Selected representative work from the lab (see also Google Scholar )

• Learning ecosystem-scale dynamics from microbiome data with MDSINE2
  T.E. Gibson, Y. Kim, S. Acharya, D.E. Kaplan, N. DiBenedetto, R. Lavin, B. Berger, J.R. Allegretti, L. Bry, G.K. Gerber
  Nature Microbiology, 2025
  paper bioRxiv GitHub

• Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain
  Y. Kim, C.J. Worby, S. Acharya, L.R. van Dijk, D. Alfonsetti, Z. Gromko, P. Azimzadeh, K. Dodson, G. Gerber, S.J. Hultgren, A.M. Earl, B.A. Berger and T.E. Gibson
  Nature Microbiology, 2025
  paper bioRxiv GitHub

• On the stability of gradient descent with second order dynamics for time-varying cost functions
  T.E. Gibson, S. Acharya, A. Parashar, J.E. Gaudio, A.M. Annaswamy
  Transactions on Machine Learning Research, 2025
  paper arXiv GitHub

• Accelerated Learning with Robustness to Adversarial Regressors
  J.E. Gaudio, A.M. Annaswamy, J.M. Moreu, M.A. Bolender, T.E. Gibson
  Conference on Learning for Dynamics and Control, 2021
  paper arXiv

• Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model
  B.B. Hsu, T.E. Gibson, V. Yeliseyev, Q. Liu, L. Bry, P.A. Silver, G.K. Gerber
  Cell Host and Microbe, 2019
  paper bioRxiv phys.org Host & Microbe preview

• Robust and Scalable Models of Microbiome Dynamics
  T.E. Gibson, G.K. Gerber
  International Conference on Machine Learning, 2018
  paper poster slides presentation arXiv

• Convergence Properties of Adaptive Systems and the Definition of Exponential Stability
  B.M. Jenkins, A.M. Annaswamy, E. Lavretsky, and T.E. Gibson
  SIAM Journal on Control and Optimization, 2018
  paper arXiv

• Universality of human microbial dynamics
  A. Bashan, T.E. Gibson, J. Friedman, V.J. Carey, S.T. Weiss, E.L. Hohmann and Y.-Y. Liu
  Nature, 2016
  paper Nature, News and Views Nature Physics, Highlight