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Employment (1)

Tufts University: Medford, Massachusetts, US

2002-09 to present | Professor and Chair (Chemical and Biological Engineering)
Employment
Source: Self-asserted source
Kyongbum Lee

Education and qualifications (2)

Massachusetts Institute of Technology: Cambridge, MA, US

1995-09 to 2002-02 | Ph.D. (Chemical Engineering)
Education
Source: Self-asserted source
Kyongbum Lee

Stanford University: Stanford, CA, US

1991-10 to 1995-06 | B.S. (Chemical Engineering)
Education
Source: Self-asserted source
Kyongbum Lee

Works (50 of 90)

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Page 1 of 2

Microbial lysates as low-cost serum replacements in cellular agriculture media formulation

Food Research International
2025-02 | Journal article
DOI: 10.1016/j.foodres.2024.115633
Contributors: James Dolgin; Damayanti Chakravarty; Sean F. Sullivan; Yiming Cai; Taehwan Lim; Pomaikaimaikalani Yamaguchi; Joseph E. Balkan; Licheng Xu; Aaron D. Olawoyin; Kyongbum Lee et al.
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Crossref

A Chalcone Synthase-like Bacterial Protein Catalyzes Heterocyclic C-Ring Cleavage of Naringenin to Alter Bioactivity Against Nuclear Receptors in Colonic Epithelial Cells

Metabolites
2025-02-21 | Journal article
DOI: 10.3390/metabo15030146
Contributors: Ebru Ece Gülşan; Farrhin Nowshad; Meredith Davis Leigh; Jimmy Walter Crott; Hyejin Park; Greg Martin; Stephen Safe; Robert S. Chapkin; Arul Jayaraman; Kyongbum Lee
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Microbial lysates as low-cost serum replacements in cellular agriculture media formulation

2024-11-02 | Preprint
DOI: 10.1101/2024.10.28.620756
Contributors: James Dolgin; Damayanti Chakravarty; Sean F. Sullivan; Yiming Cai; Taehwan Lim; Pomaikaimaikalani Yamaguchi; Joseph E. Balkan; Licheng Xu; Aaron D. Olawoyin; Kyongbum Lee et al.
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Crossref

A Chemical Reaction Similarity-Based Prediction Algorithm Identifies the Multiple Taxa Required to Catalyze an Entire Metabolic Pathway of Dietary Flavonoids

2023-10-23 | Preprint
DOI: 10.7554/eLife.89852
Contributors: Ebru Ece Gulsan; Farrhin Nowshad; Pomaikaimaikalani Yamaguchi; Xiaokun Dong; Arul Jayaraman; Kyongbum Lee
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Crossref

A Chemical Reaction Similarity-Based Prediction Algorithm Identifies the Multiple Taxa Required to Catalyze an Entire Metabolic Pathway of Dietary Flavonoids

2023-10-23 | Preprint
DOI: 10.7554/eLife.89852.1
Contributors: Ebru Ece Gulsan; Farrhin Nowshad; Pomaikaimaikalani Yamaguchi; Xiaokun Dong; Arul Jayaraman; Kyongbum Lee
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Crossref

Oral supplementation of gut microbial metabolite indole-3-acetate alleviates diet-induced steatosis and inflammation in mice

2023-09-28 | Preprint
DOI: 10.7554/eLife.87458.2
Contributors: Yufang Ding; Karin Yanagi; Fang Yang; Evelyn Callaway; Clint Cheng; Martha E Hensel; Rani Menon; Robert C. Alaniz; Kyongbum Lee; Arul Jayaraman
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Crossref

Oral supplementation of gut microbial metabolite indole-3-acetate alleviates diet-induced steatosis and inflammation in mice

2023-09-28 | Preprint
DOI: 10.7554/eLife.87458
Contributors: Yufang Ding; Karin Yanagi; Fang Yang; Evelyn Callaway; Clint Cheng; Martha E Hensel; Rani Menon; Robert C. Alaniz; Kyongbum Lee; Arul Jayaraman
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Crossref

Microbially-derived indole-3-acetate alleviates diet induced steatosis and inflammation in mice

2023-06-06 | Preprint
DOI: 10.7554/eLife.87458.1
Contributors: Yufang Ding; Karin Yanagi; Fang Yang; Evelyn Callaway; Clint Cheng; Martha E Hensel; Rani Menon; Robert C. Alaniz; Kyongbum Lee; Arul Jayaraman
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Crossref

