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Innate Immunity, Cell Signaling and Molecular Modeling Laboratory

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2023

1. Pirzada RH, Ahmad B, Qayyum N, and Choi S. Modeling structure-activity relationships with machine learning to identify GSK3-targeted small molecules as potential COVID-19 therapeutics. Front Endocrinol (Lausanne). 2023;14:1084327. DOI:10.3389/fendo.2023.1084327 |

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2. Khan AW, Farooq M, Hwang MJ, Haseeb M, and Choi S. Autoimmune Neuroinflammatory Diseases: Role of Interleukins. Int J Mol Sci. 2023 Apr 27;24(9). DOI:10.3390/ijms24097960 |

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3. Ji YB, Lee S, Ju HJ, Kim HE, Noh JH, Choi S, Park K, Lee HB, and Kim MS. Preparation and evaluation of injectable microsphere formulation for longer sustained release of donepezil. J Control Release. 2023 Apr;356:43-58. DOI:10.1016/j.jconrel.2023.02.024 |

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4. Anwar MA, Haseeb M, Choi S, and Kim KP. P176S Mutation Rewires Electrostatic Interactions That Alter Maspin Functionality. ACS Omega. 2023 Aug 8;8(31):28258-28267. DOI:10.1021/acsomega.3c01850 |

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2022

1. Khan AW, Farooq M, Haseeb M, and Choi S. Role of Plant-Derived Active Constituents in Cancer Treatment and Their Mechanisms of Action. Cells. 2022 Apr 13;11(8). DOI:10.3390/cells11081326 |

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2. Farooq M, Khan AW, Ahmad B, Kim MS, and Choi S. Therapeutic Targeting of Innate Immune Receptors Against SARS-CoV-2 Infection. Front Pharmacol. 2022;13:915565. DOI:10.3389/fphar.2022.915565 |

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3. Ji YB, Lee HY, Lee S, Kim YH, Na K, Kim JH, Choi S, and Kim MS. Electrostatically optimized adapalene-loaded emulsion for the treatment of acne vulgaris. Mater Today Bio. 2022 Dec;16:100339. DOI:10.1016/j.mtbio.2022.100339 |

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4. Haseeb M, Javaid N, Yasmeen F, Jeong U, Han JH, Yoon J, Seo JY, Heo JK, Shin HC, Kim MS, Kim W, and Choi S. Novel Small-Molecule Inhibitor of NLRP3 Inflammasome Reverses Cognitive Impairment in an Alzheimer's Disease Model. ACS Chem Neurosci. 2022 Mar 16;13(6):818-833. DOI:10.1021/acschemneuro.1c00831 |

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5. Shin GR, Kim HE, Ju HJ, Kim JH, Choi S, Choi HS, and Kim MS. Injectable click-crosslinked hydrogel containing resveratrol to improve the therapeutic effect in triple negative breast cancer. Mater Today Bio. 2022 Dec;16:100386. DOI:10.1016/j.mtbio.2022.100386 |

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6. Ahmad B and Choi S. Unraveling the Tomaralimab Epitope on the Toll-like Receptor 2 via Molecular Dynamics and Deep Learning. ACS Omega. 2022 Aug 16;7(32):28226-28237. DOI:10.1021/acsomega.2c02559 |

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7. Javaid N and Choi S. An Alternate Approach to Generate Induced Pluripotent Stem Cells with Precise CRISPR/Cas9 Tool. Stem Cells Int. 2022;2022:4537335. DOI:10.1155/2022/4537335 |

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8. Lee KG, Santos ARMP, Kang YG, Chae YJ, Shah M, Pirzada RH, Song M, Kim J, Choi S, and Park Y. Efficacy Evaluation of SDF-1α-Based Polypeptides in an Acute Myocardial Infarction Model Using Structure-Based Drug Design. ACS Biomater Sci Eng. 2022 Oct 10;8(10):4486-4496. DOI:10.1021/acsbiomaterials.2c00766 |

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9. Manan A, Pirzada RH, Haseeb M, and Choi S. Toll-like Receptor Mediation in SARS-CoV-2: A Therapeutic Approach. Int J Mol Sci. 2022 Sep 14;23(18). DOI:10.3390/ijms231810716 |

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10. Lee WH, Rho JG, Yang Y, Lee S, Kweon S, Kim HM, Yoon J, Choi H, Lee E, Kim SH, You S, Song Y, Oh YS, Kim H, Han HS, Han JH, Jung M, Park YH, Choi YS, Han S, Lee J, Choi S, Kim JW, Park JH, Lee EK, Song WK, Kim E, and Kim W. Hyaluronic Acid Nanoparticles as a Topical Agent for Treating Psoriasis. ACS Nano. 2022 Dec 27;16(12):20057-20074. DOI:10.1021/acsnano.2c07843 |

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11. Javaid N, Patra MC, Cho DE, Batool M, Kim Y, Choi GM, Kim MS, Hahm DH, and Choi S. An orally active, small-molecule TNF inhibitor that disrupts the homotrimerization interface improves inflammatory arthritis in mice. Sci Signal. 2022 Nov 8;15(759):eabi8713. DOI:10.1126/scisignal.abi8713 |

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2021

1. Jung SW, Seo JW, Park SH, Kim YG, Moon JY, Choi S, and Lee SH. A Cell-Penetrating Peptide That Blocks Toll-Like Receptor Signaling Protects Kidneys against Ischemia-Reperfusion Injury. Int J Mol Sci. 2021 Feb 5;22(4). DOI:10.3390/ijms22041627 |

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2. Ahmad B, Batool M, Kim MS, and Choi S. Computational-Driven Epitope Verification and Affinity Maturation of TLR4-Targeting Antibodies. Int J Mol Sci. 2021 Jun 1;22(11). DOI:10.3390/ijms22115989 |

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3. Park SH, Ju HJ, Ji YB, Shah M, Min BH, Choi HS, Choi S, and Kim MS. Endogenous Stem Cell-Based In Situ Tissue Regeneration Using Electrostatically Interactive Hydrogel with a Newly Discovered Substance P Analog and VEGF-Mimicking Peptide. Small. 2021 Oct;17(40):e2103244. DOI:10.1002/smll.202103244 |

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4. Ahmad B, Batool M, Ain QU, Kim MS, and Choi S. Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations. Int J Mol Sci. 2021 Aug 24;22(17). DOI:10.3390/ijms22179124 |

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5. Javaid N, Pham TLH, and Choi S. Functional Comparison between VP64-dCas9-VP64 and dCas9-VP192 CRISPR Activators in Human Embryonic Kidney Cells. Int J Mol Sci. 2021 Jan 1;22(1). DOI:10.3390/ijms22010397 |

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6. Kim DY, Ju HJ, Kim JH, Choi S, and Kim MS. Injectable in situ forming hydrogel gene depot to improve the therapeutic effect of STAT3 shRNA. Biomater Sci. 2021 Jun 15;9(12):4459-4472. DOI:10.1039/d1bm00624j |

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7. Javaid N, Hirai H, Che FS, and Choi S. Molecular Basis for the Activation of Human Innate Immune Response by the Flagellin Derived from Plant-Pathogenic Bacterium, Acidovorax avenae. Int J Mol Sci. 2021 Jun 28;22(13). DOI:10.3390/ijms22136920 |

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8. Thao NTT, Lee S, Shin GR, Kang Y, Choi S, and Kim MS. Preparation of Electrospun Small Intestinal Submucosa/Poly(caprolactone-co-Lactide-co-glycolide) Nanofiber Sheet as a Potential Drug Carrier. Pharmaceutics. 2021 Feb 11;13(2). DOI:10.3390/pharmaceutics13020253 |

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9. Pirzada RH, Haseeb M, Batool M, Kim M, and Choi S. Remdesivir and Ledipasvir among the FDA-Approved Antiviral Drugs Have Potential to Inhibit SARS-CoV-2 Replication. Cells. 2021 Apr 29;10(5). DOI:10.3390/cells10051052 |

