Ningxin Ouyang, Ph.D.

Master's student from October 2015 to January 2017
PhD student from January 2017 to January 2022
Bioinformatics Ph.D.
Current: Illimina, Inc.

Research areas

  • Gene Regulation
  • DNase Footprinting


  • B.S.: Purdue University
  • M.S.: University of Michigan

Honors and Awards

  • Rackham Graduate Student Research Grant (candidate)


Ningxin’s current project focuses on developing an unsupervised footprinting method. She works to integrate both DNase I hypersensitivity and genome sequence information in a multivariate Hidden Markov Model to detect transcription factor binding sites.

Boyle lab papers

  1. Ouyang N and Boyle AP. 2020. TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence. Genome Research. 30: 1040-1046. DOI: 10.1101/gr.258228.119.

  2. Diehl AD, Ouyang N, and Boyle AP. 2020. Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes.. Nature Communications. 1: 1796. DOI: 10.1038/s41467-020-15520-5.