A Chemical Reaction Similarity-Based Prediction Algorithm Identifies the Multiple Taxa Required to Catalyze an Entire Metabolic Pathway of Dietary Flavonoids

2023-05-05 | Preprint
DOI: 10.1101/2023.05.05.539480
Contributors: Ebru Ece Gulsan; Farrhin Nowshad; Pomaikaimaikalani Yamaguchi; Xiaokun Dong; Arul Jayaraman; Kyongbum Lee
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Crossref

Flavone and Hydroxyflavones Are Ligands That Bind the Orphan Nuclear Receptor 4A1 (NR4A1)

International Journal of Molecular Sciences
2023-05-02 | Journal article
DOI: 10.3390/ijms24098152
Contributors: Miok Lee; Srijana Upadhyay; Fuada Mariyam; Greg Martin; Amanuel Hailemariam; Kyongbum Lee; Arul Jayaraman; Robert S. Chapkin; Syng-Ook Lee; Stephen Safe
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Crossref
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Oral supplementation of gut microbial metabolite indole-3-acetate alleviates diet-induced steatosis and inflammation in mice

2023-03-23 | Preprint
DOI: 10.1101/2023.03.21.533660
Contributors: Yufang Ding; Karin Yanagi; Fang Yang; Evelyn Callaway; Clint Cheng; Martha E Hensel; Rani Menon; Robert C. Alaniz; Kyongbum Lee; Arul Jayaraman
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Crossref

Flow cytometric evaluation of yeast–bacterial cell–cell interactions

Biotechnology and Bioengineering
2023-02 | Journal article
DOI: 10.1002/bit.28253
Contributors: Ming Lei; Vikas D. Trivedi; Nikhil U. Nair; Kyongbum Lee; James A. Van Deventer
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Crossref

Metabolomics of Acute vs. Chronic Spinach Intake in an Apc–Mutant Genetic Background: Linoleate and Butanoate Metabolites Targeting HDAC Activity and IFN–γ Signaling

Cells
2022-02-07 | Journal article
DOI: 10.3390/cells11030573
Contributors: Ying-Shiuan Chen; Jia Li; Sultan Neja; Sabeeta Kapoor; Jorge Tovar Perez; Chakrapani Tripathi; Rani Menon; Arul Jayaraman; Kyongbum Lee; Wan Dashwood et al.
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Crossref
grade
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A Metabolomics Approach to Increasing Chinese Hamster Ovary (CHO) Cell Productivity

Metabolites
2021-11-30 | Journal article
DOI: 10.3390/metabo11120823
Contributors: Grace Yao; Kathryn Aron; Michael Borys; Zhengjian Li; Girish Pendse; Kyongbum Lee
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Crossref
grade
Preferred source (of 2)‎

Flow Cytometric Evaluation of Yeast-Bacterial Cell-Cell Interactions

2021-10-13 | Other
DOI: 10.1101/2021.10.13.464218
Contributors: Ming Lei; Vikas D. Trivedi; Nikhil U. Nair; Kyongbum Lee; James A. Van Deventer
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Crossref

Dietary spinach reshapes the gut microbiome in an Apc-mutant genetic background: mechanistic insights from integrated multi-omics

Gut Microbes
2021-01-01 | Journal article
DOI: 10.1080/19490976.2021.1972756
Contributors: Ying-Shiuan Chen; Jia Li; Rani Menon; Arul Jayaraman; Kyongbum Lee; Yun Huang; Wan Mohaiza Dashwood; Ke Zhang; Deqiang Sun; Roderick H. Dashwood
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Crossref

Untargeted proteomics reveals upregulation of stress response pathways during CHO-based monoclonal antibody manufacturing process leading to disulfide bond reduction

mAbs
2021-01-01 | Journal article
DOI: 10.1080/19420862.2021.1963094
Contributors: Seo-Young Park; Susan Egan; Anthony J. Cura; Kathryn L. Aron; Xuankuo Xu; Mengyuan Zheng; Michael Borys; Sanchayita Ghose; Zhengjian Li; Kyongbum Lee
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Crossref

Ridinilazole, a narrow spectrum antibiotic for treatment of Clostridioides difficile infection, enhances preservation of microbiota-dependent bile acids

