Byung-Kwan Cho

Project Scientist

I am a project scientist in the Palsson lab. Before joining this group, I completed my Ph.D. in the molecular biotechnology and biomaterials laboratory at the Seoul National University. My research project has focused on the elucidation of transcriptional regulatory networks of bacterial cells. To determine the nodes and edges in the networks, I have used the high-throughput data generation platforms such as microarrays and next-generation sequencing.

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Education and Training

2008-present: Project Scientist
Department of Bioengineering, University of California, San Diego

2003-2008: Post-Doctoral Researcher
Department of Bioengineering, University of California, San Diego

2003-2003: Post-Doctoral Researcher
Institute of Molecular Biology and Genetics, Seoul National University

School of Chemical and Biological Engineering, Seoul National University

1997-2003: Ph.D.
Molecular Biotechnology and Biomaterials Laboratory

Biochemical Engineering and Biotechnology, Seoul National University

Research Interests
Systems Biology: elucidation of various biological networks to understand phenotypes

High-throughput Molecular Biotechnology Toolbox: (1) optimization of microarrays (transcriptomics and ChIP-chip), next-generation sequencing (RNA-seq, ChIP-seq, TSS profiling), and mass spectrometry (Proteomics and Metabolomics) protocols and (2) development of novel applications of the toolbox

Protein Engineering: computer-guided and experimental protein design to generate novel proteins such as enzymes, therapeutic antibodies and peptides

Teaching Experience
Lectured Biochemical Engineering Class (undergraduate course), Spring 2003

Lectured Food Biotechnology Laboratory Class (undergraduate course), Spring 1996

Lectured Biotechnology Laboratory Class (undergraduate course), Spring 1995

Professional Activities
2001-present American Chemical Society

2007-present American Society for Microbiology

1995-present Korean Society of Biotechnology and Bioengineering

1995-present Korean Society for Microbiology and Biotechnology

2008-present Consultant services for biotech companies

2007-present Reviewer services for scientific journals

Fellowships and Awards
Brain Korea 21 Fellowship, 1999-2003

University Fellowship, 1997-1998

University Full Fellowship for the first ranked graduate student, 1995-1996

University Full Fellowship for the first ranked undergraduate student, 1991-1994

Publications

Cho, B.K., Zengler, K., Knight, E.M., Park, Y.S., Qiu, Y., Barrett, C.L., Lovley, D., and Palsson, B.O. (2009). "Genome-wide analysis of protein-DNA interactions in bacteria.", Microbial Systems Biology, in press.

Seo, J.H., Lee, G.S., Kim, J., Cho, B.K., Joo, K., Lee, J., and Kim, B.G. (2009). "Automatic protein structure prediction system enabling rapid and accurate model building for enzyme screening." Enzyme Microb. Technol., accepted.

Lewis, N.E., Cho, B.K., Knight, E.M., and Palsson, B.O. (2009). Gene Expression Profiling Data and Insight into the Use of Genome-scale In Silico Models of Escherichia coli for Analysis: Providing Context for Content. J. Bacteriol., 191:3437-3444.

Park, S.H., Park, H.Y., Cho, B.K., Yang, Y.H., Sohng, J.K., Lee, H.C., Liou, K., and Kim, B.G. (2009). Reconstitution of Antibiotics Glycosylation by Domain Exchanged Chimeric Glycosyltransferase. J Mol. Catalysis B: Enzymatic, accepted.

Hwang, J.Y., Park, J., Seo, J.H., Cha, M., Cho, B.K., Kim, J., and Kim, B.G. (2009). Simultaneous synthesis of 2-phenylethanol and L-homophenylalanine using aromatic transaminase with yeast Ehrlich pathway. Biotechnol. Bioeng., 102(5):1323-1329.

Cho, B.K., Barrett, C.L., Knight, E.M., Park, Y.S., and Palsson, B.O. (2008). Genome-scale reconstruction of Lrp-regulatory network in Escherichia coli. Proc. Natl. Acad. Sci. USA, 105:19462-19467. Supplemental Data

Cho, B.K., Knight, E.M., and Palsson, B.O. (2008). Genome-wide identification of protein binding sites on DNA by chromatin immunoprecipitation coupled with microarray. Methods in Mol. Biol., 439:131-45.

