Houston Methodist. Leading Medicine.
Houston Methodist. Leading Medicine

Publications

Publications


Journals

Zhao H, Jin G, Cui K, Ren D, Liu T, Chen P, Wong S, Li F, Fan Y, Rodriguez A, Chang J, Wong ST. Novel modeling of cancer cell signaling pathways enables systematic drug repositioning for distinct breast cancer metastases. Cancer Research. 2013 Oct 15;73(20):6149-63. PMID: 24097821
 
Yeung TL, Leung CS, Wong KK, Samimi G, Thompson MS, Liu J, Zaid TM, Ghosh S, Birrer MJ, Mok SC. TGF-β Modulates Ovarian Cancer Invasion by Upregulating CAF-Derived Versican in the Tumor Microenvironment. Cancer Res. 2013, Aug 15;73(16):5016-5028. PMID: 23824740
 
Yin Z, Sadok A, Sailem H, McCarthy A, Xia X, Li F, Garcia MA, Evans L, Barr AR, Perrimon N, Marshall CJ, Wong ST, Bakal C. A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes. Nat Cell Biol. 2013 Jul;15(7):860-71. PMID: 23748611
 
Li F, Tan H, Singh J, Yang J, Xia X, Bao J, Ma J, Zhan M, Wong ST. A 3D multiscale model of cancer stem cell in tumor development. BMC Syst Biol. 2013;7 Suppl 2:S12. PMID: 24564919
 
Fu C, Jin G, Gao J, Zhu R, Ballesteros-Villagrana E, Wong ST. DrugMap Central: an on-line query and visualization tool to facilitate drug repositioning studies. Bioinformatics. 2013 Jul 15;29(14):1834-6. PMID: 23681121
 
Li F, Yin Z, Jin G, Zhao H, Wong ST. Bioimage Informatics for Systems Pharmacology. PLoS Comput Biol. 2013 Apr;9(4):e1003043. PMID: 23633943
 
Landis MD, Lehmann BD, Pietenpol JA, Chang JC. Patient-derived breast tumor xenografts facilitating personalized cancer therapy. Breast Cancer Res. 2013 Jan 22;15(1):201. PMID: 23339383
 
Van de Ven AL, Abdollahi B, Martinez C, Burey LA, Landis MD, Chang JC, Ferrari M, Frieboes, HB. Modeling of nanotherapeutics delivery based on tumor perfusion. New J Phys. 2013 May 8;15:55004. PMID: 24039540
 
Deng T, Lyon CJ, Minze LJ, Lin J, Zou J, Liu JZ, Ren Y, Yin Z, Hamilton DJ, Reardon PR, Sherman V, Wang HY, Phillips KJ, Webb P, Wong ST, Wang RF, Hsueh WA. Class II Major Histocompatibility Complex Plays an Essential Role in Obesity-Induced Adipose Inflammation. Cell Metab. 2013 Mar 5;17(3):411-22. PMID: 23473035
 
Schott AF, Landis MD, Dontu G, Griffith KA, Layman RM, Krop I, Paskett LA, Wong H, Dobrolecki LE, Lewis MT, Froehlich AM, Paranilam J, Hayes DF, Wicha MS, Chang JC. Preclinical and clinical studies of gamma secretase inhibitors with docetaxel on human breast tumors. Clin Cancer Res. 2013 Mar 15;19(6):1512-24. PMID: 23340294
 
Wang L, Liu Q, Zhao H, Cui K, Yao L, Nie F, Jin G, Hao A, Wong ST. Differential effects of low- and high-dose GW2974, a dual epidermal growth factor receptor and HER2 kinase inhibitor, on glioblastoma multiforme invasion. J Neurosci Res. 2013 Jan;91(1):128-37. PMID: 23115024
 
Yu KD, Zhu R, Zhan M, Rodriguez AA, Yang W, Wong S, Makris A, Lehmann BD, Chen X, Mayer I, Pietenpol JA, Shao ZM, Symmans WF, Chang JC. Identification of Prognosis-Relevant Subgroups in Patients with Chemoresistant Triple Negative Breast Cancer. Clin Cancer Res. 2013; 19:2723-2733. PMID: 23549873
 
