Jinsen Li

About Me

My current research interest lies in computational biology and AI, specifically studying transcription factors and DNA interactions, from a structural biology point of view. My goal is to use machine learning to fully understand gene regulations. My recent work focused on DNA structural parameters (DNA shape) and their relationship to protein-DNA binding mechanisms.
In the past, I also worked on single-cell genomics data and developed algorithms for detecting meiotic recombination events and reconstructing haplotypes from them.

Education

• Ph.D. in Computational Biology and Bioinformatic, University of Southern California, 2021
• M.S. in Computer Science (Data Science track), University of Southern California, 2019
• B.S. in Biological Science and Computer Software (double major), Peking University, 2014

Publications

For a complete list of publications, visit my Google Scholar profile.

• Mitra, R., Li, J., Sagendorf, J.M., Jiang, Y., Chiu, T.P. and Rohs, R^#. "DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity." In review (available on Biorxiv), 2024.
• Li, J., Chiu, T.P., Rohs, R.^#. "Predicting DNA structure using a deep learning method." Nature Communications, 2024.
• Chiu, T.P., Li, J., Jiang, Y. and Rohs, R.^#. "It is in the flanks: conformational flexibility of transcription factor binding sites." Biophysical Journal, 2022.
• Lee, C.S.^*, Cheung, M.F.^*, Li, J., Zhao, Y., Lam, W.H., Ho, V., Rohs, R., Zhai, Y., Leung, D. and Tye, B.K.^#. "Humanizing the yeast origin recognition complex." Nature communications, 2021.
• Li, J., Sagendorf, J.M., Chiu, T.P., Pasi, M., Perez, A. and Rohs, R.^#. "Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding." Nucleic acids research, 2017.
• Hou, Y.^*, Fan, W.^*, Yan, L.^*, Li, R., Lian, Y., Huang, J., Li, J., Xu, L., Tang, F.^#, Xie, X.S.^# and Qiao, J.^#. "Genome analyses of single human oocytes." Cell, 2013.
• Lu, S.^*, Zong, C.^*, Fan, W.^*, Yang, M.^*, Li, J., Chapman, A.R., Zhu, P., Hu, X., Xu, L., Yan, L., Bai, F., Qiao, J., Tang, F., Li, R.^# and Xie, X.S.^#. "Probing meiotic recombination and aneuploidy of single sperm cells by Whole-Genome sequencing." Science, 2012.

* Indicates co-first authorship, # Indicates corresponding authors

Teaching Experience

• QBIO 401: Introduction to Computational Analysis of Biological Data - USC, Los Angeles, USA (2020)
  Teaching Assistant
  Leading discussions, preparing course materials, assessing student work, and providing guidance during office hours.
• BISC 427: The Global Environment - USC, Los Angeles, USA (2019)
  Teaching Assistant
  Assessing student work, and providing guidance during office hours.
• BISC 330L: Biochemistry - USC, Los Angeles, USA (2018)
  Teaching Assistant
  Teaching lab courses, instructing experiment procedures, grading lab reports and exams, and providing guidance during office hours.
• BISC 330L: Biochemistry - USC, Los Angeles, USA (2017)
  Administrative Teaching Assistant
  Helping students on all kinds of course issues including scheduling and rescheduling exams.

Contact

Email: jinsenli at usc.edu