Genomic analysis articles within Nature Reviews Genetics

Featured

  • Journal Club |

    In this Journal Club, Jessica Tollkuhn discusses how a paper describing genome-wide application of chromatin immunoprecipitation (ChIP)-on-chip inspired her own research into oestrogen-based gene regulation in the brain.

    • Jessica Tollkuhn

  • Research Highlight |

    A publication in Nature reports the data release of around 245,000 clinical-grade whole-genome sequences as part of the NIH’s All of Us Research Programme. Several companion papers highlight the value of better capturing global genomic diversity.

    • Linda Koch

  • Research Highlight |

    Three papers in Nature report on the largest open-access plasma proteomics dataset to date, a valuable resource for understanding human disease and the identification of drug targets.

    • Michael Attwaters

  • Research Highlight |

    Legnini et al. report in Nature Methods their new optogenetic method for controlling gene expression in organoids that can be coupled with single-cell and spatial transcriptomics.

    • Henry Ertl

  • Editorial |

    Single-cell omics approaches are providing unprecedented insights into cellular function and dysfunction. This Editorial highlights the remarkable potential of these technologies and their profound impact on our understanding of biology and disease.

  • Journal Club |

    In this Journal Club, Celine Vallot discusses two 2015 papers that introduced the concept of high-throughput RNA barcoding, which paved the way for today’s plethora of single-cell omic approaches.

    • Céline Vallot

  • Research Highlight |

    Zhang et al. describe two technologies for the spatially resolved co-mapping of epigenome and transcriptome at near single-cell resolution.

    • Kirsty Minton

  • Review Article |

    In this Review, the authors discuss our latest understanding of the spatial aspects of cancer evolution, including the roles of cancer subclonal structure, tissue architecture, and interactions between cancer cells and diverse cell types of the microenvironment at local and distant sites.

    • Zaira Seferbekova
    • , Artem Lomakin
    •  & Moritz Gerstung

  • Research Highlight |

    A new study in Nature Methods describes a computational method named UTAG (unsupervised discovery of tissue architecture with graphs) that aims to identify and quantify higher-level tissue domains from biological images without previous knowledge.

    • Linda Koch

  • Research Highlight |

    A new study reports Epigenomic MERFISH, an imaging method that combines CUT&Tag and MERFISH to interrogate histone marks representing cis-regulatory elements in single cells while preserving spatial information.

    • Linda Koch

  • Research Highlight |

    A new study in Cell has characterized genome-wide dosage sensitivity for 54 human disorders, providing insight into the causal genes and disease mechanisms associated with rare copy-number variants.

    • Dorothy Clyde

  • Research Highlight |

    Two new papers in Nature report copy-number-based classification systems across cancer types that provide routes for personalized therapy.

    • Darren J. Burgess

  • Review Article |

    DNA methylation-based predictors of health aim to predict outcomes such as exposure, phenotype or disease on the basis of genome-wide levels of DNA methylation. The authors review applications of existing DNA methylation-based predictors and highlight key statistical best practices to ensure their reliable performance.

    • Paul D. Yousefi
    • , Matthew Suderman
    •  & Caroline L. Relton

  • In Brief |

    A paper in Cell reports a chromosome-level genome assembly and methylome for the conifer Pinus tabuliformis. At 25.4 Gb, it the largest gymnosperm genome available to date and provides insight into conifer adaptation.

    • Dorothy Clyde

  • Research Highlight |

    A study in Nature Biotechnology describes single-cell genome and epigenome by transposases sequencing (scGET-seq), which generates euchromatin and heterochromatin profiles from the same cell, and Chromatin Velocity, a computational framework capable of predicting future epigenetic cell fate trajectories from scGET-seq data.

    • Dorothy Clyde

  • Review Article |

    In this Review, Przybyla and Gilbert describe the latest approaches for CRISPR-based functional genomics screens, including the adoption of single-cell transcriptomic read-outs and applications in characterizing the non-coding genome and mapping genetic interactions at scale.

