Pharmaco-Omics Lab facilitates the advancement of translational research and personalized medicine utilizing multi-omics technologies and data science
As to methods there may be a million and then some, but principles are few. The man who grasps principles can successfully select his own methods. The man who tries methods, ignoring principles, is sure to have trouble. -Ralph Waldo Emerson
TEAM MEMBERS
Principal Investigator
Nguyen Phuoc Long, M.D., Ph.D.
Assistant Professor (tenure-track), Department of Pharmacology, Inje University College of Medicine (2022.3 – now)
Interests: Omics, Systems Pharmacology, Personalized Medicine, Mass Spectrometry, Biostatistics
Academic Background and Working Experience
Research Professor, PharmacoGenomics Research Center, Inje University College of Medicine (2020.9 – 2022.2)
Postdoctoral Fellow, Research Institute of Pharmaceutical Sciences, Seoul National University (2020.3 – 2020.8)
Graduate Student of the Integrated M.Sc. and Ph.D. Program, College of Pharmacy, Seoul National University (2016.3 – 2020.2)
Undergraduate Student of the M.D. Program, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City (2009 – 2015)
CURRENT GRADUATE STUDENTS
Nguyen Quang Thu
M.S. Student
Translational Omics
Nguyen Tran Nam Tien
M.S. Student
Clinical Omics
AFFILIATED RESEARCH ASSOCIATES
Tam Anh Trinh
Molecular Biologist, cPMTb Staff
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VISITING FELLOWS AND INTERNS
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ALUMNI
Nguyen Ky Anh
Graduate Researcher
Clinical Omics
Noppadol Chanhom
cPMTb Visiting Intern, Pharmacologist. Ph.D. Student of Faculty of Pharmacy, Mahidol University (graduated 2023)
Nguyen Thi Hai Yen
M.S. Student
Translational and Clinical Omics
Nguyen Thi Van Anh
M.S. Student
Pharmacology
Co-mentor with Dr. Yong-Soon Cho (graduated 2023)
Nguyen Ky Phat
Graduate Researcher
Bioinformatics
Tran Minh Hung
Ph.D. student in Pharmacology (graduated in 2023)
Vo Thuy Anh Thu
Molecular biologist, Former cPMTb Staff (Ph.D. Student at Dr. Yong-Soon Cho’s lab.)
Ly Da Dat
Molecular Biologist, cPMTb Staff
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RESEARCH
Main topics:
- Metabolism-centric multi-omics and machine learning to facilitate the advancement of translational research and precision medicine.
- Pharmaco-omics and pharmacometrics to improve diagnosis, prognosis, precision dosing, treatment monitoring, and outcome prediction.
- Mechanistic studies to elucidate the underlying biological processes related to the disease progression, drug actions, and toxicity of drugs and toxicants.
Minor topics:
- Pharmaceutical and biomedical analysis.
- Medical ecology and environmental pollution research.
- Drug discovery and repurposing.
- Food science and human nutrition.
TECHNOLOGIES
Mass Spectrometry
Our metabolomics and lipidomics studies are powered by various LC-MS systems, including X500R, Q-ToF 6530, QTRAP 5500, and other QqQ platforms.
Bioinformatics
- We utilize state-of-the-art bioinformatic tools for efficient data mining.
Machine Learning
- We employ a wide range of machine learning algorithms for biomarker discovery and validation.
Molecular and Biochemical Assays
We develop and utilize a wide range of in vitro and clinical assays.
- RNA-seq and microarray-based gene expression analyses.
- Multiplex Immunoassays.
- SNaPshot® Multiplex System for SNP genotyping.
- CRISPR/Cas9-based gene knockout.
- siRNA or shRNA-based gene knockdown.
- PCR, Western Blots, and other phenotype assays.
- Mitochondrial and Mitochondria-associated ER membranes isolation.
Meta-Research
- We carry out systematic review, meta-analysis, and text mining when a comprehensive and up-to-date research topic is of high interest.
CURRENT RESEARCH APPROACH
COLLABORATIVE AND AFFILIATED CENTERS
Busan Paik Hospital
PharmacoGenomics Research Center
PUBLICATIONS
The full publication record can be found here. Some representative publications are shown below:
- Nhung TTM*, Long NP*, Nghi TD, …, Park SK. Genome-wide kinase-MAM interactome screening reveals the role of CK2A1 in MAM Ca2+ dynamics linked to DEE66. Proceedings of the National Academy of Sciences. 2023 Aug.
