Review Articles

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  • This Review discusses the types of single and multiple human organ-on-a-chip (organ chip) microfluidic devices and their diverse applications for disease modelling, drug development and personalized medicine, as well as the challenges that must be overcome for organ chips to reach their full potential.

    • Donald E. Ingber
    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
    Review Article
  • In this Review, Boulias and Greer provide an overview of current approaches for detecting and mapping N6-methyl-2′-deoxyadenosine (6mA or m6dA), and discuss the evidence for its presence and functional importance in the genomes of multicellular eukaryotes.

    • Konstantinos Boulias
    • Eric Lieberman Greer
    Review Article
  • In this Review, the authors describe technical and legal protection mechanisms for mitigating vulnerabilities in genomic data privacy. They also discuss how these protections are dependent on the context of data use such as in research, health care, direct-to-consumer testing or forensic investigations.

    • Zhiyu Wan
    • James W. Hazel
    • Bradley A. Malin
    Review Article
  • Single-cell transcriptomics is beginning to systematically define commonalities but also heterogeneity within and between organs for multiple human cell types. Here, the authors review emerging biological insights from cross-tissue single-cell transcriptomic studies into epithelial, fibroblast, vascular and immune cells.

    • Rasa Elmentaite
    • Cecilia Domínguez Conde
    • Sarah A. Teichmann
    Review Article
  • The reduction in individual and mean population fitness induced by novel deleterious genetic variation is known as the genetic load. Bertorelle et al. review the definition of the genetic load and its components as well as the impact of whole-genome sequencing on the theoretical and applied study of the genetic load.

    • Giorgio Bertorelle
    • Francesca Raffini
    • Cock van Oosterhout
    Review Article
  • In this Review, Ding, Sharon and Bar-Joseph discuss how dynamic features can be incorporated into single-cell transcriptomics studies, using both experimental and computational strategies to provide biological insights.

    • Jun Ding
    • Nadav Sharon
    • Ziv Bar-Joseph
    Review Article
  • Large-scale genetic datasets and deep learning approaches are being used to model the structures of proteins or protein complexes. This Review describes approaches based on coevolution, deep mutational scanning and genome-scale genetic or chemical–genetic interaction mapping and their application and integration to inform structural modelling.

    • Hannes Braberg
    • Ignacia Echeverria
    • Nevan J. Krogan
    Review Article
  • Synthetic RNA devices integrate sensing, processing and actuation of signals into defined, programmable functions to control cell behaviour. This Review discusses the emerging applications of RNA devices in biomedical research and biomanufacturing, as well as progress in creating new ligand sensors and new mechanisms of action with engineered RNAs.

    • Peter B. Dykstra
    • Matias Kaplan
    • Christina D. Smolke
    Review Article
  • RNA therapies can be used to manipulate gene expression or produce therapeutic proteins. Here, the authors describe the growing number of RNA therapies and their molecular mechanisms of action. They also discuss the path from preclinical drug delivery research to clinical approval of these drugs.

    • Kalina Paunovska
    • David Loughrey
    • James E. Dahlman
    Review Article
  • In this Review the authors provide an overview of key algorithmic developments, popular tools and emerging technologies used in the bioinformatic analysis of genomes. They also describe how such analysis can identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes.

    • Isidro Cortés-Ciriano
    • Doga C. Gulhan
    • Peter J. Park
    Review Article
  • The authors review the field of mammalian mitochondrial genome engineering, culminating in the recent development of mitochondrially targeted programmable nucleases and base editors. They describe research that led to the development of animal models of mitochondrial disease, as well as the potential for translating these approaches to the clinic.

    • Pedro Silva-Pinheiro
    • Michal Minczuk
    Review Article
  • Loci that encode long non-coding RNAs (lncRNAs) can be complex and function through multiple modalities. The authors provide a framework for elucidating the physiological roles of lncRNAs using genetically engineered mouse models, including whole-gene deletion, transcription termination, reporters and transgene rescue strategies.

    • Daniel Andergassen
    • John L. Rinn
    Review Article
  • Machine learning is widely applied in various fields of genomics and systems biology. In this Review, the authors describe how responsible application of machine learning requires an understanding of several common pitfalls that users should be aware of (and mitigate) to avoid unreliable results.

    • Sean Whalen
    • Jacob Schreiber
    • Katherine S. Pollard
    Review Article
  • In this Review, the authors discuss explanations for why ultraconserved sequences — which are presumed to be functionally crucial on the basis of strong evolutionary constraint — often result in surprisingly minor phenotypic consequences when experimentally disrupted. They also discuss the wider implications of extreme non-coding conservation for understanding the mechanisms of gene regulation and human variant interpretation.

    • Valentina Snetkova
    • Len A. Pennacchio
    • Diane E. Dickel
    Review Article
  • Hologenomic studies aim to further our understanding of host–microbiota interactions through the integrated analysis of host genomes and microbiota metagenomes. Here, Alberdi and colleagues discuss key considerations for designing optimal hologenomic studies and outline important biological questions that these studies can address.

    • Antton Alberdi
    • Sandra B. Andersen
    • M. Thomas P. Gilbert
    Review Article
  • The authors review overlapping sequences as fundamental features of prokaryotic, eukaryotic and viral genomes, discussing the diverse topologies and functions of overlapping genes, open reading frames and coding sequences. Moreover, they highlight the potential of harnessing sequence overlaps for synthetic biology approaches.

    • Bradley W. Wright
    • Mark P. Molloy
    • Paul R. Jaschke
    Review Article
  • In this Review, Janssen and Lorincz discuss the intricate and multilayered interplay between chromatin marks. Focusing on histone methylation and DNA methylation during mammalian development, they discuss the implications for gene regulation, differentiation and human disease.

    • Sanne M. Janssen
    • Matthew C. Lorincz
    Review Article
  • In this Review, Zhang et al. summarize our current understanding of the molecular mechanisms underlying the responses of plants to abiotic stresses, and how this knowledge can be used to improve crop resilience through genetic, chemical and microbial approaches.

    • Huiming Zhang
    • Jianhua Zhu
    • Jian-Kang Zhu
    Review Article