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Robin Pearce
Ph.D. Student, Department of Computational Medicine and Bioinformatics
Google Scholar Profile

Contact
    RM 2035B, Palmer Commons
    100 Washtenaw Ave
    Ann Arbor, MI 48109-2218
    robpearc@umich.edu
Education
  • 2019-Present, Ph.D. in Bioinformatics, University of Michigan, Ann Arbor, MI
  • 2017-2018, M.S. in Biological Chemistry, University of Michigan, Ann Arbor, MI
  • 2017-2018, M.S.E. in Biomedical Engineering, University of Michigan, Ann Arbor, MI
  • 2014-2017, B.S.E. in Biomedical Engineering, University of Michigan, Ann Arbor, MI
Research Interests
  • Algorithm development for protein design and structure prediction
  • Development of protein-based therapeutics using computational protein design
Publications
  • Pearce, R. and Zhang, Y. (2021) Deep learning techniques have significantly impacted protein structure prediction and protein design. Curr. Opin. Struct. Biol., 68: 194-207.
  • Zhang, B., Zhang, W., Pearce, R., Zhang, Y., and Shen HB. (2021) Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations. J. Phys. Chem. B, 125: 528-538.
  • Ong, E., Huang, X., Pearce, R., Zhang, Y., He, Y. (2021) Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering. Comput. Struct. Biotechnol. J., 19: 518-529.
  • Huang, X., Zhang, C., Pearce, R., Omenn, GS., and Zhang, Y. (2020) Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2. . Proteome Res., 19: 4844-4856.
  • Huang, X., Pearce, R., Zhang, Y. (2020) Computational Design of Peptides to Block Binding of the SARS-CoV-2 Spike Protein to Human ACE2. Aging, 12: 11263-11276.
  • Zhang, B., Zhang, X., Pearce, R., Shen, HB., Zhang, Y. (2020) A new protocol for atomic-level protein structure modeling and refinment using low-to-medium resolution cryo-EM density maps. Journal of Molecular Biology, 432: 5365-5377.
  • Huang, X., Pearce, R., Zhang, Y. (2020) FASPR: an open-source tool for fast and accurate protein side-chain packing. Bioinformatics, 36: 3758–3765.
  • Liu, X., Liu, J., Zhang, W., Pearce, R., Chen, M., Zhang, T., Liu, B. (2020) Effect of the Degree of Glycation on the Stability and Aggregation of Bovine Serum Albumin. Food Hydrocolloids, 106: 105892.
  • Zheng, W., Zhou, X., Wuyun, Q., Pearce, R., Li, Y., Zhang, Y. (2020) FUpred: Detecting protein domains through deep-learning based contact map prediction. Bioinformatics, 36: 3749–3757.
  • Liu, X., Zhang, W., Liu, J., Pearce, R., Zhang, Y., Zhang, K., Ruan, Q., Yu, Y., Liu, B. (2020) Mg2+ inhibits heat-induced aggregation of BSA: the mechanism and its binding site. Food Hydrocolloids, 101, 105450.
  • Huang, X., Pearce, R., Zhang, Y. (2020) EvoEF2: Accurate and fast energy function for computational protein design. Bioinformatics, 36(4), 1135-1142.
  • Huang, X., Zheng, W., Pearce, R., Zhang, Y. (2019) SSIPe: Accurately estimating protein-protein binding affinity change upon SNP mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinformatics, 36: 2429-2437.
  • Huang, X., Pearce, R., Zhang, Y. (2019) Toward the accuracy and speed of protein side-chain packing: a systematic study on rotamer libraries. Journal of Chemical Informatics and Modeling, 60(1), 410-420.
  • Zheng, W., Wuyun, Q., Li, Y., Mortuza, SM., Zhang, C., Pearce, R., Ruan, J., Zhang, Y. (2019) Detecting distant-homology protein structures by aligning deep neural-network based contact maps. PLOS Computational Biology, 15(10): e1007411.
