Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks. - Mark Hallen; Bochong Li; Yu Tanouchi; Cheemeng Tan; Mike West; Lingchong You (PLoS Comput. Biol., 2011)

Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. - Mark Hallen; Bruce Randall Donald (RECOMB, 2015)

comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. - Mark A. Hallen; Bruce Randall Donald (J. Comput. Biol., 2016)

cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. - Yuchao Pan; Yuxi Dong; Jingtian Zhou; Mark Hallen; Bruce Randall Donald; Jianyang Zeng 001; Wei Xu 005 (J. Comput. Biol., 2016)

CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions. - Mark A. Hallen; Bruce Randall Donald (Bioinform., 2017)

LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency. - Mark A. Hallen; Jonathan D. Jou; Bruce Randall Donald (J. Comput. Biol., 2017)

Protein Design by Algorithm. - Mark A. Hallen; Bruce Randall Donald (CoRR, 2018)

OSPREY 3.0: Open-source protein redesign for you, with powerful new features. - Mark A. Hallen; Jeffrey W. Martin; Adegoke A. Ojewole; Jonathan D. Jou; Anna U. Lowegard; Marcel S. Frenkel; Pablo Gainza; Hunter M. Nisonoff; Aditya Mukund; Siyu Wang; Graham T. Holt; David Zhou; et al. (J. Comput. Chem., 2018)

Protein design by provable algorithms. - Mark A. Hallen; Bruce Randall Donald (Commun. ACM, 2019)