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Sui Huang

Sui Huang, MD, PhD

Professor

ISB

Dr. Sui Huang is a molecular and cell biologist with a strong background in theoretical biology. He has devoted his research to understanding the very phenomenon of cancer from a complex systems perspective. Life scientists now readily acknowledge that the “whole is more than the sum of its parts” but the question is: What exactly is the “more” that we need in order to understand the “whole”? Can this abstract philosophical notion be reduced to a rigorous formal concept and concrete molecular entities? Pursuing this question has guided Dr. Huang‘s research in cancer and cell biology over the past decade.  Before joining the ISB in fall 2011, Dr. Huang held faculty positions at the University of Calgary (Institute of Biocomplexity and Informatics), where he helped establish biocomplexity as a discipline in research and teaching, and at Harvard Medical School (Children’s Hospital) where he obtained first experimental evidence for the existence of high-dimensional attractors in mammalian gene regulatory networks.

Sui Huang grew up in Geneva and Zurich. He received his MD degree from the University of Zurich and obtained thereafter, as the first recipient of the PhD-Program-for-Physicians Award of the Swiss National Science Foundation, his PhD in molecular biology and physical chemistry for work on interferons. As a postdoctoral fellow at Children’s Hospital Boston he investigated tumor angiogenesis and cell growth control. In that period he also studied dynamical systems through his affiliation with the New England Complex Systems Institute.

Seeing how both interferons and anti-angiogenic agents have failed to live up to their celebrated promise of curing cancer has had a lasting impact on Dr. Huang’s views. The humbling recognition of the profound complexity of the living state fostered the desire to overcome the orthodoxy of reductionist, monocausal and deterministic thinking that prevailed in biomedicine and to put to use his knowledge of complex systems theory in his experimental research. Time was ripe in the late ’90s because the arrival of the “omics technologies” and systems biology paved the way towards this interdisciplinary approach. With his move to the ISB, Dr. Huang continues to unite experiment and theory to gain insights in the essence of multi-cellularity and cancer.

MD, University of Zurich

PhD, Molecular Biology and Physical Chemistry, University of Zurich

Molecular and cell biology, cancer biology, gene regulatory networks and theory of complex systems

