PUBLICATION

JOURNAL PUBLICATIONS 

 Google Scholar Citations to the following publications

†Co-first author

42) Raman K, Kratochvíl M, Olivier BG, König M, Sengupta P, Baskaran DKK, Nguyen TVN, Lobo D, Wilken SE, Tiwari KK, Raghu AK, Palanikumar I, Raajaraam L, Ibrahim M, Balakrishnan S, Umale S, Bergmann F, Malpani T, Satagopam VP, Schneider R, Beber ME, Keating S, Anton M, Renz A, Lakshmanan M, Lee DY, Koduru L, Mostolizadeh R, Dias O, Cunha E, Oliveira A, Lee YQ, Zengler K, Santibáñez-Palominos R, Kumar M, Barberis M, Puniya BL, Helikar T, Dinh HV, Suthers PF, Maranas CD, Casini I, Loghmani SB, Veith N, Leonidou N, Li F, Chen Y, Nielsen J, Lee G, Lee SM, Kim GB, Monteiro PT, Teixeira MC, Kim HU, Lee SY, Liebal UW, Blank LM, Lieven C, Tarzi C, Angione C, Blaise ME, Aytar ÇP, Kulyashov M, Akberdin I, Kim D, Yoon SH, Xu Z, Gautam J, Scott WT, Schaap PJ, Koehorst JJ, Zuñiga C, Canto-Encalada G, Benito-Vaquerizo S, Olm IP, Suarez-Diez M, Yuan Q, Ma H, Islam MM, Papin JA, Zorrilla F, Patil KR, Basile A, Nogales J, León GS, Castillo-Alfonso F, Olivares-Hernández R, Canto-Encalada G, Vigueras-Ramírez G, Hermjakob H, Dräger A, Malik-Sheriff RS “FROG analysis ensures the reproducibility of genome scale metabolic models” bioRxiv doi: https://doi.org/10.1101/2024.09.24.614797 (2024)

41) Na H-H, Kim S, Kim J-S, Lee S, Kim Y, Kim S-H, Lee C-H, Kim D, Yoon SH, Jeong H, Kweon D, Seo HW, and Ryu C-M “Facemask acne attenuation through modulation of indirect microbiome interactions” NPJ Biofilms Microbiomes 10(1):50 (2024.06)

40) Woo H, Kim Y, Kim D, and Yoon SH “Machine learning identifies key metabolic reactions in bacterial growth on different carbon sources” Molecular Systems Biology 20(3):170-186 (2024.03) Hanbitsa

39) Han S, Kim D, Kim Y, and Yoon SH “Genome‑scale metabolic network model and phenome of solvent‑tolerant Pseudomonas putida S12” BMC Genomics 25:63 (2024.01)

38) Hong SH, Seo K, Yoon SH, Kim SK, and Chon J “Gold nanoparticle and polymerase chain reaction (PCR)-based colorimetric assay for the identification of Campylobacter spp. in chicken carcass” Food Science of Animal Resources 43(1):73-84 (2023.01)

37) Ha J†, Kim D†, Yeon J, Kim Y, Yoo SM, and Yoon SH “Identification of a gene cluster for D-tagatose utilization in Escherichia coli B2 phylogroup” iScience 25:105655 (2022.12)

36) Kim D†, Kim Y†, and Yoon SH “Development of a genome-scale metabolic model and phenome analysis of the probiotic Escherichia coli strain Nissle 1917” International Journal of Molecular Sciences 22(4):2122 (2021.02)

35) Kim S, Kim Y, Suh DH, Lee CH, Yoo SM, Lee SY, and Yoon SH “Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms” Scientific Reports 10(1):17715 (2020.10)

34) Kim H, Kim S, Kim D, and Yoon SH “A single amino acid substitution in aromatic hydroxylase (HpaB) of Escherichia coli alters substrate specificity of the structural isomers of hydroxyphenylacetate” BMC Microbiology 20:109 (2020.05)

33) Sarak S, Jeon H, Patil MD, Khobragade TP, Pagar AD, Sung S, Yoo H-W, Kim B-G, Yoon SH, and Yun H “Enzymatic synthesis of aliphatic primary ω-amino alcohols from ω-amino fatty acids by carboxylic acid reductase” Catalysis Letters 150:3079-3085 (2020.04)

32) Kim E-Y, Ashlock D, and Yoon SH “Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks” BMC Bioinformatics 20:328 (2019.06)

31) Kim S, Kim Y, and Yoon SH “Overexpression of YbeD in Escherichia coli enhances thermotolerance” J. Microbiol. Biotechnol. 29(3): 401~409 (2019.03)

30) Kim H, Kim S, and Yoon SH “Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)” PLoS ONE 13(9):e0204375 (2018.09)

