Basic
Information
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Honglue Shi
Ph.D., Chemistry Department, Duke University
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Education |
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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
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Research Experience |
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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.)
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Awards/
Honors
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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
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Selected
Publications
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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
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Summary
of Skills
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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)
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Service
Experience
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Journal reviewer: BioEssay
President, Cycling Association of Peking University
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Teaching
Experience
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2018 – 2021, Student Mentor for multiple graduate students, undergraduates, Duke University
2015 – 2016, Teaching Assistant for General Chemistry Lab (CHEM 101), Duke University
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