Bioinformatician · Cancer omics · Dhaka, Bangladesh

Md Naiem Hossain

I use genomics and bulk and single-cell transcriptomics to understand how tumours evolve and how their microenvironment is rewired, in bladder cancer, glioma and head and neck cancer. Research Officer at icddr,b.

See the projects Email me
Peer-reviewed papers
5
Manuscripts in review or preparation
5
Cancer omics case studies below
3

01

About

My main interest is cancer omics: reading tumour genomes and transcriptomes to find the mutations and cell states that drive disease. My MSc thesis at the University of Dhaka combined targeted sequencing with molecular dynamics to characterise somatic mutations in Bangladeshi bladder cancer patients, and became a first-author paper in Urologic Oncology.

Since then I have compared the mutational landscape of hypoxia-defined IDH-mutant gliomas using TCGA genomes, and built a single-cell analysis of 54,239 cells that traces immune remodelling and T cell exhaustion across head and neck cancer progression.

As a Research Officer in Dr. Firdausi Qadri's group at icddr,b, I apply the same toolkit to infectious disease, with metagenomics, bacterial transcriptomics and phage genomics for cholera research. I am comfortable on both sides of the data: at the bench running PCR, sequencing and serology, and at the terminal writing pipelines in R, Python and Bash.

What I work on

A

Cancer genomics

Somatic variant calling, tumour mutational burden and mutational landscapes, with molecular dynamics to test what a mutation does.

B

Single-cell & tumour microenvironment

scRNA-seq annotation, cell–cell communication, trajectories and T cell exhaustion, plus bulk RNA-seq subtyping.

C

Microbial omics

Metagenomics, bacterial transcriptomics and phage genomics in Vibrio cholerae research at icddr,b.

02

Projects

Each project starts from a biological question. Every card gives the question, the data, how I analysed it, and what it showed.

Cancer genomics · MSc thesis

Somatic hotspot mutations in Bangladeshi bladder cancer

PublishedFirst author
Question
Which somatic mutations in Bangladeshi bladder cancer patients are functionally relevant, and how do molecular subtypes shape the tumour microenvironment?
Data
Targeted next-generation sequencing of patient tumours, plus RNA-seq data for subtyping.
Approach
  1. Targeted NGS reads
  2. Somatic variant calling
  3. Functional prioritisation
  4. Molecular dynamics
  5. RNA-seq subtyping
Outcome
Hotspot profiling surfaced a functionally relevant mutation, which I characterised with molecular dynamics. RNA-seq analysis defined molecular subtypes and how they shape the tumour microenvironment. Published in Urologic Oncology.
  • Variant-calling pipeline
  • Molecular dynamics
  • RNA-seq

Paper

Single-cell transcriptomics · Independent analysis of public data

Immune remodelling across head and neck cancer progression

Open code & report
Question
How does the immune microenvironment change from normal tissue to leukoplakia, primary tumour and lymph-node metastasis, and how does T cell exhaustion differ between HPV+ and HPV– tumours?
Data
Public scRNA-seq dataset GEO GSE181919: 54,239 cells from 37 specimens of 23 patients, across four disease stages.
Approach
  1. Seurat object
  2. QC & Harmony batch correction
  3. CellTypist annotation
  4. Microenvironment composition
  5. UCell exhaustion scoring
  6. Differential expression
  7. CellChat communication
  8. Monocle3 trajectory
Outcome
The tumour microenvironment shifts from stromal to immune: fibroblasts collapse while T cells expand between normal tissue and lymph-node metastasis. Cell–cell interactions triple from normal tissue to tumour, and TIGIT is the only checkpoint that rises steadily along the exhaustion trajectory, which makes it the clearest progressive target.
Fibroblast share, normal → metastasis
52% → 2%
T cell share, normal → metastasis
25% → 57%
Cell–cell interactions, normal → tumour
688 → 2,123
Exhaustion module score
2.44 → 7.42

Cancer genomics · University of Dhaka

Genomic differences between hypoxia-defined IDH-mutant glioma subtypes

Preprint · under review
Question
Do severe-hypoxia and mild-hypoxia IDH-mutant gliomas differ in their somatic mutations and tumour mutational burden?
Data
TCGA genomes of IDH-mutant lower-grade glioma, grouped by hypoxia subtype.
Approach
  1. Hypoxia-defined subtypes
  2. Somatic mutation comparison (maftools)
  3. Tumour mutational burden
Outcome
My genomic comparison is part of a collaborative study on hypoxia-associated transcriptional plasticity in IDH-mutant glioma, now a preprint under review at Neuro-Oncology.

