|Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer|
YK Kim, J Yu, TS Han, SY Park, B Namkoong, DH Kim, K Hur, MW Yoo, ...
Nucleic acids research 37 (5), 1672-1681, 2009
|Network context and selection in the evolution to enzyme specificity|
H Nam, NE Lewis, JA Lerman, DH Lee, RL Chang, D Kim, BO Palsson
Science 337 (6098), 1101-1104, 2012
|Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli|
SW Seo, D Kim, H Latif, EJ O’Brien, R Szubin, BO Palsson
Nature Communications 5, 2014
|Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling|
D Kim, JSJ Hong, Y Qiu, H Nagarajan, JH Seo, BK Cho, SF Tsai, ...
PLoS genetics 8 (8), 2012
|Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli|
RL Chang, K Andrews, D Kim, Z Li, A Godzik, BO Palsson
Science 340 (6137), 1220-1223, 2013
|Multi-omic data integration enables discovery of hidden biological regularities|
A Ebrahim, E Brunk, J Tan, EJ O'brien, D Kim, R Szubin, JA Lerman, ...
Nature communications 7 (1), 1-9, 2016
|Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655|
SW Seo, D Kim, R Szubin, BO Palsson
Cell Reports 12 (8), 1289-1299, 2015
|Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states|
BK Cho, D Kim, EM Knight, K Zengler, BO Palsson
BMC biology 12 (1), 1, 2014
|The PurR regulon in Escherichia coli K-12 MG1655|
BK Cho, SA Federowicz, M Embree, YS Park, D Kim, BØ Palsson
Nucleic acids research 39 (15), 6456-6464, 2011
|Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli|
SW Seo, D Kim, EJ O’Brien, R Szubin, BO Palsson
Nature communications 6 (1), 1-8, 2015
|Determining the control circuitry of redox metabolism at the genome-scale|
S Federowicz, D Kim, A Ebrahim, J Lerman, H Nagarajan, B Cho, ...
PLoS genetics 10 (4), 2014
|Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities|
X Fang, A Sastry, N Mih, D Kim, J Tan, JT Yurkovich, CJ Lloyd, Y Gao, ...
Proceedings of the National Academy of Sciences 114 (38), 10286-10291, 2017
|Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data|
L Yang, J Tan, EJ O’Brien, JM Monk, D Kim, HJ Li, P Charusanti, ...
Proceedings of the National Academy of Sciences 112 (34), 10810-10815, 2015
|Systematic metabolic engineering of Methylomicrobium alcaliphilum 20Z for 2, 3-butanediol production from methane|
AD Nguyen, IY Hwang, OK Lee, D Kim, MG Kalyuzhnaya, R Mariyana, ...
Metabolic engineering 47, 323-333, 2018
|Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features|
JH Seo, JSJ Hong, D Kim, BK Cho, TW Huang, SF Tsai, BO Palsson, ...
BMC genomics 13 (1), 679, 2012
|Coordination-Driven Self-Assembly Using Ditopic Pyridyl–Pyrazolyl Donor and p-Cymene Ru(II) Acceptors: Catenane Synthesis and Anticancer Activities|
JH Jo, N Singh, D Kim, SM Cho, A Mishra, H Kim, SC Kang, KW Chi
Inorganic chemistry 56 (14), 8430-8438, 2017
|Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655|
Y Gao, JT Yurkovich, SW Seo, I Kabimoldayev, A Dräger, K Chen, ...
Nucleic acids research 46 (20), 10682-10696, 2018
|Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP|
D Kim, SW Seo, Y Gao, H Nam, GI Guzman, BK Cho, BO Palsson
Nucleic acids research 46 (6), 2901-2917, 2018
|Rice pectin methylesterase inhibitor28 (OsPMEI28) encodes a functional PMEI and its overexpression results in a dwarf phenotype through increased pectin methylesterification levels|
HP Nguyen, HY Jeong, SH Jeon, D Kim, C Lee
Journal of plant physiology 208, 17-25, 2017
|Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories|
D Kim, HM Woo
Applied microbiology and biotechnology 102 (22), 9471-9480, 2018