Journal papers

45. HG Lim*, Y Gao, K Rychel, C Lamoureux, A Lou, BO Palsson*, Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase, mSystems, accepted

44. S Woo, YH Han, D Baek, HK Lee, MH Noh, S Han, HG Lim, SW Seo, GY Jung, Generation of a Vibrio-based platform for efficient conversion of raffinose through adaptive laboratory evolution on a solid medium, Metabolic Engineering, 2024, 86, 300-307, doi:10.1016/j.ymben.2024.11.001

43. IA Rodionova1,*, HG Lim1, DA Rodionov, Y Hutchison, C Dalldorf, Y Gao, J Monk, BO Palsson*, CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli, Communications Biology, 2024, 7, 1160, doi:10.1038/s42003-024-06831-0

42. JH Moon, S Woo, HJ Shin, HK Lee, GY Jung*, HG Lim*, Direct itaconate production from brown macroalgae using engineered Vibrio sp. dhg, Journal of Agricultural and Food Chemistry, 2024, 72, 30, 16860–16866, doi:10.1021/acs.jafc.4c04138

41. M Kumar, JD Tibocha-Bonilla, Z Füssy, C Lieng, SM Schwenck, AV Levesque, MM Al-Bassam, A Passi, M Neal, C Zuniga, F Kaiyom, JL Espinoza, HG Lim, SW Polson, LZ Allen, K Zengler*, Mixotrophic growth of a ubiquitous marine diatom, Science Advances, 2024, 10(29):eado2623, doi:10.1126/sciadv.ado2623

40. HS Kim, MH Noh, EM White, MV Kandefer, MA Rahman, AF Wright, D Datta, HG Lim, E Smiggs, JJ Locklin, MA Rahman*, AM Feist*, JK Pokorski*, Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration, Nature Communications, 2024, 15, 3338 doi:10.1038/s41467-024-47132-8

39. C Hong, Y Kim, H Lee, S Yun, HG Lim, J Yang*, S Jang*, Vibrio species as next-generation chassis for accelerated synthetic biology, Biotechnology and Bioprocess Engineering, 2024, 29, 241-253, doi:10.1007/s12257-024-00023-7

38. AJ Borchert1, A Bleem1, HG Lim1, K Rychel, KD Dooley, ZA Kellermyer, TL Hodges, BO Palsson*, GT Beckham*, Machine learning-based analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440, mSystems, 2024, e00942-23, doi:10.1128/msystems.00942-23

37. HK Lee, S Woo, DY Baek, GY Jung*, HG Lim*, Direct and Robust Citramalate Production from Brown Macroalgae using Fast-growing Vibrio sp. dhg, Bioresource Technology, 2024, 394:130304, doi:10.1016/j.biortech.2024.130304

2023

36. Y Hirose*, S Poudel, AV Sastry, K Rychel, R Szubin, D Zelinski, HG Lim, N Menon, H Bergsten, S Uchiyama, T Hanada, S Kawabata, BO Palsson, V Nizet*, Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins, mSystems, 2023, e00247-23, doi:10.1128/msystems.00247-23

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, 2023, 76:179-192, doi:10.1016/j.ymben.2023.01.012

2022

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, 2022, 25(2):493-504, doi:10.1111/1462-2920.16296

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, 2022, 15:58, doi:10.1186/s13068-022-02157-3

31. HG Lim, K Rychel, AV Sastry, GJ Bentley, J Mueller, HS Schindel, PE Larsen, PD Laible, AM Guss, W Niu, CW Johnson, GT Beckham, 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

2021

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. Y Gao, 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

2020

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

2019

20. MJ 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*, Bicontinuous interfacially jammed emulsion gels (bijels) as media for enabling enzymatic reactive separation of a highly water insoluble substrate, 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

2018

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

2017

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

2016

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

2015

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

2014

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

2013