Experience

Research Experience

From 2024-on-ongong:

I am taking training from different labs and gained expertise on RNA sequence data analysis, western blotting, cell culture, and advanced microscopy such as fluorescent and confocal microscopy. I contributed to a craniofacial research project in Fenglei’s lab during my second semester of master’s at Tulane university where I analyzed single-cell RNA seq data. I also learned dissection, cryosection, using fluorescent and confocal microscopes, histopathology, immunostaining, and in situ hybridization. I also worked in the Wang lab for preparing research protocol for Myalgic encephalomyelitis by long covid and performed one project to test the function of extracellular vehicles (EVs) in TGF-β2-induced epithelial-mesenchymal transition (EMT) and fibrosis in ARPE-19 cells.

From 2022-2024 August:

I have developed an advanced molecular lab in the peripheral region of Bangladesh to observe antibiotic-resistant bacteria, pathogenic bacteria, and viruses from human samples such as urine, blood, feces, high vaginal swab, pus, and other samples using aerobic and anaerobic culture media. I used PCR, RT-PCR, and ELISA for the detection of pathogenic bacteria. In addition, I have mentored one student for his Master Thesis

Research project: Determinants of premature rupture of membrane (PROM) in Kishoreganj, Bangladesh: A prospective case control study. I led the project as a CO-PI and head of the research team.

From 2021-2022:

During COVID-19, I have developed molecular biology labs (5 national labs), trained others, and performed laboratory experiments, including for SARS-CoV-2 viral RNA extraction, RT-PCR, whole genome sequencing, ELISA, result interpretation, and Publication. During this time, I also worked on different research project with collaboration with KTH Royal Institute (Professor Prosun Bhattacharya), North South University (Professor Hasan Mahmud Reza, Professor Dr. Jakariya), Nottingham University (Dr. Muhammad Maqsud Hossain), Jessore Science and Technology University (Professor Iqbal Kabir Zahid).

Research project: Whole genome sequence of SARS-COV-2 from the area of the southern part of Bangladesh to observe the mutational

changes; Wastewater-based surveillance of the SARS-CoV-2 to predict early signals and monitor ongoing status.

From 2017-2021:

Research project: Identification of pathogenic and multidrug-resistant bacteria from different sources, including Poultry, Cow milk, and environmental sources, using PCR and RT-PCR-Funded by NSTU Research Cell; Identification of the effects of different drugs on obesity in Mice models. I performed bacteria identification using conventional ways such as Biochemistry, Microscopy, Antibiotic resistant pattern, PCR, RT-PCR, and ELISA. I learnt mouse model handling, dissection, extraction of blood, and performing different assay from mice blood after injecting different drugs to observe gene expression.

Teaching Experience

From 2025-on-ongong:

I am doing graduate teaching assistant with Dr. Christian Burr-Professor of Practice, Tulane University for. Here, I take undergraduate students CELL 4225 or 6225 Microbiology Lab class, mark their lab report, and prepare guidelines for midterm exam.

From 2024 ,Aug- -2024 Dec:

I performed a role as a graduate teaching assistant with Dr. Manjong Han-Senior Professor of Practice, Tulane University. I took undergraduate and graduate students CELL 1035 Heredity and Society Lab class, mark their lab report, and prepare guidelines for midterm exam.

From 2021 Aug-2024 Aug:

I was lecturer at Microbiology Department, President Abdul Hamid Medical College, Kishoreganj, Bangladesh. and taking lectures, final exams, tutorials, and laboratory sessions for medical students are my primary duties. One of the common responsibilities in my medical college is marking assignments and other evaluations. I tried to make the classroom attractive and friendly to the students. I am highly punctual and constantly maintain a timetable for taking classes and exams.

From 2017-2021: I helped Professor Firoz Ahmed departmental chair of the NSTU Microbiology to prepare notes, sheets, and questions for students. I also helped to take laboratory and academic classes. During this time, I also assisted Professor Dr. Jakariya, North South University with his teaching to make students question and presentation slides remotely.

