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Lin Research Group

Publications

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

Selected Publications († shared authorship, * corresponding author)

4. 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”, bioRxiv, 2023.08.06.552190 (2023)

3. 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. https://doi.org/10.1101/2023.03.15.532809

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., 123, 1–12, March 19 (2024)

1. Xingcheng Lin and Bin Zhang*, “Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization”, eLife, 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*, “Intracellular compaction induced by extracellular ligand-binding in epidermal growth factor receptor”, Nature Communications, 13L3709, (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)