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  • Lee SY, Jhun J, Woo JS, Lee KH, Hwang SH, Moon J, Park G, Choi SS, Kim SJ, Jung YJ, Song KY, Cho ML. Gut microbiome-derived butyrate inhibits the immunosuppressive factors PD-L1 and IL-10 in tumor-associated macrophages in gastric cancer. Gut Microbes. 2024 Jan-Dec;16(1):2300846

  • Kim J, Kim H, Lee MS, Lee H, Kim YJ, Lee WY, Yun SH, Kim HC, Hong HK, Hannenhalli S, Cho YB, Park DH, and Choi SS* (2023). Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients. Journal of Translational Medicine 21:209

  • Min HK, Na HS, Jhun J, Lee SY, Choi SS, Park GE, Lee JS, Um IG, Lee SY, Seo H, Shin TS, Kim YK, Lee JJ, Kwok SK, Cho ML, Park SH (2023). Identification of gut dysbiosis in axial spondyloarthritis patients and improvement of experimental ankylosing spondyloarthritis by microbiome-derived butyrate with immune-modulating function. Frontiers in Immunology 14:1096565

  • Lim J, Heo Y, Choi SS* (2023). Investigation of changes in DNA methylation associated with alterations in gene expression resulting in differences between lean and obese adipogenesis. Genomics 115, 110623.

  • Lee SK, Jhun JY, Lee SY, Choi SJ, Choi SS, Park MS, Lee SY, Cho KH, Lee AR, Ahn J, Choi HJ, You YK, Sung PS, Jang JW, Bae SH, Yoon SK, Cho ML, and Choi JY (2022). A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients. Gut Microbes 14(1):e2102885
  • Heo Y, Kim H, Lim J, Choi SS* (2022). Adipocyte differentiation between obese and lean conditions depends on changes in miRNA expression. Sci Reports 12:11543  
  • Choi S, Chung J, Cho ML, Park D, Choi SS* (2021). Analysis of changes in microbiome compositions related to the prognosis of colorectal cancer patients based on tissue-derived 16S rRNA sequences. J Transl Med. 19(1):485
  • Thi-Duy P, Choi SS, Park HR, Lee A, Jeong SH, Choi Y (2021). Gene Signatures associated with barrier dysfunction and infection in oral lichen planus identified by analysis of transcriptomic data. Plos One : e0257356
  • Lee YE, Lee J, Lee YS, Jang JJ, Woo H, Choi HI, Chai YG, Kim TK, Kim TS, Kim LK, and Choi SS* (2021). Identification and functional characterization of two noncoding RNAs transcribed from putative active enhancers in hepatocellular carcinoma. Mol and Cells 44(9): 658-669
  • Sin S, Choi HM, Lim J, Kim J, Bak SH, Choi SS, Park J, Lee JH, Oh YM, Lee MK, Hobbs BD, Cho MH, Silverman EK, Kim WJ (2021). A genome-wide association study of quantitative computed tomographic emphysema in Korean populations. Sci Reports 11: 16692
  • Choi HM, Lee SH, Lee MS, Park D, Choi SS* (2021). Investigation of the putative role of antisense transcripts as regulators of sense transcripts by correlation analysis of sense-antisense pairs in colorectal cancers. Faseb J. (35), e21482 (1-16).
