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

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

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

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

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

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis. - David Noren; Byron Long; Raquel Norel; Kahn Rhrissorrakrai; Kenneth R. Hess; Chenyue W. Hu; Alex Bisberg; André Schultz; Erik Engquist; Li Liu 035; Xihui Lin; Gregory M. Chen; et al. (PLoS Comput. Biol., 2016)

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

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

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

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

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

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

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