Ngoc VU (Minh Ngoc)


Université Évry Paris-Saclay
Evry · France
ngocvu.vmn@gmail.com

Minh Ngoc is a Master's student in Bioinformatics with an aspiration to pursue research in bioinformatics, medical informatics, and health data science.

Education

Université Paris-Saclay, Université d'Évry Val-d'Essonne, France


Master of Science in Bioinformatics
Program: Genomics, Informatics and Mathematics for Health and Environment
  • M1 average grade: 14.74/20
  • M1 internship project: “Comparative transcriptomics of regeneration in vertebrates” (scored 16/20)
  • Relevant courses: Structural Genomics, Genome Sequencing, Deep Learning and Data Analysis, Object-Oriented Programming, Multivariate Statistics, etc.
    • September 2024 - Present

    University of Science, Vietnam National University (VNU), Vietnam


    Bachelor of Science in Biotechnology
  • Final GPA: 3.61/4.0 (Class ranking top 1, valedictorian)
  • Recipient of the University’s scholarship for excellent students
  • Thesis title: RNA-seq analysis MCF-7 breast cancer cells co-cultured with adipose-derived stem cells (the highest scoring undergraduate thesis (9.9/10) in the Cell Biology Department (HUS-VNU) in 2024)
    • September 2020 - June 2024

    Research Interests

  • Transcriptomic analysis of cancer / cell response to chemical stimuli
  • Deep learning methods for medical diagnosis and biomedical solutions


    • Publications

    • MN Vu, HH Nguyen, A Toffano, P Larmande. (2025) Evaluating deep learning models for plant protein function prediction, JOBIM 2025, Bordeaux, France

    • MN Vu, HH Nguyen, VN Bui. (2025) Detection of peripheral blood cells using various deep learning networks, International Conference on Intelligent Systems and Networks (ICISN) 2025, Hanoi, Vietnam

    • Dan Tran, Ngoc Vu, et al. (2025) Identification of recurrent Wilms tumor-associated hub genes via RNA-seq and weighted gene coexpression network (Under review)

    • NH Tran, MN Vu, et al. (2024). Enhancement of bioactivity and biocompatibility of 3D printed scaffolds by cord blood-derived PRP and PPP coating (In submission)

    • TMP Chu, BT Ha, MN Vu, et al. (2024) The application of deep learning in lung cancerous lesions detection. medRxiv 2024.04.12.24305708; doi: https://doi.org/10.1101/2024.04.12.24305708

    • MN Vu, HD Le, et al. (2024). Integrated RNA Sequencing Analysis Revealed Early Gene Expression Shifts Associated with Cancer Progression in MCF-7 Breast Cancer Cells Cocultured with Adipose-Derived Stem Cells. Current Issues in Molecular Biology, 46(11), 11817-11834.

    • TPT Nguyen & MN Vu et al. (2023) Metagenomic characterization of archaeal and bacterial communities associated with coral, sediment, and seawater in a coral reef ecosystem of Phu Quoc Island, Vietnam. Vietnam Journal of Biotechnology, 21(4), 745–757. https://doi.org/10.15625/1811-4989/20283


    EXPERIENCE

    Bioinformatic Intern (Master 1 internship)


    Stem cells, regeneration and evolution (Gazave Lab), Institut Jacques Monod, Paris, France

    Comparative transcriptomics of regeneration in vertebrates

  • Performed differential gene expression (DGE), functional enrichment, genomic phylostratigraphy, and c-means clustering on bulk RNA-seq datasets of regeneration in 5 vertebrate species
  • Performed orthogroup analyses and clustering (PCA, CA, MDS) to identify conserved and species-specific mechanisms underlying regeneration
    • April - June 2025

    Bioinformatics Laboratory Research Assistant and Intern


    Vietnam Academy of Science and Technology (VAST), Institute of Biology, Hanoi, Vietnam

    Evaluated deep learning models for plant protein function prediction (JOBIM 2025, supervisor: Dr. Pierre Larmande, Université de Montpellier; Dr. Hoang Ha Nguyen, USTH)

  • Re-implemented top computational models (DeepGOPlus, DeepGOSE, DeepGOZero, DeepGraphGO) for predicting Gene Ontology (GO) annotations for plant proteins

    • Identification of a gene-expression signature predicting Wilms tumor recurrence

  • Performed DGE analysis and functional analyses to compare recurrent and primary Wilms tumor with public RNA-seq data from TARGET-WT
  • Performed LASSO-Cox regression and constructed a 20-gene risk score to predict recurrence probability, validated using univariate and multivariate Cox proportional-hazards regression & Kaplan-Meier disease-free survival analysis

    • Integrated RNA-seq analysis MCF-7 breast cancer cells co-cultured with adipose-derived stem cells (Bachelor’s thesis, supervisor: Dr. Bui Van Ngoc, IBT)

  • Performed quality control, processing, read mapping, and annotation for RNA-seq data
  • Conducted DGE analysis and functional analyses (hypergeometric, GSEA) to identify genes and pathways of breast cancer cells affected by the presence of stem cells

