Journals

Publication

2023

  1. Gyu-Bum Yeon, Byeong-Min Jeon, Seo Hyun Yoo, DongYun Kim, Sanghyun Park, Won-Ho Shin, Hyung Wook Kim, Dokyun Na, Dong-Wook Kim, and Dae-Sung Kim. (2023) “Differentiation of astrocytes with characteristics of ventral midbrain from human embryonic stem cells” Stem Cell Reviews and Reports (Accepted)

2022

  1. Jun Ren, Hyang-Mi Lee, JunHao Shen, and Dokyun Na* (2022) “Advanced biotechnology using methyltransferase and its applications in bacteria: a mini review” Biotechnology Letters 44: 33-44, 10.1007/s10529-021-03208-9 (2021.11.25)
  2. Bilal Shaker, Sajjad Ahmad, Junhao Shen, Hyung Wook Kim* and Dokyun Na* (2022) “Computational design of a multi-epitope vaccine against Porphyromonas gingivalis”  Frontiers in Immunology 13:806825, 10.3389/fimmu.2022.806825
    (2022.02.18)
  3. Jae Gwang Song†, Myeong-Sang Yu†, Bomi Lee, Jingyu Lee, Su-Hee Hwang, Dokyun Na*, and Hyung Wook Kim* (2022) “Analysis methods for the gut microbiome in neuropsychiatric and neurodegenerative disorders” Computational and Structural Biotechnology Journal 20: 1097-1110, 10.1016/j.csbj.2022.02.024 (2022.03.05)
  4. Jingyu Lee, Myeong-sang Yu, and Dokyun Na* (2022) “DILI-Stk: an ensemble model for the prediction of drug-induced liver injury of drug candidates” Current Bioinformatics 17(3): 296-303, 10.2174/1574893617666211228113939 (2022.03.17)
  5. Jun Ren†, Suhee Hwang†, Junhao Shen, Hyeongwoo Kim, Hyunjoo Kim, Jieun Kim, Soyoung Ahn, Min-gyun Kim, Seung-Ho Lee, Dokyun Na* (2022) “Enhancement of the solubility of recombinant proteins by fusion with a short-disordered peptide” Journal of Microbiology 60(9): 960-967, 10.1007/s12275-022-2122-z (2022.07.14)
  6. Juseong Oh, Hyi-thaek Ceong*, Dokyun Na*, Chungoo Park* (2022) “A machine learning model for classifying G-protein-coupled receptors as agonists or antagonists” BMC Bioinformatics 23(suppl 9):346, 10.1186/s12859-022-04877-7 (2022.08.18) 

