Publication

(*: Co-author; †: Correspondence)

Preprints & Accepted Papers

Soobon Ko, Sung-Hwan You, Yeojin Moon, Junsu Ko, Woong-Hee Shin and Yoonjoo Choi† (2025) Allosteric deimmunisation of a Salmonella phosphatase enhances catalytic function (Submitted)

Adam Voshall*, Jeongjun Chae*, Honglan Li, Junsu Ko, Woongyang Park†, Eunjung Alice Lee† and Yoonjoo Choi† (2025) STRUMP-I: Structure-based machine learning approach to pMHC-I binding prediction using force field energy features (Submitted)

Min Jhon*,  Ju-Wan Kim*, Kiwook Lee, Dawoon Kim, Se-Hyoun Park, Changheon Kim, Bahngtaik Lim, Seon-Young Kim,  Sung-Wan Kim, Jae-Min Kim†, Il-Seon Shin† and Yoonjoo Choi† (2025) Contactless Depression Screening via Facial Video-derived Heart Rate Variability Translational Psychiatry (Under review)

Lee, Boram*, Junseok Park*, Adam Voshall, Eduardo Maury, Yeeok Kang, Yoen Jeong Kim, Jin-Young Leem, Hye-Ran Shim, Hyo-Ju Kim, Jung-Woo Lee, Min-Hyeok Jung, Si-Cho Kim, Hoang Bao Khanh Chu, Da-Won Kim, Minjeong Kim, Eun-Ji Choi, Ok Kyung Hwang, Ho Won Lee, Kyungsoo Ha, Jung Kyoon Choi, Yongjoon Kim, Yoonjoo Choi†, Woong-Yang Park† and Eunjung Alice Lee† (2025) Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAs Nature Communications (Under review)

Soobon Ko, Honglan Li, Hongeun Kim, Woong-Hee Shin, Junsu Ko and Yoonjoo Choi† (2025) Benchmarking Sequence-Based and AlphaFold-Based Methods for pMHC-II Binding Core Prediction: Distinct Strengths and Consensus Approaches BMC Medical Genomics (Accepted) - DTMBIO 2024 Proceedings

Journal Paper

2025

45. Thanh Quang Tran, Taner Duysak, Kwangsoo Kim, Giang Chau Dang, Min-Hee Yi, Yoonjoo Choi, Jae Ho Cho, Jae‑Ho Jeong, and Hyon E. Choy Anti-cancer effect of interleukin-2 fused to flagellin expressed by tumor-targeting Salmonella Oncogene 44(37): 3449-3460.

44. Tien Duc Nguyen, Hoang Duy Le, Giang Chau Dang, Hyun Seok Jung, Yoonjoo Choi, Koemchhoy Khim, Young Kim, Shee Eun Lee† and Joon Haeng Rhee† (2025) A combined adjuvant and ferritin nanocage based mucosal vaccine against Streptococcus pneumoniae induces protective immune responses in a murine model Nature Communications 16: 2871

2024

43. Hyung Keon Park, Yoo Duk Choi, Hyun Jeong Shim, Yoonjoo Choi, Ik Joo Chung and Sook Jung Yun (2024) Comparative Whole-Genome Sequencing Analysis of In-situ and Invasive Acral Lentiginous Melanoma: Markedly Increased Copy Number Gains of: GAB2:: PAK1:: UCP2:, and: CCND1: are Associated with Melanoma Invasion The American Journal of Surgical Pathology 48(9): 1061-1071.

42. Hyeji Kwon*, Soobon Ko*, Kyungsoo Ha, Jungjoon K Lee† and Yoonjoo Choi† (2024) Assessing the Predictive Ability of Computational Epitope Prediction Methods on Fel d 1 Allergen PLoS One 19(8): e0306254

41. Sang Hoon Kim, Bo Ryeong Lee, Sung-Min Kim, Sungsik Kim, Min-seok Kim, Jaehyun Kim, Inkyu Lee, Hee-Soo Kim, Gi-Hoon Nam, In-San Kim, Kyuyoung Song, Yoonjoo Choi†, Dong-Sup Lee† and Woong-Yang Park†  (2024) The identification of effective tumor-suppressing neoantigens using a tumor-reactive TIL TCR-pMHC ternary complex Experimental & Molecular Medicine 56: 1461-1471

40. Danbi Jo, Seo Yeon Ahn, Seo Yoon Choi, Yoonjoo Choi, Dong Hoon Lee and Juhyun Song (2024) Positive Effects of Adiponectin, BDNF, and GLP-1 on Cortical Neurons Counteracting Palmitic Acid Induced Neurotoxicity Clinical Nutrition Research 13(2): 121

2023

39. Anna Jeong, Yongwoon Lim, Taewon Kook, Duk-Hwa Kwon, Young Kuk Cho, Juhee Ryu, Yun-Gyeong Lee, Sera Shin, Nakwon Choe, Yong Sook Kim, Hye Jung Cho, Jeong Chul Kim, Yoonjoo Choi, Su-Jin Lee, Hyung-Seok Kim, Hae Jin Kee, Kwang-Il Nam, Youngkeun Ahn, Myung Ho Jeong, Woo Jin Park, Young-Kook Kim, Hyun Kook (2023) Circular RNA circSMAD4 regulates cardiac fibrosis by targeting miR-671-5p and FGFR2 in cardiac fibroblasts Molecular Therapy - Nucleic Acids 34: 102071