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10. Qayyum N, Haseeb M, Kim MS, and Choi S. Role of Thioredoxin-Interacting Protein in Diseases and Its Therapeutic Outlook. Int J Mol Sci. 2021 Mar 9;22(5). DOI:10.3390/ijms22052754 |

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11. Batool M, Kim MS, and Choi S. Structural insights into the distinctive RNA recognition and therapeutic potentials of RIG-I-like receptors. Med Res Rev. 2022 Jan;42(1):399-425. DOI:10.1002/med.21845 |

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12. Farooq M, Batool M, Kim MS, and Choi S. Toll-Like Receptors as a Therapeutic Target in the Era of Immunotherapies. Front Cell Dev Biol. 2021;9:756315. DOI:10.3389/fcell.2021.756315 |

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13. Ji YB, Park JY, Kang Y, Lee S, Ju HJ, Choi S, Lee BY, and Kim MS. Scaffold printing using biodegradable poly(1,4-butylene carbonate) ink: printability, in vivo physicochemical properties, and biocompatibility. Mater Today Bio. 2021 Sep;12:100129. DOI:10.1016/j.mtbio.2021.100129 |

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14. Baek WY, Lee SM, Lee SW, Son IO, Choi S, and Suh CH. Intravenous Administration of Toll-Like Receptor Inhibitory Peptide 1 is Effective for the Treatment of Systemic Lupus Erythematosus in a Mus musculus Model. J Rheum Dis. 2021 Jul 1;28(3):133-142. DOI:10.4078/jrd.2021.28.3.133 |

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15. Farooq M, Khan AW, Kim MS, and Choi S. The Role of Fibroblast Growth Factor (FGF) Signaling in Tissue Repair and Regeneration. Cells. 2021 Nov 19;10(11). DOI:10.3390/cells10113242 |

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2020

1. Javaid N, Patra MC, Seo H, Yasmeen F, and Choi S. A Rational Insight into the Effect of Dimethyl Sulfoxide on TNF-α Activity. Int J Mol Sci. 2020 Dec 11;21(24). DOI:10.3390/ijms21249450 |

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2. Shah M, Ahmad B, Choi S, and Woo HG. Mutations in the SARS-CoV-2 spike RBD are responsible for stronger ACE2 binding and poor anti-SARS-CoV mAbs cross-neutralization. Comput Struct Biotechnol J. 2020;18:3402-3414. DOI:10.1016/j.csbj.2020.11.002 |

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3. Yasmeen F, Seo H, Javaid N, Kim MS, and Choi S. Therapeutic Interventions into Innate Immune Diseases by Means of Aptamers. Pharmaceutics. 2020 Oct 11;12(10). DOI:10.3390/pharmaceutics12100955 |

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4. Mir RH, Sawhney G, Verma R, Ahmad B, Kumar P, Ranjana S, Bhagat A, Madishetti S, Ahmed Z, Jachak SM, Choi S, and Masoodi MH. Origanum vulgare L.: In vitro Assessment of Cytotoxicity, Molecular Docking Studies, Antioxidant and Anti-inflammatory Activity in LPS Stimulated RAW 264.7 Cells. Med Chem. 2021;17(9):983-993. DOI:10.2174/1573406416666200904110828 |

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5. Kim HS, Lee BN, Choi S, Kim MS, and Kim JH. Behavior of Muscle-Derived Stem Cells on Silica Nanostructured Substrates. Nanomaterials (Basel). 2020 Aug 22;10(9). DOI:10.3390/nano10091651 |

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6. Patra MC, Shah M, and Choi S. Toll-like receptor-induced cytokines as immunotherapeutic targets in cancers and autoimmune diseases. Semin Cancer Biol. 2020 Aug;64:61-82. DOI:10.1016/j.semcancer.2019.05.002 |

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7. Patra MC, Achek A, Kim GY, Panneerselvam S, Shin HJ, Baek WY, Lee WH, Sung J, Jeong U, Cho EY, Kim W, Kim E, Suh CH, and Choi S. A Novel Small-Molecule Inhibitor of Endosomal TLRs Reduces Inflammation and Alleviates Autoimmune Disease Symptoms in Murine Models. Cells. 2020 Jul 9;9(7). DOI:10.3390/cells9071648 |

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8. Shah M, Kim GY, Achek A, Cho EY, Baek WY, Choi YS, Lee WH, Kim DJ, Lee SH, Kim W, Kim SS, Cheong JY, Suh CH, and Choi S. The αC helix of TIRAP holds therapeutic potential in TLR-mediated autoimmune diseases. Biomaterials. 2020 Jul;245:119974. DOI:10.1016/j.biomaterials.2020.119974 |

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9. Patra MC, Batool M, Haseeb M, and Choi S. A Computational Probe into the Structure and Dynamics of the Full-Length Toll-Like Receptor 3 in a Phospholipid Bilayer. Int J Mol Sci. 2020 Apr 19;21(8). DOI:10.3390/ijms21082857 |

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10. Achek A, Kwon HK, Patra MC, Shah M, Hong R, Lee WH, Baek WY, Choi YS, Kim GY, Pham TLH, Suh CH, Kim W, Hahm DH, and Choi S. A peptide derived from the core β-sheet region of TIRAP decoys TLR4 and reduces inflammatory and autoimmune symptoms in murine models. EBioMedicine. 2020 Feb;52:102645. DOI:10.1016/j.ebiom.2020.102645 |

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11. Ain QU, Batool M, and Choi S. TLR4-Targeting Therapeutics: Structural Basis and Computer-Aided Drug Discovery Approaches. Molecules. 2020 Jan 31;25(3). DOI:10.3390/molecules25030627 |

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12. Javaid N and Choi S. Toll-like Receptors from the Perspective of Cancer Treatment. Cancers (Basel). 2020 Jan 27;12(2). DOI:10.3390/cancers12020297 |

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13. Pirzada RH, Javaid N, and Choi S. The Roles of the NLRP3 Inflammasome in Neurodegenerative and Metabolic Diseases and in Relevant Advanced Therapeutic Interventions. Genes (Basel). 2020 Jan 27;11(2). DOI:10.3390/genes11020131 |

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2019

1. Haseeb M, Pirzada RH, Ain QU, and Choi S. Wnt Signaling in the Regulation of Immune Cell and Cancer Therapeutics. Cells. 2019 Nov 3;8(11). DOI:10.3390/cells8111380 |

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2. Park SH, Seo JY, Park JY, Ji YB, Kim K, Choi HS, Choi S, Kim JH, Min BH and Kim MS. An injectable, click-crosslinked, cytomodulin-modified hyaluronic acid hydrogel for cartilage tissue engineering. NPG Asia Materials volume 11, Article number: 30 (2019). DOI: 10.1038/s41427-019-0130-1

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3. Ghosh P, Shah M, Ravichandran S, Park SS, Iqbal H, Choi S, Kim KK, and Rhee DK. Pneumococcal VncR Strain-Specifically Regulates Capsule Polysaccharide Synthesis. Front Microbiol. 2019;10:2279. DOI:10.3389/fmicb.2019.02279 |

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4. Javaid N, Yasmeen F, and Choi S. Toll-Like Receptors and Relevant Emerging Therapeutics with Reference to Delivery Methods. Pharmaceutics. 2019 Sep 1;11(9). DOI:10.3390/pharmaceutics11090441 |

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5. Achek A, Shah M, Seo JY, Kwon HK, Gui X, Shin HJ, Cho EY, Lee BS, Kim DJ, Lee SH, Yoo TH, Kim MS, and Choi S. Linear and Rationally Designed Stapled Peptides Abrogate TLR4 Pathway and Relieve Inflammatory Symptoms in Rheumatoid Arthritis Rat Model. J Med Chem. 2019 Jul 25;62(14):6495-6511. DOI:10.1021/acs.jmedchem.9b00061 |

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6. Batool M, Ahmad B, and Choi S. A Structure-Based Drug Discovery Paradigm. Int J Mol Sci. 2019 Jun 6;20(11). DOI:10.3390/ijms20112783 |

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7. Kim HK, Anwar MA, and Choi S. Association of BUD13-ZNF259-APOA5-APOA1-SIK3 cluster polymorphism in 11q23.3 and structure of APOA5 with increased plasma triglyceride levels in a Korean population. Sci Rep. 2019 Jun 5;9(1):8296. DOI:10.1038/s41598-019-44699-x |

