Publications

Please refer to the full list of publications in our Google Scholar profile.

Selected Publications († shared authorship, * corresponding author)

Preprints:

6. Irene Silvernail, Yang Zhang, Xun Chen* and Xingcheng Lin*, “Charge Imbalance Drives Salt-Optimized Nucleosome Phase Separation under Physiological Conditions”, bioRxiv, DOI: 10.64898/2026.07.08.737367, (2026, July 13)

5. Yafan Zhang, Arun Kumar Ganesan and Xingcheng Lin*, “R-loop Prediction Reveals Generalization Limits of DNA Foundation Models Beyond Regulatory Genomics”, bioRxiv, DOI: 10.64898/2026.06.01.729367, (2026, June 04)

4. Thomas Thornton and Xingcheng Lin*, “Efficient RNA Folding Simulation via a Structure-Based Single-Site-Per-Nucleotide Model”, bioRxiv, DOI: 10.64898/2025.12.13.694107, (2025)

3. Yafan Zhang, Rina Li, Junhao Zhong, Xingcheng Lin*, “mIDEA: An Interpretable Structure–Sequence Model for Methylation-Dependent Protein–DNA Binding Sensitivity”, bioRxiv, DOI: 10.1101/2025.11.14.688575, (2025)

2. Eduardo Cisneros, Yafan Zhang, Xingcheng Lin*, “IRIS Integrates Sparse Sequence, Experimental, and AI-Predicted Structures for Protein-RNA Affinity Prediction and Motif Discovery”, bioRxiv, DOI: 10.1101/2025.09.10.675247, (2025)

1. Jiajia Guo, Xuyan Chen, Premashis Manna, Xingcheng Lin, Madelyn N. Scott, Wei Jia Chen, Mikaila Hoffman, Bin Zhang, Gabriela S. Schlau-Cohen* (2023, March 16). Single-molecule acceptor rise time (smART) FRET for nanoscale distance sensitivity. DOI: 10.1101/2023.03.15.532809

Peer-reviewed Publications:

10. Pingzhi Li, Hongxuan Li, Zirui Liu*, Xingcheng Lin*, Tianlong Chen*, (2026). “FlashSchNet: Fast and Accurate Coarse-Grained Neural Network Molecular Dynamics”, ICML 2026

9. Zahra S Ghoreyshi, Noah Tubo, Luca Zammataro, Xizeng Mao, Ho Ngai, Duncheng Wang, Yibin Chen, Qiuming He, Eduardo Cisneros, Shoudan Liang, Priya J Koppikar, Xingcheng Lin*, Jeffrey J Molldrem*, Jason T George*, “Biophysical modeling for accurate T cell specificity prediction of viral and tumor antigens”, Nat. Commun., DOI: 10.1038/s41467-026-74236-0, (2026)

8. Shwetha Srinivasan, Xingcheng Lin, Xuyan Chen, Raju Regmi, Wei He, Kermit L. Carraway, III, Matthew A. Coleman, Bin Zhang, Gabriela S. Schlau-Cohen*, “Active regulation of the epidermal growth factor receptor by the membrane bilayer”, eLife, DOI: 10.7554/eLife.108789.3, (2026)

7. Yunrui Qiu, Shuming Liu, Xingcheng Lin, Ilona Christy Unarta, Xuhui Huang*, Bin Zhang* “Nucleosome condensate and linker DNA alter chromatin folding pathways and rates”, Biophys. J., DOI: 10.1016/j.bpj.2025.11.2686, (2025)

6. Yafan Zhang, Irene Silvernail, Zhuyang Lin, Xingcheng Lin* “Interpretable Protein-DNA Interactions Captured by Structure-Sequence Optimization”, eLife, DOI: 10.7554/eLife.105565.3, (2025)

5. Qin Zhou, Jose Alberto de la Paz, Alexander D. Stanowick, Xingcheng Lin, Faruck Morcos, “Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing”, Nucleic Acids Res., DOI: 10.1093/nar/gkaf592, (2025)

4. Rina Li and Xingcheng Lin* “Connected Chromatin Amplifies Acetylation-modulated Nucleosome Interactions”, Biochemistry, DOI: 10.1021/acs.biochem.4c00647, (2025)

3. Ailun Wang, Xingcheng Lin*, Kevin Ng Chau, José N. Onuchic, Herbert Levine, and Jason T George* “RACER-m Leverages Structural Features for Sparse T Cell Specificity Prediction”, Sci Adv. May 17 Vol 10, Issue 20; (2024)

2. Mayu Shibata, Xingcheng Lin, José N. Onuchic, Kei Yura, and Ryan R. Cheng* “Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies”, Biophys. J., DOI: 10.1016/j.bpj.2024.01.028, (2024)

