Our systems biology tools published are available at GitHub or Bitbucket repositories:
Book chapters, Conference proceedings and Essays
Preprints
Raman K, Kratochvíl M, Olivier BG, König M, ..., Nielsen J, Lee G, Lee SM, Kim GB, ..., Kim HU, Lee SY, ..., Malik-Sheriff RS. FROG analysis ensures the reproducibility of genome scale metabolic models.
bioRxiv: https://www.biorxiv.org/content/10.1101/2024.09.24.614797v1
Jeon J1, Hong E1, Kim JY, Lee S & Kim HU. Predicting the physiological effects of multiple drugs using electronic health record. bioRxiv: https://www.biorxiv.org/content/10.1101/2024.06.30.601402v1
2024
Kwon MS1, Lee J1 & Kim HU. A machine learning framework for extracting information from biological pathway images in the literature. Metabolic Engineering 86, 1-11 (November 2024)
bioRxiv: https://www.biorxiv.org/content/10.1101/2024.06.01.596964v1
Lee J1, Lee BT1, Kwon MS1 & Kim HU. Metabolic modeling of microorganisms involved in anaerobic digestion. Biotechnology and Bioprocess Engineering 29, 613-624 (August 2024)
Park JG, Roh PR, Kang MW, Cho SW, Hwangbo S, Jung HD, Kim HU, Kim JH, Yoo JS, Han JW, Jang JW, Choi JY, Yoon SK, You YK, Choi HJ, Ryu JY & Sung PS. Intrahepatic IgA complex induces polarization of cancer-associated fibroblasts to matrix phenotypes in the tumor microenvironment of HCC. Hepatology. In press.
Bae SH1, Sim MS1, Jeong KJ, He D, Kwon I, Kim TW*, Kim HU* & Choi J*. Intracellular flux prediction of recombinant Escherichia coli producing gamma-aminobutyric acid. Journal of Microbiology and Biotechnology 34, 978-984 (April 2024)
Lee G1, Lee SM1, Lee S, Jeong CW, Song H, Lee SY, Yun H*, Koh Y*, Kim HU*. Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data. Genome Biology 25, 66 (March 2024)
bioRxiv: https://www.biorxiv.org/content/10.1101/2023.07.26.550699v1
Sharma K, Ghiffary MR, Lee G & Kim HU. Efficient production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli. Metabolic Engineering 81, 144-156 (January 2024)
bioRxiv: https://www.biorxiv.org/content/10.1101/2023.07.31.551311v1
2023
Song S1, Koh Y1, Kim S1, Lee SM, Kim HU*, Ko JM*, Lee SH*, Yoon SS* & Park S*. Systematic analysis of Mendelian disease-associated gene variants reveals new classes of cancer-predisposing genes. Genome Medicine 15, 107 (December 2023)
bioRxiv: https://www.biorxiv.org/content/10.1101/2023.02.15.528610v1
Kim WJ1, Lee Y1, Kim HU1, Ryu JY, Yang JE & Lee SY. Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes. Cell Systems 14, 990-1001 (November 2023)
Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kautsar SA, Kim H, Leao TF, Masschelein J, Rees ER, Reher R, Reker D, Schwaller P, Segler M, Skinnider MA, Walker AS, Willighagen EL, Zdrazil B, Ziemert N, Goss RJM, Guyomard P, Volkamer A, Gerwick WH, Kim HU, Müller R, van Wezel GP, van Westen GJP, Hirsch AKH, Linington RG, Robinson SL & Medema MH. Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery 22, 895-916 (November 2023)
Gu B, Kim DG, Kim DK, Kim M, Kim HU* & Oh MK*. Heterologous overproduction of oviedomycin by refactoring biosynthetic gene cluster and metabolic engineering of host strain Streptomyces coelicolor. Microbial Cell Factories 22, 212 (October 2023)
Yun KH, Sharma K, Kim HU & Bae TH. Modification of a PES microfiltration membrane to enhance sterile filtration by inhibiting protein adsorption. Journal of Industrial and Engineering Chemistry 123, 311-319 (July 2023)
Lee JA1, Kim HU1, Na JG1, Ko YS, Cho JS & Lee SY. Factors affecting the competitiveness of bacterial fermentation. Trends in Biotechnology 41, 798-816 (June 2023)
Lee G1, Lee SM1 & Kim HU. A contribution of metabolic engineering to addressing medical problems: metabolic flux analysis. Metabolic Engineering 77, 283-293 (May 2023)
Cho JS, Yang D, Prabowo CPS, Ghiffary MR, Han T, Choi KR, Moon CW, Zhou H, Ryu JY, Kim HU & Lee SY. Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs. Nature Communications 14, 2359 (April 2023)
