She is known for her work on the structure and interactions of hadrons and nuclei and her innovative use of machine learning techniques in lattice quantum field theory calculations.

[3] In her doctoral thesis, "Strangeness and Charge Symmetry Violation in Nucleon Structure," Shanahan studied the role of elementary particles called strange quarks and charge symmetry breaking in the structure of protons and neutrons in atomic nuclei using lattice quantum chromodynamics and effective field theory techniques.

[9] From 2017 to 2018, she held a joint appointment as assistant professor at the College of William & Mary and senior staff scientist at the Thomas Jefferson National Accelerator Facility.

[11] Shanahan's current research includes seeking to understand how the structures and interactions of hadrons and atomic nuclei can be calculated from the fundamental principles of the Standard Model of physics, the role of gluons in the structures of hadrons and atomic nuclei, and how supercomputers and machine learning may be used to perform low-energy quantum chromodynamics calculations.

[10][6] Shanahan received the American Physical Society's 2021 Maria Goeppert Mayer Award, which recognizes outstanding achievement by early-career women physicists, for her "key insights into the structure and interactions of hadrons and nuclei using numerical and analytical methods and pioneering the use of machine learning techniques in lattice quantum field theory calculations in particle and nuclear physics.