Preprints/Accepted Publications

Lei M, Trivedi VD, Nair NU, Lee K, Deventer JAV. (2022) Flow Cytometric Evaluation of Yeast-Bacterial Cell-Cell Interactions. bioRXiv

Selected Recent Publications

Chen Y-S, Li J, Neja S, Kapoor S, Tovar Perez JE, Tripathi C, Menon R, Jayaraman A, Lee K, Dashwood WM, Wang S, Zhang K, Kobayashi K, Rajendran P, Dashwood R. (2022) Metabolomics of Acute vs. Chronic Spinach Intake in an Apc-Mutant Genetic Background: Linoleate and Butanoate Metabolites Targeting HDAC Activity and IFN-g SignalingCells 11:573

Fiore NJ, Ganat YM, Devkota K, Batorsky R, Lei M, Lee K, Cowen LJ, Croft G, Noggle SA, Nieland TJF, Kaplan DL. (2022) Bioengineered models of Parkinson’s disease using patient-derived dopaminergic neurons exhibit distinct biological profiles in a 3D microenvironmentCell Mol Life Sci 79:78.

Yao G, Aron K, Borys M, Li Z, Pendse G, Lee K. (2021) A Metabolomics Approach to Increasing Chinese Hamster Ovary (CHO) Cell ProductivityMetabolites 11:823.

Park SY, Egan S, Cura AJ, Aron KL, Xu X, Zheng M, Borys M, Ghose S, Li Z, Lee K. (2021) Untargeted proteomics reveals upregulation of stress response pathways during CHO-based monoclonal antibody manufacturing process leading to disulfide bond reductionMAbs 13:1963094.

Chen YS, Li J, Menon R, Jayaraman A, Lee K, Huang Y, Dashwood WM, Zhang K, Sun D, Dashwood RH. (2021) Dietary spinach reshapes the gut microbiome in an Apc-mutant genetic background: mechanistic insights from integrated multi-omicsGut Microbes 13:1972756.

Lei M, Jayaraman A, Van Deventer JA, Lee K. (2021) Engineering Selectively Targeting Antimicrobial PeptidesAnnu Rev Biomed Eng doi:10.1146/annurev-bioeng-010220-095711.

Markey L, Pugliese A, Tian T, Roy F, Lee K, Kumamoto C. (2020) Decreased ecological resistance of the gut microbiota in response to clindamycin challenge in mice colonized with the fungus Candida albicansmSphere 6

Yang F, DeLuca JAA, Menon R, Garcia-Vilarato E, Callaway E, Landrock KK, Lee K, Safe SH, Chapkin RS, Allred CD, Jayaraman A.(2020) Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profilesMicrob Cell Fact 19:219

Qian X, Yanagi K, Kane AV, Alden N, Lei M, Snydman DR, Vickers RJ, Lee K, Thorpe CM. (2020) Ridinilazole, a narrow spectrum antibiotic for treatment of Clostridioides difficile infection, enhances preservation of microbiota-dependent bile acids Am J Physiol Gastrointest Liver Physiol 319: G227-G237

Park SY, Ufondu A, Jayaraman A, Lee K. (2020) Emerging computational tools and models for studying gut microbiota composition and function. Current Opinion in Biotechnology 66: 301-311.

Alden N, Raju R, McElearney K, Lambropoulos J, Kshirsagar R, Gilbert A, Lee K. (2020) Using Metabolomics to Identify Cell Line-Independent Indicators of Growth Inhibition for Chinese Hamster Ovary Cell-based BioprocessesMetabolites 10

Hassanpour N, Alden N, Menon R, Jayaraman A, Lee K, Hassoun S. (2020) Biological Filtering and Substrate Promiscuity Prediction for Annotating Untargeted MetabolomicsMetabolites 10

Lei M, Menon R, Manteiga S, Alden N, Hunt C, Alaniz RC, Lee K, Jayaraman A. (2019) Environmental chemical diethylhexyl phthalate alters intestinal microbiota community structure and metabolite profile in mice. mSystems 4

