Publications | click on paper title for links to the full paper

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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. 

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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

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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.

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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. 

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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.

 

A. Mahadevan, B.L. Long, C.W. Hu, D.T. Ryan, G.L. Britton, A. Ligeralde, A. Warmflash, J.T. Robinson, A.A. Qutub (2019) cytoNet: Network Analysis of Cell Communities. bioRxiv 180273


A. Mahadevan, N. Grandel, A. Ligeralde, J.T. Robinson, K. Francis, A.A. Qutub (2019) Living Neural Networks: Dynamic Network Analysis of Developing Neural Progenitor Cells. bioRxiv 055533

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C.W. Hu, A.J. Bisberg, A.A. Qutub (2019) Visually Guided Clustering in Biowheel: An Integration of Semi-Supervised Clustering with Interactive Visualization. bioRxiv 099739

 

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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.

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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

 
 

2016

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.

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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).

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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. 

 

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)

 
 

2014 & earlier

D.P. Noren, R. Rekhi, B.L. Long, A.A. Qutub (2014) Multiscale Models of Angiogenesis. In: Vascularization: Regenerative Medicine and Tissue Engineering. (E. Brey, ed.), CRC Press, pp. 213-234.

 

R. Rekhi, A.A. Qutub (2013) Systems Biology Approaches for Synthetic Biology: A Pathway Towards Mammalian Design, Frontiers in Computational Physiology and Medicine 4: 285.

 

S.M. Kornblau, A.A. Qutub, H. Yao, H. York, Y. Qiu, D. Graber, F. Ravandi, J. Cortes, M. Andreeff, N. Zhang, K.R. Coombes (2013) Proteomic Profiling Identifies Distinct Protein Patterns in Acute Myelogenous Leukemia CD34+CD38- Stem-Like Cells, PLoS One, 8: e78453.

 

D. Ryan, J. Hu, B. Zaunbrecher, B. Long, A.A. Qutub (2013) Predicting Endothelial Cell Phenotypes in Angiogenesis. Proceedings of the ASME 2013: Global Congress on NanoEngineering for Medicine and Biology 93124: 13-20.

 

B. Long, R. Rekhi, J. Jung, A. Abrego, A.A. Qutub (2013) Cells as State Machines: Cell Behavior Patterns Arise during Capillary Formation as a Function of BDNF and VEGF, Journal of Theoretical Biology, 326: 43-57. (PDF)

 

R. Schweller, J. Zimak, A.A. Qutub, Hittleman W.N., Diehl M.R. (2012) Multiplexed In Situ Immunofluorescence via Dynamic DNA Complexes. Angewandte Chemie 51: 9292-9296. (Link)

 

H. York, S.M. Kornblau, A.A. Qutub (2012) Network Analysis of Reverse Phase Protein Expression Data: Characterizing Protein Signatures in Acute Myeloid Leukemia Cytogenetic Categories t(8;21) and inv(16), Proteomics 12: 2084-2093.(Link)

 

M.O. Stefaninni, A.A. Qutub, F. Mac Gabhann, A.S. Popel (2012) Computational Models of VEGF-Associated Angiogenic Processes in Cancer. Math Med Biol 29: 85-94.

 

S.M. Kornblau, Y.H. Qiu, N. Zhang, N. Singh, S. Faderl, A. Ferrajoli, H. York, A.A. Qutub, K.R. Coombes, D.K. Watson (2011) Abnormal Expression of Friend Leukemia Virus Integration 1 (FLI1) Protein Is an Adverse Prognostic Factor in Acute Myeloid Leukemia, Blood 118: 5604-5612.

 

G. Liu, A.A. Qutub, P. Vempati, F. Mac Gabhann, A.S. Popel (2011) Module-Based Multiscale Simulation of Angiogenesis in Skeletal Muscle, Theoretical Biology & Medical Modelling 8: 6.

 

J.C. Nathan, A.A. Qutub (2010) “Patient-Specific Modeling of Hypoxic Response and Microvasculature Dynamics.” In: “Patient-Specific Modeling of the Cardiovascular System.” Roy Kerckhoffs (ed.). Springer, pp.183-201.

 

F. Mac Gabhann, A.A. Qutub, B.H. Annex, A.S. Popel (2010) “Systems Biology of Proangiogenic Therapeutic Strategies targeting the VEGF system.” Wiley Interdisciplinary Reviews: Systems Biology and Medicine 2: 694-707.

 

A.A. Qutub, F. Mac Gabhann, E.D. Karagiannis, A.S. Popel (2010) “Modeling Angiogenesis In Silico: From Nanoscale to Organ System.” In: “Multiscale Modeling of Particle Interactions: Applications in Biology and Nanotechnology.” Michael R. King and David J. Gee (eds.). Wiley, pp. 287-320.

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A.A. Qutub, A.S. Popel (2009) Cell Elongation, Proliferation & Migration Differentiate Endothelial Cell Phenotypes and Determine Capillary Sprouting, BMC System Biology 3.

 

A.A. Qutub, F. Mac Gabhann, E.D. Karagiannis, P. Vempati, A.S. Popel (2009) Multiscale Molecular-Based Models of Angiogenesis, IEEE Engineering in Medicine & Biology 28: 14-31.

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A.A. Qutub, G. Liu, P. Vempati, A.S. Popel (2009) Integration of Angiogenesis Modules at Multiple Scales: From Molecular to Tissue. Pacific Symposium on Biocomputing 14: 316-327.

 

A.A. Qutub, A.S. Popel (2008) Reactive Oxygen Species Regulate HIF1a Differentially in Cancer and Ischemia, Molecular and Cellular Biology 28: 5106-5119.

 

A.A. Qutub, A.S. Popel (2007) Three Autocrine Feedback Loops Determine HIF1a Expression in Chronic Hypoxia, BBA – Molecular Cell Research 1773: 1511-1525.

 

A.A. Qutub, A.S. Popel (2006) A Computational Model of Intracellular Oxygen Sensing by Hypoxia-Inducible Factor HIF1a, Journal of Cell Science 119: 3467-3480.

 

A.A. Qutub, C.A. Hunt (2005) Glucose Transport to the Brain: A Systems Model. Brain Res Rev 49: 595-617.