American Journal of Physiology-Gastrointestinal and Liver Physiology
2020-08-01 | Journal article
DOI: 10.1152/ajpgi.00046.2020
Contributors: Xi Qian; Karin Yanagi; Anne V. Kane; Nicholas Alden; Ming Lei; David R. Snydman; Richard J. Vickers; Kyongbum Lee; Cheleste M. Thorpe
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Crossref

Using Metabolomics to Identify Cell Line-Independent Indicators of Growth Inhibition for Chinese Hamster Ovary Cell-Based Bioprocesses

Metabolites
2020-05-15 | Journal article
DOI: 10.3390/metabo10050199
Contributors: Nicholas Alden; Ravali Raju; Kyle McElearney; James Lambropoulos; Rashmi Kshirsagar; Alan Gilbert; Kyongbum Lee
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Crossref

Biological Filtering and Substrate Promiscuity Prediction for Annotating Untargeted Metabolomics

Metabolites
2020-04 | Journal article | Author
DOI: 10.3390/metabo10040160
Contributors: Neda Hassanpour; Nicholas Alden; Rani Menon; Arul Jayaraman; Kyongbum Lee; Soha Hassoun
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Multidisciplinary Digital Publishing Institute
grade
Preferred source (of 2)‎

Environmental Chemical Diethylhexyl Phthalate Alters Intestinal Microbiota Community Structure and Metabolite Profile in Mice

mSystems
2019 | Journal article
DOI: 10.1128/mSystems.00724-19
Source: Self-asserted source
Kyongbum Lee

Interactions between gut microbiota and non-alcoholic liver disease: The role of microbiota-derived metabolites

Pharmacol Res
2019 | Journal article
DOI: 10.1016/j.phrs.2019.01.029
Source: Self-asserted source
Kyongbum Lee

Isoflavones as Ah Receptor Agonists in Colon-Derived Cell Lines: Structure-Activity Relationships

Chem Res Toxicol
2019 | Journal article
Source: Self-asserted source
Kyongbum Lee

Gut Microbiota-Derived Tryptophan Metabolites Modulate Inflammatory Response in Hepatocytes and Macrophages

Cell Rep
2018 | Journal article
DOI: 10.1016/j.celrep.2018.03.109
Source: Self-asserted source
Kyongbum Lee

Parabacteroides distasonis attenuates toll-like receptor 4 signaling and Akt activation and blocks colon tumor formation in high-fat diet-fed azoxymethane-treated mice

Int J Cancer
2018 | Journal article
DOI: 10.1002/ijc.31559
Source: Self-asserted source
Kyongbum Lee

Sequential Parameter Estimation for Mammalian Cell Model Based on In Silico Design of Experiments

Processes
2018-07-24 | Journal article
DOI: 10.3390/pr6080100
Part of ISSN: 2227-9717
Source: Self-asserted source
Kyongbum Lee

Biologically Consistent Annotation of Metabolomics Data

Anal Chem
2017 | Journal article
DOI: 10.1021/acs.analchem.7b02162
Source: Self-asserted source
Kyongbum Lee

An Aryl Hydrocarbon Receptor-Mediated Amplification Loop That Enforces Cell Migration in ER-/PR-/Her2- Human Breast Cancer Cells

Mol Pharmacol
2016 | Journal article
DOI: 10.1124/mol.116.105361
Source: Self-asserted source
Kyongbum Lee

Monoethylhexyl Phthalate Elicits an Inflammatory Response in Adipocytes Characterized by Alterations in Lipid and Cytokine Pathways

Environ Health Perspect
2016 | Journal article
DOI: 10.1289/EHP464
Source: Self-asserted source
Kyongbum Lee

Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity

BMC Syst Biol
2015 | Journal article
DOI: 10.1186/s12918-015-0146-2
Source: Self-asserted source
Kyongbum Lee

Microbiota metabolite regulation of host immune homeostasis: a mechanistic missing link

Curr Allergy Asthma Rep
2015 | Journal article
DOI: 10.1007/s11882-015-0524-2
Source: Self-asserted source
Kyongbum Lee

Pathways and functions of gut microbiota metabolism impacting host physiology

Curr Opin Biotechnol
2015 | Journal article
DOI: 10.1016/j.copbio.2015.08.015
Source: Self-asserted source
Kyongbum Lee

PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks

IEEE/ACM Trans Comput Biol Bioinform
2015 | Journal article
DOI: 10.1109/TCBB.2015.2394470
Source: Self-asserted source
Kyongbum Lee