29) Nguyen AD, Hwang IY, Lee OK, Hur DH, Jeon YC, Hadiyati S, Kim M-S, Yoon SH, Jeong H, and Lee EY “Functional analysis of Methylomonas sp. DH-1 genome as a promising biocatalyst for bioconversion of methane to valuable chemicals” Catalysts 8(3), 117 (2018.03) 

28) Kim SK†, Lee D-H†, Kim OC, Kim JF, and Yoon SH “Tunable control of an Escherichia coli expression system for the overproduction of membrane proteins by titrated expression of a mutant lac repressor” ACS Synthetic Biology 6(9):1766-1773 (2017.09) 

27) Jeong H, Lee S-W, Kim SH, Kim E-Y, Kim S, and Yoon SH “Global functional analysis of butanol-sensitive Escherichia coli and its evolved butanol-tolerant strain” J. Microbiol. Biotechnol. 27(6):1171–1179 (2017.06) 

26) Kim S, Jeong H, Kim E-Y, Kim JF, Lee SY, and Yoon SH “Genomic and transcriptomic landscape of Escherichia coli BL21(DE3)” Nucleic Acids Res. 45(9):5285-5293 (2017.05)  

25) Yoon SH (corresponding), Park YK, and Kim JF “PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands” Nucleic Acids Res. 43:D624-D630 (2015.01) 

24) Yoon SH, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie TJ, Slagel J, Moritz RL, Hackett M, Leigh JA, and Baliga NS “A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen” Genome Research 23(11):1839-1851 (2013.11) Hanbitsa 

23) Dai J†, Yoon SH†, Sim HY, Yang YS, Oh TK, Kim JF, and Hong JW “Charting microbial phenotypes in multiplex nanoliter batch bioreactors” Anal. Chem. 85(12):5892-5899 (2013.06) 

22) Costa KC, Yoon SH, Pan M, Burn JA, Baliga NS, and Leigh JA “Effects of H₂ and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis” J. Bacteriol. 195(7):1456-1462 (2013.04) 

21) Yoon SH, Han MJ, Jeong H, Lee CH, Xia XX, Lee DH, Shim JH, Lee SY, Oh TK, and Kim JF “Comparative multi-omics systems analysis of Escherichia coli strains B and K-12” Genome Biology 13(5):R37 (2012.05) Hanbitsa 

20) Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL, Adams MW, Barnebey A, Yannone SM, Leigh JA, and Baliga NS “Parallel evolution of transcriptome architecture during genome reorganization” Genome Research 21(11):1892-1904 (2011.11) Hanbitsa 

19) Yoon SH, Kim SK, and Kim JF “Secretory production of recombinant proteins in Escherichia coli” Recent Patents on Biotechnology 4(1):23-29 (2010.01) Hanbitsa (Highly cited)

17) Barrick JE, Yu D-S, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, and Kim JF “Genome evolution and adaptation in a long-term experiment with Escherichia coli” Nature 461(7268):1243-1247 (2009.10), Highly cited paper in Hanbitsa 

16) Kim JF, Jeong H, Yu DS, Choi S-H, Hur C-G, Park M-S, Yoon SH, Kim D-W, Ji GE, Park H-S, and Oh TK “Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. lactis AD011” J. Bacteriol. 191(2):678-679 (2009.01) 

15) Jeong H, Yoon SH, Yu D-S, Oh TK, and Kim JF “Recent progress of microbial genome projects in Korea” Biotechnol. J. 3(5):601-611 (2008.05) 

14) Nam D, Yoon SH, and Kim JF “Ensemble learning of genetic networks from time-series expression data” Bioinformatics 23(23):3225-3231 (2007.12) 

13) Yoon SH, Park YK, Lee S, Choi D, Oh TK, Hur C-G, and Kim JF “Towards pathogenomics: a web-based resource for pathogenicity islands” Nucleic Acids Res. 35:D395-D400 (2007.01) 

12) Jiang H, Shang L, Yoon SH, Lee SY, and Yu Z “Optimal production of poly-γ-glutamic acid by metabolically engineered Escherichia coli” Biotechnol. Lett. 28(16):1241-1246 (2006.08) 

11) Hur C-G, Kim S, Kim CH, Yoon SH, In YH, Kim C, and Cho HG “FASIM: Fragments assembly simulation using biased-sampling model and assembly simulation for microbial genome shotgun sequencing” J. Microbiol. Biotechnol. 16(5):683-688 (2006.05) 

10) Jeong H, Yoon SH, Lee HK, Oh TK, and Kim JF “Lessons from the sea: genome sequence of an algicidal marine bacterium Hahella chejuensis (적조 살상 해양 미생물 Hahella chejuensis의 유전체 구조)” Kor. J. Microbiol. Biotechnol. 34(1):1-6 (2006.03)

