Computational biology · Genomics · Dhaka, Bangladesh

Md Naiem Hossain

Research Officer at icddr,b. I turn sequencing data into answers about how pathogens adapt and how tumours evolve — from Vibrio cholerae and its phages to bladder cancer and glioma.

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Peer-reviewed papers
5
Under review or submitted
2
Manuscripts in preparation
3
Phage genomes assembled
36

01

About

I work in Dr. Firdausi Qadri's group at icddr,b, where I build the genomic, metagenomic and transcriptomic analyses behind our cholera research: how short-term azithromycin reshapes the gut microbiome and resistome of household contacts, how V. cholerae O1 adapts to different niches in the human gut, and how ICP1 vibriophages and their hosts co-evolve.

Before that I trained in cancer genomics at the University of Dhaka. My MSc thesis combined targeted next-generation sequencing with molecular dynamics to characterise somatic mutations in Bangladeshi bladder cancer patients, and I went on to compare the mutational landscape of hypoxia-defined subtypes of IDH-mutant glioma.

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.

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

02

Research experience

Research Officer

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

Principal Investigator: Dr. Firdausi Qadri

02/2024 — Present
Dhaka, Bangladesh

Metagenomics

Azithromycin prophylaxis in child contacts of cholera patients: a randomized controlled trial

Built a Bash and R pipeline to measure gut microbial relative abundance and diversity and to identify differentially abundant species with LEfSe in longitudinal metagenomes.

Transcriptomics

Diversity of Vibrio cholerae O1 through the human gastrointestinal tract during cholera

Analyzed V. cholerae transcriptomics across clinical samples using differential expression, KEGG pathway enrichment, and virulence gene mapping to pathogenicity islands.

Phage genomics

Specificity and host ranges of Vibrio cholerae O1 phages isolated in 2024

Assembled 36 ICP1 vibriophage genomes and screened CRISPR-Cas and anti-defense loci against host PLE and ICE genotypes to trace phage–host co-evolution.

Diagnostics

Analytical and machine learning–assisted evaluation of five commercial cholera rapid diagnostic tests

Evaluated endpoint PCR, LSHTM qPCR, and Bioperfectus qPCR for rfb and ctxA gene detection, using Cohen's kappa to quantify inter-assay agreement.

Research Assistant

System Cell Signaling Laboratory, University of Dhaka

Principal Investigator: Dr. Sajib Chakraborty

11/2023 — 01/2024
Dhaka, Bangladesh

Cancer genomics

Spatially restricted niches support hypoxia-associated transcriptional plasticity contributing to IDH-mutant glioma progression

Compared somatic mutations and tumor mutational burden (TMB) between severe and mild hypoxia-defined IDH-mutant glioma subtypes to assess genomic differences.

Graduate Research Assistant

Nutrition Genes and Human Disease Laboratory, University of Dhaka

Principal Investigator: Dr. Yearul Kabir

11/2022 — 10/2023
Dhaka, Bangladesh

MSc thesis

Targeted next-generation sequencing and molecular dynamics approaches to characterize somatic mutations in Bangladeshi bladder cancer patients

Developed an NGS variant-calling pipeline to identify functionally relevant somatic mutations and analyzed RNA-seq data to define molecular subtypes and how they shape the tumor microenvironment.

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 and expertise

Computational biology & bioinformatics

Programming
RPythonBash
Genomics
FastQCGATK Mutect2ANNOVARmaftools
Microbial genomics
ProkkaRoarySnippyUnicycler
Microbiome
Kraken2 / BrackenKrakenToolsphyloseqLEfSe
Transcriptomics & single-cell
limmaDESeq2GSEAGSVACell RangerSeuratinferCNVCellChatvelocytoSingleR
Molecular modeling
AutoDock VinaGROMACSChimeraX

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

Training, awards and teaching

  • Workshop

    Bacterial Genomics and Antimicrobial Resistance Workshop

    Child Health Research Foundation (CHRF), Dhaka

    11/2023

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

  • Workshop

    CompBio Bangladesh 2023 Workshop

    Khulna University of Engineering & Technology (KUET), Khulna

    02/2023

    Completed 15 days of introductory training analyzing public WGS (SRA) datasets in Linux and RNA-seq (GEO) datasets in R, with protein structure prediction and molecular dynamics simulations.

  • Award

    Travel and accommodation award, CompBio Bangladesh 2023 Workshop

    KUET

    02/2023

    Competitively selected for funded travel and accommodation to attend the workshop.

  • Teaching

    Academic Tutor

    Projjoy Coaching Center, Dhaka

    06/2020 — 05/2022

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

06

Let's talk about research.

I'm always glad to hear about collaborations and opportunities in genomics, microbiome science and computational biology.

naiem2217@gmail.com