    • Laralynne Przybyla
    •  & Luke A. Gilbert

  • In Brief |

    A new method called CIM-seq analyses pairwise co-occurrences of cell types across multiplets to identify cells that are in physical contact with each other in intact tissues.

    • Linda Koch

  • In Brief |

    A recent study has analysed publicly available long-read sequencing data to characterize human-specific variable number tandem repeats at high resolution.

    • Linda Koch

  • Research Highlight |

    Juliusdottir et al. use pedigree data to dissect the contributions of parental and fetal genomes to fetal growth and adult disease.

    • Joseph Willson

  • Research Highlight |

    Capturing rare protein-coding variation by whole-exome sequencing in large and diverse population samples can help identify large-effect associations and drug targets, suggest two recent publications.

    • Linda Koch

  • In Brief |

    A study in the American Journal of Human Genetics shows that using the GRCh37 versus GRCh38 version of the human reference genome makes a meaningful difference to the calling of human genetic variants, with implications for research-based and clinical-based human sequencing studies.

    • Darren Burgess

  • 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 |

    Population-scale testing is an essential component of responses to the COVID-19 pandemic and is likely to become increasingly important in public health. Here, Mercer and Salit describe the roles of testing during the COVID-19 pandemic, including in genomic surveillance, contact tracing and environmental testing.

    • Tim R. Mercer
    •  & Marc Salit

  • In Brief |

    The TOPMed consortium report whole-genome sequencing data from 53,831 ethnically diverse participants. They describe the key features of the genetic variation and produce data resources for future medical research by the wider scientific community.

    • Darren J. Burgess

  • Research Highlight |

    Two new studies report the assembled genomes of the Australian lungfish (Neoceratodus forsteri) and the African lungfish (Protopterus annectens), which provide insights into the water-to-land transition.

    • Grant Otto

  • Research Highlight |

    A report in Science describes in situ genome sequencing (IGS), a method that enables genomes to be simultaneously sequenced and imaged in intact samples, including early mouse embryos. IGS will facilitate insight into the relationship between genome sequence and organization.

    • Dorothy Clyde

  • Research Highlight |

    SHARE-seq, a new high-throughput, high-resolution multi-omics method described in Cell, measures chromatin accessibility and gene expression in the same cell and enables future potential gene expression (and therefore lineage choices) to be inferred from chromatin profiles.

    • Dorothy Clyde

  • Perspective |

    This Perspective reviews efforts to map six different RNA modifications — pseudouridine (Ψ), 5-methylcytidine (m5C), N 1-methyladenosine (m1A), N 4-acetylcytidine (ac4C), ribose methylations (Nm) and N 7-methylguanosine (m7G) — and how they differ from N 6-methyladenosine (m6A). The authors discuss the technical and analytical challenges of characterizing the epitranscriptome and provide their own conclusions on the abundance and distribution of these modifications.

    • David Wiener
    •  & Schraga Schwartz

  • Research Highlight |

    The GTEx consortium reports results from its third and final phase in several new papers. They provide unprecedented detail of human gene expression regulation across tissues.

    • Darren J. Burgess

  • Comment |

    In Africa, there is a disparity in ethics and permission requirements for molecular research on samples from living people versus ancient DNA. At the precipice of the archaeogenomics revolution, heritage agencies require updated policies and procedures for genetic and genomic research on African ancient DNA.

    • Victoria E. Gibbon

  • Research Highlight |

    A new study in Science uses chromatin accessibility profiles to reveal gene regulatory alterations associated with genetic variants in neuropsychiatric disease.

    • Darren J. Burgess

  • Research Highlight |

    A study in Nature analysing genome-wide variation in individuals from islands across Polynesia reports evidence of admixture with Native Americans related to Indigenous inhabitants of northern South America.

    • Linda Koch

  • Research Highlight |

    A new study in Nature Methods presents the ‘ZipSeq’ spatial transcriptomics approach, whereby patterned illumination is used to print barcodes onto chosen tissue regions.