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8. Yoon S, Choi JH, Kim SJ, Lee EJ, Shah M, Choi S, and Woo HG. EPHB6 mutation induces cell adhesion-mediated paclitaxel resistance via EPHA2 and CDH11 expression. Exp Mol Med. 2019 Jun 3;51(6):1-12. DOI:10.1038/s12276-019-0261-z |

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9. Ahmad B, Shah M, and Choi S. Oceans as a Source of Immunotherapy. Mar Drugs. 2019 May 10;17(5). DOI:10.3390/md17050282 |

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10. Kwon HK, Patra MC, Shin HJ, Gui X, Achek A, Panneerselvam S, Kim DJ, Song SJ, Hong R, Kim KS, Kim YG, Lee FY, Hahm DH, Lee SH, and Choi S. A cell-penetrating peptide blocks Toll-like receptor-mediated downstream signaling and ameliorates autoimmune and inflammatory diseases in mice. Exp Mol Med. 2019 Apr 26;51(4):1-19. DOI:10.1038/s12276-019-0244-0 |

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11. Anwar MA, Shah M, Kim J, and Choi S. Recent clinical trends in Toll-like receptor targeting therapeutics. Med Res Rev. 2019 May;39(3):1053-1090. DOI:10.1002/med.21553 |

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12. Han SM, Ryu HM, Suh J, Lee KJ, Choi SY, Choi S, Kim YL, Huh JY, and Ha H. Network-based integrated analysis of omics data reveal novel players of TGF-β1-induced EMT in human peritoneal mesothelial cells. Sci Rep. 2019 Feb 6;9(1):1497. DOI:10.1038/s41598-018-37101-9 |

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13. Yesudhas D, Anwar MA, and Choi S. Structural mechanism of DNA-mediated Nanog-Sox2 cooperative interaction. RSC Adv. 2019 Mar 6;9(14):8121-8130. DOI:10.1039/c8ra10085c |

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2018

1. Haseeb M, Anwar MA, and Choi S. Molecular Interactions Between Innate and Adaptive Immune Cells in Chronic Lymphocytic Leukemia and Their Therapeutic Implications. Front Immunol. 2018;9:2720. DOI:10.3389/fimmu.2018.02720 |
2. Junaid M, Shah M, Khan A, Li CD, Khan MT, Kaushik AC, Ali A, Mehmood A, Nangraj AS, Choi S, and Wei DQ. Structural-dynamic insights into the H. pylori cytotoxin-associated gene A (CagA) and its abrogation to interact with the tumor suppressor protein ASPP2 using decoy peptides. J Biomol Struct Dyn. 2019 Sep;37(15):4035-4050. DOI:10.1080/07391102.2018.1537895 |
3. Ghosh P, Luong TT, Shah M, Thach TT, Choi S, Lee S, and Rhee DK. Adenylate kinase potentiates the capsular polysaccharide by modulating Cps2D in Streptococcus pneumoniae D39. Exp Mol Med. 2018 Sep 5;50(9):1-14. DOI:10.1038/s12276-018-0141-y |
4. Khajeh Alizadeh Attar M, Anwar MA, Eskian M, Keshavarz-Fathi M, Choi S, and Rezaei N. Basic understanding and therapeutic approaches to target toll-like receptors in cancerous microenvironment and metastasis. Med Res Rev. 2018 Sep;38(5):1469-1484. DOI:10.1002/med.21480 |
5. Lee JH, Kwon HK, Shin HJ, Nam GH, Kim JH, and Choi S. Quasi-Stem Cells Derived from Human Somatic Cells by Chemically Modified Carbon Nanotubes. ACS Appl Mater Interfaces. 2018 Mar 14;10(10):8417-8425. DOI:10.1021/acsami.7b12914 |
6. Patra MC, Kwon HK, Batool M, and Choi S. Computational Insight Into the Structural Organization of Full-Length Toll-Like Receptor 4 Dimer in a Model Phospholipid Bilayer. Front Immunol. 2018;9:489. DOI:10.3389/fimmu.2018.00489 |
7. Patra MC and Choi S. Insight into Phosphatidylinositol-Dependent Membrane Localization of the Innate Immune Adaptor Protein Toll/Interleukin 1 Receptor Domain-Containing Adaptor Protein. Front Immunol. 2018;9:75. DOI:10.3389/fimmu.2018.00075 |

Book Chapters:
1. Choi S. (2018). Preface. In Encyclopedia of Signaling Molecules, Ed. S Choi, pp. v-xii. New York: Springer. PDF

2. Basith S, Manavalan B, Choi S. (2018). MyD88 (Myeloid Differentiation Primary Response Gene 88). In Encyclopedia of Signaling Molecules, Ed. S Choi, pp. 3280-91. New York: Springer. PDF

3. Manavalan B, Basith S, Choi S. (2018). IkBz. In Encyclopedia of Signaling Molecules, Ed. S Choi, pp. 2512-19. New York: Springer. PDF

4. Shah M and Choi S. (2018). Interferon Regulatory Factor, Ed. S Choi, pp. 2672-80. New York: Springer. PDF

5. Krishnan J, Anwar MA, Choi S. (2018). TLR4 (Toll-Like Receptor 4), Ed. S Choi, pp. 5472-83. New York: Springer. PDF

6. Durai P and Choi S. (2018). Toll-Like Receptor 2, Ed. S Choi, pp. 5518-24. New York: Springer. PDF

7. Anwar MA and Choi S. (2018). Receptor-Interacting Protein Kinase, Ed. S Choi, pp. 4547-4555. New York: Springer. PDF

2017

1. Park YS, Choi UJ, Nam NH, Choi SJ, Nasir A, Lee SG, Kim KJ, Jung GY, Choi S, Shim JY, Park S, and Yoo TH. Engineering an aldehyde dehydrogenase toward its substrates, 3-hydroxypropanal and NAD(+), for enhancing the production of 3-hydroxypropionic acid. Sci Rep. 2017 Dec 7;7(1):17155. DOI:10.1038/s41598-017-15400-x |
2. Yesudhas D, Anwar MA, Panneerselvam S, Kim HK, and Choi S. Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation. FEBS Open Bio. 2017 Nov;7(11):1750-1767. DOI:10.1002/2211-5463.12316 |
3. Batool M, Shah M, Patra MC, Yesudhas D, and Choi S. Structural insights into the Middle East respiratory syndrome coronavirus 4a protein and its dsRNA binding mechanism. Sci Rep. 2017 Sep 12;7(1):11362. DOI:10.1038/s41598-017-11736-6 |
4. Javaid N and Choi S. Acetylation- and Methylation-Related Epigenetic Proteins in the Context of Their Targets. Genes (Basel). 2017 Aug 7;8(8). DOI:10.3390/genes8080196 |
5. Yesudhas D, Batool M, Anwar MA, Panneerselvam S, and Choi S. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes (Basel). 2017 Aug 1;8(8). DOI:10.3390/genes8080192 |
6. Shah M and Choi S. Toll-like Receptor-Dependent Negative Effects of Opioids: A Battle between Analgesia and Hyperalgesia. Front Immunol. 2017;8:642. DOI:10.3389/fimmu.2017.00642 |
7. Durai P, Shin HJ, Achek A, Kwon HK, Govindaraj RG, Panneerselvam S, Yesudhas D, Choi J, No KT, and Choi S. Toll-like receptor 2 antagonists identified through virtual screening and experimental validation. FEBS J. 2017 Jul;284(14):2264-2283. DOI:10.1111/febs.14124 |
8. Anwar MA and Choi S. Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis. Sci Rep. 2017 Mar 8;7:43807. DOI:10.1038/srep43807 |
9. Park S, Shin HJ, Shah M, Cho HY, Anwar MA, Achek A, Kwon HK, Lee B, Yoo TH, and Choi S. TLR4/MD2 specific peptides stalled in vivo LPS-induced immune exacerbation. Biomaterials. 2017 May;126:49-60. DOI:10.1016/j.biomaterials.2017.02.023 |