  • Lee J, Park H, Lim J, Jin HS, Park Y, Jung YJ, Ko HJ, Yoon SI, Lee GS, Kim PH, Choi SS, Xiao C, Kang SG (2021). GSK3 restrains germinal center B cells to form plasma cells. J. of immunol (206): 481-493
  • Rasaei R, Kim E, Kim JY, Na S, Kim JH, Heo J, Shin DM, Choi SS, Hong SH (2020). Regulation of JAM2 expression in the lungs of streptozotocin-induced diabetic mice and human pluripotent stem cell-derived alveolar organoids. Biomedicines 8.9:346
  • Lee SH, Choi NH, Koh IU, Kim BJ, Lee S, Kim SC, Choi SS (2020). Putative positive role of inflammatory genes in fat deposition supported by altered gene expression in purified human adipocytes and preadipocytes from lean and obese adipose tissues. Journal of Translational Medicine 18:433 
  • Lee J, Lee J, Baek S, Koh JH, Kim JW, Kim SY, Chung SH, Choi SS, Cho ML, Kwok SK, Ju JH, Park SH (2019). Soluble siglec-5 is a novel salivary biomarker for primary Sjogren’s syndrome. Journal of Autoimmunity. doi: 10.1016/j.jaut.2019.03.008
  • Kim DY, Kim YJ, Kim JH, Hong SH, Choi SS (2019). Identification of putative regulatory alterations leading to changes in gene expression in chronic obstructive pulmonary disease. Molecules and Cells. doi: 10.14348/molcells.2019.2442
  • Jo S, Choi SS (2019). Analysis of the functional relevance of epigenetic chromatin marks in the first intron associated with specific gene expression patterns. Genome Biology and Evolution 11 (3): 786-897
  • Jo S, Choi SS (2019). Enrichment of rare alleles within epigenetic hromatin marks in the first intron. Genomics and informatics 17(1):e9
  • Hong Y, Hong SK, Oh YM, Shin SH, Choi SS, KIM UJ (2018). Identification of lung cancer specific differentially methylated regions using genome-wide DNA methylation study. Mol Cell Toxicol 14:315-322
  • Lee JS, Lee J, Kwok SK, Baek SY, Jang SG, Hong SM, Min JW, Choi SS, Lee JH, Cho ML, Park SH (2018). Jak-1 Inhibition Suppresses Interferon-induced Baff Production in Human Salivary Gland: Potential Therapeutic Strategy for Primary Sjögren's Syndrome. Arthritis & Rheumatology. 70:2057-2066
  • Chae HS, You BH, Kim DY, Lee H, Ko HJ, Choi YH, Choi SS, Chin YW (2018). Sauchinone controls hepatic cholesterol homeostasis by the negative regulation of PCSK9 transcriptional network. Sci Reports 8:6737
  • Im EH, Hahn YS, Choi SS (2018). Functional relevance of synonymous alleles reflected in allele rareness in the population. Genomics 110:347-354
  • Min JW, Koh Y, Kim DY, Kim HL, Han JA, Jung YJ, Yoon SS, Choi SS (2018). Identification of novel functional variants of SIN3A and SRSF1 among somatic variants in acute myeloid leukemia patients. Mol. Cells 41.5:465
  • Im EH, Choi SS (2017). Synonymous Codon Usage Controls Various Molecular Aspects. Genomics and Inform 15:1-5
  • Kim SK, Park I, Park SG, Cho S, Jin Kim JH, Ipper NS, Choi SS, Lee ES, and Hong HJ (2017). Generation, diversity determination, and application to antibody selection of a human naïve Fab library. Mol. Cells 40: 655-666
  • Cho EH, Min JW, Choi SS, Choi HS, Kim SW (2017). Identification of GCKMODY by Whole Exome Sequencing. Endocrinology and metabolism 32: 296–301
  • Ahn S, Jeong E, Min JW, Kim E, Choi SS, Kim CJ, Lee DC (2017). Identification of genes dysregulated by elevation of microRNA-210 levels in human trophoblasts cell line, Swan 71. Am J Reprod Immunol. 78:e12722
  • Cho JH, Lee HJ, Ko HJ, Yoon BI, Choe J, Kim KC, Hahn TW, Han JA, Choi SS, Jung YM, Lee KH, Lee YS, Jung YJ (2017). The TLR7 agonist imiquimod induces anti-cancer effects via autophagic cell death and enhances anti-tumoral and systemic immunity during radiotherapy for melanoma. Oncotarget 8, 24932-24948
