research

2026

1. ISMB

   Probabilistic RNA Designability via Interpretable Ensemble Approximation and Dynamic Decomposition

   Tianshuo Zhou, David H. Mathews, and Liang Huang

   Bioinformatics (Proceedings of ISMB 2026), 2026

   arXiv PDF Code
2. JCB

   Theory, Algorithms, and Applications for Identification of Undesignable RNA Secondary Structures and Motifs

   Tianshuo Zhou, Wei Yu Tang, Apoorv Malik, David H. Mathews, and Liang Huang

   Journal of Computational Biology, 2026

   DOI
3. Nat. Commun.

   SamplingDesign: RNA Design via Continuous Optimization with Coupled Variables and Monte-Carlo Sampling

   Wei Yu Tang, Ning Dai, Tianshuo Zhou, David H. Mathews, and Liang Huang

   Nature Communications, 2026

   arXiv Code
4. JMB

   Motif Server: Web Server for Undesignable RNA Motifs and Structures

   Apoorv Malik, Tianshuo Zhou, Wei Yu Tang, David H. Mathews, and Liang Huang

   Journal of Molecular Biology, 2026

   Website

2025

1. RECOMB

   Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance

   Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, and Liang Huang

   In Proceedings of RECOMB 2025, 2025

   arXiv Code Website
2. ISMB

   Messenger RNA Design for Ensemble Free Energy via Probabilistic Lattice Parsing

   Ning Dai, Tianshuo Zhou, Wei Yu Tang, David H. Mathews, and Liang Huang

   Bioinformatics (Proceedings of ISMB 2025), 2025

   PDF Code

2024

1. RECOMB

   Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition

   Tianshuo Zhou, Wei Yu Tang, David H. Mathews, and Liang Huang

   In Proceedings of RECOMB 2024, 2024

   arXiv Code

2023

1. ISMB

   RNA Design via Structure-Aware Multi-Frontier Ensemble Optimization

   Tianshuo Zhou, Ning Dai, Sizhen Li, Max Ward, David H. Mathews, and Liang Huang

   Bioinformatics (Proceedings of ISMB 2023), 2023

   PDF Code

2020

1. WSDM

   GREASE: A Generative Model for Relevance Search over Knowledge Graphs

   Tianshuo Zhou, Ziyang Li, Gong Cheng, Jun Wang, and Yu’Ang Wei

   In Proceedings of WSDM 2020, 2020

   DOI arXiv Code

2019

1. WSDM

   Relevance Search over Schema-Rich Knowledge Graphs

   Yu Gu, Tianshuo Zhou, Gong Cheng, Ziyang Li, Jeff Z. Pan, and Yuzhong Qu

   In Proceedings of WSDM 2019, 2019

   DOI Code

1. Preprint

   Title withheld during anonymous review (a paper on using LLMs to generate biological sequences)

   …, Tianshuo Zhou, and others

   Under review at ICLR 2027
2. Preprint

   Fast and Versatile RNA Design via Motif-level Divide-and-Conquer and Structure-level Rival Search

   Tianshuo Zhou, David H. Mathews, and Liang Huang

   arXiv
3. Preprint

   Sampling-based Continuous Optimization for Messenger RNA Design

   Feipeng Yue, Ning Dai, Wei Yu Tang, Tianshuo Zhou, David H. Mathews, and Liang Huang

   arXiv
4. Preprint

   Geometry-Aware Losses for Structure-Preserving Text-to-Sign Language Generation

   Zetian Wu, Tianshuo Zhou, Stefan Lee, and Liang Huang

   arXiv