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Pharmaco-OmicsLab/README.md

Pharmaco-Omics Lab – Omics for Personalized Medicine

The Pharmaco-Omics Lab leverages cutting-edge laboratory, clinical, and computational approaches to understand the molecular mechanisms of human metabolic diseases (in the broad sense), discover clinically relevant biomarkers, and develop personalized treatment strategies.

The figure below shows our laboratory's framework for personalized medicine using integrated science and technology.

Framework Figure Some of the content was inspired by Nature Medicine 25.5 (2019):792. (Created with BioRender.com and Flaticon)

Principal Investigator: Nguyen Phuoc Long

Key resources:

SepMISA - Sepsis Multi-Omics Intervention Study Analysis:

  • GAA_sepsis: Exploring the Effects of Glucogenic Amino Acids on the Multiomic Landscape of Sepsis.

LipMetAnnotCompare - A Pipeline for Verifying and Improving Lipid and Metabolite Annotations

ManuscriptSubmissionGuide - A Step-by-Step Guide for Preparing and Submitting a Scientific Manuscript

EasyPubPlot - Shiny App for Easy and Publishable Ploting

eMLe - Shiny App for Easy Machine Learning Evaluation

Research Themes:

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.

Key Publications

  • Wu Z*, Tien NTN*, Bæk O, Zhong J, Klabunde B, Nguyen TT, Yen NTH, Long NP#, Nguyen DN#. Regulation of host metabolism and defense strategies to survive neonatal infection. Biochim Biophys Acta Mol Basis Dis. 2024 Dec;1870(8):167482. doi: 10.1016/j.bbadis.2024.167482. Epub 2024 Aug 29. PMID: 39213794.

  • Anh NK*, Yen NTH*, Tien NTN, Phat NK, Park YJ, Kim HS, Vu DH, Oh JY, Kim DH, Long NP. Metabolic phenotyping and global functional analysis facilitate metabolic signature discovery for tuberculosis treatment monitoring. Biochim Biophys Acta Mol Basis Dis. 2024 Apr;1870(4):167064. doi: 10.1016/j.bbadis.2024.167064. Epub 2024 Feb 10. PMID: 38342417.

  • Nhung TTM*, Long NP*, Tran DN, Suh Y, Anh NH, Jung CW, Triet HM, Jung M, Woo Y, Yoo J, Noh S, Kim SJ, Lee SB, Park S, Thomas G, Simmen T, Mun J, Rhee HW, Kwon SW, Park SK. Genome-wide kinase-MAM interactome screening reveals the role of CK2A1 in MAM Ca2+ dynamics linked to DEE66. Proc Natl Acad Sci U S A. 2023 Aug 8;120(32):e2303402120. doi: 10.1073/pnas.2303402120. Epub 2023 Jul 31. PMID: 37523531; PMCID: PMC10410754.

  • Yen NTH, Oh JH, Van Anh NT, 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. Chem Biol Interact. 2023 Apr 25;375:110430. doi: 10.1016/j.cbi.2023.110430. Epub 2023 Mar 1. PMID: 36868495.

  • 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. Biomed Pharmacother. 2023 Feb;158:114187. doi: 10.1016/j.biopha.2022.114187. Epub 2023 Jan 3. PMID: 36916440.

  • 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. J Hazard Mater. 2020 Nov 15;399:123005. doi: 10.1016/j.jhazmat.2020.123005. Epub 2020 May 26. PMID: 32937704.

Positions

  • Graduate Students: Pharmaco-Omics Lab actively recruits and trains 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 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.

Popular repositories Loading

  1. Pharmaco-OmicsLab Pharmaco-OmicsLab Public

  2. LipMetAnnotCompare LipMetAnnotCompare Public

    A Pipeline for Verifying and Improving Lipid and Metabolite Annotations

    R

  3. ManuscriptSubmissionGuide ManuscriptSubmissionGuide Public

    A Step-by-Step Guide for Preparing and Submitting a Scientific Manuscript

  4. EasyPubPlot EasyPubPlot Public

    Shiny app to easily create publishable plots for scientific papers

  5. eMLe eMLe Public

    Shiny app to easily evaluate multiple machine learning models