2021

  1. Hyang-Mi Lee, Jun Ren, Kha Mong Tran, Byeong-Min Jeon, Won-Ung Park, Hyunjoo Kim, Kyung Eun Lee, Yuna Oh, Myungback Choi, Dae-Sung Kim, and Dokyun Na*. (2021). “Identification of efficient prokaryotic cell-penetrating peptides with applications in bacterial biotechnology” Communications Biology 4, 205 (2021.02.15) 
  2. Phuong N. Lam Vo, Hyang-Mi Lee, Jun Ren, and Dokyun Na* (2021). “Optimized expression of Hfq protein increases Escherichia coli growth” Journal of Biological Engineering 15:7 (2021.02.18)
  3. Bilal Shaker, Kha Mong Tran, Chanjin Jung, and Dokyun Na* (2021). “Introduction of advanced methods for structure-based drug discovery” Current Bioinformatics  16(3): 351-363 (2021.04.01)
  4. Sambhaji Balaso Thakar, Pradnya Namdev Ghorpade, Bilal Shaker, Jingyu Lee, and Dokyun Na* (2021) “Gas-mediated cancer therapy combined with starvation therapy, ultrasound therapy, chemotherapy, radiotherapy, and photodynamic therapy: a review” Environmental Chemistry Letters 19(4), 2981-2993 (2021.03.24)
  5. Gyu-Bum Yeon, Won-Ho Shin, Seo-Hyun Yoo, Byeong-Min Jeon, Won-Ung Park, Yeonju Bae, Jae-Yong Park, Seungkwon You, Dokyun Na*, Dae-Sung Kim* (2021). “NFIB induces functional astrocytes from human pluripotent stem cell-derived neural precursor cells mimicking in vivo astrogliogenesis” Journal of Cellular Physiology 236(11): 7625-7641 (2021.05.05)
  6. Bilal Shaker, Myeong-Sang Yu, Jin Sook Song, Sunjoo Ahn, Jae Yong Ryu, Kwang-Seok Oh, and Dokyun Na* (2021). “LightBBB: Computational prediction model of blood-brain-barrier penetration based on LightGBM” Bioinformatics 37(8) 1135-1139 (2021.04.15)
  7. Kha Mong Tran, Hyang-Mi Lee, Thi Duc Thai, Junhao Shen, Seong-il Eyun, and Dokyun Na*(2021) “Synthetically engineered microbial scavengers for enhanced bioremediation” Journal of Hazardous Materials 419, 126516 (2021.10.05)
  8. Dong-Min Kim, Myeong-June Go, Jingyu Lee,  Dokyun Na* and Seung-Min Yoo* (2021) “Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies” Molecules 26(17), 5187 (2021.08.26)
  9. Bilal Shakera, Sajjad Ahmad, Jingyu Lee, Chanjin Jung, and Dokyun Na* (2021) “In silico methods and tools for drug discovery” Computers in Biology and Medicine 137, 104851 (2021.09.08)
  10. Sung-Gwon Lee, Dokyun Na, and Chungoo Park* (2021) “Comparability of reference-based and reference-free transcriptome analysis approaches at the gene expression level” BMC Bioinformatics 22, 310 (2021.10.21)
  11. Hyang-Mi Lee, Jun Ren, Woo Young Kim, Phuong Ngoc Lam Vo, Seong-il Eyun, and Dokyun Na* (2021) “Introduction of an AU-rich element into the 5’ UTR of mRNAs enhances protein expression in Escherichia coli by S1 protein and Hfq protein” Biotechnology and Bioprocess Engineering 26, 749–757 (2021.11.08)
  12. Won Ung Park, Gyu-Bum Yeon, Myung-Sang Yu, Hui-Gwan Goo, Su-Hee Hwang, Dokyun Na*, Dae-Sung Kim* (2021) “A novel vitronectin peptide facilitates differentiation of oligodendrocytes from human pluripotent stem cells (Synthetic ECM for oligodendrocyte differentiation)”  Biology-BASEL 10 (12) 1254 (2021.12.01)
  13. Hyang-Mi Lee, Jun Ren, Myeong-Sang Yu, Hyungjoo Kim, Woo Young Kim, Junhao Shen, Seung Min Yoo, Seong-il Eyun, Dokyun Na* (2021) “Construction of a tunable promoter library to optimize gene expression in Methylomonas sp. DH-1, a methanotroph, and its application to cadaverine production” Biotechnology for Biofuels 14:228 (2021.12.05)
  14. Sanghyun Park, Jeong-Eun Yoo, Gyu-Bum Yeon, Jin Hee Kim, Jae Souk Lee, Sung Kyoung Choi, Young-Gi Hwang, Chan Wook Park, Myung Soo Cho, Jongwan Kim, Dokyun Na, Hyung Wook Kim, Dae-Sung Kim*, and Dong-Wook Kim* (2021) “Trophoblast glycoprotein: a new candidate gene for Parkinson’s disease” npj Parkinson’s Disease 7: 110 (2021.12.07)