Kwon MS, Adidjaja JJ & Kim HU. Predicting the effects of cultivation condition on gene regulation in Escherichia coli by using deep learning. Computational and Structural Biotechnology Journal 21, 2613-2620 (April 2023)
Kim Y1, Ryu JY1, Kim HU1 & Lee SY. Computational prediction of interactions between Paxlovid and prescription drugs. Proceedings of the National Academy of Sciences U S A (PNAS) 120, e2221857120 (March 2023)
Kim S1, Nam Y1, Kim MJ1, Kwon SH1, Jeon J1, Shin SJ, Park S, Chang S, Kim HU*, Lee YY*, Kim HS* & Moon M*. Proteomic analysis for the effects of non-saponin fraction with rich polysaccharide from Korean red ginseng on Alzheimer's disease in a mouse model. Journal of Ginseng Research 47, 302-310 (March 2023)
Song Y1, Lim S1, Kim YT, Park YM, Jo DA, Bae NH, Lee SJ, Choi BG, Im SG, Kim HU* & Lee KG*. Deep learning enables accurate analysis of images generated from droplet-based digital polymerase chain reaction (dPCR). Sensors and Actuators B: Chemical 379, 133241 (March 2023)
Hong E, Jeon J & Kim HU*. Recent development of machine learning models for the prediction of drug-drug interactions. Korean Journal of Chemical Engineering 40, 276-285 (February 2023)
2022
Ghiffary MR, Prabowo CPS, Adidjaja JJ, Lee SY & Kim HU*. Systems metabolic engineering of Corynebacterium glutamicum for the efficient production of β-alanine. Metabolic Engineering 74, 121-129 (November 2022)
Cho MK1, Lee BT1, Kim HU* & Oh MK*. Systems metabolic engineering of Streptomyces venezuelae for the enhanced production of pikromycin. Biotechnology and Bioengineering 119, 2250-2260 (August 2022)
Jo HG1, Adidjaja JJ1, Kim DK, Park BS, Lee N, Cho BK, Kim HU* & Oh MK*. Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin. Scientific Reports 12, 10302 (June 2022)
Lee SM1, Lee G1 & Kim HU*. Machine learning-guided evaluation of extraction and simulation methods for cancer patient-specific metabolic models. Computational and Structural Biotechnology Journal 20, 3041-3052 (June 2022)
Baek Y, Lee S, Son J, Lee T, Oh J-M, Lee SH, Kim HU, Seo SW, Park SJ, Yoo HY & Park C. Efficient production of naringin acetate with different acyl donors via enzymatic transesterification by lipases. International Journal of Environmental Research and Public Health 19, 2972 (March 2022)
2021
Koo J, Choi K, Lee P, Polley A, Pudupakam RS, Tsang J, Fernandez E, Han EJ, Park S, Swartzfager D, Xi Qi NS, Jung M, Ocnean M, Kim HU & Lim S. Predicting dynamic clinical outcomes of the chemotherapy for canine lymphoma patients using a machine learning model. Veterinary Sciences 8, 301 (December 2021)
Lee SM & Kim HU*. Development of computational models using omics data for the identification of effective cancer metabolic biomarkers. Molecular Omics 17, 881-893 (December 2021)
Jeon J1, Kang S1 & Kim HU*. Predicting biochemical and physiological effects of natural products from molecular structures using machine learning. Natural Product Reports 38, 1954-1966 (November 2021) Cover
Jung HD, Sung YJ & Kim HU*. Omics and computational modeling approaches for the effective treatment of drug-resistant cancer cells. Frontiers in Genetics 12, 742902 (October 2021)
Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO & Cho BK. Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes. Natural Product Reports 38, 1330-1361 (July 2021)
Ghiffary MR, Prabowo CPS, Sharma K, Yan Y, Lee SY* & Kim HU*. High-level production of the natural blue pigment indigoidine from metabolically engineered Corynebacterium glutamicum for sustainable fabric dyes. ACS Sustainable Chemistry & Engineering 9, 6613-6622 (May 2021) Supplementary Cover
Kim Y1, Ryu JY1, Kim HU1, Jang WD & Lee SY. A deep learning approach to evaluate the feasibility of enzymatic reactions generated by retrobiosynthesis. Biotechnology Journal 16, 2000605 (May 2021)
Kim DI1, Chae TU1, Kim HU1, Jang WD & Lee SY. Microbial production of multiple short-chain primary amines via retrobiosynthesis. Nature Communications 12, 173 (January 2021)
2020
