Sensitivity Analysis of Intracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control. - Alborz Mahdavi; Ryan E. Davey; Patrick Bhola; Ting Yin; Peter W. Zandstra (PLoS Comput. Biol., 2007)

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions. - Wenlian Qiao; Gerald T. Quon; Elizabeth Csaszar; Mei Yu; Quaid Morris; Peter W. Zandstra (PLoS Comput. Biol., 2012)

Context-explorer: Analysis of spatially organized protein expression in high-throughput screens. - Joel Ostblom; Emanuel J. P. Nazareth; Mukul Tewary; Peter W. Zandstra (PLoS Comput. Biol., 2019)

IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data. - Tiam Heydari; Matthew A. Langley; Cynthia L. Fisher; Daniel Aguilar-Hidalgo; Shreya Shukla; Ayako Yachie-Kinoshita; Michael Hughes; Kelly M. McNagny; Peter W. Zandstra (PLoS Comput. Biol., 2022)