  • Park D, Huh HJ, Kim YJ, Son DS, Jeon HJ, Im EH, Kim JW, Lee NY, Kang ES, Kang CI, Chung DR, Ahn JH, Peck KR, Choi SS, Kim YJ, Ki CS, Park WY (2016). Analysis of intra-patient heterogeneity uncovers the microevolution of Middle East respiratory syndrome coronavirus. Cold Spring Harb Mol Case Stud 2: a001214
  • Lee EK, Hong SH, Shin S, Lee HS, Lee JS, Park EJ, Choi SS, Min JW, Park D, Hwang JA, Johnson BH, Jeon SH, Kim IH, Lee YS, Lee YS (2016). nc886, a non-coding RNA and suppressor of PKR, exerts an oncogenic function in thyroid cancer. Oncotarget doi: 10.18632/oncotarget.11852
  • Park DH, Huh HJ, Kim YJ, Son DS, Jeon HJ, Im EH, Kim JW, Lee NY, Kang ES, Kang CI, Chung DR, Ahn JH, Peck KR, Choi SS, Kim YJ, Ki YJ, Ki CS, Park WY (2016). Analysis of intra-patient heterogeneity uncovers the microevolution of Middle East respiratory syndrome coronavirus. Mol Case Stud doi: 0.1101/mcs.a001214
  • Jo BS, Koh IU, Bae JB, Yu HY, Jeon ES, Lee HY, Kim JJ, Choi M, and Choi SS (2016). Data of methylome and transcriptome derived from human dilated cardiomyopathy. Data in Brief 10.1016/j.dib.2016.09.006
  • Lee EK, Hong SH, Shin S, Lee HS, Lee JS, Park EJ, Choi SS, Min JW, Park D, Hwang JA, Johnson B, Jeon SH, Kim IH, Lee YS, and Lee Y (2016). nc886, a non-coding RNA and suppressor of PKR, exerts an oncogenic function in thyroid cancer. Oncotarget 7.46 (2016): 75000.
  • Jo BS, Koh IU, Bae JB, Yu HY, Jeon ES, Lee HY, Kim JJ, Choi M, and Choi SS (2016). Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy. Genomics 108, 84-92
  • Yang JY, Kim MS, Kim E, Cheon JH, Lee YS, Kim Y, Lee SH, Seo SU, Shin SH, Choi SS, Kim B, Chang SY, Ko HJ, Bae JW, Kweon MN (2016) Enteric Viruses Ameliorate Gut Inflammation via Tolllike Receptor 3 and Toll-like Receptor 7-Mediated Interferon-b Production. Immunity doi:10.1016/j.immuni.2016.03.009
  • An HJ, Lee HJ, Jang S, Jung YJ, Choi SS, Park SC (2016). Transcription factor Sp1 prevents TRF2-induced premature senescence in human diploid fibroblasts. Mol Cell Biochem 2016 Mar;414(1-2):201-8.doi:10.1007/s11010-016-2672-7
  • Min JW, Choi SS (2015). Expressional Subpopulation of Cancers Determined by G64, a Co-regulated Module. Genomics Inform 2015;13(4):132-136
  • Jo BS, Choi SS (2015). Introns: The Functional Benefits of Introns in Genomes. Genomics Inform 2015;13(4):112-118
  • Min J-W, Kim WJ, Han JA, Jung Y-J, Kim K-T, Park W-Y, Lee H-O, Choi SS (2015). Identification of Distinct Tumor Subpopulations in Lung Adenocarcinoma via Single-Cell RNA-seq. PLoS ONE 10(8):e0135817.doi:10.1371/journal.pone.0135817
  • Shin SH, Choi SS (2015). Lengths of coding and noncoding regions of a gene correlate with gene essentiality and rates of evolution. Genes & Genomics 37: 365-374
  • Lee HJ, Kim KC, Hahn JA, Choi SS, Jung YJ (2015). The Early Induction of Suppressor of Cytokine Signaling 1 and the Downregulation of Toll-like Receptors 7 and 9 Induce Tolerance in costimulated Macrophages. Molecules and cells 38: 26-32
  • Lee HY, Han SS, Rhee H, Park JH, Lee JS, OH YM, Choi SS, Shin SS, Kim WJ (2015). Differential expression of miRNAs and their target genes in non-small-cell lung cancer. Molecular Medicine Reports 11: 2034-2040
  • Jung JI, Cho HJ, Jung YJ, Kwon SH, Her Song, Lee KW, Shin SH, Choi SS, and Park J (2015). High-fat diet-induced obesity increases lymphagiogenesis and lymph node metastasis in the B16F10 melanoma allograft model: Roles of adipocytes and M2-macrophages. International journal of Cancer 136: 258-270.
