Systems Medicine and Bioengineering (SMAB)
Our Mission
Research Areas
Our systems medicine research provides new avenues to understand the causes of diseases, identify biomarkers, discover therapeutic targets, and attain precision in disease management.
Research Areas
Diseases
- Solid adult and pediatric tumors
- Alzheimer’s disease and dementia
- Stroke
- Parkinson’s disease and movement disorders
- Diabetes and related metabolic disorders
Methods and Technologies:
- Artificial Intelligence in Medicine
- Bioinformatics and Biostatistics
- Biological and Medical Image Analysis
- Cancer Biology and Neurobiology
- Clinical Informatics
- Digital Health
- Drug Repositioning and Discovery
- Internet of Medical Things
- Neuroimaging
- Optical Microscopy and Biophotonics
- Systems Biology
Our work at Houston Methodist has led to clinical trials among all our research areas. We are also training a new generation of physicians and scientists to use systems approaches to medicine.
Bioinformatics Software
CCCEXPLORER FOR CANCER
CCCExplorer is a java-based software that predicts and visualizes the gene signaling network to aid research on crosstalk identification in the tumor microenvironment. CCCExplorer integrates a computational model that we developed to uncover cell-cell communication as a direct and connected network. These cell communications range from ligand-receptor interactions to transcription factors and their target genes. Learn more about CCCExplorer software.
Ref:
- Yeung TL, Sheng J, Leung CS, Li F, Kim J, Ho SY, Matzuk MM, Lu KH, Wong STC*, Mok SC*. Systematic Identification of Druggable Epithelial-Stromal Crosstalk Signaling Networks in Ovarian Cancer. J Natl Cancer Inst. 2018 May 31. PMID: 29860390.
- Choi H, Sheng J, Gao D, Li F, Durrans A, Ryu S, Lee SB, Narula N, Rafii S, Elemento O, Altorki NK, Wong ST*, Mittal V*. Transcriptome analysis of individual stromal cell populations identifies stroma-tumor crosstalk in mouse lung cancer model. Cell Reports. 2015 Feb 24;10(7):1187-201. PMID: 2570482
DISNEY
Systems biology-based drug repositioning identifies digoxin as a potential therapy for groups 3 and 4 medulloblastoma. Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Although outcomes have improved in recent decades, new treatments are still needed to improve survival and reduce treatment-related complications.
Drug combinations that simultaneously suppress multiple cancer driver signaling pathways increase therapeutic options and may reduce drug resistance. We have developed a computational systems biology tool, DrugComboExplorer, to identify driver signaling pathways and predict synergistic drug combinations by integrating the knowledge embedded in vast amounts of available pharmacogenomics and omics data. Learn more about DrugComboExplorer software.
DrugComboRanker is a computational tool that prioritizes synergistic drug combinations and uncovers their mechanisms of action. Learn more about DrugComboRanker.
G-CelliQ Image Processing Tool
Morphological plasticity is critical to organism development - as exemplified by the reversible conversion of embryonic non-migratory epithelial cells to motile mesenchymal cells required for tissue Morphological plasticity is critical to organism development as exemplified by the reversible conversion of embryonic non-migratory epithelial cells to motile mesenchymal cells required for tissue positioning and organization.