Conference Paper:
10. Maria Batool and Sangdun Choi (2018) Identification of druggable genome in staphylococcus aureus multidrug resistant strain. 2017 IEEE Life Sciences Conference (LSC); 13-15 Dec. 2017. Link

2016

1. Shah M, Anwar MA, Yesudhas D, Krishnan J, and Choi S. A structural insight into the negative effects of opioids in analgesia by modulating the TLR4 signaling: An in silico approach. Sci Rep. 2016 Dec 16;6:39271. DOI:10.1038/srep39271 |
2. G SB, Choi S, Krishnan J, and K R. Cigarette smoke and related risk factors in neurological disorders: An update. Biomed Pharmacother. 2017 Jan;85:79-86. DOI:10.1016/j.biopha.2016.11.118 |
3. Patra MC and Choi S. Recent Progress in the Molecular Recognition and Therapeutic Importance of Interleukin-1 Receptor-Associated Kinase 4. Molecules. 2016 Nov 13;21(11). DOI:10.3390/molecules21111529 |
4. Shin HJ, Kwon HK, Lee JH, Anwar MA, and Choi S. Etoposide induced cytotoxicity mediated by ROS and ERK in human kidney proximal tubule cells. Sci Rep. 2016 Sep 26;6:34064. DOI:10.1038/srep34064 |
5. Morris O, Liu X, Domingues C, Runchel C, Chai A, Basith S, Tenev T, Chen H, Choi S, Pennetta G, Buchon N, and Meier P. Signal Integration by the IκB Protein Pickle Shapes Drosophila Innate Host Defense. Cell Host Microbe. 2016 Sep 14;20(3):283-295. DOI:10.1016/j.chom.2016.08.003 |
6. Batool M, Anwar MA, and Choi S. Toll-like receptors targeting technology for the treatment of lymphoma. Expert Opin Drug Discov. 2016 Nov;11(11):1047-1059. DOI:10.1080/17460441.2016.1233964 |
7. Achek A, Yesudhas D, and Choi S. Toll-like receptors: promising therapeutic targets for inflammatory diseases. Arch Pharm Res. 2016 Aug;39(8):1032-49. DOI:10.1007/s12272-016-0806-9 |
8. Phukan G, Shin TH, Shim JS, Paik MJ, Lee JK, Choi S, Kim YM, Kang SH, Kim HS, Kang Y, Lee SH, Mouradian MM, and Lee G. Silica-coated magnetic nanoparticles impair proteasome activity and increase the formation of cytoplasmic inclusion bodies in vitro. Sci Rep. 2016 Jul 5;6:29095. DOI:10.1038/srep29095 |
9. Patra MC and Choi S. Recent progress in the development of Toll-like receptor (TLR) antagonists. Expert Opin Ther Pat. 2016 Jun;26(6):719-30. DOI:10.1080/13543776.2016.1185415 |
10. Shah M, Anwar MA, Kim JH, and Choi S. Advances in Antiviral Therapies Targeting Toll-like Receptors. Expert Opin Investig Drugs. 2016;25(4):437-53. DOI:10.1517/13543784.2016.1154040 |
11. Yesudhas D, Anwar MA, Panneerselvam S, Durai P, Shah M, and Choi S. Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes. PLoS One. 2016;11(1):e0147240. DOI:10.1371/journal.pone.0147240 |
12. Anwar MA, Kim S, and Choi S. The triumph of chemically enhanced cellular reprogramming: a patent review. Expert Opin Ther Pat. 2016;26(2):265-80. DOI:10.1517/13543776.2016.1118058 |

2015

1. Shin HJ, Kwon HK, Lee JH, Gui X, Achek A, Kim JH, and Choi S. Doxorubicin-induced necrosis is mediated by poly-(ADP-ribose) polymerase 1 (PARP1) but is independent of p53. Sci Rep. 2015 Nov 2;5:15798. DOI:10.1038/srep15798 |
2. Kwon HK, Lee JH, Shin HJ, Kim JH, and Choi S. Structural and functional analysis of cell adhesion and nuclear envelope nano-topography in cell death. Sci Rep. 2015 Oct 22;5:15623. DOI:10.1038/srep15623 |
3. Kwon JW, Kwon HK, Shin HJ, Choi YM, Anwar MA, and Choi S. Activating transcription factor 3 represses inflammatory responses by binding to the p65 subunit of NF-κB. Sci Rep. 2015 Sep 28;5:14470. DOI:10.1038/srep14470 |
4. Durai P, Batool M, Shah M, and Choi S. Middle East respiratory syndrome coronavirus: transmission, virology and therapeutic targeting to aid in outbreak control. Exp Mol Med. 2015 Aug 28;47(8):e181. DOI:10.1038/emm.2015.76 |
5. Shah M, Anwar MA, Park S, Jafri SS, and Choi S. In silico mechanistic analysis of IRF3 inactivation and high-risk HPV E6 species-dependent drug response. Sci Rep. 2015 Aug 20;5:13446. DOI:10.1038/srep13446 |
6. Panneerselvam S, Yesudhas D, Durai P, Anwar MA, Gosu V, and Choi S. A Combined Molecular Docking/Dynamics Approach to Probe the Binding Mode of Cancer Drugs with Cytochrome P450 3A4. Molecules. 2015 Aug 14;20(8):14915-35. DOI:10.3390/molecules200814915 |
7. Kwon HK, Shin HJ, Lee JH, Park SH, Kwon MC, Panneerselvam S, Lee CG, Kim SG, Kim JH, and Choi S. Etoposide Induces Necrosis Through p53-Mediated Antiapoptosis in Human Kidney Proximal Tubule Cells. Toxicol Sci. 2015 Nov;148(1):204-19. DOI:10.1093/toxsci/kfv182 |
8. Choi YM, Kim HK, Shim W, Anwar MA, Kwon JW, Kwon HK, Kim HJ, Jeong H, Kim HM, Hwang D, Kim HS, and Choi S. Mechanism of Cisplatin-Induced Cytotoxicity Is Correlated to Impaired Metabolism Due to Mitochondrial ROS Generation. PLoS One. 2015;10(8):e0135083. DOI:10.1371/journal.pone.0135083 |
9. Durai P, Batool M, and Choi S. Structure and Effects of Cyanobacterial Lipopolysaccharides. Mar Drugs. 2015 Jul 7;13(7):4217-30. DOI:10.3390/md13074217 |
10. Lee BS, Shin S, Jeon JY, Jang KS, Lee BY, Choi S, and Yoo TH. Incorporation of Unnatural Amino Acids in Response to the AGG Codon. ACS Chem Biol. 2015 Jul 17;10(7):1648-53. DOI:10.1021/acschembio.5b00230 |
11. Anwar MA, Panneerselvam S, Shah M, and Choi S. Insights into the species-specific TLR4 signaling mechanism in response to Rhodobacter sphaeroides lipid A detection. Sci Rep. 2015 Jan 7;5:7657. DOI:10.1038/srep07657 |
12. Luong TT, Kim EH, Bak JP, Nguyen CT, Choi S, Briles DE, Pyo S, and Rhee DK. Ethanol-induced alcohol dehydrogenase E (AdhE) potentiates pneumolysin in Streptococcus pneumoniae. Infect Immun. 2015 Jan;83(1):108-19. DOI:10.1128/IAI.02434-14 |