2020

  1. Kimin Kim, Hye Ju Yoo, Jik-Han Jung, Ruri Lee, Jae-Kyung Hyun, Ji-Ho Park, Dokyun Na, and Ju Hun Yeon*, (2020) “Cytotoxic Effects of Plant Sap-Derived Extracellular Vesicles on Various Tumor Cell Types” Journal of Functional Biomaterials 11(2): 22 (2020.04.02)
  2. Do‐Hwan Lim, Seungjae Lee, Min‐Seok Choi, Jee Yun Han, Youngmo Seong, Dokyun Na, Young‐Soo Kwon, Young Sik Lee*, (2020) “The conserved microRNA miR‐8‐3p coordinates the expression of V‐ATPase subunits to regulate ecdysone biosynthesis for Drosophila metamorphosis” FASEB Journal 00: 1-17 (2020.03.03)
  3. Bilal Shaker, Myung-Sang Yu, Jingyu Lee, Yongmin Lee, Chanjin Jung, Dokyun Na*, (2020) “User guide for the discovery of potential drugs via protein structure prediction and ligand docking simulation” Journal of Microbiology 58(3), 235-244 (2020.02.27)
  4. Jun Ren, Jingyu Lee, Dokyun Na*, (2020) “Recent advances in genetic engineering tools based on synthetic biology” Journal of Microbiology 58(1), 1-10 (2020.01.02)
  5. Dokyun Na* (2020). “DNA steganography: Hiding undetectable secret messages within the single nucleotide polymorphisms of a genome and detecting mutation-induced errors” Microbial Cell Factories  19:128 (2020.06.11)
  6. Kimin Kim, Jik-Han Jung, Hye Ju Yoo, Jae-Kyung Hyun, Ji-Ho Park, Dokyun Na, Ju Hun Yeon* (2020). “Anti-metastatic effects of plant sap-derived extracellular vesicles in a 3D microfluidic cancer metastasis model” Journal of Functional Biomaterials  11(3), 49 (2020.07.08)
  7. Ruri Lee, Hae Ju Ko, Kimin Kim, Yehjoo Sohn, Seo Yun Min, Jeong Ah Kim, Dokyun Na, and Ju Hun Yeon* (2020). “Anti-melanogenic effects of extracellular vesicles derived from plant leaves and stems in mouse melanoma cells and human healthy skin” Journal of Extracellular Vesicles 9, 1703480 (2019.12.19)
  8. Bilal Shaker, Sajjad Ahmad, Thi Thai Duc, Seong-il Eyun, and Dokyun Na* (2020). “Rational drug design for Pseudomonas aeruginosa PqsA enzyme: An in silico guided study to block biofilm formation” Frontiers in Molecular Biosciences 7, 577316 (2020.10.15)
  9. Seung Min Yoo, Seung-Woon Jung, Jinho Yeom, Sang Yup Lee*, and Dokyun Na* (2020). “Tunable gene expression system independent of downstream coding sequence” ACS Synthetic Biology  9(11): 2998-3007 (2020.10.14)
  10. Myeong-Sang Yu, Jingyu Lee, Yongmin Lee, and Dokyun Na* (2020). “2-D chemical structure image-based in silico model to predict agonist activity for androgen receptor” BMC Bioinformatics 21: 245 (2020.10.26)
  11. Jun Ren, Hyang-Mi Lee, Thai Duc Thi, and Dokyun Na* (2020). “Identification of a cytosine methyltransferase that improves transformation efficiency in Methylomonas sp. DH-1” Biotechnology for Biofuels 13:200 (2020.12.08)
  12. Kimin Kim, Yeh Joo Sohn, Ruri Lee, Hye Ju Yoo, Ji Yoon Kang, Nakwon Choi, Dokyun Na*, and Ju Hun Yeon* (2020). “Cancer-Associated Fibroblasts Differentiated by Exosomes Isolated from Cancer Cells Promote Cancer Cell Invasion” International Journal of Molecular Sciences 21(21):8153 (2020.10.31)