Cho, B.K., Knight, E.M., Barrett, C.L., and Palsson, B.O. (2008). Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res., 18(6):900-10.

Cho, B.K., Park, H.Y., Seo, J.H., Kim, J., Kang, T.J., Lee, B.S., and Kim, B.G. (2008). Redesigning ω-transaminase to synthesis of optically active aliphatic chiral amines. Biotechnol. Bioeng., 99(2):275-284.

Cho, B.K., Charusanti, P., Herggard, M., and Palsson, B.O. (2007). Microbial regulatory and metabolic networks. Curr. Opin. Biotechnol., 18(4):360-364.

Cha, M., Yun, H., Cho, B.K., and Kim, B.G. (2007). Synthesis of enantio-pure (S)-2-hydroxyphenylbutanoic acid using novel hydroxy acid dehydrogenase from Enterobacter sp. BK2K. Biotechnol. Prog., 23(3):606-612.

Kim, J., Kyung, D., Yun, H., Cho, B.K., Seo, J.H., Cha, M., and Kim, B.G. (2007). Cloning and characterization of a novel β-transaminase from Mesorhizobium sp. Strain LUK: A new biocatalyst for the synthesis of enantiomerically pure β-amino acids. Appl. Environm. Microbiol., 73(6):1772-1782.

Chung, K., Kim, J., Cho, B.K., Ko, B.J., Hwang, B.Y., and Kim, B.G. (2007). How does dextran sulfate prevent heat induced aggregation of protein?: The mechanism and its limitation as aggregation inhibitor. Biochim. Biophys. Acta: Proteins and Proteomics, 1774(2):249-257.

Cho, B.K., Knight, E.M., and Palsson, B.O. (2006). Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology, 152(8):2207-2219.

Cho, B.K., Knight, E.M., and Palsson, B.O. (2006). PCR-based tandem epitope tagging system for Escherichia coli genome engineering. Biotechniques, 40(1):67-72.

Kim, J., Kyung, D., Yun, H., Cho, B.K., and Kim, B.G. (2006). Screening and purification of a novel transaminase catalyzing the transamination of aryl β-amino acid from Mesorhizobium sp. LUK. J. Microbiol. Biotechnol., 16(11):1832-1836.

Cho, B.K., Seo, J.H., Kim, J., Lee, C.S., and Kim, B.G. (2006). Asymmetric synthesis of unnatural L-amino acid using thermophilic aromatic L-amino acid transaminase. Biotechnol. Bioproc. Eng., 11(4):299-305.

Cho, B.K., Seo, J.H., Kang, T.J., Kim, J., Park, H.Y., Lee, B.S., and Kim, B.G. (2006). Engineering aromatic L-amino acid transaminase for the asymmetric synthesis of constrained analogs of L-phenylalanine. Biotechnol. Bioeng., 94(5):842-850.

Hwang, B.Y., Cho, B.K., Yun, H., Kinnera, K., and Kim, B.G. (2005). Revisit of aminotransferase in the genomic era and its application to biocatalysis. J. Mol. Catalysis B: Enzymatic, 37(1-6):47-55.

Cho, B.K., Park, H.Y., Seo, J.H., Kinnera, K., Lee, B.S., and Kim, B.G. (2004). Enzymatic resolution for the preparation of enantiomerically enriched D-β-heterocyclic alanine derivatives using Escherichia coli aromatic L-amino acid transaminase. Biotechnol. Bioeng., 88(4):512-519.

Yun, H., Cho, B.K., and Kim, B.G. (2004). Kinetic resolution of (R,S)-sec-butylamine using ω-transaminase from Vibrio fluvialis JS17 under reduced pressure. Biotechnol. Bioeng., 87(6):772-778.

Yun, H., Lim, S.Y., Cho, B.K., and Kim, B.G. (2004). ω-amino acid:pyruvate transaminase from Alcaligenes denitrificans Y2k-2: a new catalyst for kinetic resolution of β-amino acids and amines. Appl. Environ. Microbiol., 74(4):2529-2534.

