• Honglue Shi
  • Ph.D., Chemistry Department, Duke University
  • Education

  • Department of Chemistry, Duke University, Durham, NC, USA
  • 2015-2021 Ph.D. in Chemistry
  • Department of Computer Science, Duke University, Durham, NC, USA
  • 2017-2021 M.S. in Computer Science
  • College of Chemistry and Molecular Engineering, Peking University, Beijing, China
  • 2011-2015 B.S. in Chemistry

    Research Experience

  • Graduate: Department of Chemistry, Duke University
  • 2015 – 2021, Preliminary Exam: May, 2017 (Mentor: Hashim Al-Hashimi, Ph.D.)
  • Undergraduate: College of Chemistry and Molecular Engineering, Peking University
  • 2013 – 2015, Thesis Defense: June, 2015 (Mentor: Luhua Lai, Ph.D.)



  • 2021 Student Travel Award, 65th Biophysical Society Annual Meeting
  • 2020 The Best Trainee Talk, 2020 Virtual Retreat of The Center for HIV-1 RNA Studies
  • 2019 Student Travel Stipend, 60th Experimental Nuclear Magnetic Resonance Conference
  • 2016 Outstanding Poster Award, 2016 Duke Chemistry Graduate Research Symposium
  • 2014 Wusi Scholastic Achievement Award, Peking University
  • 2012 University Service Award, Peking University
  • Selected


    Shi H.#, Kimsey I.J., Liu H.-F., Pham U., Schumacher M.A.*, Al-Hashimi H.M.* (2021) “Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA” bioRxiv
    Rangadurai A.#, Shi H.#, Xu Y.#, Liu B., Abou Assi H., Zhou H., Kimsey I.J., Al-Hashimi H.M.* (2021) “delta-Melt: Nucleic acid conformational penalties from melting experiments” bioRxiv
  • Shi H., Rangadurai A., Abou Assi H., Roy R., Case D.A.*, Yesselman J.D.*, Herschlag D.*, Al-Hashimi H.M.* (2020) “Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction” Nature Communications 11: 5531
  • Afek A., Shi H., Rangadurai A., Sahay H., Senitzki A., Xhani S., Fang M., Salinas R., Mielko Z., Pufall M.A., Poon G.M.K., Haran T.E., Schumacher M.A., Al-Hashimi H.M.*, Gordan R.* (2020) “DNA mismatches reveal conformational penalties in protein-DNA recognition” Nature 587(7833): 291-296 | This paper was featured in Nature News and Views
  • Shi H.#, Liu B.#, Nussbaumer F., Rangadurai A., Kreutz C.*, Al-Hashimi H.M.* (2019) “NMR chemical exchange measurements reveal that N6-methyladenosine slows RNA annealing” Journal of American Chemical Society 141(51): 19988-19993 | This paper was selected as JACS Spotlights
  • Summary

    of Skills

  • Programming Language: Python, Java, MATLAB
  • Data mining: SQL, MongoDB, Numpy, Pandas
  • Web Server: Amazon Web Services
  • Biochemistry: Synthesis and purification of nucleic acids for biophysical experiments
  • Experimental Biophysics: NMR spectroscopy (development of experiments, data collection and processing), Optical melting experiments, Protein binding microarray
  • Computational Methods: MD simulations (AMBER, GROMACS), Quantum mechanics calculations (GAUSSIAN, DeMon2k, AFNMR), 3D structure prediction (Rosetta), 3D structure visualization (VMD, PyMOL, Chimera), 3D structure refinement on X-ray crystallography (Phenix, COOT), 3D structure and ensemble modeling on NMR data (In-house Python script of Monte-Carlo sampling)
  • Service


  • Journal reviewer: BioEssay
  • President, Cycling Association of Peking University
  • Teaching


  • 2018 – 2021, Student Mentor for multiple graduate students, undergraduates, Duke University
  • 2015 – 2016, Teaching Assistant for General Chemistry Lab (CHEM 101), Duke University