Park H, Jin U-H, Orr A, Echegaray S, Davidson L, Allred C, Chapkin R, Jayaraman A, Lee K, Tamamis P, Safe S. (2019) Isoflavones as Ah Receptor Agonists in Colon-Derived Cell Lines: Structure-Activity Relationships. Chem Res Toxicol 32: 2353-2364

Ding Y, Yanagi K, Cheng C, Alaniz RC, Lee K, Jayaraman A. (2019) Interactions between gut microbiota and non-alcoholic liver disease: The role of microbiota-derived metabolitesPharmacol Res 141: 521-529

Krishnan S, Ding Y, Choi Y, Saedi N, Sridharan GV, Yarmush ML, Alaniz RC, Jayaraman A*, Lee K* (2018) Gut Microbiota-derived Tryptophan Metabolites Modulate Inflammatory Response in Hepatocytes and MacrophagesCell Rep 23: 1099-1111 

Koh GY, Kane A, Lee K, Xu Q, Wu X, Roper J, Mason JB, Crott JW (2018) 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

Wang Z, Sheikh H, Lee K, Georgakis C (2018) Sequential Parameter Estimation for Mammalian Cell Model based on in silico Design of ExperimentsProcesses 6:100.

Alden N, Krishnan S, Porokhin V, Raju R, McElearney K, Gilbert A, Lee K (2017) Biologically Consistent Annotation of Metabolomics DataAnal Chem 89: 13097-104

Novikov O, Wang Z, Stanford EA, Parks AJ, Ramirez-Cardenas A, Landesman E, Laklouk I, Sarita-Reyes C, Gusenleitner D, Li A, Monti S, Manteiga S, Lee K, Sherr DH (2016) An Aryl Hydrocarbon Receptor-mediated Amplification Loop that Enforces Cell Migration in ER-/PR-/Her2- Human Breast Cancer Cells.Mol Pharmacol 90:674-688 

Manteiga S, Lee K (2016) Monoethylhexyl Phthalate Elicits an Inflammatory Response in Adipocytes Characterized by Alterations in Lipid and Cytokine Pathways.Environ Health Perspect 125:615-622

Krishnan S, Alden N, Lee K (2015) Pathways and functions of gut microbiota metabolism impacting host physiologyCurr Opin Biotechnol 36: 137-145

Yousofshahi M, Manteiga S, Wu C, Lee K, Hassoun S (2015) PROXIMAL: a method for Prediction of Xenobiotic MetabolismBMC Syst Biol 9: 94.

Ullah E, Walker M, Lee K, Hassoun S (2015) PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical NetworksIEEE/ACM Trans Comput Biol Bioinform 12: 1405-1415.

Steinmeyer S, Lee K, Jayaraman A, Alaniz RC (2015) Microbiota metabolite regulation of host immune homeostasis: a mechanistic missing linkCurr Allergy Asthma Rep 15: 24.

Sims JK, Rohr B, Miller EL, Lee K (2014) Automated Image Processing for Spatially Resolved Analysis of Lipid Droplets in Cultured 3t3-L1 AdipocytesTissue Eng Part C Methods. 21:605-13

Sridharan GV, Ullah E, Hassoun S, Lee K (2014) Discovery of Substrate Cycles in Large-Scale Metabolic Networks using Hierarchical Modularity. BMC Syst Biol9: 146.

