Publications by authors named "J Shendure"
Cells are essential to understanding health and disease, yet traditional models fall short of modeling and simulating their function and behavior. Advances in AI and omics offer groundbreaking opportunities to create an AI virtual cell (AIVC), a multi-scale, multi-modal large-neural-network-based model that can represent and simulate the behavior of molecules, cells, and tissues across diverse states. This Perspective provides a vision on their design and how collaborative efforts to build AIVCs will transform biological research by allowing high-fidelity simulations, accelerating discoveries, and guiding experimental studies, offering new opportunities for understanding cellular functions and fostering interdisciplinary collaborations in open science.
View Article and Find Full Text PDFA paradigm for biology is emerging in which cells can be genetically programmed to write their histories into their own genomes. These records can subsequently be read, and the cellular histories reconstructed, which for each cell could include a record of its lineage relationships, extrinsic influences, internal states and physical locations, over time. DNA recording has the potential to transform the way that we study developmental and disease processes.
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- In situ hybridization (ISH) is a technique for examining the location of nucleic acids in fixed samples, often enhanced using fluorophores or colorimetric labels for better visibility.
- The pSABER platform is introduced as a new method for amplifying ISH signals by adding binding sites for specific oligonucleotides, which makes it possible to detect RNA and DNA more effectively in various sample types.
- pSABER provides five times more signal amplification than traditional methods and allows for multiple targets to be analyzed simultaneously, making it a valuable tool for both research and clinical applications.
Congregate homeless shelters are disproportionately affected by infectious disease outbreaks. We describe enterovirus epidemiology across 23 adult and family shelters in King County, Washington, USA, during October 2019-May 2021, by using repeated cross-sectional respiratory illness and environmental surveillance and viral genome sequencing. Among 3,281 participants >3 months of age, we identified coxsackievirus A21 (CVA21) in 39 adult residents (3.
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- Researchers found that genetic variants linked to autoimmune diseases are often located in areas that regulate gene activity in CD4 T cells, impacting disease risk through gene regulation changes.
- They analyzed over 18,000 variants associated with autoimmune diseases and identified 545 that influence gene expression, showing a strong connection to causal variants.
- The study demonstrates that these variants work through common regulatory pathways and that they affect gene networks crucial for T cell activation and proliferation, offering insights into how they may contribute to autoimmune disease risk.