Publications | click on paper title for links to the full paper
2022
A.S. Mahadevan, B.L. Long, C.W. Hu, D.T. Ryan, N.E. Grandel, G.L. Britton, M. Bustos, M. Gonzalez Porras, K. Stojkova, A. Ligeralde, H. Son, J. Shannonhouse, J.T. Robinson, A. Warmflash, E. Brey, Y.S. Kim, A.A. Qutub, cytoNet: Network Analysis of Cell Communities. bioRxiv 180273, PLOS Computational Biology, 2022, 6: e1009846.
A.S. Mahadevan, N. Grandel, A. Ligeralde, J.T. Robinson, K. Francis, A.A. Qutub, Living Neural Networks: Dynamic Network Analysis of Developing Neural Progenitor Cells. bioRxiv 055533
E.P. Pollet, A. Sathish, Z. Maloney, B.L. Long, J. Brethen, A.A. Qutub, Health Signatures During COVID-19: A Precision Fitness Case Study. medRxiv 10.1101/2020.12.07
C.W. Hu, A.J. Bisberg, A.A. Qutub, Visually Guided Clustering in Biowheel: An Integration of Semi-Supervised Clustering with Interactive Visualization. bioRxiv 099739
F.W. Hoff, A.D. van Dijk, Y.H. Qiu, C.W. Hu, R.E. Ries, A.C. Ligeralde, G.N. Jenkins, R.B. Gerbing, A.S. Gamis, R. Aplenc, E.A. Kolb, T.A. Alonz, S. Meshinchi, A.A. Qutub, E.S.J.M. de Bont, T.M. Horton, S.M. Kornblau, Clinical Relevance of Proteomic Profiling in De Novo Pediatric Acute Myeloid Leukemia: A Children’s Oncology Group study, Haematologiaca, in press.
Lauren M Sanders, Jason H Yang, Ryan T Scott, Amina Ann Qutub, Hector Garcia Martin, Daniel C Berrios, Jaden JA Hastings, Jon Rask, Graham Mackintosh, Adrienne L Hoarfrost, Stuart Chalk, John Kalantari, Kia Khezeli, Erik L Antonsen, Joel Babdor, Richard Barker, Sergio E Baranzini, Afshin Beheshti, Guillermo M Delgado-Aparicio, Benjamin S Glicksberg, Casey S Greene, Melissa Haendel, Arif A Hamid, Philip Heller, Daniel Jamieson, Katelyn J Jarvis, Svetlana V Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Christopher E Mason, Mona Matar, George I Mias, Jack Miller, Jerry G Myers Jr, Charlotte Nelson, Jonathan Oribello, Seung-min Park, Patricia Parsons-Wingerter, RK Prabhu, Robert J Reynolds, Amanda Saravia-Butler, Suchi Saria, Aenor Sawyer, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, Corey A Theriot, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Marinka Zitnik, Sylvain V Costes. Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs, arXiv preprint arXiv:2112.12582.
Ryan T Scott, Erik L Antonsen, Lauren M Sanders, Jaden JA Hastings, Seung-min Park, Graham Mackintosh, Robert J Reynolds, Adrienne L Hoarfrost, Aenor Sawyer, Casey S Greene, Benjamin S Glicksberg, Corey A Theriot, Daniel C Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E Baranzini, Afshin Beheshti, Stuart Chalk, Guillermo M Delgado-Aparicio, Melissa Haendel, Arif A Hamid, Philip Heller, Daniel Jamieson, Katelyn J Jarvis, John Kalantari, Kia Khezeli, Svetlana V Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Hector Garcia Martin, Christopher E Mason, Mona Matar, George I Mias, Jerry G Myers Jr, Charlotte Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, RK Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Frank Soboczenski, Michael Snyder, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H Yang, Marinka Zitnik, Sylvain V Costes. Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health, arXiv preprint arXiv:2112.12554
2021
R.I. Han, C.W. Hu, D.S. Loose, L. Yang, L. Li, J.P. Connell, M.J. Reardon, G.M. Lawrie, A.A. Qutub, J.D. Morrisett, K.J. Grande-Allen (2021) Differential proteome profile, biological pathways, and network relationships of osteogenic proteins in calcified human aortic valves. Hearts & Vessels: 1-12.
H.A. Abbas, V. Mohanty, R. Wang, Y. Huang, S. Liang, F. Wang, J. Zhang, Y.H. Qiu, C.W. Hu, A.A. Qutub, N. Daver, M. Konopleva, A. Futreal, K. Chen, L. Wang, S.M. Kornblau (2021) Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated with Outcomes, Frontiers in Oncology 11: 2896.