    • The application of deep learning in lung cancerous lesion detection (preprint)

  • Python programming to optimize classifiers and fine-tune hyperparameters to improve the performance of 9 Keras models to detect pneumonia and lung cancer from chest CT scans
  • Implemented gradient-weighted class activation mapping to highlight the cancerous lesions detected by the models for optimizing and explaining the models’ behavior

    • Detection of peripheral blood cells using various deep learning networks (ICISN 2025)

  • Annotated and curated a dataset of >17,000 microscopic images of 8 blood cell types, performed class-specific data augmentation to solve data imbalance
  • Trained and validated YOLOv5s, SSD300, and Faster RCNN models

    • Characterized the composition and diversity of archaea and bacteria associated with coral reefs using metagenomic analysis

  • Performed quality control for 16S rRNA sequencing data; taxonomic classification and abundance analysis; alpha and beta analysis
    • April 2022 - September 2024

    Cell Biology Laboratory Intern


    University of Science, Vietnam National University (VNU), Hanoi, Vietnam

    Analysis of tartrazine’s toxicity on human cell lines using RNA-seq and TempO-Seq data (remote in 2024)

  • Performed DGE analysis, functional analyses, and partial least squares regression to study the effects of tartrazine in vitro on human neuronal precursor cells, renal cells, and hepatocytes
  • Proposed the roles of GTPase pathways and gene candidates for experimental validations

    • Evaluated the biocompatibility of 3D-printed polycaprolactone scaffolds on mesenchymal stem cells

  • Conducted mesenchymal stem cell culture, immunofluorescence assay, and MTT assay for cytotoxicity and cell proliferation assessment
  • Experimental designs, literature reviews, and manuscript preparation
    • February 2022 - July 2023

    Data Entry Assistant (Part-time)


    Woolcock Institute of Medical Research, Hanoi, Vietnam

    Performed double entry and validated clinical data for the VQUIN project (a randomized controlled trial of levofloxacin to prevent tuberculosis, implemented by Vietnam National Lung Hospital and funded by the National Health and Medical Research Council, Australia)

    May 2022 - June 2022

    Skills

    Computational skills


    Programming languages & platforms: Python, R, Bash, SQL; remote servers & HPC clusters

    Machine learning:

  • Object detection and image classification (PyTorch, Tensorflow); object annotation; hyperparameter optimization
  • Explainable AI: gradient-weighted class activation mapping (Grad-CAM)

    • Bioinformatics and biostatistics:

  • NGS data processing: quality control, read mapping, gene annotation, etc. (nf-core rnaseq, FastQC, Qualimap, RSeQC, Cutadapt, HISAT2)
  • Transcriptomic analysis (bulk RNA-Seq, microarray, and TempO-Seq): differential gene expression (edgeR, DESeq2); functional enrichment (hypergeometric test, GSEA, GSVA); weighted gene co-expression network analysis (WCGNA); soft clustering (Mfuzz)
  • Orthologous group analysis (OrthoFinder), genomic phylostratigraphy (GenEra)
  • Protein-protein interaction network analysis (STRING, CytoHubba)
  • Multivariate statistics for feature selection (LASSO, partial least squares regression), Cox regression, Kaplan-Meier survival analysis
  • Metagenomic analysis using 16S rRNA sequencing data (DADA2, phyloseq)

    • Cell and molecular biology


  • Mesenchymal stem cell culture, MTT assay, immunofluorescence staining
  • PCR, ARMS-PCR, SDS-PAGE, gel electrophoresis

    • Languages


  • English: C1 (IELTS Academic: 8.0)
  • French

    • AWARDS

    • 2020-2024: Recipient of the Scholarship for Excellent Students, awarded by the University of Science, VNU (Vietnam) for students with GPA>3.6/4.0 each semester

    • 2023: Euréka Competition for Students’ Scientific Research: Semi-finalist (Organized by Vietnam National University - Ho Chi Minh City)

    • 2023: Student Research Conferences, Hanoi University of Science, VNU: First Prize (best presentation) at Faculty’s conference and Second Prize at University-level conference.

    • 2022: Stem Cell Innovation Competition 7th: Semi-finalist (Organized by the Stem Cell Institute of University of Science, Vietnam National University - Ho Chi Minh City)

    Extracurricular activities

    • 2024: Volunteer of the Mental Health First Aid for All Organization, the Mental Health First Aid for Educators Project (sponsored by the European Union Delegation to Vietnam and the EU Alumni Network)

    • 2022: Photographer, Faculty of Biology’s Student Research Conference, Hanoi University of Science, VNU

    • 2021: Data Entry Volunteer: entered and checked COVID-19 vaccination data of 10,000 citizens of Thanh Xuan Trung Ward, Thanh Xuan District, Hanoi, Vietnam

    • 2021 – 2024: IELTS Mentor

    • 2021 – 2024: Portrait photographer, portfolio at: Behance