Curriculum Vitae

Md. Jubayer Hossain
Department of Public Health, Daffodil International University
Daffodil Smart City, Birulia 1216

+8801622345906 | hossainmj.me@gmail.com | mdjubayerhossain.com

About Me

My research focuses on developing reproducible bioinformatics pipelines for large-scale bulk and single-cell RNA-seq data to uncover molecular biomarkers, immunological signatures, and therapeutic targets in cancer and neurological diseases. By integrating multi-omics data analysis, machine learning, and biology, I aim to advance computational methods that bridge biological discovery and clinical translation.

Technical Skills

Programming     Python, R, Julia, SQL, Bash, JavaScript
Data Science & ML     NumPy, Pandas, PyTorch, TensorFlow, scikit-learn, XGBoost, SHAP
Bulk RNA-Seq     FastQC, STAR, HISAT2, Salmon, Kallisto, DESeq2, limma, edgeR
Single-Cell RNA-Seq     Seurat, Scanpy, CellRanger, Harmony, scVI-tools, scVelo, SingleR
Spatial Transcriptomics     Squidpy, SpatialData, Seurat (spatial), Giotto, STUtility
Microbiome     QIIME 2, DADA2, Phyloseq, VSEARCH, Kraken2, MetaPhlAn
Workflow & Reproducibility     Nextflow, nf-core, Snakemake, Docker, Singularity, Git, GitHub Actions
Visualization     ggplot2, Seaborn, Matplotlib, Plotly, ComplexHeatmap, MultiQC, Quarto
Computing     UNIX/Linux, HPC clusters, SLURM, AWS, Google Cloud, Conda, Mamba

Research Experience

Visiting Scholar Sep 2025 – Present
Department of Public Health, Daffodil International University Dhaka, Bangladesh

  • Investigated computational frameworks within public health genomics to facilitate large-scale biomarker discovery and clinical validation.
  • Developed a specialized curriculum for AI-driven disease modeling, integrating neural network architectures into biomedical informatics.
  • Synthesized heterogeneous digital health records with genomic datasets to evaluate predictive models for clinical outcomes.
  • Led a multidisciplinary research initiative to translate raw sequencing data into evidence-based public health insights.

Research Associate (Bioinformatics) 2017 – 2019
Bio-Bio-1: Bioinformatics Research Discussion Group Dhaka, Bangladesh

  • Analyzed genomic and transcriptomic datasets using computational tools in R and Python, with emphasis on high-throughput sequencing data.
  • Designed and delivered training modules on sequence alignment algorithms, RNA-seq analysis pipelines, and data preprocessing workflows.
  • Evaluated and implemented peer-reviewed bioinformatics methods for transcriptomic data, ensuring reproducibility and analytical rigor.

Data Enumerator Oct 2022 – Nov 2022
School of Allied Health, Curtin University Perth, Australia

  • Collected and curated quantitative and qualitative data from 40 clinicians for a Delphi study on Patient Outcomes Measurement in Interprofessional Tuberculosis Care.
  • Performed rigorous data validation and cleaning, achieving 100% dataset accuracy for downstream statistical analysis.

Education

Master of Science in Microbiology 2019 – 2020
Jagannath University Dhaka, Bangladesh

  • Relevant Coursework: Genomics, Proteomics, Bioinformatics, Research Methodology and Scientific Writing

Bachelor of Science in Microbiology 2016 – 2019
Jagannath University Dhaka, Bangladesh

  • Relevant Coursework: Biostatistics, Public Health and Hygiene, Bioinformatics I, Bioinformatics II

Training & Certifications

Interdisciplinary Computational Biology January 2026
BRAC University Dhaka, Bangladesh

  • Mastered high-resolution protein structure prediction and molecular visualization using AlphaFold2/3 and ChimeraX to investigate complex protein-ligand interactions.
  • Applied AI/ML frameworks and docking protocols to structural data from PDB and UniProt, culminating in an interdisciplinary project on predictive molecular modeling.

AI in Public Health Sep 2023
Child Health Research Foundation (CHRF) Dhaka, Bangladesh

  • Developed predictive models and data pipelines for disease surveillance, focusing on the calculation of typhoid incidence and vaccine impact in Bangladesh.
  • Built LLM-based code generation and computer vision frameworks for medical image analysis while analyzing the ethical implications of algorithmic bias.