- Yen NTH*, Phat NK*, …, DH Kim†, Long NP†. Pathway-level Multi-Omics Analysis of the Molecular Mechanisms Underlying the Toxicity of Long-term Tacrolimus Exposure. Toxicology and Applied Pharmacology. 2023 Aug.
- Hung TM*, Jayanti RP*, …, Long NP, Cho YS, Shin JG, on behalf of cPMTb. Recommendation of Pharmacokinetics/Pharmacodynamics Target of Ethambutol to Suppress Tuberculosis Resistance: A Population Pharmacokinetics Study on Large Prospective Cohort. International Journal of Antimicrobial Agents. 2023 Jul. (2021 IF 15.441)
- Nguyen BT, Yen NTH, Tung NKT, Jeong GS, Kang JS, Long NP†, Kim HM†. Lipid class-dependent alterations of Caenorhabditis elegans under harmane exposure. Journal of Pharmaceutical and Biomedical Analysis. 2023 Jul. (Co-corresponding author, 2021 IF 3.571)
- Yen NTH*, Anh NK*, Jayanti RP, Phat NK, Vu DH, Ghim JL, Ahn S, Shin JG, Oh JY, Long NP†, Kim DH†. Multimodal plasma metabolomics and lipidomics in elucidating metabolic perturbations in tuberculosis patients with concurrent type 2 diabetes. Biochimie. 2023 Apr. (Co-corresponding author, 2021 IF 4.372)
- Yen NTH, Oh JH, Anh NTV, Le QV, Park SM, Park YJ, Cho YS, Moon KS, Nguyen HT, Shin JG, Long NP†, Kim DH†. Systems-level multi-omics characterization provides novel molecular insights into indomethacin toxicity. Chemico-Biological Interactions. 2023 Apr. (Co-corresponding author, 2021 IF 5.168)
- Anh NK*, Phat NK*, Yen NTH, Jayanti RP, Thu VTA, Park YJ, Cho YS, Shin JG, Kim DH, Oh JY†, Long NP†. Comprehensive lipid profiles investigation reveals host metabolic and immune alterations during anti-tuberculosis treatment: Implications for therapeutic monitoring. Biomedicine & Pharmacotherapy. 2023 Feb. (Co-corresponding author, 2021 IF 7.419)
- Thu VTA, Dat LD, Jayanti RP, Tu THK, Hung TM, Cho YS, Long NP†, Shin JG†. Advancing personalized medicine for tuberculosis through the application of immune profiling. Frontiers in Cellular and Infection Microbiology. 2023 Jan. (Co-corresponding author, 2021 IF 6.073)
- Yen NTH, Park SM, Thu VTA, Phat NK, Cho YS, Yoon S, Shin JG, Kim DH, Oh JH†, Long NP†. Genome-wide gene expression analysis reveals molecular insights into the drug-induced toxicity of nephrotoxic agents. Life Sciences. 2022 Oct. (Co-corresponding author, 2021 IF 6.780)
- Long NP*, Anh NK*, Yen NTH, Phat NK, Park S, Thu VTA, Cho YS, Shin JG, Oh JY, DH Kim. Comprehensive lipid and lipid-related gene investigations of host immune responses to characterize metabolism-centric biomarkers for pulmonary tuberculosis. Scientific Reports. 2022 Aug. (Co-first author, 2021 IF 4.996)
