MultiSeq: unifying sequence and structure data for evolutionary analysis. - Elijah Roberts; John Eargle; Dan Wright; Zaida Luthey-Schulten (BMC Bioinform., 2006)

Long time-scale simulations of in vivo diffusion using GPU hardware. - Elijah Roberts; John E. Stone; Leonardo Sepulveda; Wen-mei W. Hwu; Zaida Luthey-Schulten (IPDPS, 2009)

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study. - Elijah Roberts; Andrew T. Magis; Julio O. Ortiz; Wolfgang Baumeister; Zaida Luthey-Schulten (PLoS Comput. Biol., 2011)

Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. - Elijah Roberts; John E. Stone; Zaida Luthey-Schulten (J. Comput. Chem., 2013)

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations. - Michael J. Hallock; John E. Stone; Elijah Roberts; Corey Fry; Zaida Luthey-Schulten (Parallel Comput., 2014)

Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark. - Max Klein; Rati Sharma; Christopher Herrick Bohrer; Cameron M. Avelis; Elijah Roberts (Bioinform., 2017)

Modeling binary and graded cone cell fate patterning in the mouse retina. - Kiara C. Eldred; Cameron M. Avelis; Robert J. Johnston Jr; Elijah Roberts (PLoS Comput. Biol., 2020)

A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation. - Yuncong Geng; Christopher Herrick Bohrer; Nicolás Yehya; Hunter Hendrix; Lior I. Shachaf; Jian Liu; Jie Xiao; Elijah Roberts (PLoS Comput. Biol., 2022)

Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM. - Lior I. Shachaf; Elijah Roberts; Patrick Cahan; Jie Xiao (BMC Bioinform., 2023)