Leadership Experience

Founder, Bioinformatics Scientist & CEO Jan 2025 – Present
DeepBio Limited Dhaka, Bangladesh

  • Lead a team of 13 researchers executing scRNA-seq and bulk RNA-seq analysis pipelines for cancer genomics and transcriptomics projects.
  • Develop and benchmark scalable bioinformatics workflows for biomarker discovery in cancer and neurodegenerative diseases.
  • Build and maintain AI-integrated computational infrastructure for multi-omics data processing and interpretation.
  • Develop and deliver a national training program in computational biology, upskilling undergraduate researchers across Bangladesh.

Founder & Capacity Building Director June 2020 – Present
CHIRAL Bangladesh (Non-profit Research Institute) Dhaka, Bangladesh

  • Founded and lead a research institute with dedicated divisions in Bioinformatics, Public Health, Geospatial Health, and AI-Healthcare.
  • Published 20+ peer-reviewed articles in Q1/Q2 journals and 40+ conference papers in health informatics and computational biology.
  • Supervised 15+ manuscripts through analytical development and peer-review preparation in global health and bioinformatics.
  • Collaborated with Michigan State University on biomedical research capacity-building initiatives in South Asia.
  • Trained 3,000+ early-career researchers in data science, research methodology, and computational biology workflows.

Teaching Experience

Lead Organizer & Instructor June 2020 – Present
DeepBio Academy, Bioinformatics and Computational Biology Dhaka, Bangladesh

  • Designed comprehensive bioinformatics curriculum specializing in Single-Cell RNA-seq (scRNA-seq) workflows and multi-omic data integration.
  • Benchmarked computational tools for transcriptomics and genomics to ensure pipeline reproducibility and analytical rigor.
  • Supervised a technical research team in processing high-throughput omics datasets to identify transcriptional drivers of disease.

Faculty (Bioinformatics) Aug 2023 – Present
University of Dhaka (cBLAST) Dhaka, Bangladesh

  • Instructed specialized modules in Biomedical Machine Learning, focusing on the application of Python-based neural networks to sequence analysis.
  • Directed student research projects applying deep learning frameworks to identify regulatory elements in complex biological datasets.
  • Facilitated technical practicums for 100+ trainees on scalable data science methodologies for high-throughput genomic data.

Program Lead July 2025 – Dec 2025
GSA Bioinformatics Internship Dhaka, Bangladesh

  • Conducted a pan-cancer transcriptomics meta-analysis across four organ systems to identify conserved regulatory networks in tumorigenesis.
  • Optimized high-throughput pipelines for Bulk and Single-Cell RNA-seq, implementing advanced batch-effect correction and normalization protocols.
  • Mentored research interns in the utilization of High-Performance Computing (HPC) environments and R/Bioconductor analytical frameworks.

Teaching Assistant Oct 2022 – Dec 2022
Department of Microbiology, Jagannath University Dhaka, Bangladesh

  • Assisted in the delivery of research methodology training, focusing on experimental design and statistical power in public health microbiology.
  • Processed public health surveillance data to support departmental research on emerging epidemiological trends.

Community Engagement

Nextflow Ambassador 2025 – Present
Seqera Barcelona, Spain

  • Advocated for the adoption of Nextflow-based DSL2 pipelines to ensure reproducibility and scalability in high-throughput single-cell and bulk RNA-seq workflows.
  • Engineered technical tutorials and documentation for the deployment of portable scientific containers (Docker/Singularity) in cloud and HPC environments.
  • Facilitated technical workshops on workflow orchestration, training researchers to manage complex multi-omic datasets with high analytical rigor.

GBD Senior Collaborator 2025 – Present
Institute for Health Metrics and Evaluation Washington, USA

  • Contributed advanced statistical modeling and analytical validation to Global Burden of Disease (GBD) studies published in high-impact journals like The Lancet.
  • Synthesized and audited complex epidemiological datasets from 190+ countries to strengthen the robustness of global health genomic evidence.

