K. Yin, N. Lee, A. Landera, A. T. Lavarone, T. D. Young, K. Deng, Y. Chen, J. W. Gin, R. Benedict, Y. Chiu, E. Ukabiala, M. Kamruzzaman, K. Poorey, T. R. Northen, C. J. Petzold, A. George, P. Cruz-Morales, Q. Dan#, and J. D. Keasling#

Polyketide synthase-based controlled synthesis of polycyclopropanated fuel molecules

Under review.

K. Kim, J. Lee, N. Lee, and B. K. Cho

CRISPR-based approaches to engineer non-model bacteria for bioproduction and biotherapeutics

Under review.

J. Dinglasan, N. Lee, N. Pham, M. Faltane, M. Lynde, K. Louie, S. Nath, J. D. Keasling, H. Otani, N. Mouncey

A simple and versatile cell-free expression method for producing secondary metabolites

ACS Synthetic Biology, Accepted.

J. Gong*, J. S. Yi*, S. An, H. S. Cho, C. H. Shin, H. Won, N. Lee, Y. Lee, B. K. Cho, M. Noh, and Y. J. Yoon

Integrated genomic-transcriptomic analysis of clavulanic acid production in differentially productive Streptomyces clavuligerus strains

Scientific Reports, https://doi.org/10.1038/s41598-025-29509-x

N. Lee*, W. Kim*, J. Kim, Y. Lee, S. Hwang, G. Kim, H. Kim, Q. Dan, M. Schmidt, Y. Yoon, S. Cho, B. Palsson#, J. D. Keasling#, and B. K. Cho#

Regulatory orchestration of FK506 biosynthesis in Streptomyces tsukubaensis NRRL 18488 revealed through multi-omic data analysis

iScience, 28(6):112698 (2025)

S. Klass, M. Wesskamper, A. Cowan, N. Lee, S. Cheong, Z. Wang, Y. Chen, J. W. Gin, C. J. Petzold, and J. D. Keasling

Engineering controllable alteration of malonyl-CoA levels to enhance polyketide production and versatility in E. coli

Nature Chemical Biology, 21:1214-1225 (2025)

N. Lee, M. Schmidt, C. Li, C. Filbin, S. Klass, A. Yaguchi, A. L. Fear, T. W. H. Backman, B. A. Abel, Y. Kim, W. E. Kim, C. W. Johnson, Y. Chen, J. W. Gin, C. J. Petzold, E. E. K. Baidoo, Y. Gao, M. C. Burnet, G. Babnigg, P. D. Laible, C. A. Singer, W. E. Michener, D. Salvachua, H. G. Martin, R. W. Haushalter# and J. D. Keasling#

Retrobiosynthesis of unnatural lactams via reprogrammed polyketide synthase

Nature Catalysis, 8:389-402 (2025)

M. Schmidt, A. A. Vilchez, N. Lee, L. S. Keiser, A. N. Pearson, M. G. Thompson, Y. Zhu, R. W. Haushalter, A. M. Deutschbauer, S. Yuzawa, L. M. Blank, and J. D. Keasling

Engineering Pseudomonas putida for production of 3-hydroxyacids using hybrid type I polyketide synthases

Metabolic Engineering Communications, 20:e00261 (2025)

Q. Dan, Y. Chiu, N. Lee, J. H. Pereira, B. Rad, X. Zhao, K. Deng, Y. Rong, C. Zhan, Y. Chen, S. Cheong, C. Li, J. W. Gin, A. Rodrigues, T. R. Northen, T. W. H. Backman, E. E. K. Baidoo, C. J. Petzold, P. D. Adams, and J. D. Keasling

A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxyacids

Nature Catalysis, 8:147-161 (2025)

A. Nava, A. L. Fear, N. Lee, P. Mellinger, G. Lan, J. McCauley, S. Tan, N. Kaplan, G. Goyal, R. C. Coates, J. Roberts, Z. Johnson, R. Hu, B. Wu, J. Ahn, W. E. Kim, Y. Wan, K. Yin, N. Hillson, R. W. Haushalter, and J. D. Keasling