1. Xingcheng Lin and Bin Zhang*, “Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization”, eLife, 13:RP90073, Jan 30 (2024)

Prior to NCSU

• Shuming Liu^†, Xingcheng Lin^†, Bin Zhang*, “Chromatin fiber breaks into clutches under tension and crowding”, Nucleic Acids Res., 50, 17, pp 9738-9747, (2022)
• Shwetha Srinivasan^†, Raju Regmi^†, Xingcheng Lin, Steven D. Quinn, Wei He, Kermit L. Carraway, III, Matthew A. Coleman, Bin Zhang*, Gabriela S. Schlau-Cohen*, “Ligand-induced transmembrane conformational coupling in monomeric EGFR”, Nature Communications, 13:3709, (2022)
• Xingcheng Lin^†, Yifeng Qi^†, Andrew Latham, Bin Zhang*, “Multiscale Modeling of Genome Organization with Maximum Entropy Optimization” J. Chem. Phys., 155, 010901, (2021)
• Xingcheng Lin, Rachel Leicher, Shixin Liu, Bin Zhang*, “Cooperative DNA Looping by PRC2 Complexes via Allosteric Communication”, Nucleic Acids Res., 49, 11, pp 6238-6248, (2021)
• Xinqiang Ding^†, Xingcheng Lin^†, Bin Zhang*, “Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface”, Nature Communications, 12:1091, (2021)
• Xingcheng Lin^†, Jason T. George^†, Nicholas P. Schafer, Kevin Ng Chau, Cecilia Clementi, Jose N. Onuchic*, Herbert Levine*, “Rapid Assessment of T-Cell Receptor Specificity of the Immune Repertoire”, Nature Computational Science, 1, 362-373, (2021)
• Rachel Leicher, Eva J. Ge^†, Xingcheng Lin^†, Matthew J. Reynolds^†, Thomas Walz, Bin Zhang*, Tom W. Muir, Shixin Liu*, “Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin”, Proc. Natl. Acad. Sci. USA, 117, pp 30465-30475, (2020)
• Xingcheng Lin, Nicholas P. Schafer, Wei Lu, Shikai Jin, Xun Chen, Mingchen Chen, Jose N. Onuchic and Peter G. Wolynes*, “Forging tools for refining predicted protein structures”, Proc. Natl. Acad. Sci. USA, 116, pp 9400-9409, (2019)
• Mingchen Chen^†, Xingcheng Lin^†, Wei Lu^†, Nick P. Schafer, Jose N. Onuchic and Peter G. Wolynes*, “Template-Guided Structure Prediction and Refinement Using an Optimized Folding Landscape Forcefield” J. Chem. Theory Comput., 14, 11, pp 6102-6116, (2018)
• Xingcheng Lin, Jeffrey K. Noel, Qinghua Wang, Jianpeng Ma and Jose N. Onuchic*, “Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill”, Proc. Natl. Acad. Sci. USA, 115, pp E7905-E7913, (2018)
• Xingcheng Lin, Susmita Roy, Mohit K. Jolly, Federico Bocci, Nick P. Schafer, Min-Yeh Tsai, Yihong Chen, Yanan He, Alexander Grishaev, Keith Weninger, John Orban, Prakash Kulkarni, Govindan Rangarajan, Herbert Levine and Jose N. Onuchic*, “PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer”, J. Mol. Biol., 430, pp 2422-2438, (2018)
• Mingchen Chen^†, Xingcheng Lin^†, Wei Lu, Jose N. Onuchic and Peter G. Wolynes*, “Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins”, J. Phys. Chem. B, 121, pp 3473-3482, (2016)
• Xingcheng Lin^†, Jeffrey K. Noel^†, Qinghua Wang, Jianpeng Ma and Jose N. Onuchic*, “Lowered pH Leads to Fusion Peptide Release and a Highly-dynamic Intermediate of Influenza hemagglutinin”, J. Phys. Chem. B, 120, pp 9654-9660, (2016)
• Mingchen Chen, Xingcheng Lin, Weihua Zheng, Jose N. Onuchic and Peter G. Wolynes*, “Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model (AAWSEM)”, J. Phys. Chem. B, 120, pp 8557-8565, (2016)
• Xingcheng Lin^†, Nathan R. Eddy^†, Jeffrey K. Noel, Qinghua Wang, Jianpeng Ma and Jose N. Onuchic*, “Order and Disorder Control the Functional Rearrangement of Influenza Hemagglutinin”, Proc. Natl. Acad. Sci. USA, 111, pp 12049-12054, (2014)