85

Jung, J., Choi, S.C., Jung, S.,  Cho, B.K., Ahn, G.H., Ryu S.B. (2017) A transcriptome approach towards understanding fruit softening in persimmon. Front Plant Sci. 2017. accepted.

49

Cho, B.K., Kim, D.H., Knight, E.M., Zengler, K., and Palsson, B.O. (2014) Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. BMC Biology 12:4.

48

Kim, S.H., Liu, K.H., Lee, S.Y., Hong, S.J., Cho, B.K., Lee, H.K., Lee, C.G., Choi, H.K. (2013) Effects of Light Intensity and Nitrogen Starvation on Glycerolipid, Glycerophospholipid, and Carotenoid Composition in Dunaliella tertiolecta Culture. PLoS One 8(9):e72415.

47

Cho, S., Cho, Y., Lee, S., Kim, J., Yum, H., Kim, S.C., and Cho, B.K. (2013) Current challenges in bacterial transcriptomics. Genomics Informatics 11(2): 76-82.

46

Lee, B.R., Cho, S., Song, Y., Kim, S.C., and Cho, B.K. (2013) Emerging Tools for Synthetic Genome Design. Mol. Cells. 35(5): 359-370.

45

Qiu, Y., Nagarajan, H., Embree, M., Shieu, W., Abate, E., Juárez, K., Cho, B.K., Elkins, J.G., Nevin, K.P., Barrett, C.L., Lovley, D.R., Palsson B.O., and Zengler, K. (2013) Characterizing the interplay between multiple levels of organization within bacterial σ factor regulatory networks. Nat. Commun. 4: 1755.

44

Cho, S.H., Lee, B.R., Cho, B.K., Kim, J.H., and Kim, B.G. (2013) In vitro selection of sialic acid specific RNA aptamer and its application to the rapid sensing of sialic acid modified sugars. Biotechnol. Bioeng., 110(3): 905-913.

43

Seo, J.H., Hong, J.S., Kim, D., Cho, B.K., Huang, T.W., Tsai, S.F., Palsson, B.O., Charusanti, P. (2012) Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. BMC Genomics, 13(1): 679. (Selected as a highly accessed article)

42

Kim, J.G., Lee, S.I., Shin, H.S., Kim, S.C., and Cho, B.K.* (2012) Elucidation of Bacterial Genome Complexity using Next-Generation Sequencing. Biotechnol. Bioprocess Eng., 17(5): 887-899.

41

Kim, D.H., Hong, J.S.J., Qiu, Y., Nagarajan, H., Seo, J.H., Cho, B.K., Tsai, S.F., and Palsson, B.O. (2012) Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumonia by genome-wide transcription start site profiling. PLoS Genetics., 8(8): e1002867.

40

Kim, J.N., Yi, J.S., Lee, B.R., Kim, E.J., Kim, M.W., Song, Y., Cho, B.K.*, and Kim, B.G.* (2012) A versatile PCR-based tandem epitope tagging system for Streptomyces coelicolor genome. Biochem. Biophys. Res. Comm., 424(1): 22-27.

39

Cho, B.K.*, Federowicz, S., Park, Y.S., Zengler, K., and Palsson, B.O. (2012) Deciphering the transcriptional regulatory logic of metabolism. Nature Chem. Biol., 8(1): 65-71.

38

Hwang, Y.Y., Shin, D.C., Nam, Y.S., and Cho, B.K.* (2012) Characterization, stability, and pharmacokinetics of sibutramine/b-cyclodextrin inclusion complex. J. Ind. Eng. Chem., 18(4): 1412-1417.

37

Cho, B.K.*, Palsson, B.O., and Zengler, K. (2011) Deciphering the regulatory codes in bacterial genomes. Biotechnol. J., 6(9):1052-1063.

36

Cho, B.K.*, Federowicz, S., Embree, M., Park, Y.S., Zengler, K., and Palsson, B.O.* (2011) The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res., 39(15): 6456-6464.

35

Barrett, C.L., Cho, B.K., and Palsson, B.O. (2011) Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher-order derivative analysis. Nucleic Acids Res., 39(5): 1656-1665.

34

Conrad, T.M., Frazier, M., Joyce, A.R., Cho, B.K., Knight, E.M., Lewis, N.E., Landick, R., and Palsson, B.O. (2010) RNA polymerase mutants found through adaptive evolution re-program Escherichia coli for optimal growth in minimal media. Proc. Natl. Acad. Sci. USA, 107(47): 20500-20505.

33

Qiu, Y., Cho, B.K., Park, Y.S., Lovley, D., and Palsson, B.O. (2010) Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res., 20(9): 1304-1311.

32

Cho, B.K., Zengler, K., Qiu, Y., Knight, E.M., Park, Y.S., Barrett, C.L., Gao, Y., and Palsson, B.O. (2009) The transcription unit architecture of the Escherichia coli K-12 MG1655 genome. Nature Biotechnol., 27(11): 1043-1049. (Featured on the cover article of this issue).

31

Cho, B.K. and Palsson, B.O. (2009) Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect. Mol. Cell, 35(3): 255-256.

30

Cho, B.K. and Palsson, B.O. (2009) Probing the basis for genotype-phenotype relationships. Nat. Methods., 6(8): 565-566.

29

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. Emzyme Microb. Technol., 45(3): 218-225.

28

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(11): 3437-3444.

27

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, 60(1-2): 29-35.

26

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.

25

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(49): 19462-19467.

24

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-tracts. Genome Res., 18(6): 900-910. (Selected as a Faculty 1000 article)

23

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: 131-145.

22

Cho, B.K., Park, H.Y., Seo, J.H., Kim, J., Kang, T.J., Lee, B.S., and Kim, B.G. (2008) Redesigning w-transaminase to synthesis of optically active aliphatic chiral amines. Biotechnol. Bioeng., 99(2): 275-284. (Featured on the spotlighted article in this issue).

21

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

20

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.

19

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 b-transaminase from Mesorhizobium sp. Strain LUK: A new biocatalyst for the synthesis of enantiomerically pure b-amino acids. Appl. Environm. Microbiol., 73(6): 1772-1782.

18

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.

17

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 b-amino acid from Mesorhizobium sp. LUK. J. Microbiol. Biotechnol., 16(11): 1832-1836.

16

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.

15

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.

14

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.

13

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. (Featured on the highlighted article in this issue)

12

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.

11

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-b-heterocyclic alanine derivatives using Escherichia coli aromatic L-amino acid transaminase. Biotechnol. Bioeng., 88(4): 512-519.

10

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

9

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

8

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.

7

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.

6

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)-a-methylbenzylamine from racemic a-methylbenzylamine using w-transaminase/alcohol dehydrogenase/glucose dehydrogenase coupling reaction. Biotechnol. Lett., 25(10): 809-814.

5

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.

4

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.

3

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.

2

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.

1

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.

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