Automated platform for the plasmid construction process

ACS Synthetic Biology, 12(12):3506-3513 (2023)

M. Schmidt, N. Lee, C. Zhan, J. Roberts, A. Nava, L. Keiser, A. Vilchez, C. J. Petzold, Y. Chen, R. W. Haushalter, L. M. Blank, and J. D. Keasling

Maximizing heterologous expression of engineered type I polyketide synthases: Investigating codon optimization strategies

ACS Synthetic Biology, 12(11):3366-3380 (2023)

L. Waldburger, M. Thompson, A. Weisberg, N. Lee, J. Chang, J. D. Keasling, and P. Shih

Transcriptome architecture of the three main lineages of agrobacteria

mSystems, 8(4):e00333-23 (2023)

C. Zhan, N. Lee, G. Lan, Q. Dan, A. Cowan, Z. Wang, E. E. K. Baidoo, R. Kakumanu, B. Luckie, R. C. Kuo, J. McCauley, R. W. Haushalter#, and J. D. Keasling#

Improved polyketide production in C. glutamicum by preventing propionate-induced growth inhibition

Nature Metabolism, 5:1127-1140 (2023)

H. Jo*, J. J. Adidjaja*, D. Kim, B. Park, N. Lee, B. K. Cho, H. U. Kim#, and M. K. Oh#

Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin

Scientific Reports, 12:10302 (2022)

J. Shin, J. R. Noh, D. Choe, N. Lee, Y. Song, S. Cho, E. J. Kang, M. J. Go, S. K. Ha, J. H. Kim, Y. H. Kim, K. S. Kim, B. C. Kim, C. H. Lee#, and B. K. Cho#

Comprehensive 16S rRNA and metagenomics data from the gut microbiome of aging and rejuvenation mouse models

Scientific Data, 9:197 (2022)

S. Hwang, N. Lee, D. Choe, Y. Lee, W. Kim, J. H. Kim, G. Kim, H. Kim, N. Ahn, B. Lee, B. Palsson, and B. K. Cho

System-level analysis of transcriptional and translational regulatory elements in Streptomyces griseus

Frontiers in Bioengineering and Biotechnology, 10:844200 (2022)

Y. Lee, N. Lee, S. Hwang, W. Kim, S. Cho, B. Palsson, and B. K. Cho

Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information

BMC Genomics, 23:68 (2022)

J. Shin*, J. R. Noh*, D. Choe, N. Lee, Y. Song, S. Cho, E. J. Kang, M. J. Go, S. K. Ha, D. H. Chang, J. H. Kim, Y. H. Kim, K. S. Kim, H. Jung, M. H. Kim, B. H. Sung, S. G. Lee, D. H. Lee, B. C. Kim, C. H. Lee#, and B. K. Cho#

Ageing and rejuvenation models reveal changes in key microbial communities associate with healthy ageing

Microbiome, 9:240 (2021)

N. Lee*, M. Choe*, W. Kim*, S. Hwang, Y. Lee, J. H. Kim, G. Kim, H. Kim, S. Cho, B. Palsson, K. S. Jang#, and B. K. Cho#

Re-classification of Streptomyces venezuelae strains and mining secondary metabolites biosynthetic gene clusters

iScience, 24(12) (2021)

N. Lee*, S. Hwang*, W. Kim, Y. Lee, J. Kim, S. Cho, H. U. Kim, Y. J. Yoon#, M. K. Oh#, B. Palsson#, and B. K. Cho#

Systems and synthetic biology approaches on Streptomyces for enhancing the production of secondary metabolites

Natural Product Reports, 38:1330-1361 (2021)

2021 Top 10% of highly cited papers from the Royal Society of Chemistry Journals

S. Hwang, N. Lee, D. Choe, Y. Lee, W. Kim, Y. Jeong, S. Cho, B. Palsson, and B. K. Cho

Elucidating the regulatory elements for transcription termination and post-transcriptional processing in the Streptomyces clavuligerus genome

mSystems, 6(3):e01013-230 (2021)