9) Jeong H, Yim JH, Lee C, Choi SH, Park YK, Yoon SH, Hur CG, Kang HY, Kim D, Lee HH, Park KH, Park SH, Park HS, Lee HK, Oh TK, and Kim JF “Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent” Nucleic Acids Res. 33(22):7066-7073 (2005.12) 

8) Yoon SH, Hur C-G, Kang HY, Kim YH, Oh TK, and Kim JF “A computational approach for identifying pathogenicity islands in prokaryotic genomes” BMC Bioinformatics 6:184 (2005.07) 

7) Yoon SH, Han MJ, Lee SY, Jeong KJ, and Yoo JS “Combined transcriptome and proteome analysis of Escherichia coli during the high cell density culture” Biotechnol. Bioeng. 81(7):753-767 (2003.03) Hanbitsa (Highly cited)

6) Yoon SH and Lee SY "Comparison of transcript levels by DNA microarray and metabolic flux based on flux analysis for the production of poly-γ-glutamic acid in recombinant Escherichia coli" Genome Informatics 13:587-588 (2002.12)

5) Kim JS, Yoon SH, and Lee SY “Development of database systems by integrating heterogeneous metabolic databases” Genome Informatics 13:486-487 (2002.12)

4) Heo WJ, Yoon SH, and Lee SY "Global gene expression profiling of E. coli and its mutant unable to produce acetate" Genome Informatics 13:270-271 (2002.12)

3) Yoon SH, Do JH, Lee SY, and Chang HN “Production of poly-γ-glutamic acid by fed-batch culture of Bacillus licheniformis” Biotechnol. Lett. 22(7):585-588 (2000.04) 

2) Chung BH, Choi YJ, Yoon SH, Lee SY, and Lee YI “Process development for production of recombinant human insulin-like growth factor-I in Escherichia coli” J. Ind. Microbiol. Biotechnol. 24(2):94-99 (2000.02) 

1) Yoon SH, Choi J, and Lee SY “Development of DNA chip microarrayer” J. Microbiol. Biotechnol. 10(1):21-26 (2000.02) 

BOOK CHAPTERS

1) Yoon SH, Jeong H, Kwon S-K, and Kim JF “Chapter 1. Genomics, biological features, and biotechnological applications of Escherichia coli B: “Is B for better?!””, pp. 1-17, In: Systems Biology and Biotechnology of E. coli, Lee SY (ed.) Springer, Berlin, Germany (2009. 4)

PATENTS

9) Yoon SH and Kim S “High-temperature resistant microorganism overexpressing YbeD protein and method for culturing of high-temperature resistant microorganism using the same” Korean Patent number 10-2410382 (2022.06.14)

    윤성호, 김신연 “YbeD 단백질을 과발현하는 고온 내성 미생물 및 이를 이용한 고온 내성 미생물의 배양 방법” 특허출원번호: 10-2018-0009345 (2018.01.25), 특허등록번호: 10-2410382 (2022.06.14)

8) Yoon SH, Kim H “Mutant enzyme of HpaB with modified substrate specificity and uses thereof” Korean Patent: appl. 10-2020-0116319 (2020.09.10)

   윤성호, 김한설 “변형된 기질 특이성을 갖는 HpaB의 돌연변이 효소 및 이의 용도” 특허출원번호: 10-2020-0116319 (2020.09.10)

7) Yoon SH, Lee DH, Kim SK, and Kim OC “Method for producing toxic protein using the LacI protein mutant” Korean Patent number 10-1419214 (2014.07.08)

    윤성호, 이대희, 김성근, 김오철 “LacI 단백질 변이체를 이용한 독성 단백질의 생산방법” 특허출원번호 10-2013-0002227 (2013.01.08), 특허등록번호 10-1419214 (2014.07.08)

6) 김지현, 윤성호, 김성근, 이대희, 권순경, 오태광, 김오철, 정해영 “LacI 단백질 변이체를 이용한 독성 단백질의 생산 방법” (우선권내역: 10-2012-0038237 / 10-2013-0002227) PCT/KR2013/002919 (2013.04.08)

5) Kim JF, Kim SK, Kwon S-K, Oh TK, Yoon SH, Lee DH, and Jeong H “LacI protein mutant and uses thereof” Korean Patent: appl. 10-2012-0038237 (2012.04.13)

    김지현, 김성근, 권순경, 오태광, 윤성호, 이대희, 정해영 “LacI 단백질 변이체 및 이의 용도” 특허출원번호 10-2012-0038237 (2012.04.13)

4) Hong JW, Kim JF, Oh TK, and Yoon SH “Microfluidic array system for biological, chemical, and biochemical assessments” US7906074B2 (Date of Patent: March 15, 2011)

