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Items: 37


A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm.

Britton G, Heemskerk I, Hodge R, Qutub AA, Warmflash A.

Development. 2019 Oct 17;146(20). pii: dev179093. doi: 10.1242/dev.179093.


Image-based Classification of Tumor Type and Growth Rate using Machine Learning: a preclinical study.

Tang TT, Zawaski JA, Francis KN, Qutub AA, Gaber MW.

Sci Rep. 2019 Aug 29;9(1):12529. doi: 10.1038/s41598-019-48738-5.


LGALS3 is connected to CD74 in a previously unknown protein network that is associated with poor survival in patients with AML.

Ruvolo PP, Hu CW, Qiu Y, Ruvolo VR, Go RL, Hubner SE, Coombes KR, Andreeff M, Qutub AA, Kornblau SM.

EBioMedicine. 2019 Jun;44:126-137. doi: 10.1016/j.ebiom.2019.05.025. Epub 2019 May 16.


A quantitative analysis of heterogeneities and hallmarks in acute myelogenous leukaemia.

Hu CW, Qiu Y, Ligeralde A, Raybon AY, Yoo SY, Coombes KR, Qutub AA, Kornblau SM.

Nat Biomed Eng. 2019 Nov;3(11):889-901. doi: 10.1038/s41551-019-0387-2. Epub 2019 Apr 15.


Proteomic Profiling of Acute Promyelocytic Leukemia Identifies Two Protein Signatures Associated with Relapse.

Hoff FW, Hu CW, Qutub AA, Qiu Y, Hornbaker MJ, Bueso-Ramos C, Abbas HA, Post SM, de Bont ESJM, Kornblau SM.

Proteomics Clin Appl. 2019 Jul;13(4):e1800133. doi: 10.1002/prca.201800133. Epub 2019 Feb 4.


Mycoplasma contamination of leukemic cell lines alters protein expression determined by reverse phase protein arrays.

Hoff FW, Hu CW, Qutub AA, Qiu Y, Graver E, Hoang G, Chauhan M, de Bont ESJM, Kornblau SM.

Cytotechnology. 2018 Dec;70(6):1529-1535. doi: 10.1007/s10616-018-0244-2. Epub 2018 Sep 6.


Shining a light on cell signaling in leukemia through proteomics: relevance for the clinic.

Hoff FW, Hu CW, Qutub AA, de Bont ESJM, Horton TM, Kornblau SM.

Expert Rev Proteomics. 2018 Jul;15(7):613-622. doi: 10.1080/14789450.2018.1487781. Epub 2018 Jul 6. Review.


Recurrent Patterns of Protein Expression Signatures in Pediatric Acute Lymphoblastic Leukemia: Recognition and Therapeutic Guidance.

Hoff FW, Hu CW, Qiu Y, Ligeralde A, Yoo SY, Scheurer ME, de Bont ESJM, Qutub AA, Kornblau SM, Horton TM.

Mol Cancer Res. 2018 Aug;16(8):1263-1274. doi: 10.1158/1541-7786.MCR-17-0730. Epub 2018 Apr 18.


Recognition of Recurrent Protein Expression Patterns in Pediatric Acute Myeloid Leukemia Identified New Therapeutic Targets.

Hoff FW, Hu CW, Qiu Y, Ligeralde A, Yoo SY, Mahmud H, de Bont ESJM, Qutub AA, Horton TM, Kornblau SM.

Mol Cancer Res. 2018 Aug;16(8):1275-1286. doi: 10.1158/1541-7786.MCR-17-0731. Epub 2018 Apr 18.


Advances in Glioblastoma Multiforme Treatment: New Models for Nanoparticle Therapy.

Ozdemir-Kaynak E, Qutub AA, Yesil-Celiktas O.

Front Physiol. 2018 Mar 19;9:170. doi: 10.3389/fphys.2018.00170. eCollection 2018. Review.


Histone Modification Patterns Using RPPA-Based Profiling Predict Outcome in Acute Myeloid Leukemia Patients.

van Dijk AD, Hu CW, de Bont ESJM, Qiu Y, Hoff FW, Yoo SY, Coombes KR, Qutub AA, Kornblau SM.

Proteomics. 2018 Apr;18(8):e1700379. doi: 10.1002/pmic.201700379. Epub 2018 Apr 2.


Shrinkage Clustering: a fast and size-constrained clustering algorithm for biomedical applications.

Hu CW, Li H, Qutub AA.

BMC Bioinformatics. 2018 Jan 23;19(1):19. doi: 10.1186/s12859-018-2022-8.


GAIN: A graphical method to automatically analyze individual neurite outgrowth.

Long BL, Li H, Mahadevan A, Tang T, Balotin K, Grandel N, Soto J, Wong SY, Abrego A, Li S, Qutub AA.

J Neurosci Methods. 2017 May 1;283:62-71. doi: 10.1016/j.jneumeth.2017.03.013. Epub 2017 Mar 21.



Schultz A, Mehta S, Hu CW, Hoff FW, Horton TM, Kornblau SM, Qutub AA.

Pac Symp Biocomput. 2017;22:485-496. doi: 10.1142/9789813207813_0045.


A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.

Noren DP, Long BL, Norel R, Rrhissorrakrai K, Hess K, Hu CW, Bisberg AJ, Schultz A, Engquist E, Liu L, Lin X, Chen GM, Xie H, Hunter GA, Boutros PC, Stepanov O; DREAM 9 AML-OPC Consortium, Norman T, Friend SH, Stolovitzky G, Kornblau S, Qutub AA.

