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Department of Bioengineering, University of California, San Diego,
9500 Gilman Drive #0412, La Jolla, California 92093, the United States
E-mail: hyl003_AT_ucsd.edu
Research Interests
Research Interests
Microbial Systems Engineering
Systems biology and synthetic biology for metabolic engineering
Adaptive evolution of microorganisms for discovery and engineering purposes
Design and optimization of metabolic pathway for value-added chemical production
Educational Background
Educational Background
2011. 03. – 2017. 02. Ph. D. in Chemical Engineering
Pohang University of Science and Technology, Korea
Thesis: Synthetic design and optimization of metabolic pathway for
efficient conversion of low-cost carbon sources to value-added bio-chemicals
Advisor: Gyoo Yeol Jung
2006. 03. – 2011. 02. B. S. in Chemical Engineering
Pohang University of Science and Technology, Korea
Professional Experiences
Professional Experiences
2023.03 - Assistant Professor
Biological Engineering
Inha University, Korea
2018. 10. – 2023.02 Postdoctoral Scholar
Bioengineering
University of California, San Diego, the United States
Advisor: Bernhard O. Palsson & Adam M. Feist
2018. 04. – 2018. 10. Research Assistant Professor
Chemical Engineering
Pohang University of Science and Technology, Korea
Advisor: Gyoo Yeol Jung
2017. 02. – 2018. 03. Postdoctoral Research Associate
Chemical Engineering
Pohang University of Science and Technology, Korea
Advisor: Gyoo Yeol Jung
Review Activities
Review Activities
2020. 06. - Current Member of the reviewer board of Metabolites
15 Peer-reviewed journals
ACS Sustainable Chemistry & Engineering, Scientific Reports, Microbial Cell Factories, Current Genetics,
Frontiers in Bioengineering, Catalysts, Metabolites, Fermentation, Microorganisms,
Biotechnology and Bioprocess Engineering, Biochemical Engineering Journal, Energies,
Applied Biochemistry and Biotechnology, Journal of Industrial Microbiology & Biotechnology,
International Journal of Molecular Sciences
Selected Publications
Selected Publications
(1first author, *corresponding author)
7. CW Kang1 HG Lim1, J Won1, S Cha, G Shin, J-S Yang, J Sung, GY Jung*, Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production, Nature Communications, 2022, 13:6506, doi: 10.1038/s41467-022-34190-z
6. HG Lim, AV Sastry, K Rychel, AM Feist, BO Palsson*, Machine-learning from Pseudomonas putida KT2440 Transcriptomes Reveals Its Transcriptional Regulatory Network, Metabolic Engineering, 2022, 72:297-310, doi: 10.1016/j.ymben.2022.04.004
5. HG Lim, B Fong, G Alarcon, HD Magurudeniya, T Eng, R Szubin, CA Olson, BO Palsson, JM Gladden, BA Simmons, A Mukhopadhyay, SW Singer, AM Feist*, Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution, Green Chemistry, Aug, 2020; 22:5677-5690, doi:10.1039/D0GC01663B
4. HG Lim1, DH Kwak1, S Park1, S Woo1, J Yang, CW Kang, B Kim, MH Noh, SW Seo*, GY Jung*, Vibrio sp. dhg as a new promising platform for the biorefinery of brown macroalgae, Nature Communications, Jun, 2019; 10:2486, doi:10.1038/s41467-019-10371-1
3. CW Kang1, HG Lim1, J Yang, MH Noh, SW Seo*, GY Jung*, Synthetic auxotrophs for stable and tunable maintenance of plasmid copy number, Metabolic Engineering, Jul, 2018; 48:121-128, doi:10.1016/j.ymben.2018.05.020