Park, James H., Parvinder Hothi, Adrian Lopez Garcia de Lomana, Min Pan, Rachel Calder, Serdar Turkarslan, Wei-Ju Wu, et al. 2024. “Gene Regulatory Network Topology Governs Resistance and Treatment Escape in Glioma Stem-like Cells.” BioRxiv: The Preprint Server for Biology, 2024.02.02.578510. https://doi.org/10.1101/2024.02.02.578510. Cite Download
Baumgartner, Andrew, Max Robinson, Todd Golde, Suman Jaydev, Sui Huang, Jennifer Hadlock, and Cory Funk. 2024. “Fokker-Planck Diffusion Maps of Multiple Single Cell Microglial Transcriptomes Reveals Radial Differentiation into Substates Associated with Alzheimer’s Pathology.” BioRxiv: The Preprint Server for Biology, 2024.06.21.599924. https://doi.org/10.1101/2024.06.21.599924. Cite
Park, James H., Parvinder Hothi, Adrian Lopez Garcia de Lomana, Min Pan, Rachel Calder, Serdar Turkarslan, Wei-Ju Wu, et al. 2024. “Gene Regulatory Network Topology Governs Resistance and Treatment Escape in Glioma Stem-like Cells.” Science Advances 10 (23): eadj7706. https://doi.org/10.1126/sciadv.adj7706. Cite Download
Zhang, Yue, Guangrong Qin, Boris Aguilar, Noa Rappaport, James T. Yurkovich, Lance Pflieger, Sui Huang, Leroy Hood, and Ilya Shmulevich. 2024. “A Framework towards Digital Twins for Type 2 Diabetes.” Frontiers in Digital Health 6:1336050. https://doi.org/10.3389/fdgth.2024.1336050. Cite Download
Baumgartner, Andrew, Sui Huang, Jennifer Hadlock, and Cory Funk. 2024. “Dimensional Reduction of Gradient-like Stochastic Systems with Multiplicative Noise via Fokker-Planck Diffusion Maps.” arXiv. https://doi.org/10.48550/arXiv.2401.03095. Cite Download
Wang, Yue, Joseph X. Zhou, Edoardo Pedrini, Irit Rubin, May Khalil, Roberto Taramelli, Hong Qian, and Sui Huang. 2023. “Cell Population Growth Kinetics in the Presence of Stochastic Heterogeneity of Cell Phenotype.” Journal of Theoretical Biology 575:111645. https://doi.org/10.1016/j.jtbi.2023.111645. Cite Download Download
Fecho, Karamarie, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E. Thessen, Shervin Abdollahi, Sergio E. Baranzini, et al. 2023. “An Approach for Collaborative Development of a Federated Biomedical Knowledge Graph-Based Question-Answering System: Question-of-the-Month Challenges.” Journal of Clinical and Translational Science 7 (1): e214. https://doi.org/10.1017/cts.2023.619. Cite Download
Baumgartner, Andrew, Max Robinson, Sui Huang, Jennifer Hadlock, and Cory Funk. 2023. “Integration of Multiple Single Cell Microglial Datasets Reveals Radial Differentiation into Long‐lived Substates Associated with Alzheimer’s Pathology.” Alzheimer’s & Dementia 19. https://doi.org/10.1002/alz.080693. Cite
Gibbs, David L., Michael K. Strasser, and Sui Huang. 2023. “Single-Cell Gene Set Scoring with Nearest Neighbor Graph Smoothed Data (Gssnng).” Bioinformatics Advances 3 (1): vbad150. https://doi.org/10.1093/bioadv/vbad150. Cite Download
Lee, Su-Hyung, Ela W. Contreras Panta, David Gibbs, Yoonkyung Won, Jimin Min, Changqing Zhang, Joseph T. Roland, et al. 2023. “Apposition of Fibroblasts With Metaplastic Gastric Cells Promotes Dysplastic Transition.” Gastroenterology, S0016-5085(23)00731-X. https://doi.org/10.1053/j.gastro.2023.04.038. Cite
Morris, John H., Karthik Soman, Rabia E. Akbas, Xiaoyuan Zhou, Brett Smith, Elaine C. Meng, Conrad C. Huang, et al. 2023. “The Scalable Precision Medicine Open Knowledge Engine (SPOKE): A Massive Knowledge Graph of Biomedical Information.” Bioinformatics (Oxford, England) 39 (2): btad080. https://doi.org/10.1093/bioinformatics/btad080. Cite Download
Huang, Sui. 2022. “Towards a Unification of the 2 Meanings of ‘Epigenetics.’” PLoS Biology 20 (12): e3001944. https://doi.org/10.1371/journal.pbio.3001944. Cite Download
