Sangdunchoi:Papers

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Sangdun Choi Lab





Due to copyright restrictions, we are unable to provide the manuscript online for few papers. Please email (sangdunchoi@ajou.ac.kr) for an electronic reprint.


2014









2013





  • 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.



  • 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



  • Krishnan J, Basith S, Choi S. 2012. Advances in Toll-like Receptor Signaling. Advances in Systems Biology 1: 5-15. PDF








  • Choi S. 2012. As the director of the stage starring TLR, IκB-ζ and ATF3. Molecular and Cellular Biology News 2012: 1-8. *




2011















  • 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


  • 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






2010

  • Shaherin Basith and Sangdun Choi (2010) This Month in APR: Overview of human cytochrome P450 networks in chemical space. Archives of Pharmacal Research. 33: 9.PDF


  • 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


  • Oh YT, Oh KS, Choi YM, Jokiaho A, Donovan C, et al. (2010) Continuous Nictinic Acid Infusion in Rats Causes FFA Rebound by Altering Gene Expression in Adipose Tissue. Journal of Lipid Research 5(12):e14181.PMID:21386057 PDF


  • Manavalan B, Murugapiran SK, Lee G, Choi S. (2010) 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 10: 1.PMID:20067617.PDF


  • Manavalan B, Govindaraj RG, Lee G, Choi S. (2010) Molecular Modeling-based Evaluation of Dual Function of IκBζ Ankyrin Repeat Domain in Toll-like Receptor Signaling. Journal of Molecular Recognition DOI:10.1002.PMID:21472811.*


  • Manavalan B, Basith S, Choi YM, Lee G, Choi S. (2010) Structure-Function Relationship of Cytoplasmic and Nuclear IκB Proteins: An in silico analysis. PLoS ONE 5(12): e15782. PMID:21203422.PDF


  • Kim EY, Shin HY, Kim JY, Kim DG, Choi YM, et al.. (2010) ATF3 Plays a Key Role in Kdo2-Lipid A-induced TLR4-dependent Gene Expression via NF-kB Activation. PLoS ONE 5: e14181.PMID:21152039.PDF


  • Govindaraj RG, Manavalan B, Lee G, Choi S. (2010) Molecular modeling-based evaluation of hTLR10 and identification of potential ligands in Toll-like receptor signaling. PLoS ONE 5: e12713. PMID:20877634. PDF


  • Choi S, Yoon H, Oh KS, Oh YT, Kim YI, et al. (2010) Widespread effects of nicotinic acid on gene expression in insulin-sensitive tissues: implications for unwanted effects of nicotinic acid treatment. Metabolism Clinical and Experimental.PMID:20303128.[3]


  • Paik MJ, Ahn YH, Lee PH, Kang H, Park CB, et al. (2010) Polyamine patterns in the cerebrospinal fluid of patients with Parkinson's disease and multiple system atrophy. Clin Chim Acta.411: 1532-1535.PMID:20515677.*


2009

  • Krishnan J, Lee G, Choi S. (2009) Drugs Targeting Toll-like Receptors. Arch Pharm Res. 11: 1485-1502.[PMID:20091261


  • Lee KA, Shim W, Paik MJ, Lee SC, Shin JY, Park K, Kim JH, Choi S, Lee G. (2009) Analysis of changes in the viability and gene expression profiles of human mesenchymal stromal cells over time. Cytotherapy 11: 688-967.PMID:19878055.PDF


  • You MH, Kim WJ, Shim W, Lee SR, Lee G, Choi S, Kim DY, Kim YM, Kim H, Han SU. (2009) Cytosine deaminase-producing human mesenchymal stem cells mediate an antitumor effect in a mouse xenograft model. J Gastroenterol Hepatol 24: 1393-1400.PMID:19486256.PDF


  • Lee G, Lee SS, Kay KY, Kim DW, Choi S, Jun HK. (2009) Isolation and characterization of a novel adenosine deaminase inhibitor, IADA-7, from Bacillus sp. J-89. J Enzyme Inhib Med Chem 24: 59-64.PMID:18608782


  • Hwang DY, Hong S, Jeong JW, Choi S, Kim H, Kim J, Kim KS. (2009) VMAT2 and DAT are molecular targets of Pitx3 in the ventral midbrain dopamine neurons. J Neurochem 111: 1202-1212