2. MH Noh1, HG Lim1, S Park, SW Seo*, GY Jung*, Precise flux redistribution to glyoxylate cycle for 5-aminolevulinic acid production in Escherichia coli, Metabolic Engineering, Sep, 2017;43:1-8, doi: 10.1016/j.ymben.2017.07.006
1. HG Lim, MH Noh, JH Jeong, S Park*, GY Jung*, Optimum rebalancing of the 3-hydroxypropionic acid production pathway from glycerol in Escherichia coli, ACS Synthetic Biology, Nov, 2016;5(11):1247-1255, doi: 10.1021/acssynbio.5b00303
Full Publications
Full Publications
(1first author, *corresponding author)
35. RM Lennen1, HG Lim1, K Jensen1, ET Mohammed, S Malla, RA Boner, K Chekina, E Ozdemir, I Bonde, A Koza, J Maury, LE
Pedersen, LY Schoning, N Sonnenschein, BO Palsson, AT Nielsen, MOA Sommer, MJ Herrgard*, AM Feist*, Laboratory
evolution reveals general and specific tolerance mechanisms for commodity chemicals, Metabolic Engineering, accepted
34. M Park, R Gauttam, B Fong, Y Chen, HG Lim, AM Feist, A Mukhopadhay, CJ Petzold, B Simmons, SW Singer*, Oxidative
Pentose Metabolism in New Pseudomonas putida Isolates, Environmental Microbiology, accepted
33. CW Kang1 HG Lim1, J Won1, S Cha, G Shin, J-S Yang, J Sung, GY Jung*, Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production, Nature Communications, 2022, 13:6506, doi: 10.1038/s41467- 022-34190-z
32. S Woo1, HG Lim1, YH Han1, S Park, MH Noh, D Baek, JH Moon, SW Seo*, GY Jung*, A Vibrio-based microbial platform for
accelerated lignocellulosic biomass refinery, Biotechnology for Biofuels and Bioproducts, Biotechnology for Biofuels and
Bioproducts, 2022, 15:58, doi: 10.1186/s13068-022-02157-3
31. HG Lim, AV Sastry, K Rychel, AM Feist, BO Palsson*, Machine-learning from Pseudomonas putida KT2440 Transcriptomes Reveals Its Transcriptional Regulatory Network, Metabolic Engineering, 2022, 72:297-310, doi: 10.1016/j.ymben.2022.04.004
30. IA Rodionova, Y Gao, J Monk, Y Hefner, N Wong, R Szubin, HG Lim, DA Rodionov, Z Zhang, MH Saier, BO Palsson*, A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli, Scientific Reports, 2022, 12:7274, doi: 10.1038/s41598-022-11134-7
29. S Kim1, SH Jin1, HG Lim1, J Yang, B Lee, SW Seo, J Kim, C-S Lee*, GY Jung*, Synthetic cellular communication-based screening for strains with improved 3-hydroxypropionic acid secretion, Lab on a Chip, 2021, 21:4455-4463, doi:10.1039/D1LC00676B
28. IA Rodionova*, Y Gao, AV Sastry, Y Hefner, HG Lim, DA Rodionov, MH Saier*, BO Palsson*, Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli, Communications Biology, 2021, 4:991, doi:10.1038/s42003-021-02516-0
27. G Ye, HG Lim, K Chen, AV Sastry, D Quach, H Verkler, R Szubin, D Kim, BO Palsson, Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo, Nucleic Acids Research, 2021, 46(20):10682-10696. doi:10.1093/nar/gky752
26. HG Lim, T Eng, D Banerjee, G Alarcon, AK Lau, M Park, BA Simmons, BO Palsson, SW Singer, A Mukhopadhyay, AM Feist*, Generation of Pseudomonas putida KT2440 strains with efficient utilization of xylose and galactose via adaptive laboratory evolution, ACS Sustainable Chemistry & Engineering, 2021, 9(34):11512-11523, doi:10.1021/acssuschemeng.1c03765
25. JY Seok1, YH Han1, J-S Yang, J Yang, HG Lim, SG Kim, SW Seo*, GY Jung*, Synthetic biosensor accelerates evolution by rewiring carbon metabolism toward specific metabolite, Cell Reports, 2021; 36(8):109589, doi: 10.1016/j.celrep.2021.109589