Sun M, Guo X, Qian X, Wang H, Yang C, Brinkman KL, Serrano-Gonzalez M, Jope RS, Zhou B, Engler DA, Zhan M, Wong ST, Fu L, Xu B. Activation of the ATM-Snail pathway promotes breast cancer metastasis. J Mol Cell Biol. 2012 Oct;4(5):304-15. PMID: 2923499
 
Nie F, Yang J, Wen S, An YL, Ding J, Ju SH, Zhao Z, Chen HJ, Peng XG, Wong ST, Zhao H, Teng GJ. Involvement of epidermal growth factor receptor overexpression in the promotion of breast cancer brain metastasis. Cancer. 2012;118:5198-209. PMID: 22510844
 
Guven A, Rusakova IA, Lewis MT, Wilson LJ. Cisplatin@US-tube carbon nanocapsules for enhanced chemotherapeutic delivery. Biomaterials. 2012; 33(5): 1455-61. PMID: 22078812
 
Iyer V, Klebba I, McCready J, Arendt LM, Betancur-Boissel M, Wu MF, Zhang X, Lewis MT, Kuperwasser C. Estrogen promotes ER-negative tumor growth and angiogenesis through mobilization of bone marrow-derived monocytes. Cancer Res. 2012 Jun 1;72(11):2705-13. PMID: 22467173
 
Chauviere A, Hatzikirou H, Kevrekidis IG, Lowengrub JS, Cristini V. Dynamic density functional theory of solid tumor growth: Preliminary models. AIP Adv. 2012 Mar;2(1):11210. PMID: 22489279
 
Macklin P, Edgerton ME, Thompson AM, Cristini V. Patient-calibrated agent-based modelling of ductal carcinoma in situ (DCIS): from microscopic measurements to macroscopic predictions of clinical progression. J Theor Biol. 2012 May 21;301:122-40. PMID: 22342935
 
Yin Z, Fan Y, Wong ST. Computational Systems Bioinformatics for RNAi, Encyclopedia of Nanotechnology, B Bhurshan (ed), Springer, Aug 17, 2012. DOI: 10.1007/978-90-481-9751-4_103.
 
Gao D, Vahdat LT, Wong S, Chang JC, Mittal V. Microenvironmental regulation of epithelial-mesenchymal transitions in cancer. Cancer Res. 2012 Oct 1;72(19):4883-9. PMID: 23002209
 
Xia X, Wong ST. A High-Content Screening Approach to Stem Cell Research and Drug Discovery. Stem Cells. 2012 Sep;30(9):1800-7. PMID: 22821636
 
Kessler JD, Kahle KT, Sun T, Meerbrey KL, Schlabach MR, Schmitt EM, Skinner SO, Xu Q, Li MZ, Hartman ZC, Rao M, Yu P, Dominguez-Vidana R, Liang AC, Solimini NL, Bernardi RJ, Yu B, Hsu T, Golding I, Luo J, Osborne CK, Creighton CJ, Hilsenbeck SG, Schiff R, Shaw CA, Elledge SJ, Westbrook TF. A SUMOylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis. Science. 2012 Jan 20;335(6066):348-53. PMID: 22157079
 
Zheng ZY, Cheng CM, Fu XR, Chen LY, Xu L, Terrillon S, Wong ST, Bar-Sagi D, Songyang Z, Chang EC. CHMP6 and VPS4A mediate the recycling of Ras to the plasma membrane to promote growth factor signaling. Oncogene. 2012 Oct 25;31(43):4630-8. PMID: 22231449
 
Jin G, Fu C, Zhao H, Cui K, Chang J, Wong ST. A novel method of transcriptional response analysis to facilitate drug repositioning for cancer therapy. Cancer Res. Jan 1;72(1):33-44, 2012. PMID: 22108825
 
Yang C, Wang H, Xu Y, Brinkman KL, Ishiyama H, Wong ST, Xu B. The kinetochore protein Bub1 participates in the DNA damage response. DNA Repair (Amst). 2012 Feb 1;11(2):185-91. PMID: 22071147
 