38. Joon Haeng Rhee†, Koemchhoy Khim, Sao Puth, Yoonjoo Choi and Shee Eun Lee (2023) Deimmunization of flagellin adjuvant for clinical application Current Opinion in Virology 60: 101330

37. Ying Zhang, Rukhsora D Sultonova, Sung-Hwan You, Yoonjoo Choi, So-young Kim, Wan-Sik Lee, Jihyoun Seong, Jung-Joon Min*† and Yeongjin Hong*† (2023) The anticancer effect of PASylated calreticulin-targeting L-ASNase in solid tumor bearing mice with immunogenic cell death-inducing chemotherapy Biochemical Pharmacology 210: 115473

36. Youn Hee Jung, Yoonjoo Choi, Hyo-Deok Seo, Moon-Hyeong Seo*† and Hak-Sung Kim*† (2023) A conformation-selective protein binder for a KRAS mutant inhibits the interaction between RAS and RAF Biochemical and Biophysical Research Communications 645: 110-117

2022

35. Dong-Gun Kim, Hak-Sung Kim,  Yoonjoo Choi*† and Razvan Costin Stan*† (2022) Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the spike protein from SARS-CoV-2   Computational and Structural Biotechnology Journal 20: 5962-5965

34. Yoonjoo Choi† (2022) Artificial intelligence for antibody reading comprehension: AntiBERTa Patterns 3(7): 100535

33. Jarjapu Mahita*, Dong-Gun Kim*, Sumin Son, Yoonjoo Choi*†, Hak-Sung Kim*† and Chris Bailey-Kellogg*† (2022) Computational epitope binning reveals functional equivalence of sequence-divergent paratopes   Computational and Structural Biotechnology Journal 20: 2169-2180

32. Yoonjoo Choi† (2022) Computational Identification and Design of Complementary β-Strand Sequences Methods in Molecular Biology 2405: 83-94

2021

31. Koemchhoy Khim*, Yong Jun Bang*, Sao Puth, Yoonjoo Choi, Youn Suhk Lee, Kwangjoon Jeong, Shee Eun Lee*† and Joon Haeng Rhee*† (2021) Deimmunization of flagellin for repeated administration as a vaccine adjuvant npj Vaccines 6(1): 1-14

30. Jisu Hong, Young Jin Choi, Yoonjoo Choi, Jiwoo Lee, and Hyo Jeong Hong† (2021) Epitope-Paratope Interaction of A Neutralizing Human Anti-Hepatitis B Virus PreS1 Antibody That Recognizes the Receptor-Binding Motif Vaccines 9(7): 754

29. Dong-Gun Kim,  Yoonjoo Choi*†, and Hak-Sung Kim*† (2021) Epitopes of Protein Binders Are Related to the Structural Flexibility of a Target Protein Surface Journal of Chemical Information and Modeling 61(4): 2099-2017

28. Tae Yoon Kim*, Jeong Seok Cha*, Hoyoung Kim,  Yoonjoo Choi*†, Hyun-Soo Cho*† and Hak-Sung Kim*† (2020) Computationally-guided design and affinity improvement of a protein binder targeting a specific site on HER2 Computational and Structural Biotechnology Journal 19: 1325-1334

2020

27. Yoonjoo Choi*† and Arum Lee*† (2020) The Ethical Problems of CRISPR-Cas9 Gene-editing Technology The Journal of Humanities 79(1): 149-178

26. Dain Kim, Jisu Hong, Yoonjoo Choi, Jemin Han, Sangkyu Kim, Gyunghee Jo, Jun-Yeol Yoon, Heesu Chae, Hyeseon Yoon, Chankyu Lee*† and Hyo Jeong Hong*† (2020) Generation and characterization of monoclonal antibodies to the Ogawa lipopolysaccharide of Vibrio cholerae O1 from phage-displayed human synthetic Fab library Journal of Microbiology and Biotechnology 30(11): 1760-1768

25. W. James Cook, Yoonjoo Choi, Albert Gacerez, Chris Bailey-Kellogg and Charles L. Sentman† (2020) A chimeric antigen receptor that binds to a conserved site on MICA 1 ImmunoHorizons 4(10): 597-607

24. Yoonjoo Choi*, Sukyo Jeong*, Jung-Min Choi, Christian Ndong, Chris Bailey-Kellogg, Karl E. Griswold and Hak-Sung Kim† (2020) Computer-guided Binding Mode Identification and Affinity Improvement of an LRR Protein Binder without Structure Determination PLoS Computational Biology 16(8): e1008150

