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1

Kinetic modeling of mammalian cell culture bioprocessing: the quest to advance biomanufacturing

Kyriakopoulos, Sarantos, Ang, Kok Siong, Lakshmanan, Meiyappan, Huang, Zhuangrong, Yoon, Seongkyu, Gunawan, Rudiyanto, Lee, Dong-Yup

Journal:

Biotechnology Journal

Year:

2017

Language:

english

File:

PDF, 1.31 MB

english, 2017

2

N-Glycosylation Design and Control of Therapeutic Monoclonal Antibodies

Sha, Sha, Agarabi, Cyrus, Brorson, Kurt, Lee, Dong-Yup, Yoon, Seongkyu

Journal:

Trends in Biotechnology

Year:

2016

Language:

english

File:

PDF, 1.81 MB

english, 2016

3

Combined in silico modeling and metabolomics analysis to characterize fed-batch CHO cell culture

Suresh Selvarasu, Ying Swan Ho, William P. K. Chong, Niki S. C. Wong, Faraaz N. K. Yusufi, Yih Yean Lee, Miranda G. S. Yap, Dong-Yup Lee

Journal:

Biotechnology and Bioengineering

Year:

2012

Language:

english

File:

PDF, 1.45 MB

english, 2012

4

Synthetic fusion protein design and applications

Yu, Kai, Liu, Chengcheng, Kim, Byung-Gee, Lee, Dong-Yup

Journal:

Biotechnology Advances

Year:

2015

Language:

english

File:

PDF, 1.67 MB

english, 2015

5

Coopetitive Supply Chain Relationship Model: Application to the Smartphone Manufacturing Network

Kwok, Jeremy Jie Ming, Lee, Dong-Yup, Kim, Kyoung Heon

Journal:

Year:

2015

Language:

english

File:

PDF, 3.24 MB

english, 2015

6

MP criterion based multiloop PID controllers tuning for desired closed loop responses

Dong-Yup Lee, Moonyong Lee, Yongho Lee, Sunwon Park

Journal:

Korean Journal of Chemical Engineering

Year:

2003

Language:

english

File:

PDF, 98 KB

english, 2003

7

Systems biotechnology for strain improvement

Sang Yup Lee, Dong-Yup Lee, Tae Yong Kim

Journal:

Trends in Biotechnology

Year:

2005

Language:

english

File:

PDF, 427 KB

english, 2005

8

Genome-scale in silico modeling and analysis for designing synthetic terpenoid-producing microbial cell factories

Chung, Bevan Kai-Sheng, Lakshmanan, Meiyappan, Klement, Maximilian, Mohanty, Bijayalaxmi, Lee, Dong-Yup

Journal:

Chemical Engineering Science

Year:

2013

Language:

english

File:

PDF, 987 KB

english, 2013

9

Combinatorial metabolic engineering of Saccharomyces cerevisiae for terminal alkene production

Chen, Binbin, Lee, Dong-Yup, Chang, Matthew Wook

Journal:

Metabolic Engineering

Year:

2015

Language:

english

File:

PDF, 672 KB

english, 2015

10

SynLinker: an integrated system for designing linkers and synthetic fusion proteins

Liu, Chengcheng, Chin, Ju Xin, Lee, Dong-Yup

Journal:

Year:

2015

Language:

english

File:

PDF, 500 KB

english, 2015

11

Quantitative intracellular flux modeling and applications in biotherapeutic development and production using CHO cell cultures

Huang, Zhuangrong, Lee, Dong-Yup, Yoon, Seongkyu

Journal:

Biotechnology and Bioengineering

Year:

2017

Language:

english

File:

PDF, 842 KB

english, 2017

12

Multiloop PID controllers tuning for desired closed loop responses

Lee, Dong-Yup, Lee, Moonyong, Lee, Yongho, Park, Sunwon

Journal:

IFAC Proceedings Volumes

Year:

2001

Language:

english

File:

PDF, 559 KB

english, 2001

13

Towards next generation CHO cell line development and engineering by systems approaches

Hong, Jong Kwang, Lakshmanan, Meiyappan, Goudar, Chetan, Lee, Dong-Yup

Journal:

Current Opinion in Chemical Engineering

Year:

2018

Language:

english

File:

PDF, 1.51 MB

english, 2018

14

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

Song, Hyun-Seob, Lee, Joon-Yong, Haruta, Shin, Nelson, William C., Lee, Dong-Yup, Lindemann, Stephen R., Fredrickson, Jim K., Bernstein, Hans C.