Publications

Note: * indicates corresponding author

  1. Fariha, F. T. J., Fuad, M., Saha, C. S., Hossen, S., & Hossain, M. J.* (2025). Comprehensive bioinformatics analysis reveals prognostic significance and immunological roles of WNT gene family in breast cancer. Sci Rep 15, 34490. https://doi.org/10.1038/s41598-025-13315-6

  2. Ahmed, M. Z., Billah, M. M., Ferdous, J., & Hossain, M. J.* (2025). Pan-cancer analysis reveals immunological and prognostic significance of CCT5 in human tumors. Scientific Reports, 15, 14405. https://doi.org/10.1038/s41598-025-88339-z

  3. Bari, S.M., Fuad, M., Hossain, M.J. et al. (2025). A meta-analysis of public RNA-Seq data identifies conserved stress responses in rainbow trout. BMC Genomics 26, 999. https://doi.org/10.1186/s12864-025-12127-2

  4. Shanta, A. S., Islam, N., Al Asad, M., Akter, K., Habib, M. B., Hossain, M. J., Nahar, S., Godman, B., & Islam, S. (2024). Resistance and co-resistance of metallo-beta-lactamase genes in diarrheal and urinary-tract pathogens in Bangladesh. Microorganisms, 12(8), 1589. https://doi.org/10.3390/microorganisms12081589

  5. GBD 2023 Vaccine Coverage Collaborators (Hossain, M. J., 2025). Global, regional, and national trends in routine childhood vaccination coverage from 1980 to 2023 with forecasts to 2030. The Lancet. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(25)01037-2/

  6. GBD 2023 Headache Collaborators (Hossain, M. J., 2025). Global, regional, and national burden of headache disorders, 1990–2023. Lancet Neurology. https://www.thelancet.com/journals/laneur/article/PIIS1474-4422(25)00402-8/fulltext

  7. Hossain, M. J.*, Das, M., Shahjahan, M., Islam, M. W., & Towhid, S. T. (2025). Clinical and hematological manifestation of dengue patients in 2022 outbreak. Health Science Reports, 8, e70356. https://doi.org/10.1002/hsr2.70356

  8. Das, M., & Hossain, M. J.* (2025). Young stroke in Bangladesh: Addressing rare cases with diagnostic challenges. Stroke and Vascular Neurology. https://svn.bmj.com/content/early/2025/04/07/svn-2025-004178

  9. Hossain, M. J.*, Sony, S. A., Fariha, F. T. J., & Hossen, S. (2025). Preventing the silent threat: A perspective on preparing Bangladesh for Human Metapneumovirus (HMPV). Health Science Reports, 8, e71101. https://doi.org/10.1002/hsr2.71101

  10. Hossain, M. J.*, Das, M., & Munni, U. R. (2024). Urgent call for compulsory premarital screening: A crucial step towards thalassemia prevention in Bangladesh. Orphanet Journal of Rare Diseases, 19, 326. https://doi.org/10.1186/s13023-024-03344-1

  11. Islam, M. W., Shahjahan, M., Azad, A. K., & Hossain, M. J.* (2024). Factors contributing to antibiotic misuse among parents of school-going children in Dhaka City, Bangladesh. Scientific Reports, 14, 2318. https://doi.org/10.1038/s41598-024-52313-y

  12. Hossain, M. J.*, Das, M., Islam, M. W., Shahjahan, M., & Ferdous, J. (2024). Community engagement and social participation in dengue prevention. Health Science Reports, 7, e2022. https://doi.org/10.1002/hsr2.2022

  13. Hossain, M. J.*, Azad, A. K., Shahid, M. S. B., Shahjahan, M., & Ferdous, J. (2024). Prevalence, antibiotic resistance pattern for bacteriuria from patients with urinary tract infections. Health Science Reports, 7, e2039. https://doi.org/10.1002/hsr2.2039

  14. Akter, M. M., & Hossain, M. J.* (2024). Food consumption patterns and sedentary behaviors among university students. Health Science Reports, 7, e70259. https://doi.org/10.1002/hsr2.70259

  15. Hossain, M. J.*, Islam, M. W., Munni, U. R., et al. (2023). Health-related quality of life among thalassemia patients in Bangladesh using the SF-36 questionnaire. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-34205-9

  16. Towhid, S.T., Hossain, M. J., Sammo, M.A.S., & Akter, S. (2022). Perception of Students on Antibiotic Resistance and Prevention. European Journal of Biology and Biotechnology. https://doi.org/10.24018/ejbio.2022.3.3.341

  17. Hossain, M. J., Towhid, S.T., Sultana, S., Mukta, S.A., Gulshan, R., Miah, M.S. Knowledge and Attitudes towards Thalassemia among Public University Students in Bangladesh. Microbial Bioactives, 5(2). https://doi.org/10.25163/microbbioacts.526325

Papers Under Review

  1. Islam, M. W., Rahman, M. M., Naznin, H., Hossain, M. S., Akter, T., Shatabde, Z. A., & Hossain, M. J.* (2025). Integrative bioinformatics analysis reveals COL13A1 and COL23A1 as potential diagnostic and prognostic biomarkers in thyroid cancer. [Submitted to Health Science Reports].