Sridharan GV, Choi K, Klemashevich C, Wu C, Prabakaran D, Pan LB, Steinmeyer S, Mueller C, Yousofshahi M, Alaniz RC, Lee K*, Jayaraman A*(2014) Prediction and Quantification of Bioactive Microbiota Metabolites in Murine GutNat Commun5: 5492. *co-corresponding authors

Kuo CK, Lee K (2014) Extracellular Matrix Remodeling and Mechanical Stresses as Modulators of Adipose Tissue Metabolism and Inflammation. In: Gefen A, Benayahu J, editors. The Mechanobiology of Obesity and Related Diseases

Choi K, Ghaddar B, Moya C, Shi H, Lee K*, Jayaraman A*(2014) Analysis of Transcription Factor Network Underlying 3T3-L1 Adipocyte Differentiation. PLoS One 9:e100177. *co-corresponding authors

Varone A, Xylas J, Quinn KP, Pouli D, Sridharan G, McLaughlin-Drubin ME, Alonzo C, Lee K, Munger K, Georgakoudi I (2014) Endogenous Two-Photon Fluorescence Imaging Elucidates Metabolic Changes Related to Enhanced Glycolysis and Glutamine Consumption in Precancerous Epithelial TissuesCancer Res 74: 3067-3075.

Jin UH, Lee SO, Sridharan G, Lee K, Davidson LA, Jayaraman A, Chapkin R, Alaniz R, Safe SH (2014) Microbiome-Derived Tryptophan Metabolites and Their Aryl Hydrocarbon Receptor-Dependent Agonist and Antagonist ActivitiesMol Pharmacol 85: 777-788.

Quinn KP, Sridharan GV, Hayden RS, Kaplan DL, Lee K, Georgakoudi I (2013) Quantitative Metabolic Imaging Using Endogenous Fluorescence to Detect Stem Cell DifferentiationSci Rep 3: 3432.

Manteiga S, Choi K, Jayaraman A, Lee K (2013) Systems Biology of Adipose Tissue Metabolism: Regulation of Growth, Signaling and InflammationWiley Interdiscip Rev Syst Biol Med 5: 425-447.

Schiller ZA, Schiele NR, Sims JK, Lee K, Kuo CK (2013) Adipogenesis of Adipose-derived Mesenchymal Stem Cells May Be Regulated via the Cytoskeleton at Physiological Oxygen Levels In VitroStem Cell Res Ther 4: 79.

Yousofshahi M, Orshansky M, Lee K, Hassoun S. (2013) Probabilistic Strain Optimization under Constraint UncertaintyBMC Syst Biol 7: 29.

Rucker J, Paul J, Pfeifer BA, Lee K (2013) Engineering E. Coli for Triglyceride Accumulation through Native and Heterologous Metabolic ReactionsAppl Microbiol Biotechnol97: 2753-2759.

Sridharan GV, Yi M, Hassoun S, Lee K (2012) Metabolic Flux-Based Modularity Using Shortest Retroactive DistancesBMC Syst Biol 6: 155.

Quinn KP, Bellas E, Fourligas N, Lee K, Kaplan DL, Georgakoudi I (2012) Characterization of Metabolic Changes Associated with the Functional Development of 3d Engineered Tissues by Non-Invasive, Dynamic Measurement of Individual Cell Redox RatiosBiomaterials 33: 5341-5348.

Nolan RP, Lee K (2012) Dynamic Model for CHO Cell EngineeringJ Biotechnol 158: 24-33.

Lai N, Sims JK, Jeon NL, Lee K (2012) Adipocyte Induction of Preadipocyte Differentiation in a Gradient ChamberTissue Eng Part C Methods 18: 958-967.

Yousofshahi M, Lee K, Hassoun S (2011) Probabilistic Pathway ConstructionMetab Eng 13: 435-444.

Yadav V, Panilaitis B, Shi H, Numuta K, Lee K, Kaplan DL (2011) N-Acetylglucosamine 6-Phosphate Deacetylase (Naga) Is Required for N-Acetyl Glucosamine Assimilation in Gluconacetobacter XylinusPLoS One 6: e18099.

Sridharan GV, Hassoun S, Lee K (2011) Identification of Biochemical Network Modules Based on Shortest Retroactive DistancesPLoS Comput Biol 7: e1002262.

Nolan RP, Lee K (2011) Dynamic Model of Cho Cell MetabolismMetab Eng 13: 108-124.

Full list of publications