  • Review Article |

    Network propagation is based on the principle that genes underlying similar phenotypes are more likely to interact with each other. It is proving to be a powerful approach for extracting biological information from molecular networks that is relevant to human disease.

    • Lenore Cowen
    • , Trey Ideker
    •  & Roded Sharan

  • Review Article |

    Although it has been known for decades that RNA is subjected to numerous covalent modifications, there has been a recent surge in interest driven by sequencing-based transcriptome-wide detection methods and the realization that RNA modifications have important roles in diverse biological processes. This Review describes the range of detection strategies for RNA modifications, their particular strengths and limitations, and how responsible and complementary application of these techniques will be required to ensure the quality and interpretability of the rapidly accumulating data sets.

    • Mark Helm
    •  & Yuri Motorin

  • Review Article |

    Considerable resources are required to gain maximal insights into the diverse big data sets in biomedicine. In this Review, the authors discuss how crowdsourcing, in the form of collaborative competitions (known as Challenges), can engage the scientific community to provide the diverse expertise and methodological approaches that can robustly address some of the most pressing questions in genetics, genomics and biomedical sciences.

    • Julio Saez-Rodriguez
    • , James C. Costello
    •  & Gustavo Stolovitzky

  • Review Article |

    Computer simulation of next-generation sequencing data can be extremely useful for assessing and validating biological models, benchmarking sequence analysis tools or gaining an understanding of specific data sets. Here, the authors review the functionality, requirements and applications of 23 currently available simulation tools and provide a guide for the selection of the most appropriate one.

    • Merly Escalona
    • , Sara Rocha
    •  & David Posada

  • Review Article |

    Modern genomic studies are revealing widespread associations between single genetic variants and multiple distinct traits, including diseases. This Review discusses the biological underpinnings of such pleiotropy and the available bioinformatic tools for the detection and characterization of these effects, as well as the implications for understanding human disease.

    • Nadia Solovieff
    • , Chris Cotsapas
    •  & Jordan W. Smoller

  • Review Article |

    The recent explosion of genomics data has prompted the development of advanced algorithmic techniques to aid in the analysis, storage and retrieval of these data in the hunt for answers to biological questions. In this article, several examples of these algorithms are highlighted to aid in the use and selection of such algorithms.

    • Bonnie Berger
    • , Jian Peng
    •  & Mona Singh

  • Opinion |

    The concepts of orthology and paralogy are fundamental to comparative genomics and are also frequently used for the functional annotation of uncharacterized genes. However, assumptions regarding function have recently been challenged, and the implications of assigning genes as orthologues or paralogues are far from straightforward.

    • Toni Gabaldón
    •  & Eugene V. Koonin

  • Review Article |

    Evolution by natural selection at genomic loci sculpts the sequence features of not just each immediate locus but also nearby chromosomally linked sites. However, the way that this occurs substantially varies among different species, and this Review discusses potential reasons for these disparities.

    • Asher D. Cutter
    •  & Bret A. Payseur

  • Review Article |

    Functional interactions between proteins and within proteins results in co-evolutionary signatures in amino acid sequences that serve as clues to various forms of interdependence. This Review discusses the principles and distinctions of the large range of computational tools to analyse protein co-evolution and the biological insight that they are providing.

    • David de Juan
    • , Florencio Pazos
    •  & Alfonso Valencia

  • Review Article |

    As the use of next-generation sequencing has proliferated, so has the range of sequencing applications and software tools that are available for assembling sequences. To help readers to make informed choices about assembly techniques, this Review discusses the available options and practical trade-offs.

    • Niranjan Nagarajan
    •  & Mihai Pop

  • Review Article |

    A wealth of microarray gene expression data and a growing volume of RNA sequencing data are now available in public databases. The authors look at how these data are being used and discuss considerations for how such data should be analysed and deposited and how data reuse could be improved.

    • Johan Rung
    •  & Alvis Brazma

  • Review Article |

    Transposable elements are important sources of genetic and epigenetic variation in plant genomes. The author discusses the evidence that this variation has been important for plant evolution and how new genomic resources should allow a systematic assessment of this issue.

    • Damon Lisch

  • Review Article |

    Text mining — retrieving information from papers and databases — is increasingly used in data-rich fields such as genomics, systems biology and biomedical research. This Review discusses recent tools that can aid researchers and sets out the potential of enhancing integrative research using text mining.

    • Dietrich Rebholz-Schuhmann
    • , Anika Oellrich
    •  & Robert Hoehndorf

  • Review Article |

    The analysis and interpretation of genome-wide DNA methylation data poses unique bioinformatics challenges. In this article, the tools that are available for processing, visualizing and interpreting these epigenetic data sets are discussed, and the relative advantages of various methods are considered.

    • Christoph Bock

  • Review Article |

    Various studies (such as genetic linkage or 'omics'-based approaches) generate large lists of candidate genes, of which only a minority may be biologically relevant for a phenotype or disease of interest. This Review discusses computational tools for gene prioritization, emphasizing key considerations for how biologists can incorporate these tools into their research, and it includes hands-on tutorials.

    • Yves Moreau
    •  & Léon-Charles Tranchevent

  • Review Article |

    Several approaches exist for identifyingcis-regulatory modules, which are the regions in the genome that regulate gene expression. The authors describe these strategies and assess how they perform (either alone or in combination) and how they can be improved.

    • Ross C. Hardison
    •  & James Taylor

  • Review Article |

    The adoption of electronic health records will provide a rich resource for biomedical researchers. This Review discusses the potential for their use in informed decision making in the clinic, for a finer understanding of genotype–phenotype relationships and for selection of research cohorts, along with the current challenges for their mining and use.

    • Peter B. Jensen
    • , Lars J. Jensen
    •  & Søren Brunak

  • Review Article |

    Although genome sequencing is becoming routine, genome annotation is becoming increasingly challenging. The authors provide an overview of the steps and software tools that are available for annotating eukaryotic genomes, and describe the best practices for sharing, quality checking and updating the annotation.

    • Mark Yandell
    •  & Daniel Ence

Browse broader subjects

Browse Bioinformatics across other nature.com journals