Pham K, Chauviere A, Hatzikirou H, Li X, Byrne HM, Cristini V, Lowengrub J. Density-dependent quiescence in glioma invasion: instability in a simple reaction-diffusion model for the migration/proliferation dichotomy. J Biol Dyn. 2012;6 Suppl 1:54-71. PMID: 22873675
 
Yang C, Tang X, Guo X, Niikura Y, Kitagawa K, Cui K, Wong ST, Fu L, Xu B. Aurora-B Mediated ATM Serine 1403 Phosphorylation Is Required for Mitotic ATM Activation and the Spindle Checkpoint. Mol Cell. 2011 Nov 18;44(4):597-608. PMID: 22099307
 
Sigoillot FD, Huckins JF, Li F, Zhou X, Wong ST, King RW. A time-series method for automated measurement of changes in mitotic and interphase duration from time-lapse movies. PLoS One. 2011;6(9):e25511. PMID: 21966537
 
Jin G, Zhao H, Zhou X, Wong ST. An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data. Bioinformatics. 2011 Jul 1;27(13):i310-i316. PMID: 21685086
 
Zhao H, Cui K, Nie F, Wang L, Brandl MB, Jin G, Li F, Mao Y, Xue Z, Rodriguez A, Chang J, Wong ST. The effect of mTOR inhibition alone or combined with MEK inhibitors on brain metastasis: an in vivo analysis in triple-negative breast cancer models. Breast Cancer Res Treat. 2012 Jan;131(2):425-36. PMID: 21394501
 
Zhu X, Zhou X, Lewis MT, Xia L, Wong S. Cancer stem cell, niche and EGFR decide tumor development and treatment response: A bio-computational simulation study. J. Thero. Biol. 2011 Jan 21;269(1): 138-49. PMID: 20969880
 
Frieboes HB, Chaplain MA, Thompson AM, Bearer EL, Lowengrub JS, Cristini V. Physical oncology: a bench-to-bedside quantitative and predictive approach. Cancer Res. 71(2): 298-302. 2011. PMID: 21224346
 
Deisboeck TS, Wang Z, Macklin P, Cristini V. Multiscale Cancer Modeling. Annu Rev Biomed Eng. 2011 Aug 15;13:127-55. PMID: 21529163
 
Pham K, Frieboes HB, Cristini V, Lowengrub J. Predictions of tumour morphological stability and evaluation against experimental observations. J R Soc Interface. 8(54): 16-29. 2011. PMID: 20519213
 
Wise SM, Lowengrub JS, Cristini V. An Adaptive Multigrid Algorithm for Simulating Solid Tumor Growth Using Mixture Models. Math Comput Model. 53(1-2): 1-20. 2011. PMID: 21076663
 
Tektonidis M, Hatzikirou H, Chauvière A, Simon M, Schaller K, Deutsch A. Identification of intrinsic in vitro cellular mechanisms for glioma invasion. J Theor Biol. 2011 Jul 29;287C:131-147. PMID: 21816160
 
Hatzikirou H, Chauviere A, Bauer AL, Leier A, Lewis MT, Macklin P, Marquez-Lago TT, Bearer EL, Cristini V. Integrative Physical Oncology. Wiley Interdiscip Rev Syst Biol Med. 2012 Jan-Feb;4(1):1-14. PMID: 21853537
 
Edgerton ME, Chuang YL, Macklin P, Yang W, Bearer EL, Cristini V. A novel, patient-specific mathematical pathology approach for assessment of surgical volume: Application to ductal carcinoma in situ of the breast. Anal Cell Pathol (Amst). 2011 Sep 2. PMID: 21891861
 
Zhu X, Zhou X, Lewis MT, Xia L, Wong S. Cancer stem cell, niche and EGFR decide tumor development and treatment response: A bio-computational Simulation Study. Journal of Theoretical Biology. 269 (1):38-149. PMID: 20969880
 
Litzenburger BC, Creighton CJ, Tsimelzon A, Chan BT, Hilsenbeck SG, Wang T, Carboni JM, Gottardis MM, Huang F, Chang JC, Lewis MT, Rimawi MF, Lee AV. High IGF-IR activity in triple-negative breast cancer cell lines and tumorgrafts correlates with sensitivity to anti-IGF-IR therapy. Clin Cancer Res. 2011 Apr 15;17(8):2314-27. PMID: 21177763
 