Bacterial transcriptomics · icddr,b

Niche-specific gene expression of Vibrio cholerae O1 in stool and vomit

Manuscript in preparation
Question
How does V. cholerae O1 change its gene expression between the stool and vomit environments of cholera patients?
Data
V. cholerae transcriptomes from clinical stool and vomit samples.
Approach
  1. Pre-processing
  2. Differential expression (limma)
  3. PCA & heatmaps
  4. KEGG pathway enrichment
  5. Virulence genes mapped to pathogenicity islands
Outcome
A niche-by-niche view of differentially expressed genes, enriched pathways and virulence loci. The findings are being written up; the analysis code is public.
  • R
  • limma
  • clusterProfiler
  • ComplexHeatmap
  • vegan
  • rtracklayer

Code

Phage genomics · icddr,b

Phage–host co-evolution in Vibrio cholerae O1 and ICP1 vibriophages

Submitted
Question
What determines the specificity and host range of the V. cholerae O1 phages isolated in 2024?
Data
36 ICP1 vibriophage genomes and the genotypes of their V. cholerae O1 hosts.
Approach
  1. Genome assembly
  2. CRISPR-Cas & anti-defence loci screening
  3. Host PLE and ICE genotyping
  4. Phage–host comparison
Outcome
Assembled all 36 phage genomes and matched their counter-defence loci against host PLE and ICE genotypes to trace phage–host co-evolution. Submitted to Microbiology Spectrum.
  • Genome assembly
  • Comparative genomics
  • CRISPR-Cas

Shotgun metagenomics · icddr,b · Randomized controlled trial

Gut microbiome after azithromycin prophylaxis in child contacts of cholera patients

Manuscript in preparation
Question
How does short-term azithromycin prophylaxis change the gut microbiome of children living with a cholera patient, and do the changes last?
Data
Longitudinal gut metagenomes from a randomized controlled trial.
Approach
  1. Bash + R pipeline
  2. Relative abundance
  3. Diversity
  4. Differential abundance (LEfSe)
Outcome
A reusable pipeline that measures abundance and diversity over time and identifies differentially abundant species. Working title of the manuscript: “Short-term azithromycin use drives transient Enterobacteriaceae suppression and long-term resistome shifts in a cholera household contact cohort”.
  • Bash
  • R
  • LEfSe

Diagnostics evaluation · icddr,b

Agreement between PCR assays for cholera detection

Manuscript in preparationFirst author
Question
How well do endpoint PCR, LSHTM qPCR and Bioperfectus qPCR agree when detecting the V. cholerae genes rfb and ctxA?
Data
PCR and qPCR results from the CRaTE study, an evaluation of five commercial cholera rapid diagnostic tests.
Approach
  1. Assay results for rfb and ctxA
  2. Concordance analysis
  3. Cohen's kappa
  4. Agreement plots
Outcome
Inter-assay agreement quantified with Cohen's kappa across the three PCR methods. The results are being written up as a first-author manuscript; the analysis code is public.

More code, including a clear cell renal cell carcinoma single-cell atlas in progress, is on GitHub.

03

Publications

  1. PublishedFirst author

    Targeted hotspot profiling reveals a functionally relevant mutation in bladder cancer

    Hossain, M. N. et al.

    Urologic Oncology · doi:10.1016/j.urolonc.2025.08.013

  2. Published

    Rapid tests as a practical alternative to slide agglutination for the confirmation of V. cholerae O1

    Bhattacharjee, P., Hegde, S. T., Khan, A. I., Nabil, I. K., Hossain, M. N. et al.

    Journal of Clinical Microbiology · doi:10.1128/jcm.00433-25

  3. Published

    Open Diagnostic Reader (ODR): An affordable, modular, 3D-printed platform for standardized imaging and quantitative analysis of rapid diagnostic tests

    Rogers, E., Qin, Z., Bhuiyan, M. T. R., Khan, A. I., Islam, M. T., Bhattacharjee, P., Nabil, I. K., Hossain, M. N. et al.

    HardwareX 27, e00802 · doi:10.1016/j.ohx.2026.e00802

  4. Published

    Aldo-keto reductase family 1 member C3 (AKR1C3) gene polymorphism (rs12529) is associated with breast cancer in Bangladeshi population: a case-control study and computational investigation

    Shaon, M. A., Ansari, F., Mahmud, Z., Tamanna, S., Ibrahim, M. N. B., Alam, N. F., Hossain, M. N. et al.

    PLOS ONE · doi:10.1371/journal.pone.0318079

  5. Published

    Comparing the upregulations of helper T cell-specific activation-induced cell markers (AIM) among COVID-19 vaccinees in Bangladesh

    Karmakar, P. C., Kaisar, M. H., Sheikh, R., Islam, D., Tauheed, I., Ahmed, T., Khan, I. I., Akter, A., Khan, Z. H., Islam, M. T., Khanam, F., Hossain, M. N. et al.

    Scientific Reports · doi:10.1038/s41598-026-72698-2

  6. Preprint · under review

    Spatially confined niches support hypoxia-associated transcriptional plasticity contributing to malignant progression in IDH-mutant gliomas

    Das, D., Pandele, A., Jariwala, V. D., Ghariwala, N. S., Mohammed, A. O., Das, T., Krolla, C., Arosh, S. M., Hossain, M. N. et al.

    Preprint, under review at Neuro-Oncology · doi:10.64898/2026.05.31.729105

  7. Submitted

    Phage specificity across evolutionary lineages of V. cholerae O1 with distinct anti-phage defense system and resistance mechanisms

    Akhtar, M., Nafsi, N. N., Hossain, M. N. et al.

