Publications

PUBLICATIONS


BOOK CHAPTER

  1. Yoonjoo Choi, Deeptak Verma, Karl E. Griswold and Chris Bailey-Kellogg (2016), EpiSweep: Computationally-driven reengineering of therapeutic proteins to reduce immunogenicity while maintaining function, Methods in Molecular Biology (Springer Protocols), Humana Press (in press)
  2. Sebastian Kelm, Yoonjoo Choi and Charlotte M. Deane (2014), Chapter 11. Protein Modeling and Structural Prediction, Springer Handbook of Bio- and Neuroinformatics, Springer Berlin Heidelberg, 171-182

JOURNAL

  1. Yoonjoo Choi, Christian Ndong, Karl E. Griswold, Chris Bailey-Kellogg (2016), Computationally-Driven Antibody Engineering Enables Simultaneous Humanization and Thermostabilization, PEDS (Accepted)
  2. Yoonjoo Choi*, Casey Hua*, Charles L. Sentman, Margaret E. Ackerman, Chris Bailey-Kellogg (2015), Antibody humanization by structure-based computational protein design, mAbs, 7(6):1045-1057
  3. Kristina Blazanovic, Hongliang Zhao*, Yoonjoo Choi*, Wen Li, Regina S. Salvat, Daniel C. Osipovitch, Jennifer Fields, Leonard Moise, Brent L. Berwin, Steven N. Fiering, Chris Bailey-Kellogg, Karl E. Griswold (2015), Structure-based redesign of lysostaphin yields potent anti-staphylococcal enzymes that evade immune cell surveillance, Molecular Therapy - Methods and Clinical Development, 2: 15021
  4. Regina Salvat*, Yoonjoo Choi*, Alexandra Bishop, Chris Bailey-Kellogg and Karl E. Griswold (2015), Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads, Biotechnology and Bioengineering, 112(7):1306-1318 (featured as a spotlight paper)
  5. Hongliang Zhao, Deeptak Verma, Wen Li, Yoonjoo Choi, Christian Ndong, Steven N. Fiering, Chris Bailey-Kellogg, Karl E. Griswold (2015), Depletion of T cell epitopes in lysostaphin mitigates anti-drug antibody response and enhances antibacterial efficacy in vivo, Chemistry and Biology, 22(5):629-639
  6. Regina Salvat, Andrew Parker, Yoonjoo Choi, Chris Bailey-Kellogg and Karl E. Griswold (2015), Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate, PLoS Computational Biology, 11(1):e1003988
  7. Regina Salvat, Andrew Parker, Andrew Guilliams, Yoonjoo Choi, Chris Bailey-Kellogg and Karl E. Griswold (2014), Computationally Driven Deletion of Broadly Distributed T cell Epitopes in a Biotherapeutic Candidate, Cellular and Molecular Life Sciences, 71(24):4869-4880
  8. Hongliang Zhao, Kristina Blazanovic, Yoonjoo Choi, Chris Bailey-Kellogg and Karl E. Griswold (2014), Gene and protein sequence optimization for high level production of fully active and aglycosylated lysostaphin in Pichia pastoris, Applied and Environmental Microbiology, 80(9):2746-2753
  9. Sebastian Kelm, Anna Vangone, Yoonjoo Choi, Jean-Paul Ebejer, Jiye Shi and Charlotte M. Deane (2013), Fragment-based modelling of membrane protein loops - successes, failures and prospects for the future, Proteins, 82(2):175-186
  10. Yoonjoo Choi, Karl E. Griswold and Chris Bailey-Kellogg (2013), Structure-based redesign of proteins for minimal T cell epitope content, Journal of Computational Chemistry, 34(10):879-891 (featured as a cover page)
  11. Yoonjoo Choi, Sumeet Agarwal and Charlotte M. Deane (2013), How long is a piece of loop?, PeerJ, 1:e1
  12. Andrew S. Parker, Yoonjoo Choi, Karl E. Griswold and Chris Bailey-Kellogg (2013), Structure-Guided Deimmunization of Therapeutic Proteins, Journal of Computational Biology, 20(2):152-165
  13. Yoonjoo Choi and Charlotte M. Deane (2011), Predicting antibody complementarity determining region loops without classification, Molecular Biosystems, 7(12):3327-3334
  14. Yoon-Dong Yu, Yoonjoo Choi, Yik-Ying Teo and Andrew Dalby (2010), Developing stochastic models for spatial inference: bacterial chemotaxis, PLoS One, 5(5):e10464
  15. Yoonjoo Choi and Charlotte M. Deane (2010), FREAD revisited: Accurate loop structure prediction using a database search algorithm, Proteins, 78(6):1431-1440

CONFERENCE PROCEEDING

  1. Jun Ho Huh, Mirko Montanari, Derek Dagit, Rakesh B. Bobba, Dong Wook Kim, Yoonjoo Choi and Roy Campbell (2013), An empirical study on the software integrity of virtual appliances: are you really getting what you paid for?, 8th ACM Symposium on Information, Computer and Communications Security (ASIACCS 2013), 231-242
  2. Jun Ho Huh, Mirko Montanari, Derek Dagit, Rakesh B. Bobba, Dong Wook Kim, Yoonjoo Choi and Roy Campbell (2013), Assessing software integrity of virtual appliances through software whitelists: Is it any good?, Network and Distributed System Security Symposium (NDSS) 2013, Short talk paper
[*: equal contribution]

PRESS RELEASE

  1. VPR: Dartmouth researchers take aim at a deadly infection [link]
  2. WNNE: Dartmouth researchers work to fight MRSA [link]
  3. ACS noteworthy chemistry: Engineer lysostaphin to combat lethal bacteria [link]
  4. C&EN: Deimmunizing a big antibiotic [link]

SOFTWARE

  1. EpiSweep: Structure-guided deimmunisation method (Available upon request)
  2. Rosetta redesign for minimal T-cell epitope content (Available upon request)
  3. FREAD: The protein loop modelling protocol
    • FREAD modelling web-server [link]
    • FREAD binary code (written in C, old version) [link]
  4. MESMAX: a bacterial chemotaxis simulation algorithm (Available upon request)

LICENSE AND PATENT

  1. Humanized TZ47 antibody variant (US Patent filed)
  2. Deimmunized Lysostaphin and Methods of Use (US Patent filed)
  3. PyFREAD: Fragment-based loop structure prediction (Commercialisation in progress)

© Design by Andreas Viklund and modified by Yoonjoo Choi
Last updated 25/May/2016