Sharma K, Ghiffary MR, Kim HU* & Lee SY*. Engineering heterologous hosts for the enhanced production of non-ribosomal peptides. Biotechnology and Bioprocess Engineering 25, 795-809 (December 2020)
Kwon MS1, Lee BT1, Lee SY* & Kim HU*. Modeling regulatory networks using machine learning for systems metabolic engineering. Current Opinion in Biotechnology 65, 163-170 (October 2020)
Kim GB1, Kim WJ1, Kim HU* & Lee SY*. Machine learning applications in systems metabolic engineering. Current Opinion in Biotechnology 64, 1-9 (August 2020)
Jang WD1, Lee SM1, Kim HU* & Lee SY*. Systematic and comparative evaluation of software programs for template-based modeling of protein structures. Biotechnology Journal 15, 1900343 (June 2020)
Kim Y, Gu C, Kim HU & Lee SY. Current status of pan-genome analysis for pathogenic bacteria. Current Opinion in Biotechnology 63, 54-62 (June 2020)
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M & Zhang C. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology 38, 272-276 (March 2020)
bioRxiv: https://doi.org/10.1101/350991
Jeon J & Kim HU*. Setup of a scientific computing environment for computational biology: Simulation of a genome-scale metabolic model of Escherichia coli as an example. Journal of Microbiology 58, 227-234 (March 2020)
2019
Jang WD1, Kim TY1, Kim HU1, Shim WY1, Ryu JY, Park JH* & Lee SY*. Genomic and metabolic analysis of Komagataeibacter xylinus DSM 2325 producing bacterial cellulose nanofiber. Biotechnology and Bioengineering 116, 3372-3381 (December 2019)
Gwon H1, Park K1, Chung SC1, Kim RH, Kang JK, Ji SM, Kim NJ, Lee S, Ku JH, Do EC, Park S, Kim M, Shim WY, Rhee HS, Kim JY, Kim J, Kim TY, Yamaguchi Y, Iwamuro R, Saito S, Kim G, Jung IS, Park H, Lee C, Lee S, Jeon WS, Jang WD, Kim HU, Lee SY, Im D, Doo SG, Lee SY, Lee HC* & Park JH*. A safe and sustainable bacterial cellulose nanofiber separator for lithium rechargeable batteries. Proceedings of the National Academy of Sciences U S A (PNAS) 116, 19288-19293 (September 2019)
Blin K, Kim HU, Medema MH & Weber T. Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. Briefings in Bioinformatics 20, 1103-1113 (July 2019)
Ryu JY, Kim HU* & Lee SY*. Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers. Proceedings of the National Academy of Sciences U S A (PNAS) 116, 13996-14001 (July 2019)
Ghiffary MR, Kim HU* & Chang YK*. Metabolic engineering strategies for the enhanced microalgal production of long-chain polyunsaturated fatty acids (LC-PUFAs). Biotechnology Journal 14, 1900043 (June 2019)
Gu C1, Kim GB1, Kim WJ, Kim HU* & Lee SY*. Current status and applications of genome-scale metabolic models. Genome Biology 20, 121 (June 2019)
Park SH, Kim GB, Kim HU, Park SJ & Choi JI. Enhanced production of poly-3-hydroxybutyrate (PHB) by expression of response regulator DR1558 in recombinant Escherichia coli. International Journal of Biological Macromolecules 131, 29-35 (June 2019)
Lee SY, Kim HU, Chae TU, Cho JS, Kim JW, Shin JH, Kim DI, Ko YS, Jang WD & Jang YS. A comprehensive metabolic map for production of bio-based chemicals. Nature Catalysis 2, 18-33 (January 2019) Journal cover paper
Kim HT, Khang TU, Baritugo KA, Hyun SM, Kang KH, Jung SH, Song BK, Park K, Oh MK, Kim GB, Kim HU, Lee SY, Park SJ & Joo JC. Metabolic engineering of Corynebacterium glutamicum for the production of glutaric acid, a C5 dicarboxylic acid platform chemical. Metabolic Engineering 51, 99-109 (January 2019)
Mohite OS, Weber T, Kim HU* & Lee SY*. Genome-scale metabolic reconstruction of actinomycetes for antibiotics production. Biotechnology Journal 14, 1800377 (January 2019) Top 10% most downloaded papers (April 2020)
2018
Kim B1, Binkley R1, Kim HU1 & Lee SY. Metabolic engineering of Escherichia coli for the enhanced production of L-tyrosine. Biotechnology and Bioengineering 115, 2554-2564 (October 2018)
Ryu JY1, Kim HU1 & Lee SY. Deep learning improves prediction of drug-drug and drug-food interactions. Proceedings of the National Academy of Sciences U S A (PNAS) 115, E4304-E4311 (April 2018)
