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GSBSE

Molecular and Cellular Biology

Molecular and Cellular Biology seeks mechanistic understanding of broad aspects of development and disease, including cell signal transduction, stem cell fate determination, and tissue homeostasis at multiple levels that include intermolecular, cell-cell, tissue and organ function. Related research within the GSBSE ranges from basic developmental and disease processes in cell and animal models from zebrafish to mouse, to studies in humans, which emphasize vascular biology, stem cell biology, tissue development, homeostasis and pathology. Learn more >

Neuroscience

Neuroscience is an intrinsically broad discipline aimed at understanding large issues such as cognition, behavior, and neurological systems at levels that include the underlying anatomical and cellular circuits, and even the molecular events that control cell excitability, synaptic function, and development. Neuroscience research within the GSBSE ranges from psychology and psychometric studies in humans, to neuropharmacology and toxicology, to molecular genetics of neurodevelopment and neurodegenerative disease in model organisms. Learn more >

Biomedical Engineering

Biomedical Engineering may be defined as the application of engineering principles to promote and enhance the health and well-being of humans. Applications span the gamut of clinical, therapeutic and diagnostic arenas. Research strengths of the GSBSE include; artificial muscle, biomedical microdevices and microsystems, Lab-on-Chip, Biosensors, nanodevices and instruments, cell mechanics, robotic surgery, single molecule imaging, spectroscopy and microscopy of biological materials, and porous implants for tissue ingrowth. Learn more >

Toxicology

Toxicology is an applied discipline that incorporates and builds on a host of scientific disciplines to investigate the consequences of exposure to chemical agents on living organisms and the environment, and the cellular and molecular mechanisms that underlie those consequences. Research strengths of the GSBSE include; comparative marine toxicology, chemical carcinogenesis, immunotoxicology, toxicogenomics, neurotoxicology, and outer space toxicology. Learn more >

Bioinformatics and Computational Biology

Research in bioinformatics and computational biology is an interdisciplinary area of study that brings together biologists, computer and information scientists, mathematicians, engineers, biophysicists, and chemists to examine fundamental biological processes through data intensive analysis and computational modeling.
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Mingyang Lu

Mingyang Lu

Contact Information

Phone:
207-288-6350

Email/web:
Mingyang.Lu@jax.org
View Website
Download CV

Address:
600 Main St B55-2517
Bar Harbor, ME  04609

Education

Ph.D. Baylor College of Medicine 2010

Biosketch

Lu received a B.S. degree in physics from Fudan University, followed by his Ph.D. degree in Biochemistry and Molecular Biology from Baylor College of Medicine in the laboratory of Dr. Jianpeng Ma.  During that time, he conducted research on computational methodology development for coarse-grained modeling of bimolecular structures and their applications to x-ray crystallographic refinement of flexible supramolecular complexes.  In 2012, he joined the Center for Theoretical Biological Physics (CTBP) at Rice University as a postdoctoral fellow with Dr. Jose Onuchic on computational systems biology.  His work includes the design of a new theoretical framework for microRNA-based genetic circuits and its application to the epithelial-mesenchymal transition (EMT) circuit, the construction of effective landscapes for multistable genetic switches in the presence of gene expression noises, the modeling of exosome-mediated cancer-immunity interplay, and the development of a network modeling method that captures the robustness, cell-to-cell variability and heterogeneity in gene expression dynamics.  He received CPRIT postdoctoral fellowship in 2014-2015.  In 2016, he joined The Jackson Laboratory - Mammalian Genetics as an Assistant Professor. He is currently a member of the American Physical Society (APS), the Biophysical Society (BPS) and the American Association for Cancer Research (AACR). 

Research Interests

In the Lu lab at The Jackson Laboratory, we are passionate about the development and application of computational modeling methods to study the operating mechanisms of cancer genetic networks. Specifically, we use systems biology approaches to integrate computational modeling and data analysis to elucidate the relationship among robustness of network dynamics, stochasticity in gene expression and heterogeneity in cancer evolution. We are interested in the fundamental question of how cancer evolves through genetic and epigenetic alterations, especially how tumorigenesis is shaped by the architecture of gene regulatory networks. We aim to extend the scope of existing modeling scheme to large systems, and to take advantage of current available big data in the cancer biology community. Our studies will contribute to a systems-level understanding of cancer and will eventually lead to the design of personalized therapies for cancer patients.