  2. Islam, M. W., Fariha, F. T. J., Ahmed, M. Z., Ferdous, J., et al. & Hossain, M. J.* (2025). Bioinformatics-driven multi-omics profiling of CDK1 and CDK6 identifies prognostic and therapeutic roles in breast cancer. [Under Review in Health Science Reports].

  3. Billah, M. M., Mabsurah, K., Ahammad, K., et al. & Hossain, M. J.* (2025). Multi-omics pan-cancer analysis reveals an immunological role and prognostic potential of WDR76. [Under Review in Discover Oncology].

  4. Sony, S. A., Kundu, L. R., Limon, M. H., et al. & Hossain, M. J.* (2025). Predicting early antenatal care initiation at the first trimester among reproductive women in Bangladesh using machine learning. [Under Review in BMC Pregnancy and Childbirth].

  5. Hossain, M. J.*, Shahariar, M., Barsha, L.H.J., et al. (2024). Lack of knowledge and training about antibiotic resistance among community pharmacists in Bangladesh. [Under Review in Health Science Reports].

Working Papers

  1. Fezf2-Mediated Cortical Development: Multi-Omics Analysis. Integrative analysis of bulk and single-cell RNA-Seq data to elucidate Fezf2’s role in cortical neurogenesis. Tech: Python, Seurat, Scanpy, DESeq2. GitHub

  2. Single-Cell Meta-Analysis of Microglial Activation in Alzheimer’s Disease. Meta-analysis of single-cell RNA-Seq datasets to identify microglial states and activation patterns. Tech: Python, Scanpy, R/Seurat, Harmony, scVI-tools. GitHub

  3. Integrative Spatial-scRNA-seq Atlas of Immunotherapy Resistance Mechanisms Across Cancer Types. Comprehensive spatial transcriptomics and single-cell analysis to map tumor microenvironment and resistance mechanisms. Tech: Python, Scanpy, Seurat, Squidpy, SpatialData, scVI-tools. GitHub

Conference Presentations

Poster Presentations

  1. Hossain, M. J., Das, M. (2024). Diagnostic and Electrophysiological Features of Hirayama Disease in Young Adult Male: A Case Report. International Conference of Public Health, IEDCR, Dhaka, Bangladesh.

  2. Das, M., Kajol, M. M., Mim, N. A., et al. & Hossain, M. J. (2024). Level of knowledge regarding breast cancer and breast self-examination among school and college-going girls in Bangladesh. International Conference of Public Health, IEDCR, Dhaka, Bangladesh.

  3. Shahariar, M., Joarder Barsha, L. H., Shahjahan, M., et al. & Hossain, M. J. (2024). Lack of knowledge and training about antibiotic resistance among community pharmacists in Bangladesh. International Conference of Public Health, IEDCR, Dhaka, Bangladesh.

  4. Afrin, N., Howlader, G., Bhattacharjee, A., et al. & Hossain, M. J. (2024). Influence of Meteorological Factors on Dengue Incidence: A 23-Year Retrospective Analysis in Bangladesh. International Conference of Public Health, IEDCR, Dhaka, Bangladesh.

  5. Akter, N., Mim, N. A., & Hossain, M. J. (2024). Particulate Matter PM2.5 Pollution and Air Quality Index Trends Evaluation with Meteorological Factors in Dhaka City. International Conference of Public Health, IEDCR, Dhaka, Bangladesh.

Oral Presentations

  1. Tuhin, M. A. A., Mim, N. A., Akter, N., et al. & Hossain, M. J. (2024). Exploring the Factors Influencing Heat Stress Risks Using the Discomfort Index Method in Bangladesh. ICESRM 2024, Mawlana Bhashani Science and Technology University, Bangladesh.

  2. Mim, N. A., Akter, Tuhin, M. A. A., et al. & Hossain, M. J. (2024). Temporal Trends and Factors Influencing Diarrhea Prevalence Among Children in the Rangamati Hill Tract Region. ICESRM 2024, Mawlana Bhashani Science and Technology University, Bangladesh.

  3. Nayeem, M. U., Mrittika, M. A., Hossain, M. J., et al. (2023). Quantitative Microbial Risk Assessment from Vancomycin-Resistant Enterococcus. 36th Bangladesh Society of Microbiologists Annual Conference, SUST, Sylhet, Bangladesh.