Robertsen HL, Weber T*, Kim HU & Lee SY*. Toward systems metabolic engineering of streptomycetes for secondary metabolites production. Biotechnology Journal 13, 1700465 (January 2018) Top 20 most read paper in Biotechnology Journal (June 2019)
2017
Kim HU, Blin K, Lee SY & Weber T. Recent development of computational resources for new antibiotics discovery. Current Opinion in Microbiology 39, 113-120 (October 2017)
Ryu JY1, Kim HU1 & Lee SY. Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. Proceedings of the National Academy of Sciences U S A (PNAS) 114, E9740-E9749 (November 2017)
Yang D, Cho JS, Choi KR, Kim HU & Lee SY. Systems metabolic engineering as an enabling technology in accomplishing sustainable development goals. Microbial Biotechnology 10, 1254-1258 (September 2017)
Jang WD, Hwang JH, Kim HU, Ryu JY & Lee SY. Bacterial cellulose as an example product for sustainable production and consumption. Microbial Biotechnology 10, 1181-1185 (September 2017)
Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T & Medema MH. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Research 45, W36-W41 (July 2017)
Hur W1, Ryu JY1, Kim HU, Hong SW, Lee EB, Lee SY & Yoon SK. Systems approach to characterize the metabolism of liver cancer stem cells expressing CD133. Scientific Reports 7, 45557 (April 2017)
Kim WJ1, Kim HU1 & Lee SY. Current state and applications of microbial genome-scale metabolic models. Current Opinion in Systems Biology 2, 9-17 (April 2017)
Kim WJ, Ahn JH, Kim HU, Kim TY & Lee SY. Metabolic engineering of Mannheimia succiniciproducens for succinic acid production based on elementary mode analysis with clustering. Biotechnology Journal 12, 1600701 (February 2017)
2016
Choi S1, Kim HU1, Kim TY & Lee SY. Systematic engineering of TCA cycle for optimal production of a four-carbon platform chemical 4-hydroxybutyric acid in Escherichia coli. Metabolic Engineering 38, 264-273 (November 2016)
Kim HU*, Charusanti P, Lee SY & Weber T*. Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites. Natural Product Reports 33, 933-941 (July 2016)
Weber T & Kim HU. The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production. Synthetic and Systems Biotechnology 1(2), 69-79 (June 2016)
2015
Lee SY & Kim HU. Systems strategies for developing industrial microbial strains. Nature Biotechnology 33, 1061-1072 (October 2015)
Ryu JY, Kim HU & Lee SY. Human genes with a greater number of transcript variants tend to show biological features of housekeeping and essential genes. Molecular BioSystems 11, 2798-2807 (August 2015)
Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO. Minimum Information about a Biosynthetic Gene cluster. Nature Chemical Biology 11, 625-631 (August 2015)
Ryu JY1, Kim HU1 & Lee SY. Reconstruction of genome-scale human metabolic models using omics data. Integrative Biology 7, 859-868 (August 2015)
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E & Medema MH. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Research 43, W237-W243 (June 2015)
Kim HU, Ryu JY, Lee JO & Lee SY. A systems approach to traditional oriental medicine. Nature Biotechnology 33, 264-268 (March 2015)
Kim TY1, Park JM1, Kim HU1, Cho KM* & Lee SY*. Design of homo-organic acid producing strains using multi-objective optimization. Metabolic Engineering 28, 63-73 (March 2015)
Weber T, Charusanti P, Musiol-Kroll EM, Jiang X, Tong Y, Kim HU & Lee SY. Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. Trends in Biotechnology 33, 15-26 (January 2015)
2014
Park SH, Kim HU, Kim TY, Park JS, Kim SS & Lee SY. Metabolic engineering of Corynebacterium glutamicum for L-arginine production. Nature Communications 5, 4618 (August 2014)
Kim HU, Kim B, Seung D & Lee SY. Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality. Biotechnology and Bioprocess Engineering 19, 660-667 (July 2014)
Hwang KS1, Kim HU1, Charusanti P, Palsson BØ & Lee SY. Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites. Biotechnology Advances 32, 255-268 (March 2014)
2013
