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Innate Immunity, Cell Signaling and Molecular Modeling Laboratory


  1. 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 | PubMed ID:33946869 | HubMed [1]
  2. 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 | PubMed ID:33803178 | HubMed [2]

All Medline abstracts: PubMed | HubMed


  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 | PubMed ID:33322533 | HubMed [1]
  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 | PubMed ID:33200028 | HubMed [2]
  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 | PubMed ID:33050544 | HubMed [3]
  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. Oreganum Vulgare: In-vitro assessment of cytotoxicity, Molecular docking studies, Antioxidant, and evaluation of anti-inflammatory activity in LPS stimulated RAW 264.7 cells. Med Chem. 2020 Sep 4. DOI:10.2174/1573406416666200904110828 | PubMed ID:32885758 | HubMed [4]
  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 | PubMed ID:32842628 | HubMed [5]
  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 | PubMed ID:31054927 | HubMed [6]
  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 | PubMed ID:32660060 | HubMed [7]
  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 | PubMed ID:32220799 | HubMed [8]
  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 | PubMed ID:32325904 | HubMed [9]
  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 | PubMed ID:32014819 | HubMed [10]
  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 | PubMed ID:32023919 | HubMed [11]
  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 | PubMed ID:32012718 | HubMed [12]
  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 | PubMed ID:32012695 | HubMed [13]

All Medline abstracts: PubMed | HubMed


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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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  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 | PubMed ID:31283217 | HubMed [5]
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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 | PubMed ID:31028244 | HubMed [10]
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  13. Yesudhas D, Anwar MA, and Choi S. Structural mechanism of DNA-mediated Nanog–Sox2 cooperative interaction. RSC Adv. 2019;9:8121-8130. DOI: 10.1039/c8ra10085c


All Medline abstracts: PubMed | HubMed


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  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 | PubMed ID:30328798 | HubMed [2]
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All Medline abstracts: PubMed | HubMed

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


  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 | PubMed ID:29214999 | HubMed [1]
  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 | PubMed ID:29123983 | HubMed [2]
  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 | PubMed ID:28900197 | HubMed [3]
  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 | PubMed ID:28783137 | HubMed [4]
  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 | PubMed ID:28763006 | HubMed [5]
  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 | PubMed ID:28620391 | HubMed [6]
  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 | PubMed ID:28570013 | HubMed [7]
  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 | PubMed ID:28272553 | HubMed [8]
  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 | PubMed ID:28254693 | HubMed [9]

All Medline abstracts: PubMed | HubMed

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


  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 | PubMed ID:27982096 | HubMed [1]
  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 | PubMed ID:27930990 | HubMed [2]
  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 | PubMed ID:27845762 | HubMed [3]
  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 | PubMed ID:27666530 | HubMed [4]
  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 | PubMed ID:27631699 | HubMed [5]
  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 | PubMed ID:27602749 | HubMed [6]
  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 | PubMed ID:27515048 | HubMed [7]
  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 | PubMed ID:27378605 | HubMed [8]
  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 | PubMed ID:27136061 | HubMed [9]
  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 | PubMed ID:26878224 | HubMed [10]
  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 | PubMed ID:26790000 | HubMed [11]
  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 | PubMed ID:26593376 | HubMed [12]

All Medline abstracts: PubMed | HubMed


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All Medline abstracts: PubMed | HubMed


  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 | PubMed ID:25076949 | HubMed [1]
  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 | PubMed ID:25034608 | HubMed [2]
  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 | PubMed ID:24796306 | HubMed [3]
  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 | PubMed ID:24776761 | HubMed [4]
  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 | PubMed ID:24768635 | HubMed [5]
  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 | PubMed ID:24759152 | HubMed [6]

All Medline abstracts: PubMed | HubMed


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  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 | PubMed ID:23665163 | HubMed [2]
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All Medline abstracts: PubMed | HubMed

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.


  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 | PubMed ID:23346038 | HubMed [1]
  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 | PubMed ID:23166766 | HubMed [2]
  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 | PubMed ID:23166526 | HubMed [3]
  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 | PubMed ID:23151919 | HubMed [4]
  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 | PubMed ID:23028726 | HubMed [5]
  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 | PubMed ID:22941474 | HubMed [6]
  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 | PubMed ID:22830605 | HubMed [7]
  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 | PubMed ID:22496842 | HubMed [8]

All Medline abstracts: PubMed | HubMed

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.


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All Medline abstracts: PubMed | HubMed

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.


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All Medline abstracts: PubMed | HubMed

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.


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All Medline abstracts: PubMed | HubMed


  • 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.


  • 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


  • 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.


  • 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.


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  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 | PubMed ID:15585835 | HubMed [1]
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All Medline abstracts: PubMed | HubMed

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.


  • 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.


  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 | PubMed ID:12478302 | HubMed [1]
  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 | PubMed ID:12478301 | HubMed [2]

All Medline abstracts: PubMed | HubMed

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


  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 | PubMed ID:11687607 | HubMed [1]
  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 | PubMed ID:11237011 | HubMed [2]
  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 | PubMed ID:11462856 | HubMed [4]
  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. PubMed ID:11444697 | HubMed [5]

All Medline abstracts: PubMed | HubMed

  • 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


  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 | PubMed ID:10710436 | HubMed [1]
  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 | PubMed ID:10587947 | HubMed [2]

All Medline abstracts: PubMed | HubMed

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.