Nasir Mahmood Abbasi, PhD

Cancer Bioinformatician

Deciphering Sézary syndrome heterogeneity through bioinformatics approaches and single-cell genomics

PhD in Cancer Biology (defended June 23, 2026). Currently finalizing manuscript preparation and bioinformatics analyses on Sézary syndrome heterogeneity, and completing a fixed-term research contract at Bordeaux University through September 1, 2026. With more than 9 years of experience in OMICS data analysis, I specialize in developing and implementing bioinformatics tools, databases, and reproducible workflows for genomic data analysis.

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About

I am a bioinformatician with over 9 years of experience in OMICS data analysis, including bacterial genomics, metagenomics, transcriptomics, metatranscriptomics, amplicon sequencing, and single-cell analysis. I have worked extensively with Pacbio-hifi and nanopore sequencing technologies, and have experience managing HPC clusters and Galaxy servers. I recently completed my PhD in Cancer Biology at Bordeaux University (defended June 23, 2026), where I focused on deciphering Sézary syndrome heterogeneity using bioinformatics approaches. My major objectives are to analyze, develop, and implement bioinformatics tools, databases, and methods for genomic data analysis.

Research Focus

Sézary Syndrome Heterogeneity

Investigating tumor heterogeneity in Sézary syndrome using advanced bioinformatics approaches, including analysis of whole exome sequencing (WES) data, single-cell RNA sequencing, and BioNano optical mapping data.

Single-Cell Transcriptomics

Advanced single-cell RNA sequencing analysis and tumor heterogeneity characterization using state-of-the-art computational methods and quality control workflows.

WES and BioNano Analysis

Comprehensive analysis of whole exome sequencing and BioNano optical mapping data for variant identification and structural variation detection in patient genomic data.

Reproducible HPC Workflows

Development of reproducible, scalable bioinformatics workflows using containerization (Docker, Singularity), workflow management systems (Snakemake), and HPC cluster administration.

Experience

2023–2026

PhD Researcher

Bordeaux University, France

  • Research focus on deciphering Sézary syndrome heterogeneity using bioinformatics approaches
  • Analysis of whole exome sequencing (WES) data, single-cell RNA sequencing data, and BioNano optical mapping data
  • Advanced single-cell transcriptomics and tumor heterogeneity characterization
  • Thesis defended June 23, 2026; currently finalizing manuscript preparation through September 1, 2026
2022–2023

Research Engineer

IRBI Insect Biology Research Institute, France

  • HPC clusters management and data analysis (RnaSeq, Pacbio, Nanopore)
  • Performed analysis of pacbio-hifi data from ovaries of Cotesia congregata wasps
2020–2021

Research Engineer

INRAE, National Institute of Agriculture, France

  • Small RNA-seq data analysis for Brachypodium, Maize, and Wheat (siRNA and miRNA)
  • Benchmarking of bioinformatics tools for siRNA and miRNA to improve plant stress resistance
2019–2020

Research Engineer

INRAE, National Institute of Agriculture, France

  • Galaxy administration, transcriptomics data analysis, amplicon and metatranscriptomics analysis
  • Analysis of drug effects on animals using metatranscriptomics data
2017–2018

Research Assistant

Hong Kong University of Science and Technology (HKUST), Hong Kong

  • Cancer genomics data analysis, web maintenance, and data management using Synology
  • Benchmarking of tools for exome and whole genome sequencing analysis for variant identification
2017

Instructor of Bioinformatics

Virtual University of Pakistan

  • Taught courses in bioinformatics and assisted with laboratory experiments
  • Provided bioinformatics data analysis support on Unix systems
2015–2016

Research Engineer

University Miguel Hernández de Elche, Spain

  • Web development, data management, and analysis of marine prokaryotic genomes
  • Studied differences between Bacteroides species from different environments
2013–2014

Research Assistant

Evolutionary Biology Centre, Sweden

  • Genetic and epigenetic consequences of personality and social rank
  • MATLAB analysis of data
2013

