Sui Huang, MD, PhD

Professor

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

  

Pedrioli, P. G., J. K. Eng, R. Hubley, M. Vogelzang, E. W. Deutsch, B. Raught, B. Pratt, et al. 2004. “A Common Open Representation of Mass Spectrometry Data and Its Application to Proteomics Research.” Nat Biotechnol 22 (11): 1459–66. Cite
Huang, S., and J. Wikswo. 2006. “Dimensions of Systems Biology.” Reviews of Physiology, Biochemistry and Pharmacology 157: 81–104. Cite
Huang, S., and Donald E. Ingber. 2006. “A Non-Genetic Basis for Cancer Progression and Metastasis: Self-Organizing Attractors in Cell Regulatory Networks.” Breast Disease 26: 27–54. Cite
Joy, Maliackal Poulo, Donald E. Ingber, and S. Huang. 2007. “Chaotic Mean Field Dynamics of a Boolean Network with Random Connectivity.” International Journal of Modern Physics C 18: 1459–73. https://doi.org/10.1142/S0129183107011467. Cite
Huang, S., Yan-Ping Guo, Gillian May, and Tariq Enver. 2007. “Bifurcation Dynamics in Lineage-Commitment in Bipotent Progenitor Cells.” Developmental Biology 305 (2): 695–713. https://doi.org/10.1016/j.ydbio.2007.02.036. Cite
Soneji, Shamit, S. Huang, Matthew Loose, Ian John Donaldson, Roger Patient, Berthold Göttgens, Tariq Enver, and Gillian May. 2007. “Inference, Validation, and Dynamic Modeling of Transcription Networks in Multipotent Hematopoietic Cells.” Annals of the New York Academy of Sciences 1106 (June): 30–40. https://doi.org/10.1196/annals.1392.018. Cite
Bivort, Benjamin de, S. Huang, and Yaneer Bar-Yam. 2007. “Empirical Multiscale Networks of Cellular Regulation.” PLoS Computational Biology 3 (10): 1968–78. https://doi.org/10.1371/journal.pcbi.0030207. Cite
Panigrahy, Dipak, Arja Kaipainen, S. Huang, Catherine E. Butterfield, Carmen M. Barnés, Michael Fannon, Andrea M. Laforme, Deviney M. Chaponis, Judah Folkman, and Mark W. Kieran. 2008. “PPARalpha Agonist Fenofibrate Suppresses Tumor Growth through Direct and Indirect Angiogenesis Inhibition.” Proceedings of the National Academy of Sciences of the United States of America 105 (3): 985–90. https://doi.org/10.1073/pnas.0711281105. Cite
Chang, Hannah H., Martin Hemberg, Mauricio Barahona, Donald E. Ingber, and S. Huang. 2008. “Transcriptome-Wide Noise Controls Lineage Choice in Mammalian Progenitor Cells.” Nature 453 (7194): 544–47. https://doi.org/10.1038/nature06965. Cite
Hoffmann, Martin, Hannah H. Chang, S. Huang, Donald E. Ingber, Markus Loeffler, and Joerg Galle. 2008. “Noise-Driven Stem Cell and Progenitor Population Dynamics.” PloS One 3 (8): e2922. https://doi.org/10.1371/journal.pone.0002922. Cite
Andrecut, M., S. Huang, and S. A. Kauffman. 2008. “Heuristic Approach to Sparse Approximation of Gene Regulatory Networks.” Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 15 (9): 1173–86. https://doi.org/10.1089/cmb.2008.0087. Cite
Panigrahy, Dipak, Arja Kaipainen, Mark W. Kieran, and S. Huang. 2008. “PPARs: A Double-Edged Sword in Cancer Therapy?” PPAR Research, December, 350351. https://doi.org/10.1155/2008/350351. Cite
Sheehy, Sean P., S. Huang, and Kevin Kit Parker. 2009. “Time-Warped Comparison of Gene Expression in Adaptive and Maladaptive Cardiac Hypertrophy.” Circulation. Cardiovascular Genetics 2 (2): 116–24. https://doi.org/10.1161/CIRCGENETICS.108.806935. Cite
Brock, Amy, Hannah Chang, and S. Huang. 2009. “Non-Genetic Heterogeneity--a Mutation-Independent Driving Force for the Somatic Evolution of Tumours.” Nature Reviews. Genetics 10 (5): 336–42. https://doi.org/10.1038/nrg2556. Cite
Huang, S. 2009. “Reprogramming Cell Fates: Reconciling Rarity with Robustness.” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology 31 (5): 546–60. https://doi.org/10.1002/bies.200800189. Cite