Our Team
Collaborators and Support
Principal Investigators
Stephen Wong, PhD, PE
John S. Dunn Presidential Distinguished Chair in Biomedical Engineering, Houston Methodist
Professor of Computer Science and Bioengineering in Radiology, Academic Institute
Full Member, Research Institute
Department of Radiology
Associate Director, Shared Resources, Dr. Mary and Ron Neal Cancer Center
Steve Fung, MD
Eugene C. Lai, MD, PhD
Vivek Mittal, PhD
John Volpi, MD
Kelvin Wong, PhD
Weiming Xia, PhD
Zheng Yin, PhD
Jianting Sheng, PhD
Hong Zhao, MD, PhD
Associates and Students
Research Associates and Postdoctoral Fellows:
Yuliang Cao, MSc
Wenjuan Dong, PhD, Research Associate
Raksha Raghunathan, PhD, Research Engineer
Shaohua Qi, PhD, Research Associate
Lin Wang, PhD, Research Associate
Li Yang, PhD, Research Associate
Kun Han, PhD, Postdoctoral Fellow
Graduate Students:
Jonathon Cummock, TAMU-MD, PhD Student
Rahul Ghosh, MSc, TAMU-MD, PhD Student
Daniel Kermany, MSc, TAMU-MD, PhD Student
Ju Ahn Young, BSc, TAMU-MD, PhD Student
Glori Das, BSc, TAMU-MD, PhD Student
Wesley Poon, BSc, TAMU-MD, PhD Student
Orhun Davarci, MSc, TAMU EnMed Student
Natasha Nehra, BSc, TAMU EnMed Student
Gogol Bhattacharya, MSc, TAMU EnMed Student
Reid Master, BSc, TAMU EnMed Student
Patrick Sui, McGill University, PhD Student
Vo Hung, UH, PhD Student
Tongan Cao, Penn State University, PhD Student
Jihua Liu, Bsc, U Penn, Biostatistics Master Student
Undergraduate Students:
David Hunt, TAMU, Computer Science
Staff
Computational and Informatics Staff:
Yuliang Cao, MSc
Xin Wang, MSc
Zhihao Wan, MSc
Shiruo Wang, MSc
Xiaohui Yu, MSc
Lab Staff:
Dongbing Gao, MSc
Matthew Vasquez, BSc
Shan Xu, MD
Michael Chan, BSc
Bill Chan, BSc
Administrative Staff:
Tian Ding, PhD, MBA
Chika Frank Ezeana, MD, MPH
Deborah Dowell
Martha Silva
Collaborators and Support
External Collaborators
- Vahid Afshar-Kharghan, MD, Department of Pulmonary Medicine, MD Anderson Cancer Center
- Chris Bakal, PhD, The Institute of Cancer Research, U.K.
- Joseph Chang, PhD, School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore
- Sharon Glynn, PhD, National University of Ireland, Galway, Ireland
- Willa Hsueh, MD, Diabetes and Metabolism Research Center, Ohio State University
- Ching Lau, MD, PhD, Center for Cancer and Blood Disorder, Connecticut Children’s and The Jackson Laboratory
- Xiao-Nan Li, MD, PhD, Stanley Manne Children’s Research Institute, Lurie Children’s Hospital and Northwestern University
- Vivek Mittal, PhD, Ding Cheng Gao, PhD, Altorki Nasser, MD, The Neuberger Berman Lung Cancer Research Center, Weill Cornell Medicine
- Sam Mok, PhD, Department of Gynecologic Oncology and Reproductive Medicine, MD Anderson Cancer Center
- Hien Van Nguyen, PhD, Cullen College of Engineering, University of Houston
- Rudolph Tanzi, PhD, Doo Yeon Kim, PhD, Mass General Institute for Neurodegenerative Disease (MIND) laboratories, Mass General Hospital
- James Wang, PhD, Sharon Xiaolei Wang, PhD, College of Information Sciences and Technology, Penn State University
- David Wink, PhD, Center for Cancer Research, National Cancer Institute
- Weiming Xia, PhD, Alzheimer’s Disease Center, Boston University
Houston Methodist Collaborations
Funding & Support
SMAB RESEARCH PROJECTS
Cancer
C1. Brain tumor
C1.1: Tumor-astrocyte crosstalk regulating brain metastatic cancer. (NIH R01CA238727)
C1.2: Development of new PCDH7 single domain antibody therapy for brain mets. (Chao Foundation)
C1.3: Mechanism and drug target of Alzheimer’s suppression of brain tumor. (NIH R01CA238727-S1; Chao Foundation)
C1.4: Mechanism and drug repositioning of digoxin for medulloblastoma group III/IV. (Chao Foundation; Clinical Trial)
