Yang Shen

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Research Interests

    Our research theme is artificial intelligence (AI) for modeling biological intelligence (BI). Specifically, we develop optimization and machine learning, especially multimodal learning and generation across texts, images, graphs, and geometries, for structural bioinformatics, structural systems biology, and biomedical and health informatics. Some applications include

  • Protein or ligand design for binding affinity and specificity desired
  • Structural prediction of protein interactions
  • Systems biology, in particular, systems pharmacology
  • Synthetic biology, with applications in energy and therapeutics
  • Bioinformatics and big data
I am actively seeking experimental and computational collaborations.  My main motivation is to unravel molecular mechanisms and to modulate emergent behavior of biomolecular networks with the development and application of computational tools (including molecular modeling, network simulation, optimization, machine learning, graph theory, and systems and control theory).  To that end, I aim at an iterative process that models and experiments can feed each other.

Check out a video about our research.

Group Members

    Current members:

  • Dr. Jiwoong Park (Postdoctoral Research Associate, 2022.10-)
  • Yuanfei Sun (Ph.D., 2018.6-)
  • Wuwei Tan (Ph.D., 2018.6-)
  • Shaowen Zhu (Ph.D. 2019.9-)
  • Yuning You (Ph.D. 2019.9-)
  • Rujie Yin (Ph.D. 2020.9-)
  • Shuying Zhu (Ph.D. 2022.6-)
  • Alumni:


  • Dr. Su-Ping Deng (Postdoc 2018-19; Employment as of 2022: Data Scientist at the Hanover Insurance Group)
  • Dr. Tomasz Oliwa (Postdoc 2013-14; First Employer: Univ. Chicago)
  • Ph.D.

  • Yue Cao (Ph.D., Dec. 2021) Thesis: Optimization, Learning and Generation for Proteins: Docking Structures and Mapping Sequence-Function Relationships
    Internships: Facebook (2021), IBM Research (2020)
    Next: Research Scientist at Meta (formerly known as Facebook), Seattle, WA
  • Mostafa Karimi (Ph.D., Dec. 2020) Thesis: Circumventing Drug Resistance: Exact Combinatorial Optimization and Deep Generative Models
    Internships: Ancestry.com (2019) and Anadarko Petroleum (2018)
    Next: Data and Applied Scientist at Microsoft, Redmond, WA
  • M.S.

  • Yuhang Xie (M.S., May 2022)
  • Next: Ph.D. Program in Geography at TAMU
  • Yuting Gao (M.S., May 2022)
  • Next: Software Engineer at Fujitsu, Dallas, TX
  • Hao Yu Miao (Graduate Research Assistant 2021.10-2021.12 and Post-MS Researcher 2022.1-2022.3)
  • Next: Software Engineer at Meta
  • Rahul Sridhar (Graduate Research Assistant 2021.1-2021.6)
  • Next: Machine Learning Engineer at ByteDance
  • Fangtong Zhou (M.S., May 2020) Thesis: Identifying Nuclear Receptor Ligands through Sequence-Based Deep Learning
    Next: Ph.D. Program in CS at NCSU
  • Shaowen Zhu (M.S., Aug. 2019) Thesis: De Novo Protein Design of Novel Folds using Guided Conditional Wasserstein Generative Adversarial Networks (gcWGAN)
    Next: Ph.D. Program in EE at TAMU
  • Di Wu (M.S., Dec. 2018) Thesis: Structured Sparsity Learning for Coevolution-Based Protein Contact Prediction
  • Next: Research Associate at TAMU (2019-2020) then Ph.D. Program in CIS at Penn
  • Haoran Chen (M.S., Aug. 2018) Thesis: Improving molecular-level protein docking and interpreting system-level cancer mechanism through machine learning
    Next: Ph.D. Program in Comp Biol at CMU
  • Yi Yan (M.S., May 2018) Thesis: Efficiency prediction and mechanism discovery for the CRISPR-Cas9 system
  • M.E.

  • Tianliang Li (Member 2016-18; M.Eng. 2018)
  • Yuanfei Sun (Grad Summer Intern, 2016; M. Eng. 2017; Next: Ph.D. in Electrical Engineering at TAMU)
  • Kuei-Fu Chen (Grad Summer Intern, 2016; M.Eng. 2017; First Employer: Bloomberg L.P.)
  • Undergraduate

  • Andrew Shang (Undergrad Summer Research Grant (USRG), Summer 2021)
  • Nithin Goriparthi (Undergrad Summer Research Grant (USRG), Summer 2021)
  • Maxwell Huffman (Undergrad Honors Research Scholar 2020.6-2021.5) First Prize for Capstone at the 2021 Engineering Project Showcase
  • Arghamitra Talukder (Undergrad Honors Research Scholar 2020.7-2021.5) Next: Texas Instruments
  • Muhammad Ahmad (ECEN 491 Research Mentee, Fall 2019)
  • S. S. N. Vishnu Siva Sai (Research Exchange Undergrad (REU) from IIT-Hyderabad, Summer 2019)
  • Annie Rizvi (Research Intern, Summer 2018)
  • Oluwaseyi Moronfoye (Research Intern, Spring 2018; Undergrad Summer Research Grant (USRG), Summer 2018; Next: M.S. in Finance at Mays Business School at TAMU)
  • Elsherif Mahmoud (Research Exchange Undergrad (REU) from TAMU-Qatar, Summer 2017; Next: M.S. in Electrical Engineering at Columbia University)
  • Clarissa Tovias (Research Intern, Summer 2016)

Funded Projects

Physics-Constrained Modeling of Molecular Texts, Graphs, and Images for Deciphering Protein-Protein Interactions (NSF CCF-1943008 (2020-25))

Unraveling Molecular and System-level Mechanisms of Human Disease-Associated Protein Mutations (NIH R35GM124952 (2017-22))

Dimension Reduction and Optimization Methods for Flexible Refinement of Protein Docking (NSF CCF-1546278 (2013-17))