    • Darren J. Burgess

  • Research Highlight |

    Structural variants have proved difficult to characterize using traditional sequencing approaches. In two new studies in Cell, the authors demonstrate the use of pan-genome approaches to identify and explore the impact of structural variants in crop genomes and reveal variants linked to specific agronomic traits.

    • Joseph Willson

  • Research Highlight |

    A collection of seven articles from the gnomAD consortium, published in Nature, Nature Medicine and Nature Communications, showcases analyses of global human genetic variation in coding and non-coding genomic regions across this data set.

    • Linda Koch

  • Review Article |

    Genetic recombination is a fundamental biological process generating genetic variation by shuffling combinations of alleles. In this Review, Peñalba and Wolf focus on how sequencing-based approaches are providing diverse insights into recombination rate variation across levels of biological organization and timescales, from individual gametes of single individuals to populations through evolutionary history.

    • Joshua V. Peñalba
    •  & Jochen B. W. Wolf

  • Research Highlight |

    A study in Nature provides new insights into chromatin dynamics and allele-specific gene expression regulation during early mouse embryogenesis.

    • Linda Koch

  • Perspective |

    In this Perspective article, the authors discuss how Indigenous Peoples' desires for greater involvement and oversight when participating in genomic research projects can be balanced against calls for unrestricted data access. They provide practical recommendations for the handling and sharing of Indigenous genomic data, with the aim of achieving mutual benefit for the research community and participating Indigenous communities.

    • Maui Hudson
    • , Nanibaa’ A. Garrison
    •  & Stephanie Russo Carroll

  • Review Article |

    Understanding developmental trajectories has recently been enabled by progress in modern lineage-tracing methods that combine genetic lineage analysis with omics-based characterization of cell states (particularly transcriptomes). In this Review, Wagner and Klein discuss the conceptual underpinnings, experimental strategies and analytical considerations of these approaches, as well as the biological insights gained.

    • Daniel E. Wagner
    •  & Allon M. Klein

  • Review Article |

    Electronic health records (EHRs) linked to biobanks provide new opportunities for developing and applying polygenic risk scores in the clinic. The authors review the opportunities and challenges that arise when using EHR data for the systematic evaluation of patient disease susceptibilities.

    • Ruowang Li
    • , Yong Chen
    •  & Jason H. Moore

  • Review Article |

    Although single reference genomes are valuable resources, they do not capture genetic diversity among individuals. Sherman and Salzberg discuss the concept of ‘pan-genomes’, which are reference genomes that encompass the genetic variation within a given species. Focusing particularly on large eukaryotic pan-genomes, they describe the latest progress, the varied methodological approaches and computational challenges, as well as applications in fields such as agriculture and human disease.

    • Rachel M. Sherman
    •  & Steven L. Salzberg

  • Research Highlight |

    Two studies in Nature Genetics provide high-resolution maps of genetic variation across melon and watermelon species, respectively, and identify candidate loci linked to fruit quality traits through genome-wide association studies and population genomic analyses.

    • Linda Koch

  • Review Article |

    Recent methodological advances have driven the identification and characterization of cis-acting long non-coding RNAs (lncRNAs), which modulate target gene expression through various mechanisms and operate at various genomic distances. This Review discusses recent insights into the evolution and functions of these cis-acting lncRNAs.

    • Noa Gil
    •  & Igor Ulitsky

  • Review Article |

    To map the full extent of structural variation in the human genome, detection methods are needed that improve on short-read approaches. This Review discusses how ensemble algorithms and emerging sequencing technologies are helping to resolve the full spectrum of structural variations.

    • Steve S. Ho
    • , Alexander E. Urban
    •  & Ryan E. Mills

  • Research Highlight |

    Mohammadi et al. report the development of ANEVA–ANEVA-DOT, a statistical model that quantifies variation in gene dosage, and demonstrate its potential for identifying genes harbouring rare pathogenic variants.

    • Conor A. Bradley

  • Research Highlight |

    A study in Nature retraces the convergent evolution of resistance to cardiac glycosides in insects, pinpointing the adaptive alleles and their functional consequences.

    • Linda Koch

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