23. Yoo‐Kyoung Sohn, Sumin Son, Yoonjoo Choi, Da‐Eun Hwang, Hyo‐Deok Seo, Joong‐jae Lee and Hak‐Sung Kim† (2020) Effective inhibition of C3a‐mediated pro‐inflammatory response by a human C3a‐specific protein binder Biotechnology and Bioengineering 117(6): 1904-1908

22. Sukyo Jeong, Yoo-Kyoung Sohn, Yoonjoo Choi, Jinho Park and Hak-Sung Kim† (2020) A regulatory SH2 domain-targeting protein binder effectively inhibits the activity of Bruton’s tyrosine kinase and its drug-resistant variants Biochemical and Biophysical Research Communications 526(1): 8-13

2019

21. Tae-Geun Yu, Hak-Sung Kim*† and Yoonjoo Choi*† (2019) B-SIDER: Computational Algorithm for the Design of Complementary β-Sheet Sequences Journal of Chemical Information and Modeling 59(10): 4504-4511

2018

20. Woosung Heu, Jung Min Choi, Hyun-Ho Kyeong, Yoonjoo Choi, Hee Yeon Kim and Hak-Sung Kim† (2018) Repeat Module‐Based Rational Design of a Photoswitchable Protein for Light‐Driven Control of Biological Processes Angewandte Chemie International Edition 57(34): 10859-10863

19. Yoonjoo Choi, Jacob M. Furlon, Ryan B. Amos, Karl E. Griswold and Chris Bailey-Kellogg† (2018) DisruPPI: structure-based computational redesign algorithm for protein binding disruption Bioinformatics 34(13): i245-i253

18. Hyun-Ho Kyeong*, Yoonjoo Choi* and Hak-Sung Kim† (2018) GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking Bioinformatics 34(3): 469-476

2017

17. Casey K. Hua, Albert T. Gacerez, Charles L. Sentman, Margaret E. Ackerman, Yoonjoo Choi*† and Chris Bailey-Kellogg*† (2017) Computationally-driven identification of antibody epitopes eLife 6: e29023

2016

16. 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 1529: 375-398

15. Yoonjoo Choi, Christian Ndong, Karl E. Griswold*† and Chris Bailey-Kellogg*† (2016) Computationally driven antibody engineering enables simultaneous humanization and thermostabilization Protein Engineering, Design and Selection 29(10): 419-426

2015

14. Yoonjoo Choi*, Casey Hua*, Charles L. Sentman, Margaret E. Ackerman and Chris Bailey-Kellogg† (2015) Antibody humanization by structure-based computational protein design mAbs 7(6): 1045-1057

13. 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)

12. 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 and Karl E. Griswold† (2015) Structure-based redesign of lysostaphin yields potent antistaphylococcal enzymes that evade immune cell surveillance Molecular Therapy - Methods & Clinical Development 2: 15021

11. Hongliang Zhao, Deeptak Verma, Wen Li, Yoonjoo Choi, Christian Ndong, Steven N. Fiering, Chris Bailey-Kellogg*† and Karl E. Griswold*† (2015) Depletion of T Cell Epitopes in Lysostaphin Mitigates Anti-Drug Antibody Response and Enhances Antibacterial Efficacy In Vivo Chemistry & biology 22(5): 629-639

10. 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

2014

9. 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 Evironmental Microbiology 80(9): 2746-2753

7. Sebastian Kelm, Anna Vangone, Yoonjoo Choi, Jean-Paul Ebejer, Jiye Shi and Charlotte M. Deane† (2014) Fragment‐based modeling of membrane protein loops: Successes, failures, and prospects for the future Proteins: Structure, Function, and Bioinformatics 82(2): 175-186

2013

6. 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)

5. Yoonjoo Choi, Sumeet Agarwal and Charlotte M. Deane† (2013) How long is a piece of loop? PeerJ 1: e1

4. 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

2011

3. Yoonjoo Choi and Charlotte M. Deane† (2011) Predicting antibody complementarity determining region loops without classification Molecular BioSystems 7(12): 3327-3334

2010

2. 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

1. Yoonjoo Choi† and Charlotte M. Deane (2010) FREAD revisited: Accurate loop structure prediction using a database search algorithm Proteins: Structure, Function, and Bioinformatics 78(6): 1431-1440

Book Chapter

Jungjoon Lee*† and Yoonjoo Choi*† (2021) Wet Lab Goes Virtual: In Silico Tools, ELNs, and Big Data Help Scientists Generate and Analyze Wet-lab Data, Digital Transformation of the Laboratory: A Practical Guide to the Connected Lab 253-264, WILEY‐VCH GmbH

Sebastian Kelm*, Yoonjoo Choi* and Charlotte M. Deane* (2014) Chapter 11: Protein Modeling and Structural Prediction, Springer Handbook of Bio-/Neuroinformatics 171-182, Springer, Berlin, Heidelberg

Conference Proceedings

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? ASIA CCS '13 231-242

Jun Ho Huh, Mirko Montanari, Derek Dagit, Rakesh Bobba, Dong Wook Kim, Yoonjoo Choi and Roy Campbell† (2013) Assessing software integrity of virtual appliances through software whitelists: Is it any good? NDSS Symposium 2013

Patents