2019

  1. Phuong N. Lam Vo, Hyang-Mi Lee, and Dokyun Na (2019) “Synthetic bacteria for therapeutics” Journal of Microbiology and Biotechnology (2019.06.04)
  2. Hyang-Mi Lee, Myeong-Sang Yu, Sayada Reemsha Kazmi, Seong Yun Oh, Ki-Hyeong Rhee, Myung-Ae Bae, Byung Ho Lee, Dae-Seop Shin, Kwang-Seok Oh, Hyithaek Ceong, Donghyun Lee,* and Dokyun Na* (2019) “Computational determination of hERG-related cardiac toxicity of drug candidates” BMC Bioinformatics 20 (10): 250 (2019.05.29)
  3. Sayada Reemsha Kazmi, Ren Jun, Myeong-Sang Yu, Chanjin Jung, and Dokyun Na* (2019) “In silico approaches and tools for the prediction of drug metabolism and fate: A review” Computers in Biology and Medicine 106, 54-64 (2019.01.16)
  4. Jun Ren, Sandeep Karma, Hyang-Mi Lee, Seung Min Yoo, Dokyun Na* (2019). “Artificial transformation methodologies for improving the efficiency of plasmid DNA transformation and simplifying its use” Applied Microbiology and Biotechnology 103, 9205-9215  (2019.10.24)

2018

  1. Hyang-Mi Lee, Phuong N. L. Vo, Dokyun Na* (2019) “Advancement of metabolic engineering assisted by synthetic biology” Catalysts 8(12): 619 (2018.12.04)
  2. Jun Ren, Dokyun Na*, Seung Min Yoo* (2018) “Optimization of chemico-physical transformation methods for various bacterial species using diverse chemical compounds and nanomaterials”  Journal of Biotechnology 288, 55-60 (2018.12.20)
  3. Ju Hun Yeon, Hyo Eun Jeong, Hyemin Seo, Siwoo Cho, Kimin Kim, Dokyun Na, Seok Chung, Jaesung Park, Nakwon Choi, Ji Yoon Kang* (2018) “Cancer-derived exosomes trigger endothelial to mesenchymal transition followed by the induction of cancer-associated fibroblasts” Acta Biomaterialia https://doi.org/10.1016/j.actbio.2018.07.001
  4. Myeong-Sang Yu, Hyang-Mi Lee, Aaron Park, Chungoo Park, Hyithaek Ceong, Ki-Hyeong Rhee and Dokyun Na* (2018) “In silico prediction of potential chemical reactions mediated by human enzymes” BMC Bioinformatics 19(Suppl 8):207 

2017

  1. Jun Ren, Haram Lee, Seung Min Yoo, Myeong-Sang Yu, Hansoo Park*, Dokyun Na* (2017) “Combined chemical and physical transformation method with RbCl and sepiolite for the transformation of various bacterial species”  Journal of Microbiological Methods 135: 48-51 (2017.04.01)
  2. Jae-Sang Hong, Do-Hoon Lee, Ye Won Yook, Dokyun Na, Yu Jin Jang, Jong- Hoon Kim, Young Sik Lee* (2017) “MicroRNA signatures associated with thioacetamide-induced liver fibrosis in mice” Bioscience, Biotechnology and Biochemistry 1-8 (2017.04.01)

2016

  1. Hyeryeon Park, Dong-Jin Lim, Minhee Sung, Soo-Hong Lee, Dokyun Na*, Hansoo Park* (2016) “Microengineered platforms for co-cultured mesenchymal stem cells towards vascularized bone tissue engineering”  Tissue Engineering and Regenerative Medicine 13(5): 465-474 (2016.10.1)
  2. Minhui Sung, Seung Min Yoo, Ren Jun, Jae Eun Lee, Sang Yup Lee*, and Dokyun Na*. (2016) “Optimization of Phage λ Promoter Strength for Synthetic Small Regulatory RNA-based Metabolic Engineering” Biotechnology and Bioprocess Engineering 21: 483-490 (2016.9.22)
  3. Ju Hun Yeon, Florian Heinkel, Minhui Sung, Dokyun Na*, Jörg Gsponer* (2016) “System-wide identification of cis-regulatory elements in proteins” Cell Systems 2(2) 89-100 (2016.2.24)
    * Previews in Cell Systems [link]
  4. Hyeyoung Cho, Hyosil Kim, Dokyun Na, So Youn Kim, Deokyeon Jo, and Doheon Lee.  (2016) “Meta-analysis method for discoverying reliable biomarkers by integrating statistical and biological approaches: an application to liver toxicity” Biochemical and Biophysical Research Communications 471(2) 274-281 (2016.3.4)

