Projects CSE280A

Project 1: Primer design for fused transcripts Filled primers represent selection from the candidate pool. Edges indicate dimerization. All possible sums F i +R j give the possible lengths, and each length should be distinct. Forward exons F1 F2 R1

Project 1: goals All successful primer products should have distinct lengths Formulate the problem Solve on multiple real instances Project report should discuss feasibility

Project 2: Primer multiplexing for large regions Forward Reverse

Project 2 goals We need to get as many breakpoints as possible while minimizing the number of reactions Formulate the problem Solve on multiple real instances Project report should discuss feasibility. Are there creative ways of doing the design so that the quadratic expansion is reduced. Are ‘alternating designs’ better than ‘segmented designs’. Can we prove this.

Project 3: Fixation time A a Time = f(N,s)? N 1+s

Project 3 goals We have two manuscript with slightly different calculations. Reconcile, or say which one is correct Justify the theory in these two papers with extensive simulations over a variety of N and s values Provide a theory that best fits the data (optional).

Note Fixation time

Project 4: Selection in the post-fixation regime

Post-fixation

Project 5 goals There is a big gap between what is possible with a specific model and what is achieved with a general model. Try different ML based techniques to get an improvement in the post-fixation regime. Note that it is not easy to identify post-fixation so this is not sufficient, but it will provide insight.

Project 5 Introgressed sequences

Project 5 goals Discuss the techniques used in this paper and another (Reich Nature), and try to replicate the results. This is more open ended, but it doesn’t require algorithmic thinking.