cytoNet: Spatiotemporal network analysis of cell communities. - Mahadevan, Arun S.; Long, Byron L.; Hu, Chenyue W.; Ryan, David T.; Grandel, Nicolas E.; Britton, George L.; Bustos, Marisol; Porras, Maria A. Gonzalez; Stojkova, Katerina; Ligeralde, Andrew; Son, Hyeonwi; Shannonhouse, John; et al. (PLoS Comput. Biol., 2022)

Shrinkage Clustering: a fast and size-constrained clustering algorithm for biomedical applications. - Hu, Chenyue W.; Li, Hanyang; Qutub, Amina A. (BMC Bioinform., 2018)

Classification of brain tumors using texture based analysis of T1-post contrast MR scans in a preclinical model. - Tang, Tien T.; Zawaski, Janice A.; Francis, Kathleen N.; Qutub, Amina A.; Gaber, M. Waleed (2018)

Identifying Cancer Specific Metabolic Signatures Using Constraint-Based Models. - Schultz, André; Mehta, Sanket; Hu, Chenyue W.; Hoff, Fieke W.; Horton, Terzah M.; Kornblau, Steven M.; Qutub, Amina A. (2017)

Shrinkage Clustering: A Fast and Size-Constrained Algorithm for Biomedical Applications. - Hu, Chenyue W.; Li, Hanyang; Qutub, Amina A. (2017)

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA. - Schultz, André; Qutub, Amina A. (PLoS Comput. Biol., 2016)

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis. - Noren, David; Long, Byron; Norel, Raquel; Rhrissorrakrai, Kahn; Hess, Kenneth R.; Hu, Chenyue W.; Bisberg, Alex; Schultz, André; Engquist, Erik; Liu, Li; Lin, Xihui; Chen, Gregory M.; et al. (PLoS Comput. Biol., 2016)

progenyClust: an R package for Progeny Clustering. - Hu, Chenyue W.; Qutub, Amina A. (R J., 2016)

Predicting internal cell fluxes at sub-optimal growth. - Schultz, André; Qutub, Amina A. (BMC Syst. Biol., 2015)

Simulation Predicts IGFBP2-HIF1α Interaction Drives Glioblastoma Growth. - Lin, Ka Wai; Liao, Angela; Qutub, Amina A. (PLoS Comput. Biol., 2015)

DREAM 9: An Acute Myeloid Leukemia Prediction Big Data Challenge. - Noren, David; Kornblau, Steven M.; Hu, Chenyue W.; Long, Byron; Bisberg, Alex; Norel, Raquel; Stolovitzky, Gustavo; Qutub, Amina A. (2014)

Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting. - Qutub, Amina A.; Popel, Aleksander S. (BMC Syst. Biol., 2009)

Integration of Angiogenesis Modules at Multiple Scales: From Molecular to Tissue. - Qutub, Amina A.; Liu, Gang; Vempati, Prakash; Popel, Aleksander S. (2009)