24. JY Lee1, S Cha1, JH Lee, HG Lim, MH Noh, CW Kang, GY Jung*, Plug-in repressor library for precise regulation of metabolic flux in Escherichia coli, Metabolic Engineering, 2021; 67:365-372, doi:10.1016/j.ymben.2021.07.013
23. S Cha1, HG Lim1, S Kwon, D Kim, CW Kang, GY Jung, Design of mutualistic microbial consortia for stable conversion of carbon monoxide to value-added chemicals, Metabolic Engineering, Mar, 2021; 64:146-153, doi: 10.1016/j.ymben.2021.02.001
22. HG Lim, B Fong, G Alarcon, HD Magurudeniya, T Eng, R Szubin, CA Olson, BO Palsson, JM Gladden, BA Simmons, A Mukhopadhyay, SW Singer, AM Feist*, Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution, Green Chemistry, Aug, 2020; 22:5677-5690, doi:10.1039/D0GC01663B
21. MH Noh1, HG Lim1, S Park, GY Jung*, Auxotrophic selection strategy for improved production of Coenzyme B12 in Escherichia coli, iScience, Mar, 2020; 23(3):100890, doi:10.1016/j.isci.2020.100890
20. MH Kim1, MH Noh1, HG Lim*, GY Jung*, Enhanced lycopene production in Escherichia coli by expression of two MEP pathway enzymes from Vibrio sp. dhg, Catalysts, Nov, 2019; 9(12):1003, doi: 10.3390/catal9121003
19. HG Lim1, DH Kwak1, S Park1, S Woo1, J Yang, CW Kang, B Kim, MH Noh, SW Seo*, GY Jung*, Vibrio sp. dhg as a new promising platform for the biorefinery of brown macroalgae, Nature Communications, Jun, 2019; 10:2486, doi:10.1038/s41467-019-10371-1
18. S Cha1, HG Lim1, MF Haase, K Steve, GY Jung*, D Lee*, Efficient enzymatic conversion of insoluble chemicals using bicontinuous interfacially jammed emulsion gels (bijel), Scientific Reports, Apr, 2019; 9:6363, doi:10.1038/s41598-019-42769-8
17. M J1, MH Noh1, HG Lim1, CW Kang, D-K Im, M-K Oh, GY Jung*, Precise tuning of the glyoxylate cycle in Escherichia coli for efficient tyrosine production from acetate, Microbial Cell Factories, Mar, 2019; 18:57, doi: 10.1186/s12934-019-1106-0
16. HG Lim1, S Jang1, S Jang, SW Seo*, GY Jung*, Design and optimization of genetically encoded biosensors for high-throughput screening of chemicals (review), Current Opinion in Biotechnology, Dec, 2018; 54:18-25, doi:10.1016/j.copbio.2018.01.011
15. JH Lee1, SH Cha1, K Kim, HG Lim*, GY Jung*, Efficient conversion of acetate to 3-hydroxypropionic acid by engineered Escherichia coli, Catalysts, Nov, 2018; 8(11):525, doi:10.3390/catal8110525
14. SG Kim1, MH Noh1, HG Lim, S Jang, S Jang, GY Jung*, Molecular parts and genetic circuits for metabolic engineering of microorganisms (review), FEMS Microbiology Letters, Sep, 2018; 365(17): fny187, doi:10.1093/femsle/fny187
13. S Jang1, S Jang1, MH Noh, HG Lim, GY Jung*, Novel hybrid input part using riboswitch and transcriptional repressor for signal inverting amplifier, ACS Synthetic Biology, Aug, 2018; 7(9):2199-2204, doi:10.1021/acssynbio.8b00213
12. CW Kang1, HG Lim1, J Yang, MH Noh, SW Seo*, GY Jung*, Synthetic auxotrophs for stable and tunable maintenance of plasmid copy number, Metabolic Engineering, Jul, 2018; 48:121-128, doi:10.1016/j.ymben.2018.05.020
11. JY Seok1, J Yang1, SJ Choi, HG Lim, UJ Choi, K Kim, S Park, TH Yoo*, GY Jung*, Directed evolution of the 3-hydroxypropionic acid production pathway by engineering aldehyde dehydrogenase using a synthetic selection device, Metabolic Engineering, May, 2018; 47:113-120, doi:10.1016/j.ymben.2018.03.009
10. HG Lim1, JH Lee1, MH Noh, GY Jung*, Rediscovering acetate metabolism: its potential sources and utilization for bio-based transformation into value-added chemicals (review), Journal of Agricultural and Food Chemistry, Apr, 2018; 66(16) 3998-4006, doi:10.1021/acs.jafc.8b00458