C1.5: Chronic stress and brain metastasis from triple-negative breast Cancer. (Chao and Dunn Foundations)
C1.6: Prognostic gene discovery in glioblastoma patients (Dunn Foundation, Greg and Lily Nelson Fund)
C2. Ovarian cancer
C2.1: Inter-cellular exosomal communication of high grade serous ovarian cancer. (Chao Foundation)
C2.2: Prognostic biomarkers of high grade serous ovarian cancer. (Tina’s Wish Foundation, CPRIT CCBTP)
C2.3: MFAP5 immunotherapy for ovarian cancer. (Carole Walter Looke Fund and Chao Foundation)
C2.4: Immune checkpoint regulator in ovarian cancer progression. (DOD W81XWH-17-1-0126; Dunn Foundation)
C2.5: Platelets promote growth of ovarian cancer. (NIH R01CA177909)
C3. Lung Disease
C3.1: Immuno-radiotherapy crosstalk for non-small cell lung cancer. (Chao and Dunn Foundations)
C3.2: Immunotherapy for idiopathic pulmonary fibrosis. (Chao and Dunn Foundations)
C3.3: Cancer risk assessment of incidental lung nodules (Chao and Dunn Foundations)
C4. Bone Cancer
C4.1. Spatiotemporal modeling of cancer-niche interactions in bone metastasis. (NIH U01CA253553)
C4.2. Drug combinations and mechanism of metformin and imatinib for Ewing sarcoma. (Dunn Foundation)
C5. Breast Cancer
C5.1. Epithelial-mesenchymal transition in breast tumor metastasis and chemoresistance. (NIH R01CA244413)
C5.2. NOS/COX2 inhibitors for TNBC. (Dunn Foundation)
C5.3. Convergent AI for Precise Breast Cancer Risk Assessment. (NIH R01CA251710)
C5.4. Digital therapeutics (MOCHA) for post-hospitalization cancer patients and survivors (Chao and Dunn Foundations, Connie Dryer Fund)
Alzheimer’s Disease and Related Disorders
N1. Alzheimer’s Disease Mechanisms and Therapeutics
N1.1. Systematic Alzheimer's disease drug repositioning via bioinformatics-guided drug screening and image-omics. (NIH R01AG057635, Margolis Fund)
N1.2. Early and late-life metal exposures and Alzheimer’s disease (NIH R01ES024165-S4)
N1.3. Systematic modeling and prediction of cell-type-specific and spatiotemporal crosstalk pathways in Alzheimer's disease. (NIH R01AG071496)
N1.4: High content screening and analysis for drug repositioning using Alzheimer’s 3D cell assays. (Cure Alzheimer’s Fund, Gillson Longenbaugh Foundation, and Carl Anderson Foundation, Margolis Fund, Steve Cook Fund)
N1.5: Gut-brain axis, microbiome-neural interactions in Alzheimer’s disease. (Chao and Dunn Foundations)
N1.6: Mitochrondrial dysfunction and OC1AD1 in regulating Alzheimer’s disease progression. (Chao Foundation)
N1.7: Reduce risk factors of Alzheimer’s and dementia patients. (Chao Foundation)
N1.8: Multimodal optical coherence tomography probe for detection/monitoring of Alzheimer’s (Chao Foundation)
N2. Parkinson’s Disease Mechanisms and Therapeutics
N2.1: Drug repositioning for Parkinson’s disease with high content drug screening (Huffington Foundation)
N3. Stroke Precision Detection and Diagnosis
N3.1: Smart instrumentation for precision assessment of stroke. (Scurlock Foundation; Dunn Foundation)
N3.2: Multimedia intelligence for stroke screening and assessment (Scurlock Foundation; Chao Foundation)
Label-free Imaging-Guided Theragnostics
M1. Coherent anti-stroke Raman Scattering (CARS) molecular vibrational imaging for early detection of cancer, Alzheimer’s disease, and blast brain injuries. (Chao and Dunn Foundations)
M2. Dual optical coherent tomography (OCT) and CARS imaging for studying metastatic cancer initiation and progression. (Chao Foundation, Johnsson Estate)
M3. Label-free imaging-guided cold femtosecond laser single cell microablation. (Chao and Dunn Foundations)
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