We have used various strategies and assessment tools to help uncover common student difficulties related to scientific inquiry and biological concepts.  We have now completed two separate projects aimed at better understanding how students think about experimental design1 and how genetic misconceptions persist despite instruction2.  
*Complete references for the publications describing this work are given below.

References:

  1. Shi J, Power J, Klymkowsky MK (2011) Revealing student thinking about experimental design and the roles of control experiments.  International J of Scholarship of Teaching & Learning 5(2).
  2. Smith, MK and Knight, JK (in press).  Using the Genetics Concept Assessment to Document Persistent Conceptual Difficulties in Undergraduate Genetics Courses.  Genetics.