9. MH Noh1, HG Lim1, SH Woo, J Song, GY Jung*, Production of itaconic acid from acetate by engineering acid-tolerant Escherichia coli W, Biotechnology and Bioengineering, Mar, 2018;115(3):729-738, doi: 10.1002/bit.26508
8. MH Noh1, HG Lim1, S Park, SW Seo*, GY Jung*, Precise flux redistribution to glyoxylate cycle for 5-aminolevulinic acid production in Escherichia coli, Metabolic Engineering, Sep, 2017;43:1-8, doi: 10.1016/j.ymben.2017.07.006
7. DH Kwak1, HG Lim1, J Yang, SW Seo*, GY Jung*, Synthetic redesign of Escherichia coli for cadaverine production from galactose, Biotechnology for Biofuels, Jan, 2017;10:20, doi: 10.1186/s13068-017-0707-2
6. BE Min1, HG Hwang1, HG Lim, GY Jung*, Optimization of industrial microorganisms: recent advances in synthetic dynamic regulators (review), Journal of Industrial Microbiology & Biotechnology, Jan, 2017;44(1):89-98, Selected as a cover paper, doi:10.1007/s10295-016-1867-y
5. HG Lim, MH Noh, JH Jeong, S Park*, GY Jung*, Optimum rebalancing of the 3-hydroxypropionic acid production pathway from glycerol in Escherichia coli, ACS Synthetic Biology, Nov, 2016;5(11):1247-1255, doi: 10.1021/acssynbio.5b00303
4. HG Lim1, JH Lim1, GY Jung*, Modular design of metabolic network for robust production of n-butanol from galactose-glucose mixtures, Biotechnology for Biofuels, Sep, 2015;8:137, doi:10.1186/s13068-015-0327-7
3. HG Lim, DH Kwak, GY Jung*, Biofuel production from macroalgae toward bio-based economy (review), Journal of Marine Bioscience and Biotechnology, Jul, 2014:6(1):8-16, doi: 10.15433/ksmb.2014.6.1.008
2. SW Seo, J Yang, BE Min, S Jang, JH Lim, HG Lim, SC Kim, SY Kim, J Jeong, GY Jung*, Synthetic biology: tools to design microbes for the production of chemicals and fuels (review), Biotechnology Advances, Nov, 2013;31(6):811-817, doi:10.1016/j.biotechadv.2013.03.012
1. HG Lim1, SW Seo1, GY Jung*, Engineered Escherichia coli for simultaneous utilization of galactose and glucose, Bioresource Technology, May, 2013;135:564-567, doi: 10.1016/j.biortech.2012.10.124
Book chapters
Book chapters
1. S Jang, HG Lim, J Yang, SW Seo*, GY Jung*, Synthetic regulatory tools to engineer microbial cell factories for chemical production (book chapter), Current Developments in Biotechnology and Bioengineering, Nov, 2018; 115-142, doi:10.1016/B978-0-444-64085-7.00005-8
Patents
Patents
7. HG Lim, DH Kwak, GY Jung, SW Seo, Novel microorganism for rapid assimilation of carbon source derived from biomass,
Korean patent (application: 10-2017-0058781, May 11, 2017), PCT patent (application: PCT/KR2018/005437, May 11, 2018)
6. CW Kang, HG Lim, SW Seo, GY Jung, Modulation of plasmid copy number in antibiotics-free plasmid maintenance system,
Korean patent (application: 10-2018-0039841, Apr 5, 2018), PCT patent (application: PCT/KR2018/004038, Apr 5, 2018)
5. MH Noh, HG Lim, GY Jung, Recombinant microorganism producing itaconic acid and production method of itaconic acid
using the same, Korean patent (application: 10-2017-0142758, Oct 30, 2017; granted: 10-1973001, Apr 22, 2019)
4. MH Noh, HG Lim, SW Seo, GY Jung, Recombinant microorganism producing 5-aminolevulinic acid and method of producing
5-aminolevulinic acid using the same, Korean patent (application: 10-2017-0135401, 18 Oct 2017; granted: 10-2027747, Sep 26,