Cho, B.K., Cho, H.J., Yun, H., and Kim, B.G. (2003). Simultaneous synthesis of enantiomerically pure (S)-amino acids and (R)-amines using coupled transaminase reactions with two-liquid phase reaction system. J. Mol. Catalysis B: Enzymatic, 26(3-6):273-285.

Cho, B.K., Seo, J.H., Kang, T.W., and Kim, B.G. (2003). Asymmetric synthesis of L-homophenylalanine by equilibrium-shift using recombinant aromatic L-amino acid transaminase. Biotechnol. Bioeng., 83(2):226-234.

Yun, H., Yang, Y.H., Cho, B.K., Hwang, B.Y., and Kim, B.G. (2003). Simultaneous synthesis of enantiomerically pure (R)-1-phenylethanol and (R)-α-methylbenzylamine from racemic α-methylbenzylamine using ω-transaminase/alcohol dehydrogenase/glucose dehydrogenase coupling reaction. Biotechnol. Lett., 25(10):809-814.

Cho, B.K., Cho, H.J., Park, S.H., Yun, H., and Kim, B.G. (2003). Simultaneous synthesis of enantiomerically pure (S)-amino acids and (R)-amines using coupled transaminase reactions. Biotechnol. Bioeng., 81(7):783-789.

Park, B.S., Cho, B.K., Lee, S.Y., Lim, S.H., Kim, D.I., and Kim, B.G. (1999). Optimization of biotransformation process for sodium gluconate production by Aspergillus niger. Kor. J. Biotechnol. Bioeng., 14(3):309-314.

Cho, B.K. and Byun, S.Y. (1999). Purification of Paclitaxel and its derivatives by supercritical fluid chromatography (SFC). Kor. J. Biotechnol. Bioeng., 14(1):17-23.

Jeon, J.W., Cho, B.K., Moon, W.J., Kim, D.I., Chung, H.G., and Byun, S.Y. (1996). Taxol production in Taxus spp. cell culture: semisynthesis of taxol from baccatin III in cell cultures of Taxus baccata Pendula. Kor. J. Biotechnol. Bioeng., 11(3):263-269.

Suh, J.H., Cho, B.K., Byun, S.Y., and Kim, K.H. (1996). Studies on the supercritical fluid extraction of Taxol from yew tree. Kor. J. Biotechnol. Bioeng., 11(1):71-76.

Invited talks

Cho, B.K. (2008). Synthetic Biology 4.0 at Hong Kong, Oct. 10-14.

Cho, B.K. (2008). 16th Annual International Conference on Microbial Genomics at Lake Arrowhead. CA (USA), Sep. 16-19.

Cho, B.K. (2008). Bioengineering Seminar at University of California, San Diego, La Jolla, Apr. 25.

Knight, E.M., Cho, B.K., Barrett, C.L., Park, Y.S., and Palsson. B.O. (2008). Special seminar at University of Iceland, Reykjavik, Mar. 18.

Cho, B.K. and Palsson, B.O. (2008). Guest Lecturer Series at Genomatica Inc., San Diego (USA), Jan. 18.

Cho, B.K., Knight, E.M., and Palsson, B.O. (2007). Annual Geobacter Meeting at University of Massachusetts at Amherst, Amherst (USA), Oct. 21-23.

Cho, B.K., Knight, E.M., and Palsson, B.O. (2007). 15th Annual International Conference on Microbial Genomics at University of Maryland at College Park. Maryland (USA), Sep. 16-19.

Cho, B.K., Knight, E.M., and Palsson, B.O. (2007). FASEB summer research conferences: Mechanisms and regulation of prokaryotic transcription at Vermont Academy, Vermont (USA), Jun. 23-28.

Patents

Kim, B.G. and Cho, B.K. (2002). Method for asymmetric synthesis of optically pure aromatic L-amino acids using thermophilic microorganisms.

Byun, S.Y. and Cho, B.K. (1997). Equipment for the purification of taxol using online continuous process of supercritical fluid extraction.

