Collision avoidance for multiple agent systems. - Dong Eui Chang; Shawn C. Shadden; Jerrold E. Marsden; Reza Olfati-Saber (CDC, 2003)

Optimal trajectory generation in ocean flows. - Tamer Inanc; Shawn C. Shadden; Jerrold E. Marsden (ACC, 2005)

Development of an Efficient and Flexible Pipeline for Lagrangian Coherent Structure Computation. - Siavash Ameli; Yogin Desai; Shawn C. Shadden (Topological Methods in Data Analysis and Visualization, 2014)

Boolean and smoothing of discrete polygonal surfaces. - Adam Updegrove; Nathan M. Wilson; Shawn C. Shadden (Adv. Eng. Softw., 2016)

Fast Coherent Particle Advection through Time-Varying Unstructured Flow Datasets. - Mingcheng Chen; Shawn C. Shadden; John C. Hart (IEEE Trans. Vis. Comput. Graph., 2016)

SimVascular as an instructional tool in the classroom. - Craig J. Goergen; Shawn C. Shadden; Alison L. Marsden (FIE, 2017)

Adding Constraints to Bayesian Inverse Problems. - Jiacheng Wu; Jian-Xun Wang 001; Shawn C. Shadden (AAAI, 2019)

FEniCS mechanics: A package for continuum mechanics simulations. - Miguel A. Rodriguez; Christoph M. Augustin; Shawn C. Shadden (SoftwareX, 2019)

A Generalizable Deep-Learning Approach for Cardiac Magnetic Resonance Image Segmentation Using Image Augmentation and Attention U-Net. - Fanwei Kong; Shawn C. Shadden (M&Ms and EMIDEC/STACOM@MICCAI, 2020)

Interpolating the Trace of the Inverse of Matrix A + tB. - Siavash Ameli; Shawn C. Shadden (CoRR, 2020)

Whole Heart Mesh Generation for Image-Based Computational Simulations by Learning Free-From Deformations. - Fanwei Kong; Shawn C. Shadden (MICCAI (4), 2021)

A deep-learning approach for direct whole-heart mesh reconstruction. - Fanwei Kong; Nathan M. Wilson; Shawn C. Shadden (Medical Image Anal., 2021)

Multi-Centre, Multi-Vendor and Multi-Disease Cardiac Segmentation: The M&Ms Challenge. - Víctor M. Campello; Polyxeni Gkontra; Cristian Izquierdo; Carlos Martín-Isla; Alireza Sojoudi; Peter M. Full; Klaus H. Maier-Hein; Yao Zhang 010; Zhiqiang He 002; Jun Ma 016; Mario Parreño; Alberto Albiol; et al. (IEEE Trans. Medical Imaging, 2021)

Noise Estimation in Gaussian Process Regression. - Siavash Ameli; Shawn C. Shadden (CoRR, 2022)

Development of an Efficient and Flexible Pipeline for Lagrangian Coherent Structure Computation. - Siavash Ameli; Yogin Desai; Shawn C. Shadden (CoRR, 2022)

Interpolating log-determinant and trace of the powers of matrix bfA + tbfB. - Siavash Ameli; Shawn C. Shadden (Stat. Comput., 2022)

svFSI: A Multiphysics Package for Integrated Cardiac Modeling. - Chi Zhu 002; Vijay Vedula; David W. Parker; Nathan M. Wilson; Shawn C. Shadden; Alison L. Marsden (J. Open Source Softw., 2022)

LinFlo-Net: A two-stage deep learning method to generate simulation ready meshes of the heart. - Arjun Narayanan; Fanwei Kong; Shawn C. Shadden (CoRR, 2023)

Learning Whole Heart Mesh Generation From Patient Images for Computational Simulations. - Fanwei Kong; Shawn C. Shadden (IEEE Trans. Medical Imaging, 2023)

A singular Woodbury and pseudo-determinant matrix identities and application to Gaussian process regression. - Siavash Ameli; Shawn C. Shadden (Appl. Math. Comput., 2023)

Integrated Framework for Unified Cardiac and Vascular Mesh Construction from Medical Images. - Numi Sveinsson Cepero; Arjun Narayanan; Shawn C. Shadden (FIMH (2), 2025)

SeqSeg: Learning Local Segments for Automatic Vascular Model Construction. - Numi Sveinsson Cepero; Shawn C. Shadden (CoRR, 2025)