  • Park SG, Hannenhalii S, and Choi SS (2014). Conservation in first introns is positively correlated with the number of exons within genes and the presence of regulatory epigenetic signals. BMC genomics 15:526
  • Oh J, Rho HS, Yang Y, Yoon JY, Lee J, Hong YD, Kim HC, Choi SS, Kim TW, Shin SS, Cho JY (2013). Extracellular Signal-Regulated Kinase Is a Direct Target of the Anti-Inflammatory Compound Amentoflavone Derived from Torreya nucifera. Mediators of inflammation : 11 pages
  • Choi SS and Hannenhalli S (2013). Three independent determinants of protein evolutionary rate. J. Mol. Evol. 76: 98-111
  • Yang H, Ko HJ, Yang JY, Kim JJ, Seo SK, Park SG, Choi SS, Seong JK and Kweon MN (2013). Interleukin-1 promotes coagulation which is necessary for protective immunity in the lung against Streptococcus pneumoniae infection. The Journal of Infectious Disease 207: 50-60
  • Cho H, Han S, Choe J, Park SG, Choi SS, Kim YK (2013). SMG5-PNRC2 is a functionally dominant complex in mammalian nonsense-mediated mRNA decay. Nucleic Acids Res 41:1319-1328
  • Lee ME, Kim SR, Lee S, Jung YJ, Choi SS, Kim UJ, and Han JA (2012). Cyclooxygenase-2 inhibitors modulate skin aging in a catalytic activity-independent manner. Exp Mol Med. 44(9): 536–544.
  • Cho H, Kim KM, Han S, Choe J, Park SG, Choi SS, and Kim YK (2012). Staufen1-mediated mRNA decay functions in adipogenesis. Molecular cell 46, 495-506
  • Park SG, Kwon KH, and Choi SS (2012). Analysis of putative miRNA function using a novel approach, GAPPS-miRTARGE. Genes and Genomics 34, 205-216.
  • Mok YJ, Park SG, and Choi SS (2012). Comparative analysis of the structural and expressional parameters of miRNA target genes. Gene 497, 103-109.
  • Lee SY, Lee YG, Byeon SE, Han S, Choi SS, Kim AR, Lee J, Lee SJ, Hong S, and Cho JY (2010). Mitogen Activated Protein Kinases are Prime Signalling Enzymes in Nitric Oxide Production Induced by Soluble β-Glucan from Sparassis crispa. Arch Pharm Res 11, 1753-1760.
  • Park SG and Choi SS (2010). Expression breadth and expression abundance behave differently in correlation with evolutionary rates. BMC evolutionary biology 10: 241
  • Choi SS, Chung EK, and Jung YJ (2010). Newly Identified CpG ODNs, M5-30 and M6-395, stimulate mouse immune cells to secrete TNF-a and enhance Th-1 mediated immunity. The Journal of Microbiol. 48: 512-517
  • Choi SS (2010). The frequency of neural stem cells in in vitro culture systems: insights from simple modeling. Genes and Genomics 32:225-231
  • You DS, Lee J, Choi SS, Rho HS, Cho DH, Shin WC, Cho JY (2010). A modulatory effect of novel kojic acid derivatives on cancer cell proliferation and macrophage activation.  Pharmazie 65. 261-266
  • Park D, Choi SS, Ha KS (2010). Transglutaminase 2: a multi-functional protein in multiple subcellular compartments.  Amino acids 39:619-631
  • Park SG, Park D, Jung YJ, Jung EK, Choi SS (2010). Positive selection signature in the TLR7 family. Genes and Genomics 32:143-150
  • Choi SS (2009). Controversies on the rates of protein evolution. Interdisplinary Bio Central 11:1-5
  • Yi JY, Jung YJ, Choi SS, Chung E (2009). TNF-alpha downregulates E-cadherin and sensitizes responses to gamma irradiation in Caco-2 cells. Cancer Res Treat 41: 164-70
  • Yi JY, Jung YJ, Choi SS, Hwang J, Chung E (2009). Autophagy-mediated antitumoral activity of imiquimod in Caco-2 cells. BBRC 386, 455-8
  • Park D, Xiang AP, Mao FF, Walton NM, Choi SS, Lahn BT (2009). The radial glia antibody RC2 recognizes a protein encoded by Nestin. BBRC 382, 588-92
  • Park D, Park J, Park SG, Park T, Choi SS (2008). Analysis of human disease genes in the context of gene essentiality. Genomics 92, 414-418.
