Wei-Ju Wu

Software Engineer

401 Terry Ave N

Degree: MS Computer Science

Areas of Expertise: Software Engineering, Programming Languages, Software Design

Links: https://github.com/baliga-lab

Why I got into Science:

I have always been intrigued by using software techniques to help understand scientific processes, in particularly to fight diseases. I was fortunate enough that my university offered me the opportunity to combine computer science and biochemistry and be part of an Immunology research lab. Later I was lucky to contribute to the software for conducting studies for the development of the first FDA approved blood-based colon cancer product Epi proColon.

Research Highlights:

cmonkey2: The task was to create an improved implementation of the cmonkey algorithm in the programming language Python. Improvements were made in the areas of performance, usability, maintainability and distribution. In order to achieve this we created a modular, flexible and highly configurable architecture based on open web standards and best practices. cmonkey2 is easy to install through pypi.python.org.

EGRIN2: My task is to maintain and improve the usability and performance of the EGRIN2 toolset as well as simplifying the way the generated data is stored, represented and visualized.


Lorenzetti, Alan P. R., Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L G de Lomana, et al. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” MSystems 8, no. 2 (April 27, 2023): e0081622. https://doi.org/10.1128/msystems.00816-22. Cite
Arrieta-Ortiz, Mario L., Selva Rupa Christinal Immanuel, Serdar Turkarslan, Wei-Ju Wu, Brintha P. Girinathan, Jay N. Worley, Nicholas DiBenedetto, et al. “Predictive Regulatory and Metabolic Network Models for Systems Analysis of Clostridioides Difficile.” Cell Host & Microbe 29, no. 11 (November 10, 2021): 1709-1723.e5. https://doi.org/10.1016/j.chom.2021.09.008. Cite
Xavier, Joao B., Jonathan M. Monk, Saugat Poudel, Charles J. Norsigian, Anand V. Sastry, Chen Liao, Jose Bento, et al. “Mathematical Models to Study the Biology of Pathogens and the Infectious Diseases They Cause.” IScience 25, no. 4 (April 15, 2022): 104079. https://doi.org/10.1016/j.isci.2022.104079. Cite
Park, James H., Abdullah H. Feroze, Samuel N. Emerson, Anca B. Mihalas, C. Dirk Keene, Patrick J. Cimino, Adrian Lopez Garcia de Lomana, et al. “A Single-Cell Based Precision Medicine Approach Using Glioblastoma Patient-Specific Models.” NPJ Precision Oncology 6, no. 1 (August 8, 2022): 55. https://doi.org/10.1038/s41698-022-00294-4. Cite
Brooks, Aaron N., David J. Reiss, Antoine Allard, Wei-Ju Wu, Diego M. Salvanha, Christopher L. Plaisier, Sriram Chandrasekaran, Min Pan, Amardeep Kaur, and Nitin S. Baliga. “A System-Level Model for the Microbial Regulatory Genome.” Molecular Systems Biology 10 (2014): 740. Cite
Reiss, David J., Christopher L. Plaisier, Wei-Ju Wu, and Nitin S. Baliga. “CMonkey2: Automated, Systematic, Integrated Detection of Co-Regulated Gene Modules for Any Organism.” Nucleic Acids Research 43, no. 13 (July 27, 2015): e87. https://doi.org/10.1093/nar/gkv300. Cite
Hillesland, Kristina L., Sujung Lim, Jason J. Flowers, Serdar Turkarslan, Nicolas Pinel, Grant M. Zane, Nicholas Elliott, et al. “Erosion of Functional Independence Early in the Evolution of a Microbial Mutualism.” Proceedings of the National Academy of Sciences of the United States of America 111, no. 41 (October 14, 2014): 14822–27. https://doi.org/10.1073/pnas.1407986111. Cite
Wall, Matthew A., Serdar Turkarslan, Wei-Ju Wu, Samuel A. Danziger, David J. Reiss, Mike J. Mason, Andrew P. Dervan, et al. “Genetic Program Activity Delineates Risk, Relapse, and Therapy Responsiveness in Multiple Myeloma.” NPJ Precision Oncology 5, no. 1 (June 28, 2021): 60. https://doi.org/10.1038/s41698-021-00185-0. Cite
Wall, Matthew A., Serdar Turkarslan, Wei-Ju Wu, Samuel A. Danziger, David J. Reiss, Mike J. Mason, Andrew P. Dervan, et al. “Genetic Program Activity Delineates Risk, Relapse, and Therapy Responsiveness in Multiple Myeloma.” Preprint. Systems Biology, April 1, 2020. https://doi.org/10.1101/2020.04.01.012351. Cite
Turkarslan, Serdar, Elisabeth J. Wurtmann, Wei-Ju Wu, Ning Jiang, J. Christopher Bare, Karen Foley, David J. Reiss, Pavel Novichkov, and Nitin S. Baliga. “Network Portal: A Database for Storage, Analysis and Visualization of Biological  Networks.” Nucleic Acids Research 42, no. Database issue (January 2014): D184-190. https://doi.org/10.1093/nar/gkt1190. Cite