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For a good overview of issues in longitudinal data analysis, I recommend Chapter 7 of Frank Harrell's Regression Modeling Strategies. Mixed models aren't the only, or even necessarily the best, way to analyze data from studies like yours. There's a helpful table summarizing the strengths and weaknesses of several types of approaches, and references for further reading. Its emphasis is on generalized least squares rather than on mixed models, but I think it's important to understand what you gain and what you lose if you jump immediately to linear mixed models without considering alternatives.