  • Oraiqat, I., DeBruin, S., Pearce, R., Como, C., Mikell, J., Taylor, C., Way, J., Suarez, M., Rehemtulla, A., Clarke, R., El Naqa, I. (2019) Silicon Photomultipliers for Deep Tissue Cerenkov Emission Detection During External Beam Radiotherapy. IEEE Photonics Journal 11(4), 1-16.
  • Zheng, W., Li, Y., Zhang, C., Pearce, R., Mortuza, SM., Zhang, Y. (2019) Deep-learning contact-map guided protein structure prediction in CASP13. Proteins: Structure, Function, and Bioinformatics, 82(12), 1149-1164. [Server]
  • Zheng, W., Zhang, C., Wuyun, Q., Pearce, R., Li, Y., Zhang, Y. (2019) LOMETS2: Improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acid Research, 47(W1), W429-W436. [Server]
  • Pearce, R., Huang, X., Setiawana, D., Zhang, Y. (2019) EvoDesign: Designing protein-protein binding interactions using evolutionary interface profiles in conjunction with an optimized physical energy function. Journal of Molecular Biology, 431(13), 2467-2476. [PDF]
Oral Presentations at Conferences
  • Pearce, R., Zheng, W., Zhang, C., Li, Y., Mortuza, SM., Zhang, Y. (2018) Zhang Groups: Automated Structure Prediction by C-I-TASSER and C-QUARK in CASP13. 13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. Quintana Roo, Mexico.
Conference Abstracts and Papers
  • Zhang, C., Li, Y., Zheng, W., Bell, E., Huang, X., Pearce, R., Zhou, X., and Zhang, Y. (2020) Protein 3D Structure Prediction by D-QUARK in CASP14. 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. [Abstract]
  • Li, Y., Zheng, W., Zhang, C., Bell, E., Huang, X., Pearce, R., Zhou, X., and Zhang, Y. (2020) Protein 3D Structure Prediction by Zhang Human Group in CASP14. 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. [Abstract]
  • Li, Y., Zheng, W., Zhang, C., Bell, E., Huang, X., Pearce, R., Zhou, X., and Zhang, Y. (2020) Protein 3D Structure Prediction by D-I-TASSER in CASP14. 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. [Abstract]
  • Zhang, C., Pearce, R., Zhang, Y. (2019) C-QUARK: contact-assisted de novo protein structure prediction on XSEDE Comet. International Conference on Supercomputing (ICS). Phoenix, AZ. [Abstract]
  • Oraiqat, I., Taylor, C., Como, C., Way, J., Pearce, R., Debruin, S., Clarke, R., El Naqa, I. (2017) A New Approach for Cherenkov Emission Detection Using Silicon Photomultipliers. Proceedings of the 59th Annual Meeting of the American Association of Physicists in Medicine. Denver, CO.
  • Emery, N., Renberg, A., Castillo, C., Nishi, A., Haad, A., Girgis, A., Bernstein, Z., Lewin, D., Kaczmarek, C., Pearce, R., Vobbilisetty, V., Kopyeva, I., Sun, R. (2017) iGEM Report: Kinetic Modeling of a Novel Protein Detection System Using Proximity-Dependent Ligation and Nucleic Acid Sequence-Based Amplification. iGEM PLOS Collections. Boston, MA.
  • Subramanian, C., Pearce, R., Clague, M., Timmermann, B., Cohen, M. (2016) A novel naturally-derived withalonglide synergizes with cisplatin to block self-renewal, migration, and EMT transition to enhance apoptosis via targeting of translational initiation. AACR Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy. San Francisco, CA.
Honors/Awards
  • Valedictorian, Clinton High School, Clinton, MI (2014)
  • Regents Merit Scholarship, University of Michigan (2014)
  • Engineering Scholarship of Honor, University of Michigan (2014-2017)
  • James B. Angell Scholar, University of Michigan (2017)
  • Graduated Summa Cum Laude, Department of Biomedical Engineering, University of Michigan (2017)
  • Rackham Travel Grant, University of Michigan (2018)
  • Advanced Proteome Informatics of Cancer Training Program NCI Pre-doctoral Fellowship, University of Michigan (2019-2021)

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