Publications

Papers

2025

  • E. A Catoiu, J. Krishnan, G. Li, X. A Lou, K. Rychel, Y. Yuan, H. Bajpe, A. Patel, D. Choe, J. Shin, J. Burrows, P. V Phaneuf, D. C Zielinski, B. O Palsson, “iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets”, Nucleic Acids Research, 53, D99-D106. 2025 — Link

2024

  • J. Shin, D.C. Zielinski, B.O. Palsson, “Modulating Bacterial Function Utilizing A Knowledge Base of Transcriptional Regulatory Modules”, Nucleic Acids Research, gkae742. 2024 — Link

 

  • J. Shin, D.C. Zielinski, B.O. Palsson, “Deciphering Nutritional Stress Responses via Knowledge-Enriched Transcriptomics for Microbial Engineering”, Metabolic Engineering, vol. 84, 34-47. 2024 — Link

2023

  • J. Shin, K. Rychel, B.O. Palsson, “Systems biology of competency in bacteria is revealed by applying novel data analytics to the transcriptome”, Cell Reports, vol. 42, 112619. 2023 — Link

 

  • A.T. Rahman#, J. Shin#, C.H. Whang, W. Jung, D. Yoo, C. Seo, B.K. Cho, S. Jon, “Bilirubin Nanomedicine Rescues Intestinal Barrier Destruction and Restores Mucosal Immunity in Colitis”, ACS Nano, May 2023 — Link

 

  • J. Shin#, J. Bae#, H. Lee, S. Kang, S. Jin, Y. Song, S. Cho, B.K. Cho. “Genome-wide CRISPRi screen identifies enhanced autolithotrophic phenotypes in acetogenic bacterium Eubacterium limosum”, Proceedings of the National Academy of Sciences of the United States of America, vol. 120, e2216244120, Feb 2023 — Link

2022

  • Y. Song, J. Bae, S. Jin, H. Lee, S. Kang, J. Lee, J. Shin, S. Cho, B.K. Cho, “Development of highly characterized genetic bioparts for efficient gene expression in CO2-fixing Eubacterium limosum”, Metabolic Engineering, vol. 72, pp. 215-226, July 2022 — Link

 

  • 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, B.K. Cho, “Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models”, Scientific Data, vol. 9, pp. 1-7, May 2022 — Link

 

  • J. Bae, Y. Song, H. Lee,J. Shin, S. Jin, S. Kang, B.K. Cho, “Valorization of C1 gases to value-added chemicals using acetogenic biocatalysts”, Chemical Engineering Journal, vol. 428, pp. 131325, Jan 2022 — Link

2021

  • 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, B.K. Cho, “Microbiome analysis of ageing and rejuvenation models reveals changes in key microbial communities associated with healthy ageing”, Microbiome, vol. 9, pp. 240, Dec 2021. — Link

 

  • J. Shin, Y. Song, S. Kang, S. Jin, J.K. Lee, D.R. Kim, S.C. Kim, S. Cho, V. Müller, B.K. Cho, “Genome-scale analysis of Acetobacterium woodii identifies translational regulation of acetogenesis”, mSystems, vol. 31, pp. e0069621, Aug 2021. — Link

 

  • J. Sung, J. Shin, K. Kim, B.K. Cho, “Microbial production of nematicidal agents for controlling plant-parasitic nematodes”, Process Biochemistry, vol. 108, pp. 69-79, Sep 2021. Link

 

  • E. Yoo, D. Choe, J. Shin, S. Cho, B.K. Cho, “Enzyme-based DNA synthesis and selective retrieval for data storage”, Computational and Structural Biotechnology Journal, vol. 19, pp. 2468-2476, Apr 2021. Link

 

  • S. Jin, Y. Jeon, M.S., Jeon, J. Shin, Y. Song, S. Kang, J. Bae, S. Cho, J.K. Lee, D.R. Kim, B.K. Cho, “Acetogenic bacteria utilize light-driven electrons as an energy source for autotrophic growth”, Proceedings of the National Academy of Sciences of the United States of America, vol. 118, pp. e2020552118, Mar 2021. Link

 

  • Y. Song, J. Bae, J. Shin, S. Jin, J.K. Lee, S.C. Kim, S. Cho, B.K. Cho, “Transcriptome and translatome of CO2 fixing acetogens under heterotrophic and autotrophic conditions”, Scientific Data, vol. 8, 51, Feb 2021. Link

2020

  • S. Jin, J. Bae, Y. Song, N. Pearcy, J. Shin, S. Kang, N.P. Minton, P. Soucaille, B.K. Cho, “Synthetic biology on acetogenic bacteria for highly efficient conversion of C1 gases to biochemicals”, International Journal of Molecular Sciences, vol. 21, 7639, Oct 2020. Link

 

  • Y. Jeon, M.S. Jeon,J. Shin, S. Jin, J. Yi, S. Kang, S.C. Kim, B.K. Cho, J.K. Lee, D.R. Kim, “3D printed bio-responsive devices with selective permeability inspired by eggshell membrane for effective biochemical conversion”, ACS Applied Materials & Interfaces, vol. 12, pp. 30112–30119, June 2020. Link

 

  • Y. Song, J. Lee, J. Shin, G.M. Lee, S. Jin, S. Kang, J.K. Lee, D.R. Kim, E.Y. Lee, S.C. Kim, S. Cho, D. Kim, B.K. Cho,” Functional cooperation of the glycine synthase-reductase and Wood- Ljungdahl pathways for autotrophic growth of Clostridium drakei”, Proceedings of the National Academy of Sciences of the United States of America, vol. 117, pp. 7516-7523, Mar 2020. Link