2014

1. Yesudhas D, Gosu V, Anwar MA, and Choi S. Multiple roles of toll-like receptor 4 in colorectal cancer. Front Immunol. 2014;5:334. DOI:10.3389/fimmu.2014.00334 |
2. Gosu V and Choi S. Structural dynamic analysis of apo and ATP-bound IRAK4 kinase. Sci Rep. 2014 Jul 18;4:5748. DOI:10.1038/srep05748 |
3. Anwar MA and Choi S. Gram-negative marine bacteria: structural features of lipopolysaccharides and their relevance for economically important diseases. Mar Drugs. 2014 Apr 30;12(5):2485-514. DOI:10.3390/md12052485 |
4. Panneerselvam S and Choi S. Nanoinformatics: emerging databases and available tools. Int J Mol Sci. 2014 Apr 25;15(5):7158-82. DOI:10.3390/ijms15057158 |
5. Choi YM, Cho HY, Anwar MA, Kim HK, Kwon JW, and Choi S. ATF3 attenuates cyclosporin A-induced nephrotoxicity by downregulating CHOP in HK-2 cells. Biochem Biophys Res Commun. 2014 May 30;448(2):182-8. DOI:10.1016/j.bbrc.2014.04.083 |
6. Lee CG, Kim JG, Kim HJ, Kwon HK, Cho IJ, Choi DW, Lee WH, Kim WD, Hwang SJ, Choi S, and Kim SG. Discovery of an integrative network of microRNAs and transcriptomics changes for acute kidney injury. Kidney Int. 2014 Nov;86(5):943-53. DOI:10.1038/ki.2014.117 |

2013

1. Durai P, Govindaraj RG, and Choi S. Structure and dynamic behavior of Toll-like receptor 2 subfamily triggered by malarial glycosylphosphatidylinositols of Plasmodium falciparum. FEBS J. 2013 Dec;280(23):6196-212. DOI:10.1111/febs.12541 |
2. Kim EH, Kim IH, Lee MJ, Thach Nguyen C, Ha JA, Lee SC, Choi S, Choi KT, Pyo S, and Rhee DK. Anti-oxidative stress effect of red ginseng in the brain is mediated by peptidyl arginine deiminase type IV (PADI4) repression via estrogen receptor (ER) β up-regulation. J Ethnopharmacol. 2013 Jul 9;148(2):474-85. DOI:10.1016/j.jep.2013.04.041 |
3. Anwar MA, Basith S, and Choi S. Negative regulatory approaches to the attenuation of Toll-like receptor signaling. Exp Mol Med. 2013 Feb 22;45(2):e11. DOI:10.1038/emm.2013.28 |
4. Basith S, Manavalan B, Gosu V, and Choi S. Evolutionary, structural and functional interplay of the IκB family members. PLoS One. 2013;8(1):e54178. DOI:10.1371/journal.pone.0054178 |

5. Kwon H-K, Shin H-J, Choi S (2013) The Mechanisms of Cell Death: Apoptosis, Necrosis and Necroptosis. The National Academy of Sciences 52: 165-182. PDF.

Book Chapters:

1. Selvarajoo K (2013) Immuno Systems Biology. In: S. Choi, series editor. New York: Springer. pp. 150.
2. Govindaraj RG, Durai P, Choi S (2013) In Silico Approaches to Study Drug-induced Renal Toxicity. In: S.G. Kim, editor. KIDNEY:Toxicological Assessment. Boca Raton: CRC Press. pp. 103-120.

2012

1. Choi S, Chang MS, Stuecker T, Chung C, Newcombe DA, and Venkateswaran K. A fosmid cloning strategy for detecting the widest possible spectrum of microbes from the international space station drinking water system. Genomics Inform. 2012 Dec;10(4):249-55. DOI:10.5808/GI.2012.10.4.249 |
2. Gosu V, Basith S, Durai P, and Choi S. Molecular evolution and structural features of IRAK family members. PLoS One. 2012;7(11):e49771. DOI:10.1371/journal.pone.0049771 |
3. Krishnan J and Choi S. Systems Biological Approaches Reveal Non-additive Responses and Multiple Crosstalk Mechanisms between TLR and GPCR Signaling. Genomics Inform. 2012 Sep;10(3):153-66. DOI:10.5808/GI.2012.10.3.153 |
4. Gosu V, Basith S, Kwon OP, and Choi S. Therapeutic applications of nucleic acids and their analogues in Toll-like receptor signaling. Molecules. 2012 Nov 14;17(11):13503-29. DOI:10.3390/molecules171113503 |
5. Park EJ, Kwon HK, Choi YM, Shin HJ, and Choi S. Doxorubicin induces cytotoxicity through upregulation of pERK-dependent ATF3. PLoS One. 2012;7(9):e44990. DOI:10.1371/journal.pone.0044990 |
6. Basith S, Manavalan B, Yoo TH, Kim SG, and Choi S. Roles of toll-like receptors in cancer: a double-edged sword for defense and offense. Arch Pharm Res. 2012 Aug;35(8):1297-316. DOI:10.1007/s12272-012-0802-7 |
7. Shim W, Paik MJ, Nguyen DT, Lee JK, Lee Y, Kim JH, Shin EH, Kang JS, Jung HS, Choi S, Park S, Shim JS, and Lee G. Analysis of changes in gene expression and metabolic profiles induced by silica-coated magnetic nanoparticles. ACS Nano. 2012 Sep 25;6(9):7665-80. DOI:10.1021/nn301113f |
8. Kim B, Yang MS, Choi D, Kim JH, Kim HS, Seol W, Choi S, Jou I, Kim EY, and Joe EH. Impaired inflammatory responses in murine Lrrk2-knockdown brain microglia. PLoS One. 2012;7(4):e34693. DOI:10.1371/journal.pone.0034693 |

Book Chapters:

1. Krishnan J, Basith S, Choi S. 2012. Advances in Toll-like Receptor Signaling. Advances in Systems Biology 1: 5-15. PDF.
2. ManavalanB, Basith S, Choi S. 2012. IkB-ζ. In Encyclopedia of Signaling Molecules, ed. SChoi, pp. 892-9. New York: Springer.
3. Krishnan J, Choi S. 2012. TLR4, Toll-Like Receptor 4. In Encyclopedia of Signaling Molecules, ed. S Choi , pp. 1866-75. New York: Springer.
4. Choi S. 2012. As the director of the stage starring TLR, IκB-ζ and ATF3. Molecular and Cellular Biology News 2012: 1-8.
5. Choi S, ed. 2012. Encyclopedia of Signaling Molecules, Vols. 1-3. New York: Springer. 2150 pp.
6. Basith S, Manavalan B, Choi S. 2012. MyD88, Myeloid Differentiation Primary Response Gene 88. In Encyclopedia of Signaling Molecules, ed. S Choi, pp. 1149-59. New York: Springer.

2011

1. Park EJ, Kim SA, Choi YM, Kwon HK, Shim W, Lee G, and Choi S. Capric acid inhibits NO production and STAT3 activation during LPS-induced osteoclastogenesis. PLoS One. 2011;6(11):e27739. DOI:10.1371/journal.pone.0027739 |
2. Park EJ, Roh J, Kang MS, Kim SN, Kim Y, and Choi S. Biological responses to diesel exhaust particles (DEPs) depend on the physicochemical properties of the DEPs. PLoS One. 2011;6(10):e26749. DOI:10.1371/journal.pone.0026749 |
3. Park EJ, Roh J, Kim SN, Kang MS, Lee BS, Kim Y, and Choi S. Biological toxicity and inflammatory response of semi-single-walled carbon nanotubes. PLoS One. 2011;6(10):e25892. DOI:10.1371/journal.pone.0025892 |
4. Govindaraj RG, Manavalan B, Basith S, and Choi S. Comparative analysis of species-specific ligand recognition in Toll-like receptor 8 signaling: a hypothesis. PLoS One. 2011;6(9):e25118. DOI:10.1371/journal.pone.0025118 |
5. Basith S, Manavalan B, Govindaraj RG, and Choi S. In silico approach to inhibition of signaling pathways of Toll-like receptors 2 and 4 by ST2L. PLoS One. 2011;6(8):e23989. DOI:10.1371/journal.pone.0023989 |
6. Kim IH, Kim SK, Kim EH, Kim SW, Sohn SH, Lee SC, Choi S, Pyo S, and Rhee DK. Korean Red Ginseng Up-regulates C21-Steroid Hormone Metabolism via Cyp11a1 Gene in Senescent Rat Testes. J Ginseng Res. 2011 Sep;35(3):272-82. DOI:10.5142/jgr.2011.35.3.272 |
7. Manavalan B, Basith S, and Choi S. Similar Structures but Different Roles - An Updated Perspective on TLR Structures. Front Physiol. 2011;2:41. DOI:10.3389/fphys.2011.00041 |
8. Manavalan B, Govindaraj R, Lee G, and Choi S. Molecular modeling-based evaluation of dual function of IκBζ ankyrin repeat domain in toll-like receptor signaling. J Mol Recognit. 2011 Jul-Aug;24(4):597-607. DOI:10.1002/jmr.1085 |
9. Basith S, Manavalan B, Lee G, Kim SG, and Choi S. Toll-like receptor modulators: a patent review (2006-2010). Expert Opin Ther Pat. 2011 Jun;21(6):927-44. DOI:10.1517/13543776.2011.569494 |
10. Oh YT, Oh KS, Choi YM, Jokiaho A, Donovan C, Choi S, Kang I, and Youn JH. Continuous 24-h nicotinic acid infusion in rats causes FFA rebound and insulin resistance by altering gene expression and basal lipolysis in adipose tissue. Am J Physiol Endocrinol Metab. 2011 Jun;300(6):E1012-21. DOI:10.1152/ajpendo.00650.2010 |
11. Siewe BT, Kalis SL, Le PT, Witte PL, Choi S, Conway SJ, Druschitz L, and Knight KL. In vitro requirement for periostin in B lymphopoiesis. Blood. 2011 Apr 7;117(14):3770-9. DOI:10.1182/blood-2010-08-301119 |
12. Choi S, Yoon H, Oh KS, Oh YT, Kim YI, Kang I, and Youn JH. Widespread effects of nicotinic acid on gene expression in insulin-sensitive tissues: implications for unwanted effects of nicotinic acid treatment. Metabolism. 2011 Jan;60(1):134-44. DOI:10.1016/j.metabol.2010.02.013 |

