Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …

Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of
publications presenting novel methods for obtaining spatially resolved information for any …

The cerebellum contains most of the neurons in the human brain and exhibits distinctive
modes of development and aging. In this work, by developing our single-cell three …

Here we present biVI, which combines the variational autoencoder framework of scVI with
biophysical models describing the transcription and splicing kinetics of RNA molecules. We …

Pooled optical screens have enabled the study of cellular interactions, morphology, or
dynamics at massive scale, but have not yet leveraged the power of highly-plexed single …

Recent studies have demonstrated that the three-dimensional conformation of the chromatin
plays a crucial role in gene regulation, with aberrations potentially leading to various …

Chromatin is a vital and dynamic structure that is carefully regulated to maintain proper cell
homeostasis. A great deal of this regulation is dependent on histone proteins which have the …

The advent of high-throughput transcriptomics provides an opportunity to advance
mechanistic understanding of transcriptional processes and their connections to cellular …

Nuclear organization impacts gene expression activity and cell phenotype. Our current
understanding is mainly derived from ensemble-level sequencing studies that reflect the 3D …

Retrocopies are gene duplicates arising from reverse transcription of mature mRNA
transcripts and their insertion back into the genome. While long being regarded as …