PROXIMAL: a method for Prediction of Xenobiotic Metabolism

BMC Syst Biol
2015 | Journal article
DOI: 10.1186/s12918-015-0241-4
Source: Self-asserted source
Kyongbum Lee

Analysis of Transcription Factor Network Underlying 3T3-L1 Adipocyte Differentiation

PLoS One
2014 | Journal article
DOI: 10.1371/journal.pone.0100177
Source: Self-asserted source
Kyongbum Lee

Automated Image Processing for Spatially Resolved Analysis of Lipid Droplets in Cultured 3T3-L1 Adipocytes

Tissue Eng Part C Methods
2014 | Journal article
DOI: 10.1089/ten.TEC.2014.0513
Source: Self-asserted source
Kyongbum Lee

Endogenous two-photon fluorescence imaging elucidates metabolic changes related to enhanced glycolysis and glutamine consumption in precancerous epithelial tissues

Cancer Res
2014 | Journal article
DOI: 10.1158/0008-5472.CAN-13-2713
Source: Self-asserted source
Kyongbum Lee

Microbiome-derived tryptophan metabolites and their aryl hydrocarbon receptor-dependent agonist and antagonist activities

Mol Pharmacol
2014 | Journal article
DOI: 10.1124/mol.113.091165
Source: Self-asserted source
Kyongbum Lee

Prediction and quantification of bioactive microbiota metabolites in the mouse gut

Nat Commun
2014 | Journal article
DOI: 10.1038/ncomms6492
Source: Self-asserted source
Kyongbum Lee

Rational identification of diet-derived postbiotics for improving intestinal microbiota function

Curr Opin Biotechnol
2014 | Journal article
DOI: 10.1016/j.copbio.2013.10.006
Source: Self-asserted source
Kyongbum Lee

Adipogenesis of adipose-derived stem cells may be regulated via the cytoskeleton at physiological oxygen levels in vitro

Stem Cell Res Ther
2013 | Journal article
DOI: 10.1186/scrt230
Source: Self-asserted source
Kyongbum Lee

Biological Engineering

Curr Opin Chem Eng
2013 | Journal article
Source: Self-asserted source
Kyongbum Lee

Engineering E. coli for triglyceride accumulation through native and heterologous metabolic reactions

Appl Microbiol Biotechnol
2013 | Journal article
DOI: 10.1007/s00253-013-4714-3
Source: Self-asserted source
Kyongbum Lee

Extracellular Matrix Remodeling and Mechanical Stresses as Modulators of Adipose Tissue Metabolism and Inflammation

2013 | Book chapter
DOI: 10.1007/8415_2013_172
Source: Self-asserted source
Kyongbum Lee
grade
Preferred source (of 2)‎

Probabilistic strain optimization under constraint uncertainty

BMC Syst Biol
2013 | Journal article
DOI: 10.1186/1752-0509-7-29
Source: Self-asserted source
Kyongbum Lee

Quantitative metabolic imaging using endogenous fluorescence to detect stem cell differentiation

Sci Rep
2013 | Journal article
DOI: 10.1038/srep03432
Source: Self-asserted source
Kyongbum Lee

Systems biology of adipose tissue metabolism: regulation of growth, signaling and inflammation

Wiley Interdiscip Rev Syst Biol Med
2013 | Journal article
DOI: 10.1002/wsbm.1213
Source: Self-asserted source
Kyongbum Lee

Tissue, cell and engineering

Curr Opin Biotechnol
2013 | Journal article
DOI: 10.1016/j.copbio.2013.08.001
Source: Self-asserted source
Kyongbum Lee

Towards high resolution analysis of metabolic flux in cells and tissues

Curr Opin Biotechnol
2013 | Journal article
DOI: 10.1016/j.copbio.2013.07.001
Source: Self-asserted source
Kyongbum Lee

Adipocyte induction of preadipocyte differentiation in a gradient chamber

Tissue Eng Part C Methods
2012 | Journal article
DOI: 10.1089/ten.TEC.2012.0168
Source: Self-asserted source
Kyongbum Lee
Items per page:
Page 1 of 2

Peer review (4 reviews for 3 publications/grants)

Review activity for Communications biology. (1)
Review activity for Nature communications (2)
Review activity for PLoS computational biology. (1)
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