Chang H, Li Q, Moraes RC, Lewis MT, Hamel PA. Activation of ERK by sonic hedgehog independent of canonical hedgehog signaling. Intl J. of Biochem & Cell Bio. 2010 Sep; 42(9): 1462-71. PMID: 20451654
 
Klopp AH, Lacerda L, Gupta A, Debeb BG, Solley T, Li L, Spaeth E, Xu W, Zhang X, Lewis MT, Reuben JM, Krishnamurthy S, Ferrari M, Gaspar R, Buchholz TA, Cristofanilli M, Marini F, Andreeff M, Woodward WA. Mesenchymal stem cells promote mammosphere formation and decrease E-cadherin in normal and malignant breast cells. PLoS ONE. 2010 August 16; 5(8): e12180. PMID: 20808935
 
Debeb BG, Zhang X, Krishnamurthy S, Gao H, Cohen E, Li L, Rodriguez AA, Landis MD, Lucci A, Ueno NT, Robertson F, Xu W, Lacerda L, Buchholz TA, Cristofanilli M, Reuben JM, Lewis MT, Woodward WA. Characterizing cancer cells with cancer stem cell-like features in 293T human embryonic kidney cells. Mol Cancer. 2010 Jul 8;9:180. PMID: 20615238
 
Rodriguez AA, Makris A, Wu MF, Rimawi M, Froehlich A, Dave B, Hilsenbeck SG, Chamness GC, Lewis MT, Dobrolecki LE, Jain D, Sahoo S, Osborne CK, Chang JC. DNA repair signature is associated with anthracyclines response in triple negative breast cancer patients. Breast Cancer Res Treat. 2010 Aug; 123(1): 189-96. PMID: 20582464
 
De Magalhães N, Liaw LH, Berns M, Cristini V, Chen Z, Stupack D, Lowengrub J. Applications of a new In vivo tumor spheroid based shell-less chorioallantoic membrane 3-D model in bioengineering research. J Biomed Sci Eng. 2010 3(1): 20-26. PMID: 21243108
 
Chauviere AH, Hatzikirou H, Lowengrub JS, Frieboes HB, Thompson AM, Cristini V. Mathematical Oncology: How Are the Mathematical and Physical Sciences Contributing to the War on Breast Cancer?. Curr Breast Cancer Rep. 2010 2(3): 121-129. PMID:21151486
 
Frieboes HB, Jin F, Chuang YL, Wise SM, Lowengrub JS, Cristini V. Three-dimensional multispecies nonlinear tumor growth-II: Tumor invasion and angiogenesis. J Theor Biol. 2010 264(4): 1254-1278. PMID: 20303982
 
Lowengrub JS, Frieboes HB, Jin F, Chuang YL, Li X, Macklin P, Wise SM, Cristini V. Nonlinear modelling of cancer: bridging the gap between cells and tumours. Nonlinearity. 2010 23(1): R1-R91. PMID: 20808719
 
 

Conferences and Abstracts

Yanqiao Zhu, Fuhai Li, Tegy J. Vadakkan, Mei Zhang, John Landua, Wei Wei, Jinwen Ma, Mary E. Dickinson, Jeffrey M. Rosen, Michael T. Lewis, Ming Zhan, Stephen T. C. Wong. Three-dimensional vasculature reconstruction of tumour microenvironment via local clustering and classification. Interface Focus special issue of Mathematics of the Integrative Cancer Biology Program. June 25, 2013 vol.3 no.4 DOI:10.1098/rsfs.2013.0015
 
Tan H, Li F, Singh J, Xia X, Cridebring D, Yang J, Bao J, Ma JW, Zhan M, Wong ST.
A 3-Dimensional multiscale model to simulate tumor progression in response to interactions between cancer stem cells and Tumor Microenvironmental Factors”, 2012 IEEE International Conference on Systems Biology (ISB), Xi'an, China, Aug. 18-20, 2012.
 