Selected presentations

Cho, B.K., Knight, E.M., Park, Y.S., Barrett, C.L., Zengler, K., and Palsson, B.O. (2009). Deciphering sigma factor network in Escherichia coli, ASM meeting at Philadelphia (USA), May 17-21.

Park, Y.S., Cho, B.K., Zengler, K., Qiu, Y., Knight, E.M., Barrett, C.L., and Palsson, B.O. (2009). Integrated analysis of multiple genome-scale measurements reveals the meta-structure of bacterial genome, ASM meeting at Philadelphia (USA), May 17-21.

Zengler, K., Cho, B.K., Yu, Q., Barrett, C.L., Park, Y.S., Lipton, M., Lovley, D., and Palsson, B.O. (2009). Experimental genome annotation of Geobacter sulfurreducens, GTL Meeting at Bethesda, Maryland (USA), Feb. 8-11.

Cho, B.K., Zengler, K., Yu, Q., Barrett, C.L., Park, Y.S., and Palsson, B.O. (2008). Landscape of the bacterial transcriptome architecture based on the whole genome tiling microarrays and RNA sequencing, Annual Geobacter Meeting at University of Massachusetts at Amherst, Amherst (USA), Sep. 28-30.

Barrett, C.L., Zengler, K., Yu, Q., Cho, B.K., Kagan, L., Lovley, D.R., and Palsson, B.O. (2008). A method for high resolution binding site identification from genome-wide ChIP-chip and ChIP-seq binding assays, Annual Geobacter Meeting at University of Massachusetts at Amherst, Amherst (USA), Sep. 28-30.

Cho, B.K., Barrett, C.L., Knight, E.M., Park, Y.S., and Palsson, B.O. (2008). Genome-scale reconstruction of Lrp regulatory network in Escherichia coli, 16th Annual International Conference on Microbial Genomics at Lake Arrowhead. CA (USA), Sep. 16-19.

Cho, B.K., Knight, E.M., and Palsson, B.O. (2007). Genome-scale analyses of Escherichia coli transcriptomes between internal redox states. FASEB summer research conferences: Mechanisms and regulation of prokaryotic transcription at Vermont Academy, Poster session, Vermont (USA), Jun. 23-28.

Knight, E.M., Cho, B.K., Joyce, A., and Palsson, B.O. (2007). Transcriptional Networks in Adaptive Evolution. FASEB summer research conferences: Mechanisms and regulation of prokaryotic transcription at Vermont Academy, Oral and poster session, Vermont (USA), Jun. 23-28 (Selected as an oral presentation by conference organizers).

Cho, B.K., Knight, E.M., and Palsson, B.O. (2006). Elucidation and adaptation of the transcriptional network in Escherichia coli. The 3rd International E. Coli Alliance Conference on Systems Biology, Jeju Island (Korea), Oct. (Keynote talk given by B.O.P).

Cho, B.K., Knight, E.M., and Palsson, B.O. (2005). Genome-wide maps of transcription factor-DNA association in E. coli. Annual International Meeting on Microbial Genomics, Poster session, Wisconsin (USA), Sep.

Cho, B.K. and Kim, B.G. (2003). Bioinformatical screening of ω-transaminases and its applications to the production of chiral amines. Gordon Research Conferences: Enzymes, Coenzymes and Metabolic Pathways, Poster session, New Hampshire (USA), Jul.

Upcoming meetings

FASEB SRC at Vermont, June 21-26, 2009.

q-bio conference on cellular information processing at Santa Fe, August 5-9, 2009.

The 10th International Conference on Systems Biology at Stanford University, August 30 - September 4, 2009.

17th Annual International Conference on Microbial Genomics at Maryland, October 11-15, 2009.

Contact Information

Email Address: bcho@ucsd.edu

Phone: (858)822-3076

Mailing Address: 9500 Gilman Drive, Mail Code 0412, La Jolla, CA 92093-0412

Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

Contact Us

Contact Us

In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

FAX:   858-822-3120

Website Concerns: sbrgit@ucsd.edu

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