Selected Publications

  • Y. Suzuki*, M.Lu*, E. Ben-Jacob, and J. Onuchic. Periodic, quasi-periodic and chaotic dynamics in simple gene elements with time delays. (2016) Sci. Rep. 6: 21037 (*equal contribution) Read Abstract
  • Darash-Yahana M*, Pozniak Y*, Lu M*, Sohn Y-S, Karmi O, Tamir S, et al. (2016). Breast cancer tumorigenicity is dependent on high expression levels of NAF-1 and the lability of its Fe-S clusters. Proc. Natl. Acad. Sci. U.S.A. 113:10890-5 (*equal contribution) Read Abstract
  • B. Huang, M. Jolly, M. Lu, E. Ben-Jacob, I. Tsarfaty, and J. Onuchic. Modeling the tranition between collective and solitary migration phenotypes in cancer metastasis. (2015) Sci. Rep. 5:17379
  • M. Jolly, M. Boareto, B. Huang, D. Jia, M. Lu, J. Onuchic, H. Levine, and E. Ben-Jacob. (2015) Implications of the hybrid epithelial/mesenchymal phenotype in metastasis. Front. Oncol. 5:155
  • M. Jolly, M. Boareto, M. Lu, J. Onuchic, C. Clementi, and E. Ben-Jacob. (2015) Operating principles of Notch–Delta–Jagged module of cell–cell communication. New J. Phys. 17 (5):055021
  • M. Boareto, M. Jolly, M. Lu, J. Onuchic, C. Clementi, and E. Ben-Jacob. (2015) Jagged-Delta asymmetry in Notch signaling can give rise to a sender/receiver hybrid phenotype. Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1416287112
  • E. Ben-Jacob, M. Lu, D. Schultz, J. Onuchic. (2015) The physics of bacterial decision making. Front. Cell. Infect. Microbiol. 4: 154
  • M. Lu, B. Huang, S. Hanash, J. Onuchic and E. Ben-Jacob. (2014) Modeling putative therapeutic implications of exosome exchange between tumor and immune Cells. Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1416745111
  • M. Lu, M. Jolly, J. Onuchic and E. Ben-Jacob. (2014) Toward decoding the principles of cancer metastasis circuits. Cancer Res. 74(17):4574-4587
  • M. Lu, J. Onuchic and E. Ben-Jacob. (2014) Construction of an Effective Landscape for Multistate Genetic Switches. Phys. Rev. Lett. 113 (7): 078102
  • M. Jolly, B. Huang, M. Lu, S. Mani, H. Levine and E. Ben-Jacob. (2014) Towards elucidating the connection between epithelial-mesenchymal transitions and stemness. J. R. Soc. Interface. 11:20140962
  • B. Huang, M. Lu, M. Jolly, I. Tsarfaty, J. Onuchic and E. Ben-Jacob. (2014) The three-way switch operation of Rac1/RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition. Sci. Rep. 4:6449
  • M. Lu, M. Jolly, H. Levine, J. Onuchic and E. Ben-Jacob. (2013) MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination. Proc. Natl. Acad. Sci. U.S.A. 110:18144-18149
  • M. Lu, M. Jolly, R. Gomoto, B. Huang, J. Onuchic and E. Ben-Jacob. (2013) Tristability in Cancer-Associated MicroRNA-TF Chimera Toggle Switch. J. Phys. Chem. B. 117:13164-13174
  • D. Schultz*, M. Lu*, T. Stavropoulos, J. Onuchic and E. Ben-Jacob. (2013) Turning Oscillations Into Opportunity Spikes: A Lesson from Bacterial Decision Gate. Sci. Rep. 3:1668 (*equal contribution)
  • M. Lu, and J.Ma. (2013) PIM: Phase Integrated Method for Normal Mode Analysis of Biomolecules in Crystalline Environment. J. Mol. Biol. 425: 1082-1098
  • M. Lu, D.Ming and J. Ma. (2012) fSUB: Normal Mode Analysis with Flexible Substructures. J. Phys. Chem. B. 116(29): 8636-45
  • M. Lu and J. Ma. (2011) Normal mode analysis with molecular geometry restraints: Bridging molecular mechanics and elastic models. Arch. Biochem. Biophys. 508 (1): 64-71
  • M. Lu and J. Ma. (2009) A Minimalist Network Model for Studying Biomolecular Vibration. Book Chapter in Proteins: Energy, Heat and Signal Flow. CRC Press: 229 - 245.
  • X. Chen, M. Lu, B. K. Poon, Q. Wang, and J. Ma. (2009) Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement. Acta D 65:339-347.
  • Wang, Q. H., F. Cheng, M. Lu, X. Tian, and J. P. Ma. (2008) Crystal structure of unliganded influenza B virus hemagglutinin. J. Virol. 82:3011-3020.
  • M. Lu and J. Ma. (2008) A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. Proc. Natl. Acad. Sci. U.S.A. 105:15358-15363.
  • M. Lu, A. D. Dousis, and J. Ma. (2008) OPUS-Rota: A fast and accurate method for side-chain modeling. Protein Sci. 17:1576-1585.
  • M. Lu, A. D. Dousis, and J. Ma. (2008) OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing. J. Mol. Biol. 376:288-301.
  • B.K. Poon, X. Chen, M. Lu, N. K. Vyas, F. A. Quiocho, Q. Wang, and J. Ma. (2007) Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution. Proc. Natl. Acad. Sci. U.S.A. 104:7869-7874.
  • Y. Wu*, M. Lu*, M. Chen, J. Li, and J. Ma. (2007) OPUS-Ca: A knowledge-based potential function requiring only C alpha positions. Protein Sci. 16:1449-1463. (*equal contribution)
  • M. Lu, B.K. Poon, and J. Ma. (2006) A new method for coarse-grained elastic normal-mode analysis. J. Chem. Theory and Comput. 2:464-471.
  • Y. Wu, X. Tian, M. Lu, M. Chen, Q. Wang, and J. Ma. (2005) Folding of small helical proteins assisted by small-angle X-ray scattering profiles. Structure 13:1587-1597.
  • M. Lu and J. Ma. (2005) The role of shape in determining molecular motions. Biophys. J. 89:2395-2401.
  • Y. Wu, M. Chen, M. Lu, Q. Wang, and J. Ma. (2005) Determining protein topology from skeletons of secondary structures. J. Mol. Biol. 350:571-586.
  • Eichinger, et.al. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43-57.


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Our Programs

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We offer 3 degree programs in five research focus areas. Learn more


UMaine The Jackson Laboratory Maine Medical Center Research Institute The Mount Desert Island Biological Laboratory University of Southern Maine University of New England
 
For more information about the program, please contact:
Tammy Crosby • 207-581-4654 • gsbse@maine.edu