Mingyang Lu

About

Mingyang Lu is an Associate Professor in the Department of Bioengineering at Northeastern University. He received his BS degree in Physics from Fudan University in 2003 and earned his PhD in Biochemistry and Molecular Biology with a Biophysics Track from Baylor College of Medicine in 2010. Prior to joining Northeastern, he established his independent research lab as an Assistant Professor at The Jackson Laboratory in 2016. His research interests focus on methodology development in computational systems biology, integrating mathematical modeling and bioinformatics to study gene regulatory networks, single cell genomics, epithelial-mesenchymal transition, coarse-graining, reverse engineering, machine learning, stochasticity, and heterogeneity in gene expression. Dr. Lu's work aims to model cellular state transitions by analyzing genomics data through computational approaches. He has received recognition for his research, including a five-year Maximizing Investigators' Research Award (MIRA) from the National Institute of General Medical Sciences.

Research topics

• Computer Science
• Computational biology
• Biology
• Genetics
• Cell biology
• Algorithm
• Bioinformatics

Selected publications

• NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity

  Genome biology · 2022 · 62 citations

  Senior authorCorresponding

  A major question in systems biology is how to identify the core gene regulatory circuit that governs the decision-making of a biological process. Here, we develop a computational platform, named NetAct, for constructing core transcription factor regulatory networks using both transcriptomics data and literature-based transcription factor-target databases. NetAct robustly infers regulators' activity using target expression, constructs networks based on transcriptional activity, and integrates mat…

  DOI

• A quantitative evaluation of topological motifs and their coupling in gene circuit state distributions

  iScience · 2023-01-23 · 5 citations

  articleOpen accessSenior authorCorresponding

  One of the major challenges in biology is to understand how gene interactions collaborate to determine overall functions of biological systems. Here, we present a new computational framework that enables systematic, high-throughput, and quantitative evaluation of how small transcriptional regulatory circuit motifs, and their coupling, contribute to functions of a dynamical biological system. We illustrate how this approach can be applied to identify four-node gene circuits, circuit motifs, and m…

  PublisherOA PDFDOI

• A computational approach for perturbation-induced EMT transitions

  npj Systems Biology and Applications · 2025-11-13 · 4 citations

  articleOpen access

  The Epithelial-mesenchymal transition (EMT) is a cellular state transition fundamental to development, wound healing, and cancer metastasis. The gene regulatory mechanisms underlying EMT have been extensively documented, revealing gene regulatory networks (GRNs) involving groups of mutually inhibiting transcription factors and microRNAs. Despite significant progress from both experimental and computational approaches, the details of how the EMT GRN initiates EMT in response to various external i…

  PublisherOA PDFDOI

• Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML

  npj Systems Biology and Applications · 2024-04-09 · 4 citations

  articleOpen accessSenior author

  Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of poorly differentiated myeloid cells, with a heterogenous mutational landscape. Mutations in IDH1 and IDH2 are found in 20% of the AML cases. Although much effort has been made to identify genes associated with leukemogenesis, the regulatory mechanism of AML state transition is still not fully understood. To alleviate this issue, here we develop a new computational approach that integrates genomic data from diverse sou…

  PublisherOA PDFDOI

• Comparative Assessment of Two Numerical Methods for Eddy Current Nondestructive Evaluation: Insights from Benchmark Studies

  Progress In Electromagnetics Research M · 2025-01-01

  articleOpen access
  PublisherDOI

Recent grants

• New Computational Systems Biology Methods for Modeling Gene Regulatory Circuits

  NIH · $3.3M · 2018–2029

Frequent coauthors

• Eshel Ben‐Jacob

  122 shared

• José N. Onuchic

  Rice University

  120 shared

• Herbert Levine

  Northeastern University

  81 shared

• Dongya Jia

  63 shared

• Benjamin Clauss

  Tufts University

  53 shared

• Bin Huang

  Guangzhou University

  52 shared

• Sheng Li

  Jackson Laboratory

  47 shared

• Jianpeng Ma

  45 shared

Labs

• Computational Systems Biology LabPI

Education

• Ph.D., Biochemistry and Molecular Biology

  Baylor College of Medicine

  2010

• B.S., Physics

  Fudan University

  2003

Awards & honors

• Maximizing Investigators' Research Award (MIRA) from the Nat…

Similar researchers at Northeastern University

• Raimond Winslowh-72
• Neel Joshih-60