Xiling Shen


Hawkins Family Associate Professor

Dr. Shen’s research interests lie at precision medicine and systems biology. His lab integrates engineering, computational and biological techniques to study cancer, stem cells, microbiota and the nervous system in the gut. This multidisciplinary work has been instrumental in initiating several translational clinical trials in precision therapy. He is the director of the Woo Center for Big Data and Precision Health (DAP) and a core member of the Center for Genomics and Computational Biology (GCB).

Appointments and Affiliations

  • Hawkins Family Associate Professor
  • Associate Professor in the Department of Biomedical Engineering
  • Associate Professor in the Department of Electrical and Computer Engineering
  • Associate Professor in Molecular Genetics and Microbiology
  • Member of the Duke Cancer Institute
  • Affiliate of the Regeneration Next Initiative

Contact Information


  • Ph.D. Stanford University, 2008
  • M.Sc. Stanford University, 2001
  • B.Sc. Stanford University, 2001

Research Interests

Precision medicine for cancer, regeneration, microbiome, and gut-brain axis. Multi-omics approaches including organoid, epigenetics, CRISPR, single-cell, metabolomics, machine learning, droplet microfluidics, humanized immune model and intravital imaging.

Courses Taught

  • BME 493: Projects in Biomedical Engineering (GE)
  • BME 590: Special Topics in Biomedical Engineering
  • BME 590L: Special Topics with Lab
  • BME 791: Graduate Independent Study
  • ECE 899: Special Readings in Electrical Engineering

In the News

Representative Publications

  • Bu, P; Chen, K-Y; Xiang, K; Johnson, C; Crown, SB; Rakhilin, N; Ai, Y; Wang, L; Xi, R; Astapova, I; Han, Y; Li, J; Barth, BB; Lu, M; Gao, Z; Mines, R; Zhang, L; Herman, M; Hsu, D; Zhang, G-F; Shen, X, Aldolase B-Mediated Fructose Metabolism Drives Metabolic Reprogramming of Colon Cancer Liver Metastasis., Cell Metab, vol 27 no. 6 (2018), pp. 1249-1262.e4 [10.1016/j.cmet.2018.04.003] [abs].
  • Rakhilin, N; Barth, B; Choi, J; Muñoz, NL; Kulkarni, S; Jones, JS; Small, DM; Cheng, Y-T; Cao, Y; LaVinka, C; Kan, E; Dong, X; Spencer, M; Pasricha, P; Nishimura, N; Shen, X, Simultaneous optical and electrical in vivo analysis of the enteric nervous system., Nature Communications, vol 7 (2016) [10.1038/ncomms11800] [abs].
  • Bu, P; Wang, L; Chen, K-Y; Srinivasan, T; Murthy, PKL; Tung, K-L; Varanko, AK; Chen, HJ; Ai, Y; King, S; Lipkin, SM; Shen, X, A miR-34a-Numb Feedforward Loop Triggered by Inflammation Regulates Asymmetric Stem Cell Division in Intestine and Colon Cancer., Cell Stem Cell, vol 18 no. 2 (2016), pp. 189-202 [10.1016/j.stem.2016.01.006] [abs].
  • Chen, HJ; Sun, J; Huang, Z; Hou, H; Arcilla, M; Rakhilin, N; Joe, DJ; Choi, J; Gadamsetty, P; Milsom, J; Nandakumar, G; Longman, R; Zhou, XK; Edwards, R; Chen, J; Chen, KY; Bu, P; Wang, L; Xu, Y; Munroe, R; Abratte, C; Miller, AD; Gümüş, ZH; Shuler, M; Nishimura, N; Edelmann, W; Shen, X; Lipkin, SM, Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting., Nature Biotechnology, vol 33 no. 6 (2015), pp. 656-660 [10.1038/nbt.3239] [abs].
  • Bu, P; Chen, K-Y; Chen, JH; Wang, L; Walters, J; Shin, YJ; Goerger, JP; Sun, J; Witherspoon, M; Rakhilin, N; Li, J; Yang, H; Milsom, J; Lee, S; Zipfel, W; Jin, MM; Gümüş, ZH; Lipkin, SM; Shen, X, A microRNA miR-34a-regulated bimodal switch targets Notch in colon cancer stem cells., Cell Stem Cell, vol 12 no. 5 (2013), pp. 602-615 [10.1016/j.stem.2013.03.002] [abs].