 

  • S. Kang#, Y. Song#, S. Jin, J. Shin, J. Bae, D.R. Kim, J.K. Lee, S.C. Kim, S. Cho, B.K. Cho, “Adaptive laboratory evolution of Eubacterium limosum ATCC 8486 on carbon monoxide”, Frontiers in Microbiology, vol. 11, 402, Mar 2020. Link

 

  • D.H. Chang#, J. Shin#, S. Lim, K.R. Park, M.S. Rhee, B.K. Cho, I.H. Chung, S.K. Lee, B.C. Kim, “Characterization of vaginal microbiota profiles in native Korean women related with high risk pregnancies”, Journal of Microbiology and Biotechnology, vol. 30, pp. 248–258, Feb 2020. Link

2019

  • J. Shin#, S. Kang#, Y. Song, S. Jin, J. Lee, J.K. Lee, D.R. Kim, S.C. Kim, S. Cho, B.K. Cho, “Genome engineering of Eubacterium limosum using expended genetic tools and CRISPR-Cas9 system”, ACS Synthetic Biology. vol. 8, pp. 2059-2068, Aug 2019. Link

 

  • J. Shin#, J.R. Noh#, D.H. Chang, Y.H. Kim, M.H. Kim, E.S. Lee, S. Cho, B.J. Ku, M.S. Rhee, B.C. Kim, C.H. Lee, B.K. Cho. “Elucidation of Akkermansia muciniphila probiotic traits driven by mucin depletion”, Frontiers in Microbiology, vol. 10, 1137, May 2019. Link

2018

  • Y. Song, J. Shin, S. Jin, J.K. Lee, D.R. Kim, S.C. Kim, S. Cho, B.K. Cho, “Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth”, BMC Genomics, vol. 19, 837, Nov 2018. Link

 

  • J. Shin, Y. Song, S. Jin, J.K. Lee, D.R. Kim, S.C. Kim, S. Cho, B.K. Cho, “Genome-scale analysis of Acetobacterium bakii reveals the cold adaptation of psychrotolerant acetogens by post-transcriptional regulation”, RNA, vol. 24, pp. 1839-1855, Sep 2018. Link

 

  • S. Cho, J. Shin, B.K. Cho, “Applications of CRISPR/Cas system to bacterial metabolic engineering”, International Journal of Molecular Sciences, vol. 19, 1089, Apr 2018. Link

 

  • M.S. Jeon, Y. Jeon, J.H. Hwang, C.S. Heu, S. Jin, J. Shin, Y. Song, S.C. Kim, B.K. Cho, J.K. Lee, D.R. Kim, “Fabrication of three-dimensional porous carbon scaffolds with tunable pore sizes for effective cell confinement”, Carbon, vol. 130, pp. 814-821, Apr 2018. Link

 

  • H. Shin, E. Lee, J. Shin, S.R. Ko, H.S. Oh, C.Y. Ahn, H.M. Oh, B.K. Cho, S. Cho, “Elucidation of the bacterial communities associated with the harmful microalgae Alexandrium tamarense and Cochlodinium polykrikoides using nanopore sequencing”, Scientific Reports, vol. 8, 5323, Mar 2018. Link

2017

  • Y. Song, J. Shin, Y. Jeong, S. Jin, J.K. Lee, D.R. Kim, S.C. Kim, S. Cho, B.K. Cho, “Determination of the genome and primary transcriptome of syngas fermenting Eubacterium limosum ATCC 8486”, Scientific Reports, vol. 7, 13694, Oct 2017. Link

2016

  • J. Shin, Y. Song, Y. Jeong, B.K. Cho, “Analysis of the core genome and pan-genome of autotrophic acetogenic bacteria”, Frontiers in Microbiology, vol. 7, 1531, Sep 2016. Link

 

  • J. Shin#, S. Lee#, M.J. Go, S.Y. Lee, S.C. Kim, C.H. Lee, B.K. Cho, “Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing”, Scientific Reports, vol. 6, 29681, Jul 2016. Link

 

  • N. Lee#, J. Shin#, J. Park, G.M. Lee, S. Cho, B.K. Cho, “Targeted gene deletion using DNA-free RNA-guided Cas9 nuclease accelerates adaptation of CHO cells to suspension culture”, ACS Synthetic Biology, vol. 5, pp. 1211-1219, Feb 2016. Link

2015

  • J. Shin#, N. Lee#, Y. Song, J. Park, T.J. Kang, S.C. Kim, G.M. Lee, B.K. Cho, “Efficient CRISPR/Cas9-mediated multiplex genome editing in CHO cells via high-level sgRNA-Cas9 complex”, Biotechnology and Bioprocess Engineering, vol. 20, pp. 825-833, Nov 2015. Link

 

  • Y. Kang, Y.W. Kim, J. Yun, J. Shin, A. Kim, “KLF1 stabilizes GATA-1 and TAL1 occupancy in the human β-globin locus”, Biochimica et Biophysica Acta, vol. 1849, pp. 282-289, Mar 2015. Link








Lab: SSyn Lab (Systems and Synthetic Biology Lab) 시스템 및 합성생물학 연구실 ㅣ Principal Investigator: Jongoh Shin
Address: Room 418, Natural Science Building 1, Chonnam National University, 77, Yongbong-ro, Buk-gu, Gwang-ju, Republic of Korea. 61186

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