Professional Experience

Aug 2024-2025 Graduate Teaching Assistant: Cell and Molecular Biology, Tulane University, USA

Aug 2021- 2024 Lecturer, Lab Incharge & Head: President Abdul Hamid Medical College, Bangladesh

Aug 2021-2024 Member, Institutional Review Board, President Abdul Hamid Medical College, Bangladesh

July 2020-July 2021 Research Assistant: Genome Center, Jessore University of Science & Technology, Bangladesh

Oct 2020-Dec 2020 Research Assistant and Trainer: Gonoshasthaya-Molecular Diagnostic Center, Bangladesh

April 2020-May 2020 Trainer: Dept. of Microbiology, Cumilla Medical College, Cumilla, Bangladesh

May 2020 Lab In-Charge and Team Leader: NSTU COVID-19 Diagnostic Lab, Noakhali, Bangladesh

May 2019 Research Assistant: Red Green Research Center, Dhaka, Bangladesh

Research Training and Skills

Microbiology Techniques

Bacteria and virus-related experiences

Preparation of microbial media (differential and natural, modified for uncultured organisms) and reagents for bacterial identification using conventional biochemistry and molecular techniques.

Handling and culturing facultative and obligatory anaerobic bacteria using GasPak jars, anaerobic chambers, or candle jars.

Examined biofilm formation and quantification using crystal violet, confocal microscopy, and microtiter plate methods.

Researched bacterial growth and protein expression using UV-vis spectrophotometry, FTIR, TLC, and HPLC.

Identification and characterization of microorganisms or microbial communities using MALDI-TOF MS, microscopy, partial sequencing, whole-genome sequencing, and metagenomics.

Antimicrobial susceptibility testing using disk diffusion, E-test, MIC, and MBC

Detection of multidrug-resistant bacterial genes using PCR or WGS

Performed bioassays for antimicrobial activity using agar well diffusion, broth microdilution, and time-kill assay.

Isolation, characterization, and enrichment of bacteriophage, including plaque assay, and phage typing.

Analyzed phenotypic and genotypic typing of bacterial characters using PFGE, MLST, rep-PCR, RAPD, or VNTR.

Conducted transformation via electroporation and heat shock protocols.

Isolation/purification, and identification of bacterial plasmid DNA and any kind of pathogenic gene using PCR, qPCR, DNA/RNA, and sequencing.

Isolation and identification of viruses from human and other in-vivo samples.

Viral cell culture, maintenance, handling primary and continuous cell line, including TCID₅₀, hemagglutination assay (HA), or qPCR quantification of viral load.

Amplification and purification of adenovirus and lentivirus for in-viro and in-vitro work

Isolation, quantification, and identification of nucleic acids and proteins

Master in DNA, RNA, miRNA, protein extraction from in-vivo model or human samples using TRI- and kit-based protocols, without degrading samples.

Analyzed diverse human and bacterial gene expression using real-time qPCR via Taqman-based assay.

Detected specific targeted DNA sequences using Southern blots.

Isolated protein from transgenic mice, identified protein levels by Western blotting, and applied co-immunoprecipitation experiments.

Cloning

An expert in all steps performed for conditional knockout mice to observe blood vessel abnormalities.

Cell culture

Cultured cells in various cell lines, including ARP-19, HeLa, and MEFs.

Proficient in transfection using CaPO4 transfection, Lipofectamine treatment, cell counting, fluorescent microscopy, cell cloning, and cell proliferation assay.

Murine experiments

Managed the breeding and maintenance of several mouse colonies across multiple conditional knockout projects to efficiently generate desired genotypes and screen for phenotypes relevant to the study.

Performed genotyping, tail-clipping, and dissection to isolate specific organs and tissue for examination, and embryo isolation/dissection.

Fluorescence-Activated Cell Sorting (FACS) experiments

Examined cell cycle via Propidium Iodide staining.

Immunology

Performed Enzyme-antibody conjugation, sandwich ELISA, immunohistochemical staining, and isolation of murine immune cells, mixed lymphocyte reaction.

Histology

Performed cryosection, immunocytochemistry, cell proliferation assays (BrdU, EdU, Ki-67, etc.), Apoptosis Assays (TUNEL, Annexin V, etc.), Nissl, DAPI, HE, and Hoechst staining.

In-vivo pharmacological studies for plant-based natural products and other drugs.