Research Engineer

Karolinska Hospital, Sweden

  • Bioinformatics analysis of bacterial genomes (Capnocytophaga)
  • Studied newly characterized Capnocytophaga species and discovered Capnocytophaga stomatitis
2009–2010

Research Assistant

COMSATS University, Pakistan

  • Wet lab experiments and bioinformatics analysis (exome sequencing data)
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Skills

Programming Languages

R Unix/Linux Python Perl PHP SQL C/C++ JavaScript

Single-Cell Analysis

Seurat Scanpy SingleCellExperiment DoubletFinder Scrublet SCTransform Harmony PAGA Slingshot Monocle3 Velocyto scVelo

Differential Expression & Annotation

LIBRA DESeq2 edgeR MAST Wilcoxon Azimuth SingleR scType

Visualization & Analysis

ggplot2 ComplexHeatmap SCpubr Nebulosa dittoSeq inferCNV SCENIC GENIE3 DoRothEA LIANA CellChat

Systems & HPC

Unix/Linux HPC Clusters (Slurm) Galaxy Administration Docker Singularity Conda Snakemake Git/GitHub Cloud Computing

Genomics & Sequencing

Whole Genome Sequencing (WGS) Whole Exome Sequencing (WES) Transcriptomics Metatranscriptomics Amplicon Sequencing Metagenomics Small RNA-seq Pacbio-hifi Nanopore Phylogenetics

Databases & Markup

MySQL Oracle Microsoft Access HTML CSS

Publications

Zajitschek, S., James E. Herbert-Read, Abbasi N, Immler. Paternal personality and social status influence offspring personality in offsprings. BMC Evolutionary Biology (2017) 17:157

Zangenah S, Abbasi N, Anders F A, Bergman P. Whole Genome Sequencing Reveals Novel Species of genus Capnocytophaga isolated from dog and cat bite wounds in humans. Scientific Reports (2016)

Ajmal M, Khan M, Neveling K, Tayyab A, Jaffar S, Sadeque A, Ayub H, Abbasi N, Riaz M, Micheal S, Gilissen C, Ali S, Azam M, Collin R, Cremers F, Qamar R. Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome. Molecular Vision (2013)

Conferences & Seminars

  • The Mathematics of Deep Learning, Hong Kong
  • The Hong Kong Epigenomics Project, Hong Kong
  • GDEC-Bioinfo-Workshop #2 - Tidyverse / R-Markdown for Genomics, France
  • Flash Talk and Poster Presentation - SBM Day, France (September 2024 & 2025)
  • Poster Presentation - Doctoral School Day 2025, France
View full research profile on ORCID →

Education

2023–2026

PhD in Cancer Biology

Bordeaux University, France

(Thesis defended June 23, 2026)

2010–2012

Master of Science: Bioinformatics

Sweden

Projects

Sézary Syndrome Heterogeneity

Current PhD project: Deciphering Sézary syndrome heterogeneity using bioinformatics approaches, including WES data, single-cell RNA data, and BioNano optical mapping data.

Adaptive Evolution in Birds

Research-based project on adaptive evolution in birds using genomic and evolutionary analysis methods.

Rough Set-Based HIV-1 Model

Machine learning project on Rough Set-based model of HIV-1 using Dmlab for Monte Carlo feature selection and Rosetta.

Laboratory Information Management System

Web development project (Drug Assistant) in laboratory information management system using PHP and MySQL.

Spironucleus Genome Composition

Base composition analyses in the Spironucleus salmonicidi genome using Linux, Perl, R, and GC tools.

Eye Gene Regulatory Regions

Analysis of regulatory regions of genes expressed in the eye in collaboration with Dr. Mehmood Ahmed Kayani and Dr. Ansar.

Contact

Open to postdoctoral and research opportunities from September 2026 onward. I am interested in collaborations in cancer bioinformatics and single-cell genomics. Feel free to reach out to discuss research opportunities, collaborations, or inquiries.

Location: Bordeaux, France

Email: nmabbasi@gmail.com

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