3) Jeong H, Han JH, Yoon SH, Ryu C-M, Kim JF, Oh TK, Jung MH, and Yoon SP “Method for Selecting Alcohol Resistant Variants of Microorganism Using Mutagenesis by Proton Beam Irradiation” Korean Patent: appl. 10-2009-0080393 (2009.08.28)

    정해영, 한지희, 윤성호, 류충민, 김지현, 오태광, 정명환, 윤상필 “양성자 빔 조사에 의한 돌연변이 유도방법을 이용한 알코올 내성 미생물 변이체의 선별 방법” 특허출원번호 10-2009-0080393 (2009.08.28)

2) Hong JW, Kim JF, Oh TK, and Yoon SH “A fluidic array system for biological, chemical, and biochemical assessments” WO2008124781A1 / US20080248960A1 (PCT/US08/59777) (filed on April 9, 2008)

1) Lee SY and Yoon SH "Methods for producing high concentration of poly (gamma-glutamic acid) by fed-batch culture of Bacillus licheniformis" Korean Patent: appl. 97-67605 (1997.12.10), registered 250627 (2000.01.05)

    이상엽, 윤성호 "바실러스 리케니포니스에 의한 폴리글루탐산(g-PGA)의 고효율 생산방법" 특허출원번호 10-1997-0067605 (1997.12.10), 등록번호 1002506270000 (2000.01.05)

PROGRAM REGISTRATIONS

3) 윤성호 “방향성 있는 바이오네트워크의 topology(토폴로지)를 분석하는 cascade(캐스케이드) 알고리즘”, 정보통신산업진흥원, 등록번호: ASSET_0006293 (2019.06.25)

2) 김지현, 윤성호, 허철구, 오태광. “미생물 유전체 내에서 외래에서 유입된 병원성 유전자군인 pathogenicity island를 예측하는 방법” (등록일자: 2007.07.30; 등록번호: S-2007-003962)

1) 김지현, 윤성호, 허철구, 박영규, 오태광. “미생물 유전체 내에서 외래에서 유입된 병원성 유전자군인 pathogenicity island를 분석, 예측하는 시스템” (등록일자: 2007.07.30; 등록번호: S-2007-003964)

ESSAYS

12) 윤성호 “미생물의 대사 네트워크 및 유전자조절 네트워크 모델링 기법 개발” BT News, 한국생물공학회, 24(2) (2017.10.09)

11) 윤성호 “대사경로 재설계를 통한 유용 화학물질 생산 전략” 지능형 바이오시스템 설계 및 합성 연구단 뉴스레터 2(3) (2014.10.23)

10) 윤성호 “Bio-CAD를 이용한 지능형 바이오시스템 설계” 지능형 바이오시스템 설계 및 합성 연구단 뉴스레터 1(1) (2013.01.18)

9) 윤성호, 이정민 “합성생물학 윤리 및 기술에 관한 미대통령 정책자문 보고서” (NEW DIRECTIONS: The Ethics of Synthetic Biology and Emerging Technologies 번역요약본) KOSEN21 (한민족과학기술자 네트워크, http://www.kosen21.org) (2011. 10. 17)

8) 윤성호 “합성생물학에서의 미생물 유전자회로 및 대사회로개발” 생명공학정책연구센터 바이오인(BioIn), 16 (2010)

7) 윤성호 “Institute for Systems Biology” e-Bioindustry News (e-생물산업, 한국미생물/생명공학회 소식지), 22(4) (2009)

6) 윤성호 “Systems and Synthetic Biology” In State of the Art Report on Microbial Genomics (미생물유전체 연구동향 분석연구), Ministry of Science and Technology, Korea (2007)

5) 윤성호 “Biolog사의 Phenotype Microarray (PM) Technology” 미생물과 산업, 32(2): 28-29, 한국미생물학회 (2006)

4) 이승구, 김지현, 정흥채, 송재준, 류충민, 윤성호 “바이오기반 경제구축을 위한 합성생물학 핵심기술 개발” (Development of Platform Technologies for Synthetic Biology), KRIBB, Korea (2006)

3) 김지현, 정해영, 윤성호, 박승환 “시스템 미생물학 : 유전체 해독에서 네트워크 재설계까지” (Systems Microbiology : From Genome Sequencing to Network Engineering), e-Bioindustry News (e-생물산업, 한국미생물/생명공학회 소식지), 16(3) (2003)

2) 김진식, 윤성호, 이상엽 “미생물 게놈 연구”, BioZine (http://biozine.kribb.re.kr) (2001.6)

1) 이상엽, 윤성호, 임근배, 조윤경 “Genomics와 DNA chip” News & Information for Chemical Engineers (NICE), 18(3): 307-311 (2000)