Huang, S., Ingemar Ernberg, and Stuart Kauffman. 2009. “Cancer Attractors: A Systems View of Tumors from a Gene Network Dynamics and Developmental Perspective.” Seminars in Cell & Developmental Biology 20 (7): 869–76. https://doi.org/10.1016/j.semcdb.2009.07.003. Cite
Foster, David V., Jacob G. Foster, S. Huang, and Stuart A. Kauffman. 2009. “A Model of Sequential Branching in Hierarchical Cell Fate Determination.” Journal of Theoretical Biology 260 (4): 589–97. https://doi.org/10.1016/j.jtbi.2009.07.005. Cite
Huang, S. 2009. “Non-Genetic Heterogeneity of Cells in Development: More than Just Noise.” Development (Cambridge, England) 136 (23): 3853–62. https://doi.org/10.1242/dev.035139. Cite
Bracha, Abigail L., Arvind Ramanathan, S. Huang, Donald E. Ingber, and Stuart L. Schreiber. 2010. “Carbon Metabolism-Mediated Myogenic Differentiation.” Nature Chemical Biology 6 (3): 202–4. https://doi.org/10.1038/nchembio.301. Cite
Huang, S. 2010. “Cell Lineage Determination in State Space: A Systems View Brings Flexibility to Dogmatic Canonical Rules.” PLOS Biol 8 (5): e1000380. https://doi.org/10.1371/journal.pbio.1000380. Cite Download
Wang, Jin, Li Xu, Erkang Wang, and S. Huang. 2010. “The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation.” Biophysical Journal 99 (1): 29–39. https://doi.org/10.1016/j.bpj.2010.03.058. Cite
Panigrahy, Dipak, Arja Kaipainen, Emily R. Greene, and S. Huang. 2010. “Cytochrome P450-Derived Eicosanoids: The Neglected Pathway in Cancer.” Cancer and Metastasis Reviews 29 (4): 723–35. https://doi.org/10.1007/s10555-010-9264-x. Cite Download
Zernicka-Goetz, Magdalena, and S. Huang. 2010. “Stochasticity versus Determinism in Development: A False Dichotomy?” Nature Reviews. Genetics 11 (11): 743–44. https://doi.org/10.1038/nrg2886. Cite
Andrecut, Mircea, Julianne D. Halley, David A. Winkler, and S. Huang. 2011. “A General Model for Binary Cell Fate Decision Gene Circuits with Degeneracy: Indeterminacy and Switch Behavior in the Absence of Cooperativity.” PloS One 6 (5): e19358. https://doi.org/10.1371/journal.pone.0019358. Cite
Zhou, Joseph Xu, Lutz Brusch, and S. Huang. 2011. “Predicting Pancreas Cell Fate Decisions and Reprogramming with a Hierarchical Multi-Attractor Model.” PloS One 6 (3): e14752. https://doi.org/10.1371/journal.pone.0014752. Cite
Zhou, Joseph X., and S. Huang. 2011. “Understanding Gene Circuits at Cell-Fate Branch Points for Rational Cell Reprogramming.” Trends in Genetics: TIG 27 (2): 55–62. https://doi.org/10.1016/j.tig.2010.11.002. Cite
Guo, Yuchun, Ying Feng, Niraj S. Trivedi, and S. Huang. 2011. “Medusa Structure of the Gene Regulatory Network: Dominance of Transcription Factors in Cancer Subtype Classification.” Experimental Biology and Medicine (Maywood, N.J.) 236 (5): 628–36. https://doi.org/10.1258/ebm.2011.010324. Cite
Huang, S. 2011. “On the Intrinsic Inevitability of Cancer: From Foetal to Fatal Attraction.” Semin Cancer Biol 21 (3): 183–99. Cite
Huang, S. 2011. “Systems Biology of Stem Cells: Three Useful Perspectives to Help Overcome the Paradigm of Linear Pathways.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 366 (1575): 2247–59. https://doi.org/10.1098/rstb.2011.0008. Cite
Greene, Emily R., S. Huang, Charles N. Serhan, and Dipak Panigrahy. 2011. “Regulation of Inflammation in Cancer by Eicosanoids.” Prostaglandins & Other Lipid Mediators, Eicosanoids and disease, 96 (1–4): 27–36. https://doi.org/10.1016/j.prostaglandins.2011.08.004. Cite
Ho, Hsiu J., Tsung I. Lin, Hannah H. Chang, Steven B. Haase, S. Huang, and Saumyadipta Pyne. 2012. “Parametric Modeling of Cellular State Transitions as Measured with Flow Cytometry.” BMC Bioinformatics 13 Suppl 5: S5. https://doi.org/10.1186/1471-2105-13-S5-S5. Cite
Torres-Sosa, Christian, S. Huang, and Maximino Aldana. 2012. “Criticality Is an Emergent Property of Genetic Networks That Exhibit Evolvability.” PLoS Comput Biol 8: e1002669. https://doi.org/10.1371/journal.pcbi.1002669. Cite