    Submitted to Microbiology Spectrum

  8. In preparation

    Transcriptomic insights into niche-specific adaptation of Vibrio cholerae across stool and vomit environments

    Rahman, S. I. A., Hossain, M. N. et al.

  9. In preparation

    Short-term azithromycin use drives transient Enterobacteriaceae suppression and long-term resistome shifts in a cholera household contact cohort

    Akhtar, M., Hossain, M. N. et al.

  10. In preparationFirst author

    Comparative performance and agreement of PCR-based diagnostic assays for cholera detection

    Hossain, M. N. et al.

Conference presentations

  • Oral presentation · 2025

    Targeted hotspot profiling reveals a functionally relevant mutation in bladder cancer

    Hossain, M. N. et al. 2nd RSG Bangladesh ComBio Symposium, ISCB RSG Bangladesh, Department of Biochemistry and Molecular Biology, University of Dhaka.

  • Poster · EANO 2025

    Hypoxia-driven EGFR signaling promotes a quiescent-activation axis in IDH-mutant low-grade gliomas

    Das, D., Jariwala, V. D., Pandele, A., Mohammed, A. O., Das, T., Ghariwala, N. S., Krolla, C., Arosh, S. M., Hossain, N. et al. Neuro-Oncology (2025).

04

Skills, tied to the work

Each group links to the projects where I used it.

Computational biology & bioinformatics

Programming
RPythonBash

Used in every project

Genomics
FastQCGATK Mutect2ANNOVARmaftools

Used in bladder cancer, glioma

Microbial genomics
ProkkaRoarySnippyUnicycler

Used in phage–host co-evolution

Microbiome
Kraken2 / BrackenKrakenToolsphyloseqLEfSe

Used in azithromycin and the gut microbiome

Transcriptomics & single-cell
limmaDESeq2GSEAGSVACell RangerSeuratinferCNVCellChatvelocytoSingleR

Used in V. cholerae transcriptomics, head and neck cancer atlas

Molecular modeling
AutoDock VinaGROMACSChimeraX

Used in bladder cancer

Statistics for diagnostics
Cohen's kappaConcordance analysis

Used in PCR assay agreement

Experimental & laboratory techniques

Molecular biology
DNA extraction (blood, tissue, microbial)PCRqPCRRestriction digestionGel electrophoresis
Genomics
Illumina sequencingIon Torrent AmpliSeq
Microbiology
Bacterial cultureAntimicrobial susceptibility testing
Immunology & serology
ELISALuminex multiplex assayVibriocidal assay
Phage biology
Plaque assayDye assay
Cell & antibody techniques
Hybridoma cultureMonoclonal antibody production
Analytical
TLC

05

Experience and education

Research

  1. Research Officer

    International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b)

    Principal Investigator: Dr. Firdausi Qadri

    Metagenomic, transcriptomic and phage-genomic analyses for cholera research, and evaluation of PCR diagnostics. Projects: gut microbiome, V. cholerae transcriptomics, phage genomics, PCR agreement.

    02/2024 — Present
    Dhaka, Bangladesh

  2. Research Assistant

    System Cell Signaling Laboratory, University of Dhaka

    Principal Investigator: Dr. Sajib Chakraborty

    Somatic mutation and tumour mutational burden comparison in hypoxia-defined IDH-mutant glioma. Project: glioma subtypes.

    11/2023 — 01/2024
    Dhaka, Bangladesh

  3. Graduate Research Assistant

    Nutrition Genes and Human Disease Laboratory, University of Dhaka

    Principal Investigator: Dr. Yearul Kabir

    MSc thesis on targeted next-generation sequencing and molecular dynamics of somatic mutations in Bangladeshi bladder cancer patients. Project: bladder cancer.

    11/2022 — 10/2023
    Dhaka, Bangladesh

Education

  1. Master of Science, Biochemistry and Molecular Biology

    University of Dhaka

    11/2022 — 12/2023

  2. Bachelor of Science, Biochemistry and Molecular Biology

    University of Dhaka

    01/2018 — 10/2022

Training, awards and teaching

  1. Bacterial Genomics and Antimicrobial Resistance Workshop

    Child Health Research Foundation (CHRF), Dhaka

    Read quality control, trimming and bacterial genome assembly from raw Illumina reads; genome annotation, AMR and plasmid detection, MLST typing, and SNP phylogenies.

    11/2023

  2. CompBio Bangladesh 2023 Workshop

    Khulna University of Engineering & Technology (KUET), Khulna

    15 days of training analysing public WGS (SRA) datasets in Linux and RNA-seq (GEO) datasets in R, with protein structure prediction and molecular dynamics simulations. Competitively selected for funded travel and accommodation.

    02/2023

  3. Academic Tutor

    Projjoy Coaching Center, Dhaka

    Taught biology and chemistry to 30 A-Level students, designing lessons and practice tests to monitor individual progress.

    06/2020 — 05/2022

06

Let's talk about research.

I'm glad to hear about collaborations and opportunities in cancer genomics, single-cell omics and computational biology. Email is the fastest way to reach me.

naiem2217@gmail.com