Molecular Biology

Performed all the steps for plasmid preparation, ligation, and transformation.

Applied recombinant DNA techniques for several experiments.

cDNA synthesis using a kit, and analyzed gene expression using RT-PCR for RNA virus.

Used CRISPR-Cas gene editing to study bacterial or viral genomes for functional studies.

Designed Cre-loxp experiments and handled in-vivo mice for blood vessel formation.

Performed library prep for Next Generation Sequencing for Illumina, Nanopore, or PacBio platforms.

Plasmid mapping and cloning design by silico tools (e.g., SnapGene, Benchling) for cloning or expression vector construction.

Genomics, Bioinformatics & Proteomics

16S metagenomics and bioinformatics

Performed quality control, taxonomic classification, and diversity profiling using tools like QIIME2, MEGA, or Kraken, trimming & adapter removal (Trimmomatic), alignment (BWA), local Blast, assembly, SNPs calling, immunoinformatics (IEDB), and multi-omics integration.

Mutational and Phylogenetic Study

MEGA, FigTree, Unipro UGENE, Jalview, etc.

NGS Data Analysis (Genome Assembly, Annotation & Comparative Genomics)

Gene prediction & functional annotation: Conducted gene prediction and functional annotation of assembled genomes. Tools: Prokka, eggNOG.
Pan-genome construction & ortholog clustering: Built pan-genome profiles and performed ortholog clustering. Tools: Roary, BPGA, Analyzed gene presence/absence matrices and derived biological insights from core vs accessory genomes
Advanced pan-genome & comparative genomics: Downloaded and curated genome datasets for pan-genome workflows, Constructed core-genome phylogenetic trees and performed comparative genomics, Interpreted accessory genes: identified unique genes linked to specific functions, including AMR and virulence-associated factors
Functional enrichment, pathway & ontology analyses: Performed functional enrichment analysis for core and accessory genes, Conducted pathway analysis and gene ontology (GO) analysis
Specialized analyses: Detected CAZymes, Identified secondary metabolite gene clusters, Evaluated antimicrobial resistance (AMR) features

RNA-Seq Data Analysis

Data preparation & quality control: Worked with RNA-seq data formats: FASTQ, BAM, count matrices, Extracted datasets from public repositories: NCBI, GEO, SRA, Performed normalization for downstream analysis using: RPKM, TPM, TMM
Dimensionality reduction & visualization: Explored gene-expression patterns using PCA and clustering, Visualized sample relationships and expression structure across conditions, Differential expression & biological interpretation
Performed differential expression analysis using DESeq2: Identified significantly regulated genes and interpreted biological relevance, Clustered samples based on gene-expression profiles to assess separation and consistency
Differential expression result visualization: Generated and interpreted MA plots, volcano plots, and heatmaps, Highlighted significant genes for follow-up analysis using R libraries
Pathway enrichment & functional analysis: Conducted pathway and functional enrichment analyses to link gene changes to biology (e.g., cancer pathways, immune response), Tools/Databases: KEGG, Reactome, Enrichr, iLINCS
Protein–protein interaction (PPI) networks & hub gene analysis: Built PPI networks from differentially expressed genes and assessed key interactions. Tools: STRING (PPI network generation), Identified hub genes and functional modules using network properties (nodes/edges/centrality), Tools: Cytoscape (network clustering, hub gene identification, module visualization)

Protein Structure, Docking, and Molecular Simulation Study

Small Molecule Optimization by Gaussian, Molecular docking using different software, Protein optimization & Energy Minimization, Structure Analysis- Protein & ligand complex,
Molecular Dynamics Simulation and Explanation of different MD Parameters graph (RMSD, RMSF, Rg, SASA, No. of H-bond)

Computer, Programming, and Statistical

Familiar with Windows, Linux, and Mac operating systems

MS Office (Word, Excel, and PowerPoint), Adobe Photoshop, Sigma Plot, Chem Draw, and PubMed search,

Applied programming languages (R (RStudio), Python (2.7, 3.8))

Extracted secondary data from various sources and used SPSS, R, and Python libraries for analyzing, including meta-analysis, secondary meta-analysis, and statistical correlation.