Angelini, Erin, Yue Wang, Joseph Xu Zhou, Hong Qian, and Sui Huang. 2022. “A Model for the Intrinsic Limit of Cancer Therapy: Duality of Treatment-Induced Cell Death and Treatment-Induced Stemness.” PLoS Computational Biology 18 (7): e1010319. https://doi.org/10.1371/journal.pcbi.1010319. Cite Download
Tercan, Bahar, Boris Aguilar, Sui Huang, Edward R. Dougherty, and Ilya Shmulevich. 2022. “Probabilistic Boolean Networks Predict Transcription Factor Targets to Induce Transdifferentiation.” IScience 25 (9). https://doi.org/10.1016/j.isci.2022.104951. Cite Download
Baranzini, Sergio E., Katy Börner, John Morris, Charlotte A. Nelson, Karthik Soman, Erica Schleimer, Michael Keiser, et al. 2022. “A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology.” AI Magazine 43 (1): 46–58. https://doi.org/10.1002/aaai.12037. Cite Download
Fecho, Karamarie, Anne E. Thessen, Sergio E. Baranzini, Chris Bizon, Jennifer J. Hadlock, Sui Huang, Ryan T. Roper, et al. 2022. “Progress toward a Universal Biomedical Data Translator.” Clinical and Translational Science. https://doi.org/10.1111/cts.13301. Cite
Huang, Sui. 2021. “Should Biophysics Study Nonphysical Quantities of Biological Systems? Take Max Delbrück for Inspiration.” Biophysics Reviews 2 (4): 040401. https://doi.org/10.1063/5.0079700. Cite Download
Haak, Victoria M., Sui Huang, and Dipak Panigrahy. 2021. “Debris-Stimulated Tumor Growth: A Pandora’s Box?” Cancer Metastasis Reviews 40 (3): 791–801. https://doi.org/10.1007/s10555-021-09998-8. Cite Download
Park, James H., Adrian Lopez Garcia de Lomana, Diego M. Marzese, Tiffany Juarez, Abdullah Feroze, Parvinder Hothi, Charles Cobbs, et al. 2021. “A Systems Approach to Brain Tumor Treatment.” Cancers 13 (13): 3152. https://doi.org/10.3390/cancers13133152. Cite Download
Huang, Sui. 2021. “Reconciling Non-Genetic Plasticity with Somatic Evolution in Cancer.” Trends in Cancer. https://doi.org/10.1016/j.trecan.2020.12.007. Cite
Tian, Xiao-Jun, Dong Zhou, Haiyan Fu, Rong Zhang, Xiaojie Wang, Sui Huang, Youhua Liu, and Jianhua Xing. 2020. “Sequential Wnt Agonist Then Antagonist Treatment Accelerates Tissue Repair and Minimizes Fibrosis.” IScience 23 (5): 101047. https://doi.org/10.1016/j.isci.2020.101047. Cite Download
Fishbein, Anna, Weicang Wang, Haixia Yang, Jun Yang, Victoria M. Hallisey, Jianjun Deng, Sanne M. L. Verheul, et al. 2020. “Resolution of Eicosanoid/Cytokine Storm Prevents Carcinogen and Inflammation-Initiated Hepatocellular Cancer Progression.” Proceedings of the National Academy of Sciences of the United States of America 117 (35): 21576–87. https://doi.org/10.1073/pnas.2007412117. Cite
Sinha, Saurabh, Beryl M. Jones, Ian M. Traniello, Syed A. Bukhari, Marc S. Halfon, Hans A. Hofmann, Sui Huang, et al. 2020. “Behavior-Related Gene Regulatory Networks: A New Level of Organization in the Brain.” Proceedings of the National Academy of Sciences of the United States of America 117 (38): 23270–79. https://doi.org/10.1073/pnas.1921625117. Cite Download
Su, Yapeng, Daniel Chen, Dan Yuan, Christopher Lausted, Jongchan Choi, Chengzhen L. Dai, Valentin Voillet, et al. 2020. “Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19.” Cell, S0092867420314446. https://doi.org/10.1016/j.cell.2020.10.037. Cite Download
Su, Yapeng, Melissa E. Ko, Hanjun Cheng, Ronghui Zhu, Min Xue, Jessica Wang, Jihoon W. Lee, et al. 2020. “Multi-Omic Single-Cell Snapshots Reveal Multiple Independent Trajectories to Drug Tolerance in a Melanoma Cell Line.” Nature Communications 11 (1): 2345. https://doi.org/10.1038/s41467-020-15956-9. Cite Download
Johnson, Kaitlyn E., Grant Howard, William Mo, Michael K. Strasser, Ernesto A. B. F. Lima, Sui Huang, and Amy Brock. 2019. “Cancer Cell Population Growth Kinetics at Low Densities Deviate from the Exponential Growth Model and Suggest an Allee Effect.” PLoS Biology 17 (8). https://doi.org/10.1371/journal.pbio.3000399. Cite Download
