Regeneration of the lung following severe injury is often incomplete and can result in permanently altered tissue structure and impaired lung function. In the lung alveolus, the small air sacs responsible for gas exchange, repair can proceed through adaptive regeneration that restores normal architecture or through maladaptive pathways that generate abnormal tissue incapable of supporting lung function. The Jones Lab studies how signals from supportive cells in the lung, known as mesenchymal cells, and from the surrounding extracellular environment instruct lung stem cell function during these regenerative processes. Current projects in the lab focus on defining how distinct populations of alveolar mesenchymal cells regulate epithelial stem cell behavior after injury. One line of work examines how mesenchymal cells, or fibroblasts, proliferate and establish disease-specific signaling programs, including mesenchymal-epithelial pathways such as Notch, that shape adaptive versus maladaptive alveolar regeneration following viral and fibrotic lung injury. Additional work explores how changes in extracellular matrix composition and tissue mechanics influence mesenchymal cell state and long-term regenerative capacity. Core assays used in our laboratory include transgenic mouse models, single-cell transcriptomic and epigenomic analyses, 3D organoid systems, and advanced high-resolution imaging. The long-term goal of our research is to define fundamental mechanisms of lung repair and leverage this knowledge to guide the development of improved therapies for chronic lung disease.