2015

  1. Amit Kumar Chaudhary, Dokyun Na*, Eun Yeol Lee* (2015) “Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs” Biotechnology Advances 33(6) 914-930 (2015.11.1)
  2. Jae-Sang Hong, Nam-Hoon Kim, Chang-Yong Choi, Jun-Seong Lee, Dokyun Na, Taehoon Chun, and Young Sik Lee (2015). “Changes in cellular microRNA expression induced by porcine circovirus type 2-encoded proteins” Veterinary Research 46:39 (2015.4.10)
  3. Changyoon Baek, Hee Yeon Kim, Dokyun Na*, and Junhong Min* (2015). “A microfluidic system for the separation and detection of E. coli O157:H7 in soil sample using ternary interactions between humic acid, bacteria, and a hydrophilic surface” Sensors and Actuators B: Chemical  208: 238-244 (2015.03.01)

2014

  1. Dokyun Na, Hyungbin Son, and Jörg Gsponer* (2014). “Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity” BMC Genomics 15: 1091 (2014.12.11)
  2. Muhammad Qasim, Phornsawat Baipaywad, Nopphadol Udomluck, Dokyun Na*, and Hansoo Park* (2014) “Enhanced Therapeutic Efficacy of Lipophilic Amphotericin B Against Candida albicans with Amphiphilic Poly(N-isopropylacrylamide) Nanogels” Macromolecular Research 22(10): 1125-1131 (2014.09.29)
  3. Muhammad Qasim, Dong-Jin Lim, Hansoo Park* and Dokyun Na* (2014). “Nanotechnology for diagnosis and treatment of infectious diseases” Journal of Nanoscience and Nanotechnology 14: 7374-7387 (2014.10.1)
  4. Byoungjin Kim, Hyegwon Park, Dokyun Na, and Sang Yup Lee (2014). “Metabolic engineering of Escherichia coli for the production of phenol from glucose” Biotechnology Journal 9: 621-629 (2014.5.1)

2013

  1. Dokyun Na, Mushfiqur Rouf, Cahir J O’Kane, David C Rubinsztein and Jörg Gsponer (2013) “NeuroGeM, a knowledgebase of genetic modifiers in neurodegenerative diseases” BMC Medical Genomics 6:52 (2013.11.14)
  2. Eric T. C. Wong, Dokyun Na, and Jörg Gsponer (2013) “On the importance of polar interactions for complexes containing intrinsically disordered proteins” PLOS Computational Biology 9(8): e1003192. (2013.8.22)
  3. Seung Min Yoo*, Dokyun Na*, Sang Yup Lee (2013) “Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli” Nature Protocols 8, 1694–1707. (2013.8.8)
    * Equally contributed.
    * Cover paper
  4. Dokyun Na, Seung Min Yoo, Hannah Chung, Hyegwon Park, Jin Hwan Park, Sang Yup Lee. (2013) “Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs” Nature Biotechnology 31(2): 170-174 (2013.1.20)
    * Research Highlight in Nature Reviews Genetics

2012

  1. Ju Hun Yeon, Dokyun Na, Kyungsun Choi, Seung-Wook Ryu, Chulhee Choi, and Je-Kyun Park. (2012) “Reliable permeability assay system in a microfluidic device mimicking cerebral vasculatures” Biomedical Microdevices 14(6):1141-1148 (2012.7.22)
  2. Jeong Wook Lee, Dokyun Na, Jong Myoung Park, Joungmin Lee, Sol Choi, and Sang Yup Lee. (2012) “Systems metabolic engineering of microorganisms for natural and non-natural chemicals” Nature Chemical Biology 8: 536-546 (2012.5.17)
  3. Dokyun Na (2012). “Meeting Report: Cold Spring Harbor Asia – Design and Synthesis of Biological System.” Biotechnology Journal 10.1002/biot.201100490

