UNAGI deciphers cellular dynamics from human disease time-series single-cell data and facilitates in silico drug perturbations to discover drugs potentially active against complex human diseases.

Image-based spatial transcriptomics deliver gene expression measurements of RNA transcripts in tissue slices with single-molecule resolution and spatial context preserved. Modern Graph Neural Network ...

Peroxisomes are vital but often overlooked metabolic organelles. We found that excessive interferon signaling remodeled macrophage peroxisomes. This loss of peroxisomes impaired inflammation resolutio...

Nature Genetics - Simultaneous profiling of the genome, methylome, epigenome and transcriptome using single-molecule chromatin fiber sequencing and multiplexed arrays isoform sequencing identifies...

The impact of synonymous mutations remains elusive. Here, the authors demonstrate that synonymous mutations can promote tumorigenesis by disrupting post-transcriptional m6A modification. The findings ...

Xenium spatial transcriptomic profiling of pulmonary fibrosis characterizes cell composition dynamics and histopathological features associated with the disease.

Worldwide, we are still recovering from probably the biggest pneumonia pandemic in recent history, coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Even before COVID-19, pneumonia was by far the most common serious infectious disease and among the top causes of death in low- and middle-income countries (LMICs) and the top five or six causes of death in developed economies (1). Because it is a very common misconception that pneumonia is no longer a serious disease because it can easily be cured with antibiotic treatment, it is very appropriate that we have World Pneumonia Day to highlight the enormous societal burden of this disease. In fact, worldwide, a child dies of pneumonia every 43 seconds (2). However, the common misconception should be correct: we have all the tools in our hands to slash mortality from pneumonia, but they are left to gather dust. It is painful to compare the focus and drive that brought the COVID-19 pandemic under control, with tremendous science producing effective RNA vaccines and their widespread deployment, with the pitiful attempts to prevent pneumonia deaths, particularly in childhood. For the latter, we do not need new vaccines or monoclonal treatments. We have the tools, but worldwide apathy means they are not used.

Recent massively-parallel approaches to decipher gene regulatory circuits have focused on the discov

Many human genes, including transcription factor (TF) genes, produce alternative coding isoforms. Al

To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, se...

Author Contributions: Study concept and design: S.P.B. Acquisition, analysis, or interpretation of data: all authors. Drafting of the manuscript: S.P.B. Critical revision of the manuscript for important intellectual content: all authors. Statistical analysis: S.P.B. Study supervision: all authors.

The American Thoracic Society is the world's leading medical society dedicated to accelerating the advancement of global respiratory health through…