13. Park JH, Choi S. (2011) Gene Expression Analysis of Gα13-/- Knockout Mouse Embryos Reveals Perturbations in Gα13 Signaling Relatedto Angiogenesis and Hypoxia. Genomics&Informatics. 9: 161-172. Download PDF.

14. Kim SN, Kang MS, Han YA, Kim JH, Roh J, et al. (2011) Toxicity Analysis of Carbon Nanotubes Based on Their Physicochemical Properties. Clean Technology 17: 273-279.PDF.

15. Paik M-J, Shim W, Moon SM, Kim YM, Kim DW, et al. (2011) Altered Amino Acid Metabolic Patterns in the Plasma of Rat Models with Adenovirus Infection. Bull Korean Chem Soc 32: 1569-1574.PDF.

16. Paik M-J, Nguyen D-T, Youn J, Cho I-S, Shim W, et al. (2011) Selective 3,4-Dihydroxyphenylalanine Analysis in Human Urine as Ethoxycarbonyltert-butyldimethylsilyl Derivatives by Gas Chromatography-Mass Spectrometry. Bull Korean Chem Soc 32: 977-980. PDF.

Book Chapters:

1. Basith S, Manavalan B, Choi S (2011) MyD88, MYELOID DIFFERENTIATION PRIMARY RESPONSE GENE 88. In:Choi S, editor. Encyclopedia of Signaling Molecules. 1 ed. New York: Springer. pp. 2500.

2. Manavalan B, Basith S, Choi S (2011) IkBz , IKAPPABZETA In: Choi S, editor. Encyclopedia of Signaling Molecules. 1 ed. New York: Springer. pp. 2500.

3. Krishnan J, Choi S (2011) TLR4,TOLL-LIKE RECEPTOR 4. In: Choi S, editor. Encyclopedia of Signaling Molecules. 1 ed. New York: Springer. pp. 2500.

4. Choi S, editor (2011) Encyclopedia of Signaling Molecules. 1 ed. New York: Springer. 2500 p.

5. Booß-Bavnbek B, Klösgen B, Larsen J, Pociot F, Renström E, editors (2011) Systems Biology of Regulated Exocytosis in Pancreatic ß-Cells. 1 ed. New York: Springer. 440 p.

2010

1. Manavalan B, Basith S, Choi YM, Lee G, and Choi S. Structure-function relationship of cytoplasmic and nuclear IκB proteins: an in silico analysis. PLoS One. 2010 Dec 23;5(12):e15782. DOI:10.1371/journal.pone.0015782 |
2. Kim EY, Shin HY, Kim JY, Kim DG, Choi YM, Kwon HK, Rhee DK, Kim YS, and Choi S. ATF3 plays a key role in Kdo2-lipid A-induced TLR4-dependent gene expression via NF-κB activation. PLoS One. 2010 Dec 2;5(12):e14181. DOI:10.1371/journal.pone.0014181 |
3. Basith S and Choi S. Overview of human cytochrome P450 networks in chemical space. Arch Pharm Res. 2010 Sep;33(9):1289-91. DOI:10.1007/s12272-010-0900-3 |
4. Govindaraj RG, Manavalan B, Lee G, and Choi S. Molecular modeling-based evaluation of hTLR10 and identification of potential ligands in Toll-like receptor signaling. PLoS One. 2010 Sep 16;5(9):e12713. DOI:10.1371/journal.pone.0012713 |
5. Paik MJ, Ahn YH, Lee PH, Kang H, Park CB, Choi S, and Lee G. Polyamine patterns in the cerebrospinal fluid of patients with Parkinson's disease and multiple system atrophy. Clin Chim Acta. 2010 Oct 9;411(19-20):1532-5. DOI:10.1016/j.cca.2010.05.034 |
6. Manavalan B, Murugapiran SK, Lee G, and Choi S. Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases. BMC Struct Biol. 2010 Jan 12;10:1. DOI:10.1186/1472-6807-10-1 |

7. Paik MJ, Nguyen DT, Cho IS, Shim W, kim KR, et al. (2010) Seletive dopa analysis in human urine as ethoxycarbony/tert-butyldimethysily derivatives by Gas chromatography-Mass spectrometry. Analytical Letters. PDF.

Book Chapters:

1. Choi S, ed. (2010) Systems Biology Approaches: Solving New Puzzles in a Symphonic Manner. Systems Biology for Signaling Networks. Springer Inc., NewYork.

2. Choi S, ed. (2010) Systems Biology for Signaling Networks. Springer Inc., NewYork.

2009

1. Krishnan J, Lee G, and Choi S. Drugs targeting Toll-like receptors. Arch Pharm Res. 2009 Nov;32(11):1485-502. DOI:10.1007/s12272-009-2100-6 |
2. Lee KA, Shim W, Paik MJ, Lee SC, Shin JY, Ahn YH, Park K, Kim JH, Choi S, and Lee G. Analysis of changes in the viability and gene expression profiles of human mesenchymal stromal cells over time. Cytotherapy. 2009;11(6):688-97. DOI:10.3109/14653240902974032 |
3. You MH, Kim WJ, Shim W, Lee SR, Lee G, Choi S, Kim DY, Kim YM, Kim H, and Han SU. Cytosine deaminase-producing human mesenchymal stem cells mediate an antitumor effect in a mouse xenograft model. J Gastroenterol Hepatol. 2009 Aug;24(8):1393-400. DOI:10.1111/j.1440-1746.2009.05862.x |
4. Lee G, Lee SS, Kay KY, Kim DW, Choi S, and Jun HK. Isolation and characterization of a novel adenosine deaminase inhibitor, IADA-7, from Bacillus sp. J-89. J Enzyme Inhib Med Chem. 2009 Feb;24(1):59-64. DOI:10.1080/14756360801906863 |
5. Hwang DY, Hong S, Jeong JW, Choi S, Kim H, Kim J, and Kim KS. Vesicular monoamine transporter 2 and dopamine transporter are molecular targets of Pitx3 in the ventral midbrain dopamine neurons. J Neurochem. 2009 Dec;111(5):1202-12. DOI:10.1111/j.1471-4159.2009.06404.x |
6. Lee G, Santat LA, Chang MS, and Choi S. RNAi methodologies for the functional study of signaling molecules. PLoS One. 2009;4(2):e4559. DOI:10.1371/journal.pone.0004559 |
7. Tsuchiya M, Piras V, Choi S, Akira S, Tomita M, Giuliani A, and Selvarajoo K. Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages. PLoS One. 2009;4(3):e4905. DOI:10.1371/journal.pone.0004905 |
8. Paik MJ, Li WY, Ahn YH, Lee PH, Choi S, Kim KR, Kim YM, Bang OY, and Lee G. The free fatty acid metabolome in cerebral ischemia following human mesenchymal stem cell transplantation in rats. Clin Chim Acta. 2009 Apr;402(1-2):25-30. DOI:10.1016/j.cca.2008.12.022 |

2008

• Krishnan J, Chen J, Shin KJ, Hwang JI, Han SU, Lee G, Choi S. (2008) Gene expression profiling of light-induced retinal degeneration in phototransduction gene knockout mice. Exp Mol Med 40: 495-504. PDF.