PLoS Comput Biol. 2016 Jun 28;12(6):e1004890. doi: 10.1371/journal.pcbi.1004890. eCollection 2016 Jun.


Reconstruction of Tissue-Specific Metabolic Networks Using CORDA.

Schultz A, Qutub AA.

PLoS Comput Biol. 2016 Mar 4;12(3):e1004808. doi: 10.1371/journal.pcbi.1004808. eCollection 2016 Mar.


Endothelial cells decode VEGF-mediated Ca2+ signaling patterns to produce distinct functional responses.

Noren DP, Chou WH, Lee SH, Qutub AA, Warmflash A, Wagner DS, Popel AS, Levchenko A.

Sci Signal. 2016 Feb 23;9(416):ra20. doi: 10.1126/scisignal.aad3188.


Inferring causal molecular networks: empirical assessment through a community-based effort.

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.

Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22.


Progeny Clustering: A Method to Identify Biological Phenotypes.

Hu CW, Kornblau SM, Slater JH, Qutub AA.

Sci Rep. 2015 Aug 12;5:12894. doi: 10.1038/srep12894.


Recapitulation and Modulation of the Cellular Architecture of a User-Chosen Cell of Interest Using Cell-Derived, Biomimetic Patterning.

Slater JH, Culver JC, Long BL, Hu CW, Hu J, Birk TF, Qutub AA, Dickinson ME, West JL.

ACS Nano. 2015 Jun 23;9(6):6128-38. doi: 10.1021/acsnano.5b01366. Epub 2015 May 22.


Predicting internal cell fluxes at sub-optimal growth.

Schultz A, Qutub AA.

BMC Syst Biol. 2015 Apr 3;9:18. doi: 10.1186/s12918-015-0153-3.


Simulation predicts IGFBP2-HIF1α interaction drives glioblastoma growth.

Lin KW, Liao A, Qutub AA.

PLoS Comput Biol. 2015 Apr 17;11(4):e1004169. doi: 10.1371/journal.pcbi.1004169. eCollection 2015 Apr.


Systems approaches for synthetic biology: a pathway toward mammalian design.

Rekhi R, Qutub AA.

Front Physiol. 2013 Oct 9;4:285. doi: 10.3389/fphys.2013.00285. eCollection 2013.


Cells as state machines: cell behavior patterns arise during capillary formation as a function of BDNF and VEGF.

Long BL, Rekhi R, Abrego A, Jung J, Qutub AA.

J Theor Biol. 2013 Jun 7;326:43-57. doi: 10.1016/j.jtbi.2012.11.030. Epub 2012 Dec 22.


Multiplexed in situ immunofluorescence using dynamic DNA complexes.

Schweller RM, Zimak J, Duose DY, Qutub AA, Hittelman WN, Diehl MR.

Angew Chem Int Ed Engl. 2012 Sep 10;51(37):9292-6. doi: 10.1002/anie.201204304. Epub 2012 Aug 15. No abstract available.


Abnormal expression of FLI1 protein is an adverse prognostic factor in acute myeloid leukemia.

Kornblau SM, Qiu YH, Zhang N, Singh N, Faderl S, Ferrajoli A, York H, Qutub AA, Coombes KR, Watson DK.

Blood. 2011 Nov 17;118(20):5604-12. doi: 10.1182/blood-2011-04-348052. Epub 2011 Sep 13.


Module-based multiscale simulation of angiogenesis in skeletal muscle.

Liu G, Qutub AA, Vempati P, Mac Gabhann F, Popel AS.

Theor Biol Med Model. 2011 Apr 4;8:6. doi: 10.1186/1742-4682-8-6.


Computational models of VEGF-associated angiogenic processes in cancer.

Stefanini MO, Qutub AA, Mac Gabhann F, Popel AS.

Math Med Biol. 2012 Mar;29(1):85-94. doi: 10.1093/imammb/dqq025. Epub 2011 Jan 25.


Systems biology of pro-angiogenic therapies targeting the VEGF system.

Mac Gabhann F, Qutub AA, Annex BH, Popel AS.

Wiley Interdiscip Rev Syst Biol Med. 2010 Nov-Dec;2(6):694-707. doi: 10.1002/wsbm.92. Review.


Multiscale models of angiogenesis.

Qutub AA, Mac Gabhann F, Karagiannis ED, Vempati P, Popel AS.

IEEE Eng Med Biol Mag. 2009 Mar-Apr;28(2):14-31. doi: 10.1109/MEMB.2009.931791. Review. Erratum in: IEEE Eng Med Biol Mag. 2009 May-Jun;28(3):65.


Integration of angiogenesis modules at multiple scales: from molecular to tissue.

Qutub AA, Liu G, Vempati P, Popel AS.

Pac Symp Biocomput. 2009:316-27.


Reactive oxygen species regulate hypoxia-inducible factor 1alpha differentially in cancer and ischemia.

Qutub AA, Popel AS.

Mol Cell Biol. 2008 Aug;28(16):5106-19. doi: 10.1128/MCB.00060-08. Epub 2008 Jun 16.


Three autocrine feedback loops determine HIF1 alpha expression in chronic hypoxia.

Qutub AA, Popel AS.

Biochim Biophys Acta. 2007 Oct;1773(10):1511-25. Epub 2007 Jul 20.


Glucose transport to the brain: a systems model.

Qutub AA, Hunt CA.

Brain Res Brain Res Rev. 2005 Nov;49(3):595-617. Epub 2005 Apr 20. Review.


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