Choi S, Kim HU, Kim TY, Kim WJ, Lee MH & Lee SY. Production of 4-hydroxybutyric acid by metabolically engineered Mannheimia succiniciproducens and its conversion to γ-butyrolactone by acid treatment. Metabolic Engineering 20, 73-83 (November 2013)
Shin JH1, Kim HU1, Kim DI & Lee SY. Production of bulk chemicals via novel metabolic pathways in microorganisms. Biotechnology Advances 31, 925-935 (November 2013)
Kim HU & Lee SY. Applications of genome-scale metabolic network models in the biopharmaceutical industry. Pharmaceutical Bioprocessing 1(4), 337-339 (October 2013)
Kim HU1, Kim WJ1 & Lee SY. Flux-coupled genes and their use in metabolic flux analysis. Biotechnology Journal 8, 1035-1042 (September 2013) Selected for “In this issue” of the journal
2012
Park JM, Park HM, Kim WJ, Kim HU, Kim TY & Lee SY. Flux variability scanning based on enforced objective flux for identifying gene amplification targets. BMC Systems Biology 6, 106 (August 2012)
Kim HU, Sohn SB & Lee SY. Metabolic network modeling and simulation for drug targeting and discovery. Biotechnology Journal 7, 330-342 (March 2012) Inside Cover of the Journal
2011
Kim HU1, Kim TY1* & Lee SY*. Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network. BMC Systems Biology 5(Suppl 2), S14 (December 2011) Presented at GIW 2011/BIOINFO 2011: BRIC VOD: http://bric.postech.ac.kr/vod/vod_detail.php?nNum=11844
Lee JW, Kim HU, Choi S, Yi J & Lee SY. Microbial production of building block chemicals and polymers. Current Opinion in Biotechnology 22, 758-767 (December 2011)
Kim HU1, Kim SY1, Jeong H, Kim TY, Kim JJ, Choy HE, Yi KY, Rhee JH* & Lee SY*. Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Molecular Systems Biology 7, 460 (January 2011)
2010
Kim TY1, Kim HU1 & Lee SY. Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks. Metabolic Engineering 12(2), 105-111 (March 2010)
Kim TY, Kim HU & Lee SY. Data integration and analysis of biological networks. Current Opinion in Biotechnology 21, 78-84 (February 2010) Journal cover paper
Kim HU, Kim TY & Lee SY. Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE. Molecular BioSystems 6(2), 339-348 (February 2010) Journal cover paper
2009
Kim TY1, Kim HU1, Song H & Lee SY. In silico analysis of the effects of H2 and CO2 on the metabolism of a capnophilic bacterium Mannheimia succiniciproducens. Journal of Biotechnology 144(3), 184-189 (November 2009)
Lee SY, Kim HU, Park JH, Park JM & Kim TY. Metabolic engineering of microorganisms: general strategies and drug production. Drug Discovery Today 14, 78-88 (January 2009) Top 10 articles on “metabolic engineering” topic since this publication – BioMedLib (March 10, 2011)
2008
Park JH, Lee SY, Kim TY & Kim HU. Application of systems biology for bioprocess development. Trends in Biotechnology 26, 404-412 (August 2008) Journal cover paper
Kim TY, Sohn SB, Kim HU & Lee SY. Strategies for systems-level metabolic engineering. Biotechnology Journal 3, 612-623 (May 2008)
Kim HU, Kim TY & Lee SY. Metabolic flux analysis and metabolic engineering of microorganisms. Molecular BioSystems 4, 113-120 (February 2008) Top 50 most cited in the journal (September 14, 2010)
2007
Lee KH, Park JH, Kim TY, Kim HU & Lee SY. Systems metabolic engineering of Escherichia coli for L-threonine production. Molecular Systems Biology 3, 149 (December 2007)
Kim TY, Kim HU, Park JM, Kim JS, Song H & Lee SY. Genome-scale analysis of Mannheimia succiniciproducens metabolism. Biotechnology and Bioengineering 97(4), 657-671 (July 2007)
2006
Barrett CL, Kim TY, Kim HU, Palsson BØ & Lee SY. Systems biology as a foundation for genome-scale synthetic biology. Current Opinion in Biotechnology 17, 488-492 (October 2006)
Lee SY, Kim DH, Kim JS, Kim HU & Yun H. Korean systems biology and biotechnology research. Asia Pacific Biotech News 10(17), 967-977 (September 2006)
Kim JS, Yun H, Kim HU, Choi HS, Kim TY, Woo HM & Lee SY. Resources for systems biology research. Journal of Microbiology and Biotechnology 16(6), 832-848 (June 2006)