• Paik MJ, Yu J, Hu MB, Kim SJ, Kim KR, Ahn YH, Choi S, Lee G. (2008) Gas chromatographic-mass spectrometric analyses of cholesterol and its precursors in rat plasma as tert-butyldimethylsilyl derivatives. Clin Chim Acta 396: 62-5. PDF.

• Paik MJ, Moon SM, Kim KR, Choi S, Ahn YH, Lee G. (2008) Target metabolic profiling analysis of free amino acids in plasma as EOC/TBDMS derivatives by GC-SIM-MS. Biomed Chromatogr 22: 339-42. PDF.

• Paik MJ, Cho EY, Kim H, Kim KR, Choi S, Ahn YH, Lee G. (2008) Simultaneous clinical monitoring of lactic acid, pyruvic acid and ketone bodies in plasma as methoxime/tert-butyldimethylsilyl derivatives by gas chromatography-mass spectrometry in selected ion monitoring mode. Biomed Chromatogr 22: 450-3. PDF.

• Krishnan J, Lee G, Han SU, Choi S. (2008) Characterization of phototransduction gene knockouts revealed important signaling networks in the light-induced retinal degeneration. J Biomed Biotechnol 2008: 327468. PDF.

2007

• Krishnan J, Selvarajoo K, Tsuchiya M, Lee G, Choi S. (2007) Toll-like receptor signal transduction. Experimental and Molecular Medicine 39: 421-38. PDF.

• Cho MK, Kim WD, Ki SH, Hwang JI, Choi S, Lee CH, Kim SG. (2007) Role of Galpha12 and Galpha13 as novel switches for the activity of Nrf2, a key antioxidative transcription factor. Mol Cell Biol 27: 6195-208. PDF.

• Choi S, ed. (2007) Introduction to Systems Biology. Humana Press Inc., Totowa, NJ.

• Piras V, Selvarajoo K, Fujikawa N, Choi S, Tomita M, Giuliani A, Tsuchiya M. (2007) Statistical Analysis of Gene Expression in Innate Immune Responses: Dynamic Interactions between MicroRNA and Signaling Molecules. Genomics & Informatics 5: 95-100.

• Krishnan J, Lee G, Han S-U, Choi S. (2007) Signaling Networks Involved in Retinal Degeneration in Mice. IEEE 2007: 3-6.

• Jeon H, Choi S. (2007) Fluorescence Quenching Causes Systematic Dye Bias in Microarray Experiments Using Cyanine Dye. Genomics & Informatics 5: 113-8

2006

• Zhu X, Chang MS, Hsueh RC, Taussig R, Smith KD, Simon MI, Choi S. (2006) Dual ligand stimulation of RAW 264.7 cells uncovers feedback mechanisms that regulate TLR-mediated gene expression. J Immunol 177: 4299-310.PDF.

• Kim DH, Behlke MA, Rose SD, Chang MS, Choi S, Rossi JJ. (2006) Enhancing RNAi with Synthetic RNA Duplexes. Non-viral Gene Therapy: 465-75.

• Yu Y, Santat LA, Choi S. (2006) Bioinformatics packages for sequence analysis. In Genes, Genomics & Bioinformatics, ed. D Arora, R Berka, G Singh, The Netherlands: Elsevier Science, pp. 143-60. PDF.

• Nam JS, Turcotte TJ, Smith PF, Choi S, Yoon JK. (2006) Mouse cristin/R-spondin family proteins are novel ligands for the Frizzled 8 and LRP6 receptors and activate beta-catenin-dependent gene expression. J Biol Chem 281: 13247-57. PDF.

• Lee JA, Sinkovits RS, Mock D, Rab EL, Cai J, Yang P, Saunders B, Hsueh RC, Choi S, Subramaniam S, Scheuermann RH. (2006) Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics 7: 237. PDF.

• Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF, 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK. (2006) A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 24: 832-40. PDF.

• Choi S, Seo J-S. (2006) Single and dual ligand effects on gene expression changes in mouse macrophage cells. Genomics and Informatics 4: 57-74.

• Choi S. (2006) Construction of chromosome-specific BAC libraries from the filamentous ascomycete Ashbya gossypii. Genomics and Informatics 4: 80-6.

2005

• Kim DH, Behlke MA, Rose SD, Chang MS, Choi S, Rossi JJ. (2005) Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol 23: 222-6.PMID:15619617. PDF.

• Hwang JI, Choi S, Fraser ID, Chang MS, Simon MI. (2005) Silencing the expression of multiple Gbeta-subunits eliminates signaling mediated by all four families of G proteins. Proc Natl Acad Sci U S A 102: 9493-8. PDF.

• Choi S, Liu X, Li P, Akimoto T, Lee SY, Zhang M, Yan Z. (2005) Transcriptional profiling in mouse skeletal muscle following a single bout of voluntary running: evidence of increased cell proliferation. J Appl Physiol 99: 2406-15. PDF.

• Xiaocui Zhu and Sangdun Choi (2005) Understanding cellular signaling networks in mouse macrophage cells. In Introduction to Systems Biology. Humana Press Inc., Totowa, NJ.

• Sangdun Choi, ed. (2005) Introduction to Systems Biology. Humana Press Inc., Totowa, NJ.

• Winston P. Kuo, Peter J. Park, and Sangdun Choi (2005) DNA microarrays and statistical genomic techniques (D. Allison, G. Page, M. Beasley, J. Edwards, Eds). Marcel Dekker Inc., New York.

2004

1. Zhu X, Hart R, Chang MS, Kim JW, Lee SY, Cao YA, Mock D, Ke E, Saunders B, Alexander A, Grossoehme J, Lin KM, Yan Z, Hsueh R, Lee J, Scheuermann RH, Fruman DA, Seaman W, Subramaniam S, Sternweis P, Simon MI, and Choi S. Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands. J Immunol. 2004 Dec 15;173(12):7141-9. DOI:10.4049/jimmunol.173.12.7141 |
2. Levenson JM, Choi S, Lee SY, Cao YA, Ahn HJ, Worley KC, Pizzi M, Liou HC, and Sweatt JD. A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel. J Neurosci. 2004 Apr 21;24(16):3933-43. DOI:10.1523/JNEUROSCI.5646-03.2004 |
3. Hwang JI, Fraser ID, Choi S, Qin XF, and Simon MI. Analysis of C5a-mediated chemotaxis by lentiviral delivery of small interfering RNA. Proc Natl Acad Sci U S A. 2004 Jan 13;101(2):488-93. DOI:10.1073/pnas.0307549100 |
4. Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, and Choi S. Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J Biotechnol. 2004 Sep 9;112(3):225-45. DOI:10.1016/j.jbiotec.2004.05.006 |
5. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pöhlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, and Philippsen P. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 2004 Apr 9;304(5668):304-7. DOI:10.1126/science.1095781 |
6. Kim JH, Ha IS, Hwang CI, Lee YJ, Kim J, Yang SH, Kim YS, Cao YA, Choi S, and Park WY. Gene expression profiling of anti-GBM glomerulonephritis model: the role of NF-kappaB in immune complex kidney disease. Kidney Int. 2004 Nov;66(5):1826-37. DOI:10.1111/j.1523-1755.2004.00956.x |
7. Deane JA, Trifilo MJ, Yballe CM, Choi S, Lane TE, and Fruman DA. Enhanced T cell proliferation in mice lacking the p85beta subunit of phosphoinositide 3-kinase. J Immunol. 2004 Jun 1;172(11):6615-25. DOI:10.4049/jimmunol.172.11.6615 |

Book Chapters:

1.Choi S. (2004) DNA Chips and Microarray Analysis: An Overview. In Handbook of fungal biotechnology, ed. D Arora, pp. 173-9. New York, NY: Marcel Dekker, Inc.Book weblink.