Journal:

Frontiers in Microbiology

Year:

2019

Language:

english

File:

PDF, 1.99 MB

english, 2019

15

Characterizing Escherichia coli DH5α growth and metabolism in a complex medium using genome-scale flux analysis

Suresh Selvarasu, Dave Siak-Wei Ow, Sang Yup Lee, May May Lee, Steve Kah-Weng Oh, Iftekhar A. Karimi, Dong-Yup Lee

Journal:

Biotechnology and Bioengineering

Year:

2009

Language:

english

File:

PDF, 867 KB

english, 2009

16

Elucidation of metabolism in hybridoma cells grown in fed-batch culture by genome-scale modeling

Suresh Selvarasu, Victor V.T. Wong, Iftekhar A. Karimi, Dong-Yup Lee

Journal:

Biotechnology and Bioengineering

Year:

2009

Language:

english

File:

PDF, 523 KB

english, 2009

17

Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis

Hanifah Widiastuti, Jae Young Kim, Suresh Selvarasu, Iftekhar A. Karimi, Hyungtae Kim, Jeong-Sun Seo, Dong-Yup Lee

Journal:

Biotechnology and Bioengineering

Year:

2011

Language:

english

File:

PDF, 3.36 MB

english, 2011

18

Multiobjective flux balancing using the NISE method for metabolic network analysis

Young-Gyun Oh, Dong-Yup Lee, Sang Yup Lee, Sunwon Park

Journal:

Biotechnology Progress

Year:

2009

Language:

english

File:

PDF, 663 KB

english, 2009

19

Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis

Dave Siak-Wei Ow, Dong-Yup Lee, Miranda Gek-Sim Yap, Steve Kah-Weng Oh

Journal:

Biotechnology Progress

Year:

2009

Language:

english

File:

PDF, 270 KB

english, 2009

20

In silico genome-scale modeling and analysis for identifying anti-tubercular drug targets

Dong-Yup Lee, Bevan Kai Sheng Chung, Faraaz N.K. Yusufi, Suresh Selvarasu

Journal:

Drug Development Research

Year:

2011

Language:

english

File:

PDF, 160 KB

english, 2011

21

Mathematical modeling and sensitivity analysis of the integrated TNFα-mediated apoptotic pathway for identifying key regulators

Geoffrey Koh, Dong-Yup Lee

Journal:

Computers in Biology and Medicine

Year:

2011

Language:

english

File:

PDF, 2.60 MB

english, 2011

22

A linear diversity constraint – Application to scheduling in microgrids

Pavan Kumar Naraharisetti, I.A. Karimi, Abhay Anand, Dong-Yup Lee

Journal:

Year:

2011

Language:

english

File:

PDF, 685 KB

english, 2011

23

Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: Overexpression of malate dehydrogenase II

William P.K. Chong, Satty G. Reddy, Faraaz N.K. Yusufi, Dong-Yup Lee, Niki S.C. Wong, Chew Kiat Heng, Miranda G.S. Yap, Ying Swan Ho

Journal:

Journal of Biotechnology

Year:

2010

Language:

english

File:

PDF, 453 KB

english, 2010

24

Combined data preprocessing and multivariate statistical analysis characterizes fed-batch culture of mouse hybridoma cells for rational medium design

Suresh Selvarasu, Do Yun Kim, Iftekhar A. Karimi, Dong-Yup Lee

Journal:

Journal of Biotechnology

Year:

2010

Language:

english

File:

PDF, 1.06 MB

english, 2010

25

Metabolomics-based identification of apoptosis-inducing metabolites in recombinant fed-batch CHO culture media

William P.K. Chong, Faraaz N.K. Yusufi, Dong-Yup Lee, Satty G. Reddy, Niki S.C. Wong, Chew Kiat Heng, Miranda G.S. Yap, Ying Swan Ho

Journal:

Journal of Biotechnology

Year:

2011

Language:

english

File:

PDF, 538 KB

english, 2011

26

Complementary identification of multiple flux distributions and multiple metabolic pathways

Dong-Yup Lee, L.T. Fan, Sunwon Park, Sang Yup Lee, Shahram Shafie, Botond Bertók, Ferenc Friedler

Journal:

Metabolic Engineering

Year:

2005

Language:

english

File:

PDF, 828 KB

english, 2005

27

Colored Petri net modeling and simulation of signal transduction pathways

Dong-Yup Lee, Ralf Zimmer, Sang Yup Lee, Sunwon Park

Journal:

Metabolic Engineering

Year:

2006

Language:

english

File:

PDF, 586 KB

english, 2006

28

Modeling and optimization of a multi-product biosynthesis factory for multiple objectives

Fook Choon Lee, Gade Pandu Rangaiah, Dong-Yup Lee

Journal:

Metabolic Engineering

Year:

2010

Language:

english

File:

PDF, 586 KB

english, 2010

29

Integrative analysis workflow for the structural and functional classification of C-type lectins

Geoffrey Koh, Ariana Low, Daren Poh, Yujian Yao, Say Kong Ng, Victor Vai Tak Wong, Vincent Vagenende, Kong-Peng Lam, Dong-Yup Lee

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.05 MB

english, 2011

30

Systems-level analysis of genome-scalein silicometabolic models using MetaFluxNet

Sang Yup Lee, Han Min Woo, Dong-Yup Lee, Hyung Seok Choi, Tae Yong Kim, Hongseok Yun

Journal:

Biotechnology and Bioprocess Engineering

Year:

2005

File:

PDF, 782 KB

2005

31

An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins

Faraaz Noor Khan Yusufi, Wonjun Park, May May Lee, Dong-Yup Lee

Journal:

Bioprocess and Biosystems Engineering

Year:

2009

Language:

english

File:

PDF, 525 KB

english, 2009

32

NADPH-dependent pgi-gene knockout Escherichia coli metabolism producing shikimate on different carbon sources

Jungoh Ahn, Bevan K.S. Chung, Dong-Yup Lee, Myongsoo Park, Iftekhar A. Karimi, Joon-Ki Jung, Hongweon Lee

Journal:

FEMS Microbiology Letters

Year:

2011

Language:

english

File:

PDF, 276 KB

english, 2011

33

Robust optimization for engineering design

Kang, Jin-Su, Lee, Tai-Yong, Lee, Dong-Yup

Journal:

Engineering Optimization

Year:

2012

Language:

english

File:

PDF, 477 KB

english, 2012

34

LC-MS-based metabolic characterization of high monoclonal antibody-producing Chinese hamster ovary cells

William Pooi Kat Chong, Shu Hui Thng, Ai Ping Hiu, Dong-Yup Lee, Eric Chun Yong Chan, Ying Swan Ho

Journal:

Biotechnology and Bioengineering

Year:

2012

Language:

english

File:

PDF, 315 KB

english, 2012

35

Genome-scale metabolic reconstruction andin silicoanalysis of methylotrophic yeastPichia pastorisfor strain improvement

Bevan KS Chung, Suresh Selvarasu, Andrea Camattari, Jimyoung Ryu, Hyeokweon Lee, Jungoh Ahn, Hongweon Lee, Dong-Yup Lee

Journal:

Microbial Cell Factories

Year:

2010

Language:

english

File:

PDF, 2.42 MB

english, 2010

36

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

Bevan Kai Sheng Chung, Dong-Yup Lee

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 1.69 MB

english, 2009

37

Baseline heavy metal concentrations in the Antarctic clam, Laternula elliptica in Maxwell Bay, King George Island, Antarctica

In-Young Ahn, Soo Hyung Lee, Kyung Tae Kim, Jeong Hee Shim, Dong-Yup Kim

Journal:

Marine Pollution Bulletin

Year:

1996

Language:

english

File:

PDF, 694 KB

english, 1996

38

Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants

Hyung Seok Choi, Tae Yong Kim, Dong-Yup Lee, Sang Yup Lee

Journal:

Journal of Biotechnology

Year:

2007

Language:

english

File:

PDF, 920 KB

english, 2007

39

Genome-scale in silico design and analysis of E. coli systems via interactive web application

Journal:

Journal of Biotechnology

Year:

2008

Language:

english

File:

PDF, 85 KB

english, 2008

40

Metabolic reconstruction and flux analysis of industrialPichiayeasts

Chung, Bevan Kai-Sheng, Lakshmanan, Meiyappan, Klement, Maximilian, Ching, Chi Bun, Lee, Dong-Yup

Journal:

Applied Microbiology and Biotechnology

Year:

2013

Language:

english

File:

PDF, 308 KB

english, 2013

41

Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice

Bijayalaxmi Mohanty, Venura Herath, Edward Wijaya, Hock Chuan Yeo, Benildo G. de los Reyes, Dong-Yup Lee

Journal:

Year:

2012

Language:

english

File:

PDF, 481 KB

english, 2012

42

Computational codon optimization of synthetic gene for protein expression

Bevan Kai-Sheng Chung, Dong-Yup Lee

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.09 MB

english, 2012

43

Translatome analysis of CHO cells to identify key growth genes

Courtes, Franck C., Lin, Joyce, Lim, Hsueh Lee, Ng, Sze Wai, Wong, Niki S.C., Koh, Geoffrey, Vardy, Leah, Yap, Miranda G.S., Loo, Bernard, Lee, Dong-Yup

Journal:

Journal of Biotechnology

Year:

2013

Language:

english

File:

PDF, 2.01 MB

english, 2013

44

Understanding translational control mechanisms of the mTOR pathway in CHO cells by polysome profiling

Courtes, Franck C., Vardy, Leah, Wong, Niki S.C., Bardor, Muriel, Yap, Miranda G.S., Lee, Dong-Yup

Journal:

New Biotechnology

Year:

2014

Language:

english

File:

PDF, 2.33 MB

english, 2014

45

Enhanced Production of Neuroprogenitors, Dopaminergic Neurons, and Identification of Target Genes by Overexpression of Sonic Hedgehog in Human Embryonic Stem Cells

Wu, Selena Meiyun, Tan, Ker Sin, Chen, Huishan, Beh, Thian Thian, Yeo, Hock Chuan, Ng, Stanley Kwang-Loong, Wei, Shunhui, Lee, Dong-Yup, Choo, Andre Boon-Hwa, Chan, Ken Kwok-Keung

Journal:

Stem Cells and Development

Year:

2012

Language:

english

File:

PDF, 1.20 MB

english, 2012

46

Enhanced expression of codon optimized interferon gamma in CHO cells

Chung, Bevan Kai-Sheng, Yusufi, Faraaz N.K., Mariati,, Yang, Yuansheng, Lee, Dong-Yup

Journal:

Journal of Biotechnology

Year:

2013

Language:

english

File:

PDF, 3.77 MB

english, 2013

47

Identifying essential genes/reactions of the rice photorespiration byin silicomodel-based analysis

Lakshmanan, Meiyappan, Mohanty, Bijayalaxmi, Lee, Dong-Yup

Journal:

Year:

2013

Language:

english

File:

PDF, 280 KB

english, 2013

48

Mechanistic elements and critical factors of cellular reprogramming revealed by stepwise global gene expression analyses

Park, Sung-Jin, Yeo, Hock Chuan, Kang, Nam-Young, Kim, Hanjo, Lin, Joyce, Ha, Hyung-Ho, Vendrell, Marc, Lee, Jun-Seok, Chandran, Yogeswari, Lee, Dong-Yup, Yun, Seong-Wook, Chang, Young-Tae

Journal:

Stem Cell Research

Year:

2014

Language:

english

File:

PDF, 2.72 MB

english, 2014

49

28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures

Courtes, Franck C., Gu, Chen, Wong, Niki S.C., Dedon, Peter C., Yap, Miranda G.S., Lee, Dong-Yup

Journal:

Journal of Biotechnology

Year:

2014

Language:

english

File:

PDF, 1.50 MB

english, 2014

50

Scheduling of Actual Size Refinery Processes Considering Environmental Impacts with Multiobjective Optimization

Song, Jehoon, Park, Hyungjin, Lee, Dong-Yup, Park, Sunwon

Journal:

Industrial & Engineering Chemistry Research

Year:

2002

Language:

english

File:

PDF, 538 KB

english, 2002

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