2011

  1. Dokyun Na, Sunjae Lee, Gwan-Su Yi, and Doheon Lee. (2011). “Synthetic inter-species cooperation of host and virus for targeted genetic evolution.” Journal of Biotechnology 153: 35-41 (2011.3.9)

~2010

  1. Dokyun Na and Doheon Lee. (2010). “RBSDesigner: software for designing synthetic ribosome binding sites that yield a desired level of protein expression.” Bioinformatics 26(20): 2633-2634. (2010.8.11)
  2. Ju Hun Yeon, Dokyun Na, Je-Kyun Park. (2010). “Heptatotoxicity assay using human hepatocytes trapped in microholes of a microfluidic device.” Electrophoresis 31: 3167-3174. (2010.9.20)
  3. Dokyun Na, Sunjae Lee and Doheon Lee. (2010). “Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes.” BMC Systems Biology 4, 71. (2010.5.26)
    * Invited to give a talk in PEPTALK, San Diego(2011).
  4. Dokyun Na, Tae Yong Kim and Sang Yup Lee. (2010). “Construction and optimization of synthetic pathways in metabolic engineering.” Current Opinion in Microbiology 13, 363-370. (2010.3.10)
  5. KiYoung Lee, Dae-Won Kim, Dokyun Na, Kwang H. Lee, and Doheon Lee. (2006). “PLPD: reliable protein localization prediction from imbalanced and overlapped datasets.” Nucleic Acids Research. 34, 4655-4666. (2006.9.11)
  6. Dokyun Na, Dongsup Kim, and Doheon Lee. (2006). “Mathematical modeling of humoral immune response suppression by passively administered antibodies in mice.” Journal of Theoretical Biology 241, 830-851.
  7. Inho Park, Dokyun Na, Kwang H. Lee, and Doheon Lee. (2005). “Fuzzy continuous Petri Net-based approach for modeling helper T cell differentiation.” Lecture Notes in Computer Science 3627, 331-338
  8. Dokyun Na and Doheon Lee. (2005). “Mathematical modeling of immune suppression.” Lecture Notes in Computer Science 3627, 182-192
  9. Hyeong Jun An, Dokyun Na, Doheon Lee, Kwang Hyung Lee, and Jonghwa Bhak. (2004). “High correlation between Alu elements and the conversion of 3’ UTR of mRNAs processed pseudogenes.” Genomics and Informatics 2(2), 94-100.
  10. Dokyun Na, Inho Park. Kwang H. Lee, and Doheon Lee. (2004). “Integration of Immune Models Using Petri Nets.” Lecture Notes in Computer Science 3239, 205-216
  11. Kwang-Seok Oh, Dokyun Na, Mee-Hyang Kweon, and Ha-Chin Sung. (2003). “Expression and purification of delta-sleep-inducing peptide in Escherichia coli.” J. Microbiol. Biotechnol. 13(4), 620-623
  12. Kwang-Seok Oh, Dokyun Na, Mee-Hyang Kweon, and Ha-Chin Sung. (2002). “Expression and purification of the anticomplementary peptide Sh-CRIT-ed1 (formerly Sh-TOR-ed1) as a tetramultimer in Escherichia coli.” Protein Expression and Purification 27, 202-209
Books
  1. 나도균 외 (2020) “미생물학: 기초에서 응용까지, Chapter 10: 유전공학, 유전체학, 생물정보학” (Book, 범문에듀케이션)
  2. Dokyun Na, JH Park, YS Jang, JW Lee, SY Lee. (2012) “Systems metabolic engineering of Escherichia coli for chemicals, materials, biofuels, and pharmaceuticals (chapter 5)” Systems Metabolic Engineering (Book, Springer)
  3. Dokyun Na, MY Kim, JY Park, and SY Lee. (2011) “Systems metabolic engineering for the production of non-innate chemical compounds.” Comprehensive Biotechnology (3rd). (Book, Elsevier)