2.Choi S. (2004) Large DNA Transformation. In Bacterial Artificial Chromosomes: Functional Studies, ed. S Zhao, J Walker, pp. 57-68. Totowa, NJ: Humana Press Inc.Goolge book link.

3.Roach T, Choi S, Han H, Zhu H. (2004) Cultured transgenic human Bcl-2 B cells as an alternative signaling model for primary B cells. In Nature - The Signaling Gateway: AfCS Research Reports, pp. 13BC.

2003

• Yan Z, Choi S, Liu X, Zhang M, Schageman JJ, Lee SY, Hart R, Lin L, Thurmond FA, Williams RS. (2003) Highly coordinated gene regulation in mouse skeletal muscle regeneration. J Biol Chem 278: 8826-36. PMID:12477723.PDF.

• Cao YA, Lee SY, Kim JW, Chang MS, Choi S. (2003) Cross comparison of DNA microarray platforms. In Nature - The Signaling Gateway: AfCS Research Reports, pp. DA0010.PDF.

• Sangdun Choi (2003). Systems Biology. Korea Genome Organization (KOGO) News 3(4), p7-9.

• Mi Sook Chang, Yun Anna Cao, and Sangdun Choi (2003) Microarray Protocol for Agilent Inkjet-Deposited Presynthesized Oligo Arrays? Aminoallyl Method. Nature-The Signaling Gateway. PDF.

• Sangdun Choi (2003) G-Protein Coupled Receptor from Molecular Tinkering to Drug Target. KOGO News 3(3), 8-10.

• Sangdun Choi (2003) Biodiversity. KOGO News 3(2), 8-10.

• J.M. Levenson, S. Choi, K.C. Worley, H. Zheng, M. Simon, J.D. Sweatt (2003) Regulation of histone acetylation and gene expression during consolidation of long-term memory in the hippocampus (Neuroscience).

• Sangdun Choi (2003) The DNA structure made Watson and Crick. KOGO News. 3(1), 9-11.

• Yun Anna Cao and Sangdun Choi (2003) Affimetrix Microarray Analysis. Nature-The Signaling Gateway.

• Yun Anna Cao and Sangdun Choi (2003) Microarray Protocol for Agilent Inkjet-Deposited Presynthesized Oligo Arrays. Nature-The Signaling Gateway.

• Jonathan M. Levenson, Sangdun Choi, Sun-Young Lee, Melvin I. Simon, J. David Sweatt (2003) RNA expression profiling of long-term memory consolidation in normal and Alzheimer's hippocampus. Learning & Memory. Cold Spring Harbor Laboratory.

2002

1. Sambrano GR, Chandy G, Choi S, Decamp D, Hsueh R, Lin KM, Mock D, O'Rourke N, Roach T, Shu H, Sinkovits B, Verghese M, and Bourne H. Unravelling the signal-transduction network in B lymphocytes. Nature. 2002 Dec 12;420(6916):708-10. DOI:10.1038/nature01305 |
2. Gilman AG, Simon MI, Bourne HR, Harris BA, Long R, Ross EM, Stull JT, Taussig R, Bourne HR, Arkin AP, Cobb MH, Cyster JG, Devreotes PN, Ferrell JE, Fruman D, Gold M, Weiss A, Stull JT, Berridge MJ, Cantley LC, Catterall WA, Coughlin SR, Olson EN, Smith TF, Brugge JS, Botstein D, Dixon JE, Hunter T, Lefkowitz RJ, Pawson AJ, Sternberg PW, Varmus H, Subramaniam S, Sinkovits RS, Li J, Mock D, Ning Y, Saunders B, Sternweis PC, Hilgemann D, Scheuermann RH, DeCamp D, Hsueh R, Lin KM, Ni Y, Seaman WE, Simpson PC, O'Connell TD, Roach T, Simon MI, Choi S, Eversole-Cire P, Fraser I, Mumby MC, Zhao Y, Brekken D, Shu H, Meyer T, Chandy G, Heo WD, Liou J, O'Rourke N, Verghese M, Mumby SM, Han H, Brown HA, Forrester JS, Ivanova P, Milne SB, Casey PJ, Harden TK, Arkin AP, Doyle J, Gray ML, Meyer T, Michnick S, Schmidt MA, Toner M, Tsien RY, Natarajan M, Ranganathan R, Sambrano GR, and Participating investigators and scientists of the Alliance for Cellular Signaling. Overview of the Alliance for Cellular Signaling. Nature. 2002 Dec 12;420(6916):703-6. DOI:10.1038/nature01304 |

• Sangdun Choi (2002) Transcript Profiling by Microarray Analysis. Nature-The Signaling Gateway.

• Sangdun Choi (2002) Size matters = afcs.org. Korea Genome Organization News. 2(2): p3-5.

• Sangdun Choi (2002) Eternal Life. Korea Genome Organization News. 2(3): p9-11.

• Sangdun Choi (2002) Current issues and technologies of DNA microarrays. Korea Genome Organization News. 2(1): p2-4.

• Jonathan M. Levenson, Sangdun Choi, Melvin I. Simon, J. David Sweatt (2002) Genomic blueprint for formation of contextual fear memory. Neuroscience, Nov. 2-7, 2002. Orlando, FL. 84.14.

2001

1. Choi S, Hao W, Chen CK, and Simon MI. Gene expression profiles of light-induced apoptosis in arrestin/rhodopsin kinase-deficient mouse retinas. Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):13096-101. DOI:10.1073/pnas.201417498 |
2. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, and International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921. DOI:10.1038/35057062 |

3. Hiroaki Shizuya, Sangdun Choi, and Yu-Juin Chen (2001) Supplementary Information. Initial sequencing and analysis of the human genome.

4. Choi S and Kim UJ. Construction of a bacterial artificial chromosome library. Methods Mol Biol. 2001;175:57-68. DOI:10.1385/1-59259-235-X:057 |
5. Yang ZN, Ye XR, Choi S, Molina J, Moonan F, Wing RA, Roose ML, and Mirkov TE. Construction of a 1.2-Mb contig including the citrus tristeza virus resistance gene locus using a bacterial artificial chromosome library of Poncirus trifoliata (L.) Raf. Genome. 2001 Jun;44(3):382-93.

• Sangdun Choi (2001) Gene Stories. Korea Genome Organization News. 1(5): p10-11.
• Sangdun Choi (2001) Array of Arrays. Korea Genome Organization News. 1(4): p4-6.
• Sangdun Choi (2001) Genome Era. Korea Genome Organization News. 1(2): p3-5.
• Sangdun Choi et al. (2001) Light-induced apoptosis. The Scientist

2000

1. Choi S, Begum D, Koshinsky H, Ow DW, and Wing RA. A new approach for the identification and cloning of genes: the pBACwich system using Cre/lox site-specific recombination. Nucleic Acids Res. 2000 Apr 1;28(7):E19. DOI:10.1093/nar/28.7.e19 |
2. Tomkins JP, Miller-Smith H, Sasinowski M, Choi S, Sasinowska H, Verce MF, Freedman DL, Dean RA, and Wing RA. Physical map and gene survey of the Ochrobactrum anthropi genome using bacterial artificial chromosome contigs. Microb Comp Genomics. 1999;4(3):203-17. DOI:10.1089/omi.1.1999.4.203 |

Book Chapters:

1. Sangdun Choi and Rod A. Wing (2000) Construction of Bacterial Artificial Chromosome (BAC) Libraries. In Plant Molecular Biology Manual (2 ed) Kluwer Academic Publishers, The Netherlands (S. Gelvin and R. Schilperoort, Eds.) H5, 1-28.

• Sangdun Choi (2000) Functional genomics. The Biochemistry News 19(3): 215-219.