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This qualitative case study examined how generative artificial intelligence (genAI) tools can be integrated to support students’ higher-order thinking in graduate coursework. By analyzing student reflections and artifacts, this research explored the ways that students used genAI tools to support analysis, synthesis, evaluation, as well as critical and creative thinking. Findings revealed that students developed iterative prompting strategies for genAI collaboration, using it to compare theoretical frameworks, synthesize multiple perspectives, and challenge their reasoning. When properly scaffolded, genAI tools can serve as thinking partners that can prompt deeper understanding and support learning processes. This work contributes to understanding how graduate educators can harness genAI tools to help prepare students for an AI-enhanced professional landscape while supporting essential cognitive skills.