Artificial intelligence (AI) is changing the way biomedical research is conducted by making it possible to integrate diverse types of biological data and tackle questions that were previously difficult to address. At the same time, its growing use …
Inferring cellular dynamics from static single-cell data remains a central challenge in genomics. We introduce ArchVelo, a computational framework for modeling gene regulation and inferring trajectories from paired single-cell chromatin accessibility …
Mammalian reproduction requires substantial immune adaptations to safeguard reproductive success and to ultimately shape the evolutionary trajectories of a species. Systemic and placental immunity shift towards tolerance during pregnancy; however, …
Recent studies have advanced understanding of chromosomal organization and its role in gene regulation, yet most analyses focus on short-range interactions (
Interactions between cells are central to tissue organization and function in health and disease. Labeling immune partnerships by sortagging intercellular contacts (LIPSTIC) quantitatively measures direct physical cell-cell interactions. Combined …
Regulatory T (Treg) cells, expressing the transcription factor Foxp3, are obligatory gatekeepers of immune responsiveness, yet the mechanisms by which Foxp3 governs the Treg transcriptional network remain incompletely understood. Using a novel …
3D chromatin structure is critical for the regulation of gene expression during development. Here we used Micro-C assays at 100-bp resolution to map genome organization in Drosophila melanogaster throughout the first half of embryogenesis. These …
Marsupial neonates are born with immature immune systems, making them vulnerable to pathogens. While neonates receive maternal protection, they can also independently combat pathogens, although the mechanisms remain unknown. Using the sugar glider …
We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA libraries for targeting coding and non-coding regions in …
Regulatory T (Treg) cells are a specialized CD4+ T cell lineage with essential anti-inflammatory functions. Analysis of Treg cell adaptations to non-lymphoid tissues that enable their specialized immunosuppressive and tissue-supportive functions …