  • Kwon, Y.K., Choi S.S., Cho, K.H. (2007). Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling. BMC Bioinformatics 8, 384
  • Choi, S.S., Vallender, E.J., Lahn, B.T. (2006). Systematically Assessing the Influence of Three-Dimensional Structural Context on the Molecular Evolution of Mammalian Proteomes. Mol. Biol. Evo. 23:2131-2133
  • Choi, S.S., Bush, E. Lahn, B.T. (2006). Different classes of tissue-specific genes show different levels of noncoding conservation. Genomics 87:433-436.
  • Choi, S.S., Li, W., Lahn, B.T (2005). Robust signals of coevolution of interacting-residue in mammalian proteomes identified by phylogeny-aided structural analysis. Nature Genet. 12:1367-1371
  • Dorus, S., Evans, P.D., Wyckoff, G.J., Choi, S.S., & Lahn, B.T. (2004). Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity. Nature Genet. 36: 1326-1329.
  • Hong, S.H., Kim, J.S., Lee, S.Y., In, Y.H., Choi, S.S., Rih, J.-K., Kim, C.H., Jeong, H.Y., Hur, C.G., & Kim, J.J. (2004). The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nature Biotech. 22: 1275-1281.
  • Evans, P.D., Anderson, J.R., Vallender, E.J., Choi, S.S., Lahn, B.T. (2004).  Reconstructing the evolutionary history of Microcephalin, a gene controlling human brain size. Hum Mol Genet. 13:1139-1145.
  • Choi, S.S., Lahn, B.T. (2003). Adaptive evolution of MRG, a neuron-specific gene family implicated in nociception. Genome Res 13: 2252-2259.
  • Choi, S.S., Kang, Y.S., Kim, U.-J., Lee, K.H., Shin, H.-S. (1999). Chromosomal localization of ESTs from human fetal liver via BAC-mediated FISH mapping. Mol. Cells 9: 403-409.
  • Jung-Ha, H., Kim, D., Lee, S.-B., Hong, S.-I., Park, S.-Y., Huh, J., Kim, C.-W., Kim S.-S., Lee, Y., Choi, S.S., Shin, H.-S. (1998). Expression of Bfl-1 in Normal and Tumor Tissues: Bfl-1 Overexpression in cancer due to its preferential expression in infiltrating inflammatory cells. Human pathology 29: 723-728.
  • Park, I.C., Lee, S.H., Whang, D.Y., Hong, W.S., Choi, S.S., Shin, H.S., Chae, T.B., Hong, S.I (1997). Expression of a novel Bcl-2-related gene, Bfl-1, in various human cancers & cancer cell lines.  Anticancer Res. 17, 4619-4622.
  • Choi, S.S., Park, S.H., Kim, U.-J., Shin, H.-S. (1997). Bfl-1, a Bcl-2-related gene, is the human homolog of the murine A1, and maps to Chromosome 15q24.3. Mamm. Genome 8, 781-782.
  • Kim, U.-J., Shizuya, H., Kang, H.-L., Choi, S.S., Garrett, C.L., Smink, L.J., Birren, B.W., Korenberg, J.R., Dunham, I., and Simon, M.I. (1996). A bacterial artificial chromosome-based framework contig map of human chromosome 22q. Proc. Natl. Acad. Sci. USA 93: 6297-6301.
  • Choi, S.S., Yun, J.W., Choi, E.K., Cho, Y.G., Sung, Y.C., Shin, H.-S. (1995b). Construction of a gene expression profile of a human fetal liver by single-pass cDNA sequencing. Mamm. Genome 6, 653-657.
  • Choi, S.S., Park, I.C., Yun, J.W., Sung, Y.C., Hong, S.I., Shin, H.-S. (1995a). A novel Bcl-2 related gene, Bfl-1, is overexpressed in stomach cancer and preferentially expressed in bone marrow. Oncogene 11, 1693-1698.