Full Publications

Selected Publications
  1. A. Katebi, V. Kohar, M. Lu. (2020) Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle. iScience. 23(6): 101150 PDF
  2. D. Ramirez, V. Kohar, M. Lu. (2020) Toward Modeling Context-Specific EMT Regulatory Networks Using Temporal Single Cell RNA-Seq Data. Front Mol Biosci. 7:54 PDF
  3. D. Jia, M. Lu, K.H. Jung, J.H. Park, L. Yu, J. Onuchic, B.A. Kaipparettu, H. Levine. (2019) Elucidating Cancer Metabolic Plasticity by Coupling Gene Regulation with Metabolic Pathways, Proc. Natl. Acad. Sci. U.S.A. 116(9): 3909-18 PDF
  4. D. Jia, J. George, S. Tripathi, D. Kundnani, M. Lu, S. Hanash, J. Onuchic, M.K. Jolly, H. Levine. (2019) Testing the gene expression classification of the EMT spectrum. Phys. Biol.16(2): 025002
  5. V. Kohar and M. Lu. (2018) Role of noise and parametric variation in the dynamics of gene regulatory circuits. NPJ Syst. boil. Appl. 4: 40 PDF
  6. B. Huang, D. Jia, J. Feng, H. Levine, J.N Onuchic, M. Lu. (2018) RACIPE: a computational tool for modeling gene regulatory circuits using randomization. BMC Syst. Biol. 12(1): 74
  7. F. Bocci, Y. Suzuki, M. Lu, J.N. Onuchic. (2018) Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion. Proc. Natl. Acad. Sci. U.S.A. 115(16): 4288-4293
  8. F. Ye, D. Jia, M. Lu, H. H. Levine, M. W. Deem. (2018) Modularity of the metabolic gene network as a prognostic biomarker for hepatocellular carcinoma. Oncotarget. 9(19): 15015-26
  9. D. Jia, M.K. Jolly, S.C. Tripathi, P.D. Hollander, B. Huang, M. Lu, M. Celiktas, E. Ramirez-Peña, E. Ben-Jacob, J.N. Onuchic, S.M. Hanash, S.A. Mani, H. Levine. (2017) Distinguishing mechanisms underlying EMT tristability. Cancer Converg. 1:2
  10. X. Tian, B. Huang, X. Zhang, M. Lu, F. Liu, J. Onuchic, W. Wang. (2017) Modeling the response of a tumor-suppressive network to mitogenic and oncogenic signals. Proc. Natl. Acad. Sci. U.S.A. 114(21):5337-42
  11. B. Huang*, M. Lu*, D. Jia, E. Ben-Jacob, H. Levine, J. Onuchic. (2017) Interrogating the topological robustness of gene regulatory circuits by randomization. PLoS Comput Biol.13(3):e1005456 (*equal contribution) PDF
  12. L. Yu*, M. Lu*#, D. Jia*, J. Ma, E. Ben-Jacob, H. Levine, K.B. Kaipparettu, J. Onuchic (2017). Modeling the Genetic Regulation of Cancer Metabolism: Interplay Between Glycolysis and Oxidative Phosphorylation. Cancer Res. 77(7): 1564 (*equal contribution, #co-corresponding author) PDF
  13. M. Darash-Yahana*, Y. Pozniak*, M. Lu*, Y-S. Sohn, O. Karmi, S. Tamir, 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)
  14. Y. Suzuki*, M. Lu*, E. Ben-Jacob, J. Onuchic. (2016). Periodic, quasi-periodic and chaotic dynamics in simple gene elements with time delays. Sci. Rep. 6:21037(*equal contribution)
  15. B. Huang, M. Jolly, M. Lu, E. Ben-Jacob, I. Tsarfaty, J. Onuchic. (2015). Modeling the tranition between collective and solitary migration phenotypes in cancer metastasis. Sci. Rep. 5:17379
  16. 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
  17. M. Jolly, M. Boareto, M. Lu, J. Onuchic, C. Clementi, and E. Ben-Jacob. (2015). Operating principles of Notch-Delat-Jagged module of cell-cell communication. New J. Phys.17(5):055021
  18. 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
  19. E. Ben-Jacob, M. Lu, D. Schultz, J. Onuchic. (2015). The physics of bacterial decision making. Front. Cell. Infect. Microbiol. 4:154
  20. 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
  21. 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
  22. 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
  23. 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 (*equal contribution)
  24. M. Lu, J. Onuchic and E. Ben-Jacob. (2014). Construction of an Effective Landscape for Multistate Genetic Switches. Phys. Rev. Lett. 113(7):078102 PDF
  25. 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 (*equal contribution) PDF
  26. 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
  27. 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

Early Studies:

  1. 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
  2. M. Lu, D.Ming and J. Ma. (2012). fSUB: Normal Mode Analysis with Flexible Substructures. J. Phys. Chem. B. 116 (29): 8636-45
  3. 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
  4. M. Lu and J. Ma. (2009). A Minimalist Network Model for Studying Biomolecular Vibration. Book Charpter in Proteins: Energy, Heat and Signal Flow. CRC Press: 229 – 245
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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)
  12. 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
  13. 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
  14. M. Lu and J. Ma. (2005). The role of shape in determining molecular motions. Biophys. J.89:2395-2401
  15. 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
  16. Eichinger, et.al. (2005). The genome of the social amoeba Dictyostelium discoideum. Nature 435:43-57