2009

Krishnan J, Lee G, Choi S. 2009. Drugs Targeting Toll-like Receptors. Arch Pharm Res. 11: 1485-1502

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

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

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

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

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

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

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. Totowa, NJ.: Humana Press Inc.

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

   (S, 6.387) 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.

   (S, 5.85) 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

   (S, 4.958) 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

   (S, 22.738) 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

   (S, 22.738) 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

   (S, 10.231) 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

   (S, 3.037) 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 (Ed. Sangdun Choi). Humana Press Inc., Totowa, NJ.

   Sangdun Choi (2005) Introduction to Systems Biology (Book, Editor: Sangdun Choi) Humana Press Inc., Totowa, NJ.

   Sangdun Choi, Leah T. Santat, Mi Sook Chang, Jong-Ik Hwang, Iain D.C. Fraser, and Melvin I. Simon. Silencing the expression of G protein alpha i2 and beta 2 by small interfering RNAs, small hairpin RNAs or antisense oligonucleotides in mouse macrophage RAW 267.4 cells and their comprehensive comparisons by DNA microarray analyses (submitted to Nature Biotechnology)

   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 (in press)

   Tomoki Ito, Yui-Hsi Wang, Norihiko Watanabe, Shino Hanabuchi, Toshiyuki Hori, Guy J Delespesse, Sangdun Choi, Wei Chen, Xiao-Feng Qin, Wei Cao and Yong-Jun Liu. TSLP-activated dendritic cells trigger TH2 responses by a positive TH2-polarizing signal and a default mechanism (submitted to J Experimental Medicine)

   Jamie A. Lee, Robert S. Sinkovits, Dennis Mock, Eva Rab, Jennifer Cai, Peng Yang, Brian Saunders, Robert C. Hsueh, Sangdun Choi, Shankar Subramaniam and Richard H. Scheuermann. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation (submitted to Blood)

   Jamie A. Lee, Robert Sinkovits, Dennis Mock, Jennifer Cai, Peng Yang, Eva Rab, Brian Saunders, Robert C. Hsueh, Sangdun Choi, Tamara I. A. Roach, Shankar Subramaniam, and Richard H. Scheuermann. Experimental validation of CLASSIFI: a tool for functional classification of microarray gene clusters (submitted to PNAS)

   Sangdun Choi, Kum-Joo Shin, Yun Anna Cao, Sun Young Lee, and Melvin I. Simon. Phototransduction signaling in light-induced retinal degeneration. (submitted to Molecular Vision)

   Dennis Mock, Robert Hsueh, Paul Sternweis, Sangdun Choi, Melvin I. Simon, and Shankar Subramaniam. The analysis of signaling network-based transcriptional network response in murine B-cells (submitted to The Journal of Immunology)

   Sangdun Choi, Xiaocui Zhu, Mi Sook Chang, Robert Hsueh, Paul Sternweis, and Melvin Simon. Regulation of molecular mechanism in B lymphocytes by IL4, AIG, CD40L, and LPS. (in preparation)

   Sangdun Choi, Xiaocui Zhu, Mi Sook Chang, Robert Hsueh, Paul Sternweis, and Melvin Simon. Transcriptional regulation of pathways activated by lipopolysaccharide in RAW 264.7 cells (in preparation)

   Xiaocui Zhu, Robert Hsueh, Paul Sternweis, Melvin I. Simon, and Sangdun Choi. Gene expression profiling reveals interactions of signals activated by different proliferative ligands in B cells (in preparation)

2004

   (S, 6.387) 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 "This Week in The Journal" page of the April 21 issue of The Journal of Neuroscience)

   (S, 7.506) 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

   (S, 10.231) 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

   (S, 2.687) 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

   (S, 30.927) 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

   (S, 4.927) 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.

   (S, 0.3) 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

   (S, 6.387) 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

   (S, 5.85) 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

   (S, 29.273) 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

   (S, 29.273) 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

   Sangdun Choi, Wenshan Hao, Ching-Kang Chen, and Melvin I. Simon (2001). Gene expression profiling: transcription analysis of light-induced visual degeneration using mouse oligonucleotide microarrays. Proc. Natl. Arcd. Sci. USA 98:13096-13101

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

   Hiroaki Shizuya, Sangdun Choi, and Yu-Juin Chen (2001) Supplementary Information for "Initial Sequencing and Analysis of the Human Genome" Nature, V412, 565

   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, Dilara Begum, Heather Koshinsky, David Ow, D. and Rod A. Wing (2000). (S. Choi: corresponding author) A new approach for the identification and cloning of genes: pBACwich system using Cre-lox site specific recombination. Nucleic Acid Research 1; 28(7): E19

   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