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High-throughput RNA sequencing (RNA-seq) is a powerful method for transcriptome-wide analysis that has recently been applied to single cells. This Review discusses the analytical and computational challenges of processing and analysing single-cell RNA-seq data, paying special consideration to differences relative to the analysis of RNA-seq data generated from bulk cell populations and discussing how single-cell-specific biological insights can be obtained.
The use of mathematical modelling to elucidate genetic, molecular and cellular processes is an integral part of systems biology. This Review presents the main methods to model and simulate molecular and gene networks (kinetic and logic modelling), describes their inherent advantages and limitations, and highlights recent developments that reveal the potential of hybrid approaches.
Synthetic biology approaches to characterize gene regulation have largely used transcription factor circuits in bacteria. However, the multilayered regulation of genes by chromatin in eukaryotes provides opportunities for more sophisticated control of gene expression. This Review describes diverse approaches for engineering eukaryotic chromatin states, the insights gained into physiological gene regulation principles, and the broad potential applications throughout biomedical research and industry.
Copy number variation (CNV) accounts for much of the variability across genomes and can influence phenotypes. In this Analysis, the authors construct a CNV map using high-quality data from published studies to provide more detailed insights into CNV, which will be useful for both clinical and research applications in the future.
Transposable elements are key drivers of evolutionary innovation across many species. This Opinion article proposes evolutionary scenarios in which transposable elements have acted on innate immunity loci to generate adaptive immune systems and discusses striking parallels between the evolution of different adaptive immune systems: CRISPR–Cas in bacteria and archaea, and V(D)J recombination in vertebrates.
