Articles in 2023

Dramatic advances in protein structure prediction have sparked debate as to whether the problem of predicting structure from sequence is solved or not. Here, I argue that AlphaFold2 and its peers are currently limited by the fact that they predict only a single structure, instead of a structural distribution, and that this realization is crucial for the next generation of structure prediction algorithms.

Mechanoimmunology methods help dissect the mechanical forces within the immune system.

CRISPR systems can be leveraged to direct recombinases to integrate gene-sized DNA sequences.

Strategies to overcome poor reproducibility in MRI studies are needed.

In vitro models and single-cell atlases help uncover the mysteries of human embryogenesis.

Computational approaches are pushing the limits of unknown metabolite annotation.

Advances in fluorescence microscopy and spectroscopy show their promise for applications that complement in situ structural biology methods like cryoelectron tomography.

The combination of microscopy, targeted illumination and single-cell sequencing is driving applications from direct evolution to spatial omics.

Data integration methods weave genomics data into holistic pictures of biological systems.

Many scientists are active on social media, especially Twitter. The social media world is changing, but these researchers want to stay socially connected.

Planaria are a group of worms within the phylum Platyhelminthes (flatworms). Many species, including Schmidtea mediterranea, have the ability to regenerate their body from small pieces of tissue and are easy to keep in the laboratory, which makes them a prime model system for studying whole-body regeneration.

Long-read sequencing powers a more complete reading of genomic information.

Long-read sequencing has made closed microbial genomes a routine task, and the dramatic increase in quality and quantity now paves the way to a complete microbial tree of life through genome-centric metagenomics.

Advances in long-read sequencing technologies have broadened our understanding of genetic variation in the human population, uncovered new complex structural variants and offered an opportunity to elucidate new variant associations with disease.

Spatially resolved and single-cell transcriptomics provide insights into tumor heterogeneity and tumor–microbiome interactions.

Long-read sequencing has become a widely employed technology that enables a comprehensive view of RNA transcripts. Here, we discuss the importance of long-read sequencing in interpreting the variables along RNA molecules, such as polyadenylation sites, transcription start sites, splice sites and other RNA modifications. In addition, we highlight the history of short-read and long-read technologies and their advantages and disadvantages, as well as future directions in the field.

To large-scale projects and individual labs, long-read sequencing has delivered new vistas and long wish lists for this technology’s future.

The year 2022 will be remembered as the turning point for accurate long-read sequencing, which now establishes the gold standard for speed and accuracy at competitive costs. We discuss the key bioinformatics techniques needed to power long reads across application areas and close with our vision for long-read sequencing over the coming years.