Li, Jeremiah H., Felix X.-F. Ye, Hong Qian, and Sui Huang. 2019. “Time-Dependent Saddle-Node Bifurcation: Breaking Time and the Point of No Return in a Non-Autonomous Model of Critical Transitions.” Physica D. Nonlinear Phenomena 395:7–14. https://doi.org/10.1016/j.physd.2019.02.005. Cite Download
Su, Yapeng, Guideng Li, Melissa E. Ko, Hanjun Cheng, Ronghui Zhu, Min Xue, Jessica Wang, et al. 2019. “Trajectories from Snapshots: Integrated Proteomic and Metabolic Single-Cell Assays Reveal Multiple Independent Adaptive Responses to Drug Tolerance in a BRAF-Mutant Melanoma Cell Line.” BioRxiv, 767988. https://doi.org/10.1101/767988. Cite Download
Panigrahy, Dipak, Allison Gartung, Jun Yang, Haixia Yang, Molly M. Gilligan, Megan L. Sulciner, Swati S. Bhasin, et al. 2019. “Preoperative Stimulation of Resolution and Inflammation Blockade Eradicates Micrometastases.” The Journal of Clinical Investigation 130. https://doi.org/10.1172/JCI127282. Cite
Gilligan, Molly M., Allison Gartung, Megan L. Sulciner, Paul C. Norris, Vikas P. Sukhatme, Diane R. Bielenberg, Sui Huang, Mark W. Kieran, Charles N. Serhan, and Dipak Panigrahy. 2019. “Aspirin-Triggered Proresolving Mediators Stimulate Resolution in Cancer.” Proceedings of the National Academy of Sciences of the United States of America 116 (13): 6292–97. https://doi.org/10.1073/pnas.1804000116. Cite
Cuvitoglu, Ali, Joseph X. Zhou, Sui Huang, and Zerrin Isik. 2019. “Predicting Drug Synergy for Precision Medicine Using Network Biology and Machine Learning.” Journal of Bioinformatics and Computational Biology 17 (2): 1950012. https://doi.org/10.1142/S0219720019500124. Cite
Gartung, Allison, Jun Yang, Vikas P. Sukhatme, Diane R. Bielenberg, Djanira Fernandes, Jaimie Chang, Birgitta A. Schmidt, et al. 2019. “Suppression of Chemotherapy-Induced Cytokine/Lipid Mediator Surge and Ovarian Cancer by a Dual COX-2/SEH Inhibitor.” Proceedings of the National Academy of Sciences, 201803999. https://doi.org/10.1073/pnas.1803999116. Cite
Zhou, Joseph X., Roberto Taramelli, Edoardo Pedrini, Theo Knijnenburg, and Sui Huang. 2018. “Author Correction: Extracting Intercellular Signaling Network of Cancer Tissues Using Ligand-Receptor Expression Patterns from Whole-Tumor and Single-Cell Transcriptomes.” Scientific Reports 8 (1): 17903. https://doi.org/10.1038/s41598-018-36408-x. Cite Download
Joo, Jae Il, Joseph X. Zhou, Sui Huang, and Kwang-Hyun Cho. 2018. “Determining Relative Dynamic Stability of Cell States Using Boolean Network Model.” Scientific Reports 8 (1): 12077. https://doi.org/10.1038/s41598-018-30544-0. Cite Download
Chang, Jaimie, Swati S. Bhasin, Diane R. Bielenberg, Vikas P. Sukhatme, Manoj Bhasin, Sui Huang, Mark W. Kieran, and Dipak Panigrahy. 2018. “Chemotherapy-Generated Cell Debris Stimulates Colon Carcinoma Tumor Growth via Osteopontin.” FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology, fj201800019RR. https://doi.org/10.1096/fj.201800019RR. Cite
Trachana, Kalliopi, Rhishikesh Bargaje, Gustavo Glusman, Nathan D. Price, Sui Huang, and Leroy E. Hood. 2018. “Taking Systems Medicine to Heart.” Circulation Research 122 (9): 1276–89. https://doi.org/10.1161/CIRCRESAHA.117.310999. Cite
Grosse-Wilde, Anne, Rolf E. Kuestner, Stephanie M. Skelton, Ellie MacIntosh, Aymeric Fouquier d’Hérouël, Gökhan Ertaylan, Antonio Del Sol, Alexander Skupin, and Sui Huang. 2018. “Loss of Inter-Cellular Cooperation by Complete Epithelial-Mesenchymal Transition Supports Favorable Outcomes in Basal Breast Cancer Patients.” Oncotarget 9 (28): 20018–33. https://doi.org/10.18632/oncotarget.25034. Cite
