The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis. - Xiongwu Wu; Yidong Chen 002; Bernard R. Brooks; Yan A. Su (EURASIP J. Adv. Signal Process., 2004)

Modeling Of Macromolecular Assemblies with Map Objects. - Xiongwu Wu; Bernard R. Brooks (BIOCOMP, 2007)

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water. - Xiongwu Wu; Bernard R. Brooks (PLoS Comput. Biol., 2015)

Self-guided Langevin dynamics via generalized Langevin equation. - Xiongwu Wu; Bernard R. Brooks; Eric Vanden-Eijnden (J. Comput. Chem., 2016)

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges. - Naohiro Nishikawa; Kyungreem Han; Xiongwu Wu; Florentina Tofoleanu; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2018)

AmberTools. - David A. Case; Hasan Metin Aktulga; Kellon Belfon; David S. Cerutti; G. Andrés Cisneros; Vinícius Wilian D. Cruzeiro; Negin Forouzesh; Timothy J. Giese; Andreas W. Götz; Holger Gohlke; Saeed Izadi; Koushik Kasavajhala; et al. (J. Chem. Inf. Model., 2023)

Recent Developments in Amber Biomolecular Simulations. - David A. Case; David S. Cerutti; Vinícius Wilian D. Cruzeiro; Thomas A. Darden; Robert E. Duke; Mahdieh Ghazimirsaeed; George M. Giambasu; Timothy J. Giese; Andreas W. Götz; Julie A. Harris; Koushik Kasavajhala; Tai-Sung Lee; et al. (J. Chem. Inf. Model., 2025)