Inverse Monte Carlo procedure for conformation determination of macromolecules. - Mark Bathe; Gregory C. Rutledge (J. Comput. Chem., 2003)

The subspace iteration method in protein normal mode analysis. - Reza Sharifi Sedeh; Mark Bathe; Klaus-Jürgen Bathe (J. Comput. Chem., 2010)

Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies. - Do-Nyun Kim; Josiah Altschuler; Campbell Strong; Gaël McGill; Mark Bathe (Nucleic Acids Res., 2011)

A Bayesian framework for high-throughput T cell receptor pairing. - Patrick V. Holec; Joseph Berleant; Mark Bathe; Michael E. Birnbaum (Bioinform., 2019)

DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. - Victor Kulikov; Syuan-Ming Guo; Matthew Stone; Allen Goodman; Anne E. Carpenter; Mark Bathe; Victor S. Lempitsky (PLoS Comput. Biol., 2019)

Isometric Hamming embeddings of weighted graphs. - Joseph Berleant; Kristin Sheridan; Anne Condon; Virginia Vassilevska Williams; Mark Bathe (Discret. Appl. Math., 2023)

Factorization and pseudofactorization of weighted graphs. - Kristin Sheridan; Joseph Berleant; Mark Bathe; Anne Condon; Virginia Vassilevska Williams (Discret. Appl. Math., 2023)

Characterizing DNA Origami Nanostructures in TEM Images Using Convolutional Neural Networks. - Xingfei Wei; Qiankun Mo; Chi Chen; Mark Bathe; Rigoberto Hernandez (J. Chem. Inf. Model., 2025)

DNA Origami Nanostructures Observed in Transmission Electron Microscopy Images can be Characterized through Convolutional Neural Networks. - Xingfei Wei; Qiankun Mo; Chi Chen; Mark Bathe; Rigoberto Hernandez (CoRR, 2025)