- Anh NH, Yoon YC, Min YJ, Long NP, Jung CW, Kim SJ, Kim SW, Lee EG, Wang D, Wang X, Kwon SW. Caenorhabditis elegans deep lipidome profiling by using integrative mass spectrometry acquisitions reveals significantly altered lipid networks. Journal of Pharmaceutical Analysis. 2022 Jun 24. (2021 IF 14.026)
- Soedarsono S, Jayanti RP, Mertaniasih NM, Kusmiati T, Permatasari A, Indrawanto DW, Charisma AN, Yuliwulandari R, Long NP, Choi YK, Hoa PQ et al. Development of population pharmacokinetics model of isoniazid in Indonesian patients with tuberculosis. International Journal of Infectious Diseases. 2022 Apr 1;117:8-14. (2021 IF 12.074)
- Long NP, Oh JH, Park SM, Yen NT, Phat NK, Cho YS, Kim HM, Yoon S, Shin JG, Kim DH. Delineation of the molecular mechanisms underlying Colistin-mediated toxicity using metabolomic and transcriptomic analyses. Toxicology and Applied Pharmacology. 2022 Feb 19:115928. (2021 IF 4.460)
- Long NP, Heo DY, Park S, Yen NTH, Cho YS, Shin JG, Oh JY, Kim DH. Molecular perturbations in pulmonary tuberculosis patients identified by pathway-level analysis of plasma metabolic features. PloS ONE. 2022 Jan 24;17(1):e0262545. (2021 IF 3.752)
- Long NP, Phat NK, Yen NT, Park S, Park Y, Cho YS, Shin JG. A 10-gene biosignature of tuberculosis treatment monitoring and treatment outcome prediction. Tuberculosis. 2021 Dec 1;131:102138. (2021 IF 2.973)
- Long NP, Heo D, Kim HY, Kim TH, Shin JG, Lee A, Kim DH. Metabolomics-guided global pathway analysis reveals better insights into the metabolic alterations of breast cancer. Journal of Pharmaceutical and Biomedical Analysis. 2021 Aug 5;202:114134. (2021 IF 3.571)
- Long NP, Kim HM. Distinct metabolic alterations in different Caenorhabditis elegans mitochondrial mutants. Journal of Chromatography B. 2021 Aug 1;1179:122863. (2021 IF 3.318)
- Kim SJ, Long NP, Jung CW, Anh NH, Min JE, Kim HM, Kwon SW. Exposure to nano-polystyrene induces metabolic alteration in lipid homeostasis in Caco-2. Environmental Science: Nano. 2021;8(5):1408-24 (2021 IF 9.473).
- Kim HM*, Long NP*, Min JE, Anh NH, Kim SJ, Yoon SJ, Kwon SW. Comprehensive phenotyping and multi-omic profiling in the toxicity assessment of nanopolystyrene with different surface properties. Journal of Hazardous Materials. 2020 Nov 15;399:123005. (Co-first author, 2021 IF 14.224)
- Long NP*, Min JE*, Anh NH, Kim SJ, Park S, Kim HM, Yoon SJ, Lim J, Lee SJ, Kwon SW. Isolation and metabolic assessment of cancer cell mitochondria. ACS Omega. 2020 Oct 12;5(42):27304-13. (Co-first author, 2021 IF 4.132)
- Long NP*, Nghi TD*, Kang YP, Anh NH, Kim HM, Park SK, Kwon SW. Toward a standardized strategy of clinical metabolomics for the advancement of precision medicine. Metabolites. 2020 Feb;10(2):51. (The affiliated journal of The Metabolomics Society (MetSoc), Co-first author, 2021 IF 5.581) (Selected to be the cover story!)
