Publications

Recent Publications

1. B. Clauss, and M. Lu. (2023) A Quantitative Evaluation of Topological Motifs and Their Coupling in Gene Circuit State Distributions. iScience. 26(2): 106029
2. C. Caranica, and M. Lu. (2023) A Data-Driven Optimization Method for Coarse-Graining Gene Regulatory Networks. iScience. 26(2): 105927
3. D.B. Uthaya Kumar, E. Motakis E, M. Yurieva, V. Kohar, J. Martinek, T.C. Wu, J. Khoury, J. Grassmann, M. Lu, K. Palucka, N. Kaminski, J.L. Koff, A. Williams. (2022) Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro. Am J Physiol Lung Cell Mol Physiol. 322(6): L822-L841
4. K. Su, A. Katebi, V. Kohar, B. Clauss, D. Gordin, Z.S. Qin, R.K.M. Karuturi, S. Li, M. Lu. (2022) NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity. Genome Biology. 23, 270 
5. L. Huang, B. Clauss, M. Lu. (2022) What Makes a Functional Gene Regulatory Network? A Circuit Motif Analysis. J. Phys. Chem. B. 126, 10374–10383
6. A. Katebi, D. Ramirez, M. Lu. (2021) Computational systems-biology approaches for modeling gene networks driving epithelial–mesenchymal transitions. Comput. Syst. Oncol. 1(2):e1021
7. V. Kohar, D. Gordin, A. Ketabi, M. Lu. (2021) Gene Circuit Explorer (GeneEx): an interactive web-app and database for visualizing, simulating and analyzing gene regulatory circuits. Bioinformatics. 37(9):1327-29
8. B. Huang, M. Lu, M. Galbraith, H. Levine, J. Onuchic, D. Jia. (2020) Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation. J. R. Soc. Interface. 17(169):20200500
9. A. Katebi, V. Kohar, M. Lu. (2020) Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle. iScience. 23(6): 101150
10. 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
11. 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

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News Articles

Inaugural AJC Merit Research Scholars – Northeastern University College of Engineering 

Understanding microRNA Roles in Stochastic Multistable Networks – Northeastern University College of Engineering 

Assuring that Self-Driving Cars are Accessible to Those with Disabilities – Northeastern University College of Engineering

COE Faculty Awarded Seed Funding in Collaboration with University of Maine – Northeastern University College of Engineering