Panigrahy, Dipak, Matthew L. Edin, Craig R. Lee, S. Huang, Diane R. Bielenberg, Catherine E. Butterfield, Carmen M. Barnés, et al. 2012. “Epoxyeicosanoids Stimulate Multiorgan Metastasis and Tumor Dormancy Escape in Mice.” J Clin Invest 122 (January): 178–91. https://doi.org/10.1172/JCI58128. Cite
Huang, S. 2012. “The Molecular and Mathematical Basis of Waddington’s Epigenetic Landscape: A Framework for Post-Darwinian Biology?” BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology 34 (2): 149–57. Cite
Halley, J. D., K. Smith-Miles, D. A. Winkler, T. Kalkan, S. Huang, and A. Smith. 2012. “Self-Organizing Circuitry and Emergent Computation in Mouse Embryonic Stem Cells.” Stem Cell Res 8 (March): 324–33. https://doi.org/10.1016/j.scr.2011.11.001. Cite
Huang, S. 2012. “Tumor Progression: Chance and Necessity in Darwinian and Lamarckian Somatic (Mutationless) Evolution.” Progress in Biophysics and Molecular Biology, May. Cite
DeGracia, Donald J., Zhi-Feng Huang, and S. Huang. 2012. “A Nonlinear Dynamical Theory of Cell Injury.” J Cereb Blood Flow Metab 32 (June): 1000–1013. https://doi.org/10.1038/jcbfm.2012.10. Cite
Zhou, J. X., M. D. Aliyu, E. Aurell, and S. Huang. 2012. “Quasi-Potential Landscape in Complex Multi-Stable Systems.” Journal of the Royal Society, Interface / the Royal Society, August. Cite
Pisco, A. O., A. Brock, J. Zhou, A. Moor, M. Mojtahedi, D. Jackson, and S. Huang. 2013. “Non-Darwinian Dynamics in Therapy-Induced Cancer Drug Resistance.” Nat Commun 4: 2467. Cite
Huang, S. 2013. “When Peers Are Not Peers and Don’t Know It: The Dunning-Kruger Effect and Self-Fulfilling Prophecy in Peer-Review.” BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology, February. Cite
Heinäniemi, Merja, Matti Nykter, Roger Kramer, Anke Wienecke-Baldacchino, Lasse Sinkkonen, Joseph Xu Zhou, Richard Kreisberg, Stuart A. Kauffman, S. Huang, and Ilya Shmulevich. 2013. “Gene-Pair Expression Signatures Reveal Lineage Control.” Nat Methods 10 (June): 577–83. https://doi.org/10.1038/nmeth.2445. Cite
Huang, S., and S. Kauffman. 2013. “How to Escape the Cancer Attractor: Rationale and Limitations of Multi-Target Drugs.” Semin Cancer Biol 23 (4): 270–78. Cite
Huang, S. 2013. “Hybrid T-Helper Cells: Stabilizing the Moderate Center in a Polarized System.” PLoS Biol 11 (8): e1001632. Cite
Panigrahy, Dipak, Brian T. Kalish, S. Huang, Diane R. Bielenberg, Hau D. Le, Jun Yang, Matthew L. Edin, et al. 2013. “Epoxyeicosanoids Promote Organ and Tissue Regeneration.” Proc Natl Acad Sci U S A 110 (August): 13528–33. https://doi.org/10.1073/pnas.1311565110. Cite
Huang, S. 2013. “Genetic and Non-Genetic Instability in Tumor Progression: Link between the Fitness Landscape and the Epigenetic Landscape of Cancer Cells.” Cancer Metastasis Rev 32 (3–4): 423–48. Cite
Zhou, Joseph Xu, Angela Oliveira Pisco, Hong Qian, and S. Huang. 2014. “Nonequilibrium Population Dynamics of Phenotype Conversion of Cancer Cells.” PloS One 9 (12): e110714. https://doi.org/10.1371/journal.pone.0110714. Cite
Pisco, Angela Oliveira, Dean Andrew Jackson, and S. Huang. 2014. “Reduced Intracellular Drug Accumulation in Drug-Resistant Leukemia Cells Is Not Only Solely Due to MDR-Mediated Efflux but Also to Decreased Uptake.” Frontiers in Oncology 4: 306. https://doi.org/10.3389/fonc.2014.00306. Cite
Mojtahedi, Mitra, Aymeric Fouquier d’Hérouël, and S. Huang. 2014. “Direct Elicitation of Template Concentration from Quantification Cycle (Cq) Distributions in Digital PCR.” Nucleic Acids Research 42 (16): e126. https://doi.org/10.1093/nar/gku603. Cite
Huang, S. 2014. “When Correlation and Causation Coincide.” Bioessays 36 (January): 1–2. https://doi.org/10.1002/bies.201370003. Cite
Rebhahn, Jonathan A., Nan Deng, Gaurav Sharma, Alexandra M. Livingstone, S. 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