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김동혁
Kim, Donghyuk

김동혁

School of Energy and Chemical Engineering(에너지화학공학과)

  • Systems Biology and Machine Learning Lab.
  • Website
Research Interests
Systems Biology;Machine Learning;Metabolic engineering;NGS;시스템생물학;머신러닝;대사공학;차세대염기서열분석법
Lab Description
The research areas of Systems Biology and Machine Learning Lab are primarily based on the systems biology and machine learning approaches and their applications to study - Transcriptional regulation of bacterial pathogens including Salmonella and E. coli- Characterization of high-value bacterial strains- Anti-microbial resistance- Machine learning approaches for biological information
We have been applying the systems biology approaches to study bacteria, but there are also collaborators who expect us to apply those approaches to other types of organisms including yeast, fungi, and human cells.
Researcher ID Research Gate ORCiD Scopus Google Scholar
Previous
Developing the PIP-eco: An integrated genomic pipeline for identification and characterization of Escherichia coli pathotypes encompassing hybrid forms File

Ko, Seyoung , Nguyen, Huynh Minh Triet , Lee, Woojung , Kim, Donghyuk

Article Issue Date2024-12 View30
Behavioral biometric optical tactile sensor for instantaneous decoupling of dynamic touch signals in real time File

Son, Changil , Kim, Jinyoung , Kang, Dongwon , Park, Seojoung , Ryu, Chaeyeong , Baek, Dahye , Jeong, Geonyoung , Jeong, Sanggyun , Ahn, Seonghyeon , Lim, Chanoong , et al

Article Issue Date2024-09 View18
Use of acetate as substrate for sustainable production of homoserine and threonine by Escherichia coli W3110: A modular metabolic engineering approach File

Vo, Toan Minh , Park, Joon Young , Kim, Donghyuk , Park, Sunghoon

Article Issue Date2024-07 View21
Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure File File

Ko, Seyoung , Kim, Jaehyung , Lim, Jaewon , Lee, Sang-Mok , Park, Joon Young , Woo, Jihoon , Scott-Nevros, Zoe K. , Kim, Jong R. , Yoon, Hyunjin , Kim, Donghyuk

Article Issue Date2024-01 View20
Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution File

Lee, Sang-Mok , Le, Hoa Thi , Taizhanova, Assiya , Nong, Linh Khanh , Park, Joon Young , Lee, Eun-Jin , Palsson, Bernhard O. , Kim, Donghyuk

Article Issue Date2024-01 View31
Pan-genome Analysis Reveals Comparative Genomic Features of Central Metabolic Pathways in Methylorubrum extorquens File

Lee, Gyu Min , Scott-, NevrosZoe K. , Lee, Sang-Mok , Kim, Donghyuk

Article Issue Date2023-12 View28
A deep learning-based framework for battery reusability verification: one-step state-of-health estimation of pack and constituent modules using a generative algorithm and graphical representation File

Park, Seojoung , Lim, Dongjun , Lee, Hyunjun , Jung, Dawoon , Choi, YunSeok , Lim, Hankwon , Kim, Donghyuk

Article Issue Date2023-11 View80
Comparative Genomic Analysis and BTEX Degradation Pathways of a Thermotolerant Cupriavidus cauae PHS1 File File

Sathesh-Prabu, Chandran , Woo, Jihoon , Kim, Yuchan , Kim, Suk Min , Lee, Sun Bok , Jeon, Che Ok , Kim, Donghyuk , Lee, Sung Kuk

Article Issue Date2023-07 View26
Design of synthetic promoters for cyanobacteria with generative deep-learning model File

Seo, Euijin , Choi, Yun-Nam , Shin, Ye Rim , Kim, Donghyuk , Lee, Jeong Wook

Article Issue Date2023-07 View18
The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets File File

Gao, Ye , Bang, Ina , Seif, Yara , Kim, Donghyuk , Palsson, Bernhard O.

Article Issue Date2023-05 View33
Deep-learning based spatio-temporal generative model on assessing state-of-health for Li-ion batteries with partially-cycled profiles File

Park, Seojoung , Lee, Hyunjun , Scott-Nevros, Zoe K. K. , Lim, Dongjun , Seo, Dong-Hwa , Choi, Yunseok , Lim, Hankwon , Kim, Donghyuk

Article Issue Date2023-04 View66
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling File

Bang, Ina , Lee, Sang-Mok , Park, Seojoung , Park, Joon Young , Nong, Linh Khanh , Gao, Ye , Palsson, Bernhard O , Kim, Donghyuk

Article Issue Date2023-03 View17
Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing File

Choe, Donghui , Kim, Uigi , Hwang, Soonkyu , Seo, Sang Woo , Kim, Donghyuk , Cho, Suhyung , Palsson, Bernhard , Cho, Byung-Kwan

Article Issue Date2023-02 View20
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli File File

Park, JoonYoung , Lee, Sang-Mok , Ebrahim, Ali , Scott-Nevros, ZoeK , Kim, Jaehyung , Yang, Laurence , Sastry, Anand , Seo, SangWoo , Palsson, Bernhard O , Kim, Donghyuk

Article Issue Date2023-01 View14
Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction File File

Kim, Youngju , Lee, Sang-Mok , Nong, Linh Khanh , Kim, Jaehyung , Kim, Seung Bum , Kim, Donghyuk

Article Issue Date2023-01 View24
A Machine Learning Approach Reveals a Microbiota Signature for Infection with Mycobacterium avium subsp. paratuberculosis in Cattle File

Lee, Sang-Mok , Park, Hong-Tae , Park, Seojoung , Lee, Jun Ho , Kim, Danil , Yoo, Han Sang , Kim, Donghyuk

Article Issue Date2023-01 View18
ChEAP: ChIP-exo analysis pipeline and the investigation of Escherichia coli RpoN protein-DNA interactions File File

Bang, Ina , Nong, Linh Khanh , Park, Joon Young , Le, Hoa Thi , Lee, Sang-Mok , Kim, Donghyuk

Article Issue Date2023-01 View18
Characterization of an Entner-Doudoroff pathway-activated Escherichia coli File File

Kim, Ye Eun , Cho, Kyung Hyun , Bang, Ina , Kim, Chang Hee , Ryu, Young Shin , Kim, Yuchan , Choi, Eun Mi , Nong, Linh Khanh , Kim, Donghyuk , Lee, Sung Kuk

Article Issue Date2022-11 View21
Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis File File

Park, Hong-Tae , Lee, Sang-Mok , Ko, Seyoung , Kim, Suji , Park, Hyun-Eui , Shin, Min-Kyoung , Kim, Donghyuk , Yoo, Han Sang

Article Issue Date2022-09 View17
Enhanced production of nonanedioic acid from nonanoic acid by engineered Escherichia coli File

Lee, Yongjoo , Sathesh-Prabu, Chandran , Kwak, Geun Hwa , Bang, Ina , Jung, Hyun Wook , Kim, Donghyuk , Lee, Sung Kuk

Article Issue Date2022-03 View26
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