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We previously established an in vitro model for<jats:italic>Borrelia burgdorferi<\/jats:italic>infection of human neuroglial cells. To expand on our earlier study, we performed<jats:italic>B. burgdorferi<\/jats:italic>whole-genome expression analysis following a 20-hour infection of human neuroglial cells to identify borrelial genes that were differentially regulated during host-cell association compared with cultured<jats:italic>Borrelia<\/jats:italic>in cell-free medium. 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