Exploring cis-regulatory models of the genome to predict epigenetic state and variation
Author(s)
Kang, Daniel D
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Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.
Advisor
David Gifford.
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We introduce a new model called CCM+ that rectifies the inability of previous sequence-based methods to generalize across cell-types. We permit generalization by introducing arbitrary base-pair resolution covariates. We show that the addition of base-pair resolution chromatin accessibility covariate greatly aids in the prediction of cis-regulatory marks. Additionally, we show that by using cell-type specific covariates, CCM+ can generalize across cell-types. Finally, we show CCM+ can be used for downstream analysis that matches state-of-the-art methods when chromatin accessibility is used as a covariate.
Description
Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015. Cataloged from student-submitted PDF version of thesis. Includes bibliographical references (pages [18]-[20]).
Date issued
2015Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer SciencePublisher
Massachusetts Institute of Technology
Keywords
Electrical Engineering and Computer Science.