Xiling Shen


Adjunct Professor in the Department of Pathology

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

  • Adjunct Professor in the Department of Pathology

Contact Information


  • Ph.D. Stanford University, 2008
  • Ph.D. Stanford University, 2008
  • B.Sc. Stanford University, 2001
  • M.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 590: Special Topics in Biomedical Engineering
  • BME 791: Graduate Independent Study
  • BME 792: Continuation of Graduate Independent Study

In the News

Representative Publications

  • Huang, Q; Cohen, MA; Alsina, FC; Devlin, G; Garrett, A; McKey, J; Havlik, P; Rakhilin, N; Wang, E; Xiang, K; Mathews, P; Wang, L; Bock, C; Ruthig, V; Wang, Y; Negrete, M; Wong, CW; Murthy, PKL; Zhang, S; Daniel, AR; Kirsch, DG; Kang, Y; Capel, B; Asokan, A; Silver, DL; Jaenisch, R; Shen, X, Intravital imaging of mouse embryos., Science, vol 368 no. 6487 (2020), pp. 181-186 [10.1126/science.aba0210] [abs].
  • Kaelberer, MM; Buchanan, KL; Klein, ME; Barth, BB; Montoya, MM; Shen, X; Bohórquez, DV, A gut-brain neural circuit for nutrient sensory transduction., Science, vol 361 no. 6408 (2018) [10.1126/science.aat5236] [abs].
  • 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].
  • 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].
  • 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].