Lin Yang, USC Dana and David Dornsife College of Letters, Arts and Sciences, Computational Biology and Bioinformatics

2016 Recipients of the PhD Achievement Award

Lin Yang, USC Dana and David Dornsife College of Letters, Arts and Sciences, Computational Biology and Bioinformatics

Faculty Advisor: Remo Rohs

Graduated from the University of Science and Technology of China, Lin Yang received
the Viterbi Fellowship and joined the program of Molecular and Computational Biology
at USC in the fall of 2010. He later joined Professor Remo Rohs’ lab in the summer
of 2011. In the Rohs lab, Lin’s research focuses on the study of transcription
factor (TF)-DNA binding specificity, i.e., the DNA binding preference of TFs.
Specifically, he applied machine learning methods to build quantitative models of
TF-DNA binding specificity. In his work, he showed that incorporating DNA “shape”
features that characterize the structure of DNA to a model that is purely based on
mononucleotide features can significantly boost the model performance,
quantitatively demonstrating the importance of “DNA shape readout” by TFs. As a
novel computational component in the Abe et al. 2015 Cell paper, Lin used machine
learning in combination with feature selection techniques to reveal the DNA shape
readout mechanism in Drosophila Hox TFs at base-pair resolution. In 2015, Lin
received the international Dan David Prize Scholarship in support of his research
project. In the same year, Lin also received the Harrison M. Kurtz Award from the
Department of Biological Sciences at USC. In 2014, Lin’s first-author paper,
published on the peer-reviewed journal Nucleic Acids Research (NAR), received a
RECOMB/ISCB Top-10 Paper Award and was selected as an NAR Breakthrough Article for
its originality, significance and scientific impact. Lin defended his dissertation
on June 6 th , 2016, with ten published papers listing him as a co-author.