M. Gonzalez Porras, K. Stojkova, M.K. Vaicik, A. Pellowe, A. Goddi, A. Carmona, B. Long, A.A. Qutub, R.N. Cohen, A. Gonzalez, E. Brey (2021) Integrins and extracellular matrix proteins module adipocyte thermogenic capacity. Scientific Reports 11: 1-14.
2019
C.W. Hu, Y.H. Qiu, A. Ligeralde, A.Y. Raybon, S.Y. Yoo, K.R. Coombes, A.A. Qutub+, S.M. Kornblau+, +co-senior authors (2019) Quantifying Proteomic Heterogeneities and Hallmarks in Acute Myelogenous Leukaemia, Nature Biomedical Engineering 3: 889-901.
-
Highlighted by Nature BME "News & Views" Prognostic Hallmarks in AML (Nov 2019)
G. Britton, I. Heemskerk, R. Hodge, A.A. Qutub, A. Warmflash (2019) A Novel Self-Organizing Embryonic Stem Cell System Reveals Signaling Logic Underlying the Patterning of Human Ectoderm. Development, 2019, 146: dev179093
-
Highlighted by Development's (Micro)patterning the Human Ectoderm (Oct 2019)
T.T. Tang, J. Zawaski, K. Francis, A.A. Qutub, M.W. Gaber (2019) Image-based Classification of Tumor Type and Growth Rate using Machine Learning: a preclinical study, Scientific Reports 9: 12529.
P.P. Ruvolo, C.W. Hu, Y.H. Qu, K.R. Coombes, M. Andreeff, A.A. Qutub, S.M. Kornblau (2019) Galectin 3 is connected to CD74 in a previously unknown protein network that is associated with poor survival in patients with AML, EBioMedicine 44: 126–137.
F.W. Hoff, C.W. Hu, A.A. Qutub, Y. Qiu, M.J. Hornbaker, C. Bueso-Ramos, H.A. Abbas, S.M. Post, E.S.J.M., de Bont, S.M. Kornblau (2019) Proteomic Profiling of Acute Promyelocytic Leukemia Identifies Two Protein Signatures Associated with Relapse. Proteomics – Clinical Applications 16: e1800133.
F. Hoff, C.W. Hu, Y.H. Qiu, A. Ligeralde, E. de Bont, S.Y. Yoo, A.A. Qutub, T. Horton, S.M. Kornblau (2018) Recurrent Patterns of Protein Expression Signatures in Pediatric Acute Lymphoblastic Leukemia (ALL): Recognition and Therapeutic Guidance, Molecular Cancer Research 16: 1263-1274.
F. Hoff, C.W. Hu, Y.H. Qiu, S.Y. Yoo, E. de Bont, H. Mahmud, A.A. Qutub, T. Horton, S.M. Kornblau (2018) Recognition of Recurrent Protein Expression Patterns in Pediatric Acute Myeloid Leukemia (AML) Suggest New Therapeutic Targets, Molecular Cancer Research 16: 1275-1286.
E.O. Kaynak, A.A. Qutub, O.Y. Celiktas (2018) Advances in Glioblastoma Multiforme Treatment: New Models for Nanoparticle Therapy, Frontiers in Physiology 9: 170.
A.D. van Dijk, C.W. Hu, E.S.J.M. de Bont, Y.H. Qiu, F.W. Hoff, S.Y. Yoo, K.R. Coombes, A.A. Qutub, S.M. Kornblau (2018) Histone Modification Patterns using RPPA-based Profiling Predict Outcome in Acute Myeloid Leukemia Patients, Proteomics 18: e1700379.
F.W. Hoff, C.W. Hu, A.A. Qutub, Y. Qiu, E. Graver, G. Hoang, M. Chauhan, E.S.J.M. de Bont, S.M. Kornblau (2018) Mycoplasma contamination of leukemic cell lines alters protein expression determined by reverse phase protein arrays. Cytotechnology 70: 1529-1535.
C.W. Hu, H. Li, A.A. Qutub (2018) Shrinkage Clustering: A Fast and Size-Constrained Algorithm for Biomedical Applications, BMC Bioinformatics 19: 19.
C. Lantos, S.M. Kornblau, A.A. Qutub (2018) Quantitative Morphological and Cytological Analyses in Leukemia. In: Hematology: Latest Research & Clinical Advances.
C.W. Hu, A.A. Qutub (2018) Proteomics in Acute Myeloid Leukemia. In: Myeloid Leukemia.