Robinson, Max, Jennifer Hadlock, Jiyang Yu, Alireza Khatamian, Aleksandr Y. Aravkin, Eric W. Deutsch, Nathan D. Price, Sui Huang, and Gustavo Glusman. 2018. “Fast and Simple Comparison of Semi-Structured Data, with Emphasis on Electronic Health Records.” BioRxiv, 293183. https://doi.org/10.1101/293183. Cite Download
Huang, Sui, Fangting Li, Joseph X. Zhou, and Hong Qian. 2017. “Processes on the Emergent Landscapes of Biochemical Reaction Networks and Heterogeneous Cell Population Dynamics: Differentiation in Living Matters.” Journal of the Royal Society, Interface 14 (130). https://doi.org/10.1098/rsif.2017.0097. Cite
Bargaje, Rhishikesh, Kalliopi Trachana, Martin N. Shelton, Christopher S. McGinnis, Joseph X. Zhou, Cora Chadick, Savannah Cook, Christopher Cavanaugh, Sui Huang, and Leroy Hood. 2017. “Cell Population Structure Prior to Bifurcation Predicts Efficiency of Directed Differentiation in Human Induced Pluripotent Cells.” Proceedings of the National Academy of Sciences, 201621412. https://doi.org/10.1073/pnas.1621412114. Cite
Brock, Amy, and Sui Huang. 2017. “Precision Oncology: Between Vaguely Right and Precisely Wrong.” Cancer Research. https://doi.org/10.1158/0008-5472.CAN-17-0448. Cite
Yuan, Ruoshi, Suzhan Zhang, Jiekai Yu, Yanqin Huang, Demin Lu, Runtan Cheng, Sui Huang, et al. 2017. “Beyond Cancer Genes: Colorectal Cancer as Robust Intrinsic States Formed by Molecular Interactions.” Open Biology 7 (11). https://doi.org/10.1098/rsob.170169. Cite
Zhou, Joseph X., Roberto Taramelli, Edoardo Pedrini, Theo Knijnenburg, and Sui Huang. 2017. “Extracting Intercellular Signaling Network of Cancer Tissues Using Ligand-Receptor Expression Patterns from Whole-Tumor and Single-Cell Transcriptomes.” Scientific Reports 7 (1): 8815. https://doi.org/10.1038/s41598-017-09307-w. Cite
Li, Qin, Anders Wennborg, Erik Aurell, Erez Dekel, Jie-Zhi Zou, Yuting Xu, Sui Huang, and Ingemar Ernberg. 2016. “Dynamics inside the Cancer Cell Attractor Reveal Cell Heterogeneity, Limits of Stability, and Escape.” Proceedings of the National Academy of Sciences of the United States of America 113 (10): 2672–77. https://doi.org/10.1073/pnas.1519210113. Cite
Huang, Sui. 2016. “Where to Go: Breaking the Symmetry in Cell Motility.” PLoS Biology 14 (5): e1002463. https://doi.org/10.1371/journal.pbio.1002463. Cite
Mojtahedi, Mitra, Alexander Skupin, Joseph Zhou, Ivan G. Castaño, Rebecca Y. Y. Leong-Quong, Hannah Chang, Kalliopi Trachana, Alessandro Giuliani, and Sui Huang. 2016. “Cell Fate Decision as High-Dimensional Critical State Transition.” PLoS Biology 14 (12): e2000640. https://doi.org/10.1371/journal.pbio.2000640. Cite
Marr, Carsten, Joseph X. Zhou, and Sui Huang. 2016. “Single-Cell Gene Expression Profiling and Cell State Dynamics: Collecting Data, Correlating Data Points and Connecting the Dots.” Current Opinion in Biotechnology 39:207–14. https://doi.org/10.1016/j.copbio.2016.04.015. Cite
Pisco, A. O., and Sui Huang. 2015. “Non-Genetic Cancer Cell Plasticity and Therapy-Induced Stemness in Tumour Relapse: ’What Does Not Kill Me Strengthens Me’.” Br J Cancer 112 (May):1725–32. https://doi.org/10.1038/bjc.2015.146. Cite
Papadakis, A. I., C. Sun, T. A. Knijnenburg, Y. Xue, W. Grernrum, M. Holzel, W. Nijkamp, et al. 2015. “SMARCE1 Suppresses EGFR Expression and Controls Responses to MET and ALK Inhibitors in Lung Cancer.” Cell Research, February. Cite
Rebhahn, Jonathan A., Nan Deng, Gaurav Sharma, Alexandra M. Livingstone, Sui Huang, and Tim R. Mosmann. 2014. “An Animated Landscape Representation of CD4+ T-Cell Differentiation, Variability, and Plasticity: Insights into the Behavior of Populations versus Cells.” European Journal of Immunology 44 (8): 2216–29. https://doi.org/10.1002/eji.201444645. Cite