Jin G, Gao JF, Wong ST.
A new computational model using multi-objective optimization to identify activated cancer signaling networks from heterogeneous genomic data. 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, CA. July 15-17, 2012.
 
Peikai Chen, Y. S. Hung, Yubo Fan, ST Wong.
An integrative bioinformatics approach for identifying subtypes and subtype-specific drivers in cancer. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2012: San Diego, CA, USA, May 9-12: 169-176.
 
Hua Tan, Fuhai Li, Jaykrishna Singh, Xiaofeng Xia, Derek Cridebring, Jian Yang, Jiguang Bao, Jinwen Ma, Ming Zhan, Stephen T.C. Wong.
A 3-Dimentional Multiscale Model to Simulate Tumor Progression in Response to Interactions between Cancer Stem Cells and Tumor Microenvironmental Factors. IEEE 6th International Conference on Systems Biology (ISB), 2012.
 
Lewis M.
Xenograft models of the normal and malignant human breast. Translational Animal Models in Drug Discovery and Development, 2012, Bentham Science Publishers. pp122-138. ISBN 978-60805-591-3
 
Fuhai Li, Jaykrishna Singh, Jinwen Ma, Ming Zhan, Stephen T.C. Wong.
Modeling Cell-Cell Communication in Cancer Stem Cell Microenvironment by Considering Molecular and Cellular Heterogeneities. NCI’s Integrative Cancer Biology Program (ICBP) Mathematical Modeling Cancer Systems, Tampa, Florida, March 18-20, 2012.
 
Fuhai Li, Hua Tan, Jaykrishna Singh, Jian Yang, Xiaofeng Xia, Jinwen Ma1, Mei Zhang, Mary Dickinson, Jeffrey M. Rosen, Michael T. Lewis, Ming Zhan and Stephen T.C. Wong.
A 3D Imaging-Driven Computational Model for Simulating and Predicting Tumor Development and Re-growth under Tumor Microenvironment. NCI’s Integrative Cancer Biology Program (ICBP) Mathematical Modeling Cancer Systems, Tampa, Florida, March 18-20, 2012.
 
Guangxu Jin, Junfeng Gao, Stephen T. C. Wong.
A computational model of pathway activation facilitates target discovery. NCI’s Integrative Cancer Biology Program (ICBP) Mathematical Modeling Cancer Systems, Tampa, Florida, March 18-20, 2012.
 
Yanqiao Zhu, Fuhai Li, John Landua, Tegy J. Vadakkan, Mei Zhang, Wei Wei, Jinwen Ma, Mary Dickinson, Jeffrey M. Rosen, Michael T. Lewis, Ming Zhan and Stephen T.C. Wong.
Quantitative Characterization of 3D Vasculature Spatial Patterns within Tumor Microenvironment of Breast Cancer Stem Cells. NCI’s Integrative Cancer Biology Program (ICBP) Mathematical Modeling Cancer Systems, Tampa, Florida, March 18-20, 2012.
 
Jianting Sheng, Fuhai Li, Yubo Fan, Yuho Hayashi, Jinwen Ma, Ming Zhan, Stephen T.C. Wong.
A network prediction strategy coupling disease driver genes with geometric diffusion analysis toreconstruct signaling networks and repurpose known drugs for treatment of cancer. NCI’s Integrative Cancer Biology Program (ICBP) Mathematical Modeling Cancer Systems, Tampa, Florida, March 18-20, 2012.
 
Jinwen Ma, Jianting Sheng, Fuhai Li, Ming Zhan and Stephen T.C. Wong.
A 3D Computational Model for Studying Self-organization of the Development of Epithelial Lesions with Cancer Mutations. NCI’s Integrative Cancer Biology Program (ICBP) Mathematical Modeling Cancer Systems, Tampa, Florida, March 18-20, 2012.
 
Zheng Yin, Xiaofeng Xia, Ming Zhan, Norbert Perriman, Stephen T.C. Wong.
Modeling heterogeneous cellular responses to combinations of RNAi treatments using Reversible JumpMarkov Chain Monte Carlo. NCI’s Integrative Cancer Biology Program (ICBP) Mathematical Modeling Cancer Systems, Tampa, Florida, March 18-20, 2012.