- Kim HM, Long NP, Yoon SJ, Anh NH, Kim SJ, Park JH, Kwon SW. Omics approach reveals perturbation of metabolism and phenotype in Caenorhabditis elegans triggered by perfluorinated compounds. Science of The Total Environment. 2020 Feb 10;703:135500. (2021 IF 10.753)
- Kim HM, Lee DK, Long NP, Kwon SW, Park JH. Uptake of nanopolystyrene particles induces distinct metabolic profiles and toxic effects in Caenorhabditis elegans. Environmental Pollution. 2019 Mar 1;246:578-86. (2021 IF 9.988, highly cited article)
- Kim HM, Long NP, Yoon SJ, Nguyen HT, Kwon SW. Metabolomics and phenotype assessment reveal cellular toxicity of triclosan in Caenorhabditis elegans. Chemosphere. 2019 Dec 1;236:124306. (2021 IF 8.943)
- Long NP*, Jung KH*, Anh NH, Yan HH, Nghi TD, Park S, Yoon SJ, Min JE, Kim HM, Lim JH, Kim JM. An integrative data mining and omics-based translational model for the identification and validation of oncogenic biomarkers of pancreatic cancer. Cancers. 2019 Feb;11(2):155. (Co-first author, 2021 IF 6.575)
- Long NP, Yoon SJ, Anh NH, Nghi TD, Lim DK, Hong YJ, Hong SS, Kwon SW. A systematic review on metabolomics-based diagnostic biomarker discovery and validation in pancreatic cancer. Metabolomics. 2018 Aug;14(8):1-26. (2021 IF 4.747)
- Lim DK*, Long NP*, Mo C, Dong Z, Cui L, Kim G, Kwon SW. Combination of mass spectrometry-based targeted lipidomics and supervised machine learning algorithms in detecting adulterated admixtures of white rice. Food Research International. 2017 Oct 1;100:814-21. (Co-first author, 2021 IF 7.425)
- Long NP*, Lim DK*, Mo C, Kim G, Kwon SW. Development and assessment of a lysophospholipid-based deep learning model to discriminate geographical origins of white rice. Scientific reports. 2017 Aug 17;7(1):1-0. (Co-first author, 2021 IF 4.996)
- Tam NT, Huy NT, Thoa LT, Long NP, Trang NT, Hirayama K, Karbwang J. Participants’ understanding of informed consent in clinical trials over three decades: systematic review and meta-analysis. Bulletin of the World Health Organization. 2015;93:186-98H. (Official Journal of WHO, highly cited article, 2021 IF 13.831)
LAB NEWS
- 2023.04.20-21 – PharmOmicsLab participated in the annual conference (2023) of the Pharmaceutical Society of Korea with 3 poster presentations.
- 2023.04.06-07 – PharmOmicsLab participated in the annual conference (2023) of the Korea Metabolomics Society with 4 poster presentations.
- 2023.03.20 – The editorial entitled “Editorial: Reviews in metabolomics: Personalized and predictive medicine of infectious diseases” Dr. Long co-editted with Dr. Ilse Du Preez was published (full text). This is part of his participation in the research topic with the same name.
- 2023.03.08 – Dr. Long gave a keynote presentation at Metabolomics Symposium Vietnam. TDTU and Agilent organized the symposium.
- 2023.02.09 – Dr. Long received the Metabolites 2022 Outstanding Reviewer Award. He has received this award 3 times (2020, 2021, 2022).
- 2022.11.30 – 2022.12.02: PharmOmicsLab participated in the 2022 Conference organized by Korean Society of Clinical Pharmacology (KSCPT).
- 2022.11.10 – 2022.11.11: PharmOmicsLab participated in the 2022 Conference organized by Korean Society of Pharmacology.
- 2022.10-30 – 2022.11.05 – Dr. Long joined other professors in a business trip to Vietnam, participated in scientific meetings at Hanoi University of Pharmacy, Hanoi Medical University, and University of Medicine and Pharmacy at Ho Chi Minh City, and signed an MoU contract with Ton Duc Thang University (university news).
- 2022.10.07 – Dr. Long joined other professors in the department to welcome the delegates of Hai Phong University of Medicine and Pharmacy.
- 2022.06.29 – Dr. Long presented at the seminar entitled “Pharmaceutical Sciences: Recent trends and application”. The seminar was an international event organized by College of Pharmacy, Ton Duc Thang University.
- 2022.06.02 – Dr. Long presented in an invited seminar at College of Pharmacy, Seoul National University. The presentation was about “Integrated Framework for the Advancement of Personalized and Predictive Medicine”.
- 2022.03.12 – Dr. Long received the Metabolites 2021 Outstanding Reviewer Award. He also got this award last year.
2022.03.01 – Dr. Long has been officially appointed an assistant professor at Inje University College of Medicine.
FUNDINGS
Inje University Internal Grant
AVAILABLE POSITIONS
Graduate Students
- Pharmaco-Omics Lab aims at recruiting and training highly potential and self-motivated graduate students. The candidate is expected to have to some degree either (1) computational and programming skills or (2) experimental skills. Please send your motivation letter, updated academic transcript, and CV to the PI (email: bsngphuoclong<at>gmail<dot>com) for a scheduled interview.
Postdoctoral Fellows
- Our lab always welcomes talented and highly self-motivated young scientists with an omics background to work with us. Please send your cover letter and updated academic CV to the PI for a scheduled interview.
Inje University Symbol Mark
Inje University College of Medicine
