Post Doctoral Associate
Department of Chemical Engineering
Massachusetts Institute of Technology
77 Massachusetts Avenue, Room: E18-524
Cambridge, MA 02139 USA
Phone: (617) 258-8037
Email: yosebiba@mit.edu
Education
Ph.D. in Biological Engineering, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 2019
B.S. in Biochemistry and Cell Biology, Department of Biology, University of California San Diego, 2010
Publications
1. 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”, P.N.A.S., vol. 9, pp. 118, March 2021.
2. Y. Song†, J. Bae†, J. Shin, S. Jin, J. K. Lee, S. C. Kim, S. Cho, and B. K. Cho, “Transcriptome and translatome of four CO2 fixing acetogens under heterotrophic and autotrophic conditions”, Sci. Data, vol. 8, pp. 51, Feb 09 2021
3. S. Jin, J. Bae, Y. Song, N. Pearcy, J. Shin, S. Kang, N.P. Minton, P. Soucaille, and B. K. Cho, “Synthetic biology on acetogenic bacteria for highly efficient conversion of C1 gases to biochemicals”, Int J Mol Sci, vol. 21, pp. 7639, Oct 25 2020
4. S. Kang†, Y. Song†, S. Jin, J. Shin, J. Bae, D. R. Kim, J. K. Lee, S. C. Kim, S. Cho, and B. K. Cho, “Adaptive laboratory evolution of Eubacterium limosum ATCC 8486 on carbon monoxide”, Front Microbiol, vol. 11, pp. 402, 2020.
5. Y. Song, J. Lee, G. Lee, J. Shin, S. Jin, S. Kang, J. K. Lee, D. R. Kim, E. Y. Lee, S. C. Kim, S. Cho, D. Kim, and B. K. Cho, “Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei”, P.N.A.S., vol. 117, pp. 7516, Mar 2020.
6. J. Shin, S. Kang, Y. Song, S. Jin, J. Lee, J. Lee, D. R. Kim, S. C. Kim, S. Cho, and B. K. Cho, “Genome engineering of Eubacterium limosum using expended genetic tools and CRISPR-Cas9 system”, ACS Synth Biol, vol. 9, pp. 2059, Aug 2 2019
7. S. Park, E. Ko, J. H. Lee, Y. Song, C. H. Cui, J. Hou, B. M. Jeon, H. S. Kim, S. C. Kim, “Gypenoside LXXV Promotes Cutaneous Wound Healing In Vivo by Enhancing Connective Tissue Growth Factor Levels Via the Glucocorticoid Receptor Pathway”, Molecules, vol. 24, pp. 1595, Apr 23 2019.
8. Y. Song, J. Shin, S. Jin, J. K. Lee, D. R. Kim, S. C. Kim, S. Cho, and B. K. Cho, “Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth”, BMC Genomics, vol. 19, pp. 837, Nov 23 2018.
9. J. Shin, Y. Song, S. Jin, J. K. Lee, D. R. Kim, S. C. Kim, S. Cho, and 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, Dec 2018.
10. 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 et al., “Fabrication of three-dimensional porous carbon scaffolds with tunable pore sizes for effective cell confinement”, Carbon, vol. 130, pp. 814-821, Apr 2018.
11. Y. Song, J. Shin, Y. Jeong, S. Jin, J.-K. Lee, D. R. Kim, S. C. Kim, S. Cho, and B.-K. Cho, “Determination of the Genome and Primary Transcriptome of Syngas Fermenting Eubacterium limosum ATCC 8486″, Scientific Reports, vol. 7, pp. 13694, 2017/10/20 2017.
12. J. Shin, Y. Song, Y. Jeong, and B. K. Cho, “Analysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria”, Front Microbiol, vol. 7, pp. 1531, 2016.
13. S. Hwang, Y. Song, and B. K. Cho, “Draft Genome Sequence of Acetobacterium bakii DSM 8239, a Potential Psychrophilic Chemical Producer through Syngas Fermentation”, Genome Announc, vol. 3, pp., Sep 24 2015.
14. 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”, Biotechnol Bioproc E, vol. 20, pp. 825-833, Sep 2015.
15. Y. Song, B. R. Lee, S. Cho, Y. B. Cho, S. W. Kim, T. J. Kang, S. C. Kim, and B. K. Cho, “Determination of single nucleotide variants in Escherichia coli DH5alpha by using short-read sequencing”, Fems Microbiol Lett, vol. 362, pp., Jun 2015.
16. Y. Song, S. Hwang, and B. K. Cho, “Draft Genome Sequence of Clostridium aceticum DSM 1496, a Potential Butanol Producer through Syngas Fermentation”, Genome Announc, vol. 3, pp., Apr 30 2015.
17. Y. Song and B. K. Cho, “Draft Genome Sequence of Chemolithoautotrophic Acetogenic Butanol-Producing Eubacterium limosum ATCC 8486”, Genome Announc, vol. 3, pp., Feb 12 2015.
18. S. Lee, Y. Song†, D. Choe, S. Cho, S. J. Yu, Y. Cho, S. C. Kim, and B. K. Cho, “Reconstruction of Acetogenesis Pathway Using Short-Read Sequencing of Clostridium aceticum Genome”, J Nanosci Nanotechnol, vol. 15, pp. 3852-3861, May 2015.
19. Y. Jeong, Y. Song, H. S. Shin, and B. K. Cho, “Draft Genome Sequence of Acid-Tolerant Clostridium drakei SL1T, a Potential Chemical Producer through Syngas Fermentation”, Genome Announc, vol. 2, pp., May 15 2014.
20. Y. Song, Y. Jeong, H. S. Shin, and B. K. Cho, “Draft Genome Sequence of Clostridium scatologenes ATCC 25775, a Chemolithoautotrophic Acetogenic Bacterium Producing 3-Methylindole and 4-Methylphenol”, Genome Announc, vol. 2, pp., May 15 2014.
21. B. R. Lee, S. Cho, Y. Song, S. C. Kim, and B. K. Cho, “Emerging tools for synthetic genome design”, Mol Cells, vol. 35, pp. 359-370, May 2013.
22. J. N. Kim, J. S. Yi, B. R. Lee, E. J. Kim, M. W. Kim, Y. Song, B. K. Cho, and B. G. Kim, “A versatile PCR-based tandem epitope tagging system for Streptomyces coelicolor genome”, Biochem Biophys Res Commun, vol. 424, pp. 22-27, Jul 20 2012.