2018
2017 & earlier
A. Schultz, S. Mehta, F. Hoff, C.W. Hu, T. Horton, S.M. Kornblau, A.A. Qutub (2017) Identifying Cancer-Specific Metabolic Signatures Using Constraint-Based Models, Pacific Symposium on Biocomputing 22: 485-496.
A. Quintás-Cardama, C.W. Hu, A.A. Qutub, Y.H. Qiu, X. Zhang, S. Post, N. Zhang, K. Coombes, S. M. Kornblau (2017) p53 Pathway Dysfunction is Highly Prevalent in Acute Myeloid Leukemia Independent of TP53 Mutational Status, Leukemia 6: 1296-1305.
B. Long, H.Q. Li, T. Tang, N.E. Grandel, A. Mahadevan, A. Abrego, K. Balotin, S.Y. Wong, J. Soto, S. Li, A.A. Qutub (2017) GAIN: A Graphical Method to Automatically Analyze Individual Neurite Outgrowths, J Neuroscience Methods, 283, 62-71.
L. Liu, Y. Chang, T. Yang, D.P. Noren, B.L. Long, S.M. Kornblau, A.A. Qutub, J. Ye (2016) Evolution-Informed Modeling Improves Outcome Prediction for Cancers, Evolutionary Applications, 10: 68-76. (PDF)
C.W. Hu, A.A. Qutub (2016) progenyClust: an R package for Progeny Clustering, The R Journal, in press.
D.P. Noren, B. Long, R. Norel, K. Rhrissorrakrai, K. Hess, C.W. Hu, A. Bisberg, A. Schultz, E. Engquist, L. Liu, E. Lin, G. Chen, H. Xie, G. Hunter, AML DREAM Consortium, T. Norman, S. Friend, G.B. Mills, G. Stolovitzky, S.M. Kornblau, A.A. Qutub (2016) A Crowd Sourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis, PLOS Computational Biology, 12:e1004890. (PDF)
A. Schultz, A.A. Qutub (2016) Reconstruction of Tissue-Specific Metabolic Networks Using CORDA, PLOS Computational Biology, 12(3).
D.P. Noren, W.H. Chou, S.H. Lee, A.A. Qutub, A. Warmflash, D.S. Wagner, A.S. Popel, A. Levchenko (2016) Endothelial cells decode VEGF-mediated Ca2+ signaling patterns to produce distinct functional responses, Science Signaling 9: ra20.
-
Cover & Science Signaling Editor’s Choice; PDF, Faculty 1000
S.M. Hill, L. Heiser, T. Cokelear, M. Unger, D. Carlin, Y. Zhang, A. Sokolov, E. Paul, C.K. Wong, K. Graim, A. Bivol, H. Wang, F. Zhu, B. Afsari, L.V. Danilova, A.V. Favorov, W.S. Lee, D. Taylor, C.W. Hu, D.P. Noren, B.L. Long, A.J. Bisberg, HPN-DREAM Consortium, G.B. Mills, J.W. Gray, M. Kellen, T. Norman, S. Friend, A.A. Qutub, E.J. Fertig, Y. Guan, M. Song, J. Stuart, H. Koeppl, P.T. Spellman, G. Stolovitzky, J.S.-Rodriguez, S. Mukherjee (2016) Empirical Assessment of Causal Network Inference through A Community-Based Effort, Nature Methods, 13: 310-318. (Interactive DREAM 8 Breast Cancer Data Portal; Highlights Biowheel)
C.W. Hu, S.M. Kornblau, J.H. Slater, A.A. Qutub (2015) Progeny Clustering: A Method to Identify Biological Phenotypes, Scientific Reports 5: 12894. (R package available; Highlighted in Health Data Management) (PDF)
J.H. Slater, J.C. Culver, B. Long, C.W. Hu, J. Hu, T. Birk, A.A. Qutub, M.E. Dickinson, J.L. West (2015) Recapitulation of the Cellular Architecture of a User-Chosen Cell-of-Interest Using Cell-Derived, Biomimetic Patterning, ACS Nano, 9: 6128–6138.
K.W. Lin, A. Liao, A.A. Qutub (2015) Simulation Predicts IGFBP2-HIF1 Signaling Drives Glioblastoma Growth, PloS Computational Biology, 11: e1004169.
-
Highlighted in JAMA, 2015, Targeting Insulin Pathways to Treat Brain Tumors 313: 2114. doi:10.1001/jama.2015.5140
A. Schultz, A.A. Qutub (2015) Predicting Internal Cell Fluxes at Sub-Optimal Growth, BMC Systems Biology, 9:18.
-
Highlighted as one of the best papers of 2015 by BMC