CV

Education

• B.S. in Biology (Undergraduate Honors Program in Biology), Peking University,July 2018
• M.S. in Computer Science, Rice University, Dec. 2024 (expected)
• Ph.D. in Bioengineering, Advisor: Dr. Oleg Igoshin, Rice University, Dec. 2024 (expected)

Skills

• Programming language
  • Python
  • C/C++
  • JAVA
• Data analysis
  • MATLAB
  • R
• ML framework
  • pyTorch
  • TensorFlow
• Parallel computation
  • OpenMP
  • MPI
  • CUDA
• Hardware Description Language
  • Verilog
• Frontend
  • javascript(React)
  • html

Publications

Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images

Zhang, J.; Comstock, J.A.; Cotter, C.R.; Murphy, P.A.; Nie, W.; Welch, R.D.; Patel, A.B.; Igoshin, O.A. Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images. Microorganisms 2021, 9, 1954.

Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins

Wang L, Zhang J, Wang D, Song C (2022) Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins. PLoS Comput Biol 18(3): e1009972.

Cell behaviors underlying Myxococcus xanthus aggregate dispersal

Murphy, P., Comstock, J., Khan, T., Zhang, J., Welch, R. D., & Igoshin, O. A. (2023). Cell behaviors underlying Myxococcus xanthus aggregate coarsening. bioRxiv, 2023-05.

Talks

Using Deep Learning to Quantify Bacterial Self-organization Patterns

November 10, 2020

Trainee Talk at 2nd Annual Translational Imaging Conference AI and Machine Learning in Imaging, Houston, TX

Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images

October 27, 2021

Workshop Technical Presentation at 2021 Ken Kennedy AI and Data Science Conference, Houston, TX

Quantification of Myxococcus xanthus Aggregation and Rippling Behaviors: Deep-Learning Transformation of Phase-Contrast into Fluorescence Microscopy Images

October 27, 2021

Contributed talk at The 46.5th Annual International Meeting on the Biology of the Myxobacteria, online

Quantification of Myxococcus xanthus Aggregation Behaviors with Deep Learning Approaches

May 31, 2022

Presentation at Session II: Collective phenomena, 2022 Annual Meeting of the International Physics of Living Systems (iPOLS) network, Montpellier, France

Quantification of Myxococcus xanthus Aggregation Behaviors with Deep Learning Approaches

November 18, 2022

Presentation at Computational system biology meeting, Center for Theoretical Biological Physics, online

Quantification of Myxococcus xanthus Aggregation Behaviors with Deep Learning Approaches

January 31, 2023

Presentation at Center for Theoretical Biological Physics (CTBP) Student/Postdoc Workshop, online

Quantification of Myxococcus xanthus Aggregation Behaviors with Deep Learning Approaches

June 16, 2023

Presentation at The 48th International Conference on the Biology of Myxobacteria, Princeton, NJ

Teaching

Computational Biology

Biostatistics

Service and leadership

• Deputy Secretary-General, Houston Beida Alumni Association， Sep 2021 - Present
• Vice President, Rice Chinese Students and Scholars Association， May 2019 – May 2020
• Assistant Secretary General, Peking University New Youth Network Culture Studio， Sep 2016 – Jul 2017
• Director, Publicity Department, Student Union, School of Life Sciences， Sep 2014 – Jul 2016
• Volunteer, Summer Social Practice in Taiwan， Aug 2015