J. Kim*, N. Lee*, S. Hwang, W. Kim, Y. Lee, S. Cho, B. Palsson, and B. K. Cho

Discovery of novel secondary metabolites encoded in actinomycetes genomes through coculture

Journal of Industrial Microbiology & Biotechnology, 1-16 (2021)

Y. Lee, N. Lee, S. Hwang, W. Kim, Y. Jeong, S. Cho, B. Palsson, and B. K. Cho

Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

Scientific Data, 7:436 (2020)

Y. Lee, N. Lee, S. Hwang, K. Kim, W. Kim, J. Kim, S. Cho, B. Palsson, and B. K. Cho

System-level understanding of gene expression in Streptomyces for discovery of secondary metabolites

Journal of Industrial Microbiology & Biotechnology, 47:739-752 (2020)

N. Lee, S. Hwang, J. Kim, S. Cho, B. Palsson, and B. K. Cho

Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces

Computational and Structural Biotechnology Journal, 18:1548-1556 (2020)

W. Kim, N. Lee, S. Hwang, Y. Lee, J. Kim, S. Cho, B. Palsson, and B. K. Cho

Comparative genomics determines strain-dependent secondary metabolite production in Streptomyces venezuelae strains

Biomolecules, 10(6):864 (2020)

S. Hwang, N. Lee, S. Cho, B. Palsson, and B. K. Cho

Repurposing modular polyketide synthases and non-ribosomal peptide synthetases for novel chemical biosynthesis

Frontiers in Molecular Biosciences, 7:87 (2020)

W. Kim*, S. Hwang*, N. Lee*, Y. Lee, S. Cho, B. Palsson, and B. K. Cho

Transcriptome and translatome profiling of five Streptomyces species in distinct growth phases

Scientific Data, 7:138 (2020)

N. Lee*, W. Kim*, S. Hwang, Y. Lee, S. Cho, B. Palsson, and B. K. Cho

Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters

Scientific Data, 7:55 (2020)

N. Lee, W. Kim, J. Chung, Y. Lee, S. Cho, K. S. Jang, S. C. Kim, B. Palsson, and B. K. Cho

Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus

ISME Journal, 14:1111-1124 (2020)

Y. Lee, N. Lee, Y. Jeong, S. Hwang, W. Kim, S. Cho, B. Palsson, and B. K. Cho

The transcription unit architecture of Streptomyces lividans TK24

Frontiers in Microbiology, 10:2074 (2019)

H. Cho, J. Jo, C. H. Shin, N. Lee, J. S. Choi, B. K. Cho, J. H. Roe, C. W. Kim, H. J. Kwon#, and Y. Yoon#

Improved production of clavulanic acid by reverse engineering and overexpression of the regulatory genes in an industrial Streptomyces clavuligerus strain

Journal of Industrial Microbiology & Biotechnology, 46:1205-1215 (2019)

S. Hwang, N. Lee, Y. Jeong, Y. Lee, W. Kim, S. Cho, B. Palsson, and B. K. Cho

Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome

Nucleic Acids Research, 47(12):6114-6129 (2019)

N. Lee, S. Hwang, Y. Lee, S. Cho, B. Palsson, and B. K. Cho

Synthetic biology tools for novel secondary metabolite discovery in Streptomyces

Journal of Microbiology and Biotechnology, 29(5):667-686 (2019)

JMB outstanding paper

N. Lee*, J. Shin*, J. H. Park, G. M. Lee, S. Cho, and B. K. Cho

Targeted gene deletion using DNA-free RNA-guided Cas9 nuclease accelerates adaptation of CHO cells to suspension culture

ACS Synthetic Biology, 5(11):1211-1219 (2016)

J. Shin*, N. Lee*, Y. Song, J. Park, T. J. Kang, S. C. Kim, G. M. Lee, and B. K. Cho

Efficient CRISPR/Cas9-mediated multiplex genome editing in CHO cells via high-level sgRNA-Cas9 complex

Biotechnology and Bioprocess Engineering, 20(5):825-833 (2015)