  4. Hossain, M. J., Habiba, U., Rozario, C., et al. (2023). Factors influencing heat stress risk in Bangladesh. 9th International Public Health Conference, BMRC, Bangladesh.

  5. Hossain, M. J., Nowshin, N., Momtaj, et al. (2023). Monitoring Water-Borne Disease (Vibrio cholerae) using NASA Earth observation data. 9th International Public Health Conference, BMRC, Bangladesh.

Invited Talks

  1. Computational Biology and Bioinformatics Research in Resource-Limited Settings: Strategies, Tools and Opportunities (2025). Speaker, Jagannath University Higher Study and Research Society.
  2. Mastering Biomedical Data Management (2024). Speaker, IFMSA Bangladesh, Dhaka, Bangladesh.
  3. Undergraduate Research - Importance, Benefits, and Challenges (2022). Speaker, CHIRAL Bangladesh, Dhaka, Bangladesh.
  4. State the Art of Microbial Genome Analysis (2022). Speaker, Jagannath University, Dhaka, Bangladesh.

Research Mentoring

Bulk RNA-Seq Meta-Analysis of Liver, Kidney, Pancreatic, and Gastrointestinal Cancers for Biomarker and Immune Signature Discovery (July 2025 – present)

  • Rahnuma Tabassum (Biochemistry & Molecular Biology, Jagannath University) – Liver Cancer
  • Fayez Ahmad (Notre Dame College) – Esophageal Cancer
  • Sabbir Khan (Doctor of Veterinary Medicine, Gazipur Agricultural University) – Kidney Cancer
  • Md Shakil Ahamed (Biotechnology & Genetic Engineering, Mawlana Bhashani Science & Technology University) – Colon Cancer
  • Lamisa Manha Aditee (Biotechnology, BRAC University) – Pancreatic Cancer

Bioinformatics Workflows

  1. Bulk RNA-Seq Meta-Analysis Pipeline. Nextflow-based pipeline for meta-analysis of public RNA-Seq data with automated QC and differential expression. Tech: Nextflow, nf-core, Python, R/Bioconductor, Docker. GitHub

  2. Single-Cell Meta-Analysis Pipeline. Pipeline for single-cell RNA-Seq integration, cell type annotation, and batch correction. Tech: Python, Scanpy, R/Seurat, Harmony, scVI-tools. GitHub

  3. Salmon RNA-Seq Quantification Pipeline. End-to-end pipeline for ultra-fast transcript quantification and quality assessment. Tech: Salmon, FastQC, MultiQC, R/Bioconductor. GitHub

  4. Biomarker Identification using Machine Learning. ML framework for biomarker discovery with feature selection and model interpretability. Tech: Python, Scikit-learn, XGBoost, SHAP. GitHub

  5. GEO Differential Expression & ML Dataset Prep. Automated GEO data retrieval, differential expression analysis, and ML dataset generation. Tech: R/Bioconductor, Python, GEOquery, limma, DESeq2. GitHub

  6. 16S rRNA Microbiome Analysis Pipeline. Comprehensive microbiome pipeline combining QIIME 2 and DADA2 for taxonomic profiling. Tech: QIIME 2, R/DADA2, Phyloseq, VSEARCH. GitHub

  7. 16S-OHJU Pipeline. Bioinformatics pipeline for processing and analyzing 16S rRNA gene sequencing data from microbial community studies. Tech: QIIME 2, Python, R, FastQC, MultiQC, Cutadapt. GitHub

  8. Shotgun Metagenomics Pipeline. Comprehensive automated pipeline for shotgun metagenomic analysis from raw reads through metagenome-assembled genomes (MAGs). Tech: Kraken2, MetaPhlAn4, HUMAnN3, MEGAHIT, metaSPAdes, MetaBAT2, CheckM. GitHub

GenAI Projects

  1. DeepTrust AI (Prototype). AI-powered tool to detect and counter health misinformation with NLP and credibility scoring features. Tech: Python, NLP, Transformers, FastAPI, Streamlit. Demo

  2. GenMed AI (Prototype). AI-driven platform accelerating drug discovery through disease data analysis, protein target identification, and therapeutic compound generation. Tech: Python, BioPython, RDKit, DeepChem, Transformers, PyTorch. Demo

Media Coverage

  1. Parental lack of antibiotic knowledge imperils child health in Bangladesh: Study. The Business Standard (TBS), 2024.
  2. What the rise in self-medication tells us about the country’’s healthcare system. The Business Standard (TBS), 2024.

References

References available upon request.