Web-based collaborative annotation tools can facilitate communication among students and their instructors through online reading and communication. Collaborative reading fosters peer interaction and is an innovative way to facilitate discussion and participation in larger enrollment courses. It can be especially powerful as it creates an environment where all students are able to ask questions and contribute to a discussion about science. An online annotation tool, Nota Bene (NB), was tested in two biology courses: intermediate-level Molecular Biology (89 students) and upper level Cancer Biology (26 students). Student participation in these graded reading assignments ranged from 79% to 93%. A typical reading assignment from the upper level course generated 105 student comments, 68% of which led to responses, and a typical assignment from the midlevel course generated 183 comments, 44.8% of which generated further discussion. NB also helped uncover misunderstandings and misconceptions about biological phenomena. Coded student responses revealed evidence of knowledge transfer and synthesis, especially in the upper level biology course. We suggest that this type of collaborative reading activity could be useful in a variety of postsecondary classroom settings as it encourages collaborative learning and promotes inclusion of students who might not participate otherwise.