Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces. - Rex A. Kerr; Thomas M. Bartol; Boris Kaminsky; Markus Dittrich; Jen-Chien Jack Chang; Scott B. Baden; Terrence J. Sejnowski; Joel R. Stiles (SIAM J. Sci. Comput., 2008)

MCell. - Thomas M. Bartol; Markus Dittrich; James R. Faeder (Encyclopedia of Computational Neuroscience, 2014)

Design Automation for Biological Models: A Pipeline that Incorporates Spatial and Molecular Complexity. - Devin P. Sullivan; Rohan Arepally; Robert F. Murphy; José Juan Tapia; James R. Faeder; Markus Dittrich; Jacob Czech (ACM Great Lakes Symposium on VLSI, 2015)

Registering large volume serial-section electron microscopy image sets for neural circuit reconstruction using FFT signal whitening. - Arthur W. Wetzel; Jennifer Bakal; Markus Dittrich; David G. C. Hildebrand; Josh L. Morgan; Jeff W. Lichtman (AIPR, 2016)

A Virtual File System for On-Demand Processing of Multidimensional Datasets. - Arthur W. Wetzel; Jennifer Bakal; Markus Dittrich (XSEDE, 2016)

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. - Rory M. Donovan; José Juan Tapia; Devin P. Sullivan; James R. Faeder; Robert F. Murphy; Markus Dittrich; Daniel M. Zuckerman (PLoS Comput. Biol., 2016)