2019)
3. HG Lim, GY Jung, S Park, EH Seol, 3-Hydroxypropionic acid-producing recombinant microorganism and method of producing
3-hydroxypropionic acid using the same, Korean patent (application: 10-2016-0002175, Jan 7, 2016; granted:10-1760340, Jul
17, 2017)
2. HG Lim, SW Seo, GY Jung, Novel galactose metabolizing bacteria and methods for metabolizing biomass using the same,
Korean patent (application:10-2013-0097310, Aug 16, 2013; granted: 10-1476047, Dec 17, 2014)
1. MH Oh, JS Ham, KH Seol, AR Jang, DH Kim, GY Jung, GW Shin, BR Chung, HS Hwang, JK Na, BE Min, JH Lim, S Jang, SW Seo, J
Yang, HG Lim, W Choi, SC Kim, HJ Lee, Probe, probe set for food borne pathogens and the detecting method thereof, Korean
patent (application: 10-2011-0117805, Nov 11, 2011; granted: 10-1347735, Dec 27, 2013)
Selected Presentations
Selected Presentations
8. HG Lim, MH Noh, CW Kang, SW Seo, GY Jung, Accelerating microbial production of value-added biochemicals via precise
control of gene expression in Escherichia coli, i-BioS, Singapore (Dec 18-20, 2017) as an oral presentation
7. HG Lim, MH Noh, JH Jung, S Park, GY Jung, Synthetic Design and Optimization of Biosynthetic Pathway for 3-
Hydroxypropionic Acid Production in Escherichia coli, i-BioP, Busan, Korea (Dec 16-18, 2016) as an oral presentation
6. HG Lim, MH Noh, JH Jung, S Park, GY Jung, Optimal Pathway Rebalancing for 3-Hydroxypropionic acid Production from
glycerol in Escherichia coli, 251st ACS National Meeting & Exposition, San Diego, United States (Mar 10-14, 2015) as an oral
presentation
5. HG Lim, JH Lim, GY Jung, Modular Engineering for Robust n-Butanol Production from Galactose-Glucose mixtures in
Escherichia coli, The 12th Asian Congress on Biotechnology (ACB 2015), Kuala Lumpur, Malaysia (Nov 15-19, 2015) as an oral
presentation
4. HG Lim, JH Lim, GY Jung, Optimization of Modular Pathway for Production n-Butanol from Red Seaweed Hydrolysate in
Escherichia coli, 5th International Conference on Biomolecular Engineering, Texas, United States (Jan 11-14, 2015) as a poster
presentation
3. HG Lim, JH Lim, GY Jung, Enhanced Utilization of Non-Favored Sugars from Marine Biomass By Re-Designed Escherichia coli,
Metabolic Engineering X, Vancouver, Canada (June 15-19, 2014) as a poster presentation.
2. HG Lim, SW Seo, GY Jung, Simultaneous Utilization of Galactose and Cellobiose by Engineered Escherichia coli, 245th ACS
National Meeting & Exposition, New Orleans, United States (Apr, 7-11, 2013) as an oral presentation
1. HG Lim, SW Seo, GY Jung, Simultaneous Utilization of Glucose and Galactose by Re-design of Galactose Metabolism pathway
in Escherichia coli, 15th International Biotechnology Symposium(IBS) and Exhibition, Korea (Sep, 16-21, 2012) as a poster
presentation
Awards and Honors
Awards and Honors
2006 – 2011 The Korean Presidential Scholarship supported by Korean Government
Dec, 2011 Member of Young Engineers Honor Society (NAEK-YEHS) supported by
the National Academy of Engineering of Korea
April, 2012 Best Student Poster Award at Korean Society for Biotechnology and Bioengineering,
Spring Meeting, Korea
October, 2012 Best Student Poster Award at the Korean Institute of Chemical Engineering
Fall Meeting, Korea
April, 2014 Best Oral Presentation Award at Korean Society for Biotechnology and Bioengineering
Fall Meeting, Korea
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