  • Lee G, Santat LA, Chang MS, Choi S. (2009) RNAi methodologies for the functional study of signaling molecules. PLoS ONE 4: e4559.PMID:19238203.PDF


  • Tsuchiya M, Piras V, Choi S, Akira S, Tomita M, Giuliani A, Selvarajoo K. (2009) Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages. PLoS ONE 4: e4905.PMID:19300509.PDF


  • Paik MJ, Li WY, Ahn YH, Lee PH, Choi S, Kim KR, Kim YM, Bang OY, Lee G. (2009) The free fatty acid metabolome in cerebral ischemia following human mesenchymal stem cell transplantation in rats. Clin Chim Acta 402: 25-30.PMID:19161994

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


  • 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


  • 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


  • 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


  • 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


2007

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


  • 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


  • 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


  • 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.


  • 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


  • 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


  • 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


  • 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


  • 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


  • 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


  • 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

  • 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, Choi S. (2004) Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands. J Immunol 173: 7141-9


  • Jonathan M. Levenson, Sangdun Choi, Sun-Young Lee, Yun Anna Cao, Kim Worley, Hui Zheng, and David Sweatt (2004) A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-Rel. The Journal of Neuroscience. 24, p3933-3943 (also chosen for the


  • Levenson JM, Choi S, Lee SY, Cao YA, Ahn HJ, Worley KC, Pizzi M, Liou HC, Sweatt JD. (2004) A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel. J Neurosci 24: 3933-43


  • Hwang JI, Fraser ID, Choi S, Qin XF, Simon MI. (2004) Analysis of C5a-mediated chemotaxis by lentiviral delivery of small interfering RNA. Proc Natl Acad Sci U S A 101: 488-93


  • Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S. (2004) Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J Biotechnol 112: 225-45


  • Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K,Steiner S, Mohr C, Pohlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304: 304-7


  • Kim JH, Ha IS, Hwang CI, Lee YJ, Kim J, Yang SH, Kim YS, Cao YA, Choi S, Park WY. (2004) Gene expression profiling of anti-GBM glomerulonephritis model: the role of NF-kappaB in immune complex kidney disease. Kidney Int 66: 1826-37


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


  • 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.


  • 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


  • Deane JA, Trifilo MJ, Yballe CM, Choi S, Lane TE, Fruman DA. (2004) Enhanced T cell proliferation in mice lacking the p85beta subunit of phosphoinositide 3-kinase. J Immunol 172: 6615-25


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


  • 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


  • 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


  • 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

  • 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, Bourne H. (2002) Unravelling the signal-transduction network in B lymphocytes. Nature 420: 708-10


  • 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. (2002) Overview of the Alliance for Cellular Signaling. Nature 420: 703-6


  • 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


  • Eric Lander .. Sangdun Choi, et al. (2001) Initial sequencing and analysis of the human genome. Nature (2001) 409:860-921. PMID: 11237011



  • Sangdun Choi and Ung-Jin Kim (2001) Construction of a bacterial artificial chromosome library. In Genomics Protocol. Methods Mol Biol. The Humana Press Inc., U.K. (R. Elaswarapu and M. Starkey, Eds.) 175: p57-68


  • Yang, Z. N., Ye, X. R., Choi, S., Molina, J., Moonan, F., Wing, R. A., Roose, M. L., and Mirkov. (2001) T. E. Construction of a 1.2 MB contig in the Citrus Tristeza virus resistance gene locus using a bacterial artificial chromosome library of Poncirus trifoliate (L.) RAF. Genome 44:382-393


  • Sangdun Choi and Ung-Jin Kim (2001) Construction of a bacterial artificial chromosome library. In Genomics Protocol. Methods Mol Biol. The Humana Press Inc., U.K. (R. Elaswarapu and M. Starkey, Eds.) 175: p57-68


  • 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


  • 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


  • Tomkins, J. P., Miller-Smith, H., Sasinowski, M., Choi, S., Sasinowska, H., Verce, M., Freedman, D. L., Dean, R. A., and Wing, R. A. (2000) Physical map and organization of the Ochrobactrum anthropi genome using bacterial artificial chromosome contigs. Microbial & Comparative Genomics 4(3): 203-217
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