Dr. Rezwan
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Profile

Breakthrough in CMN Research

Image Credit: Sky News

Personal Snippet

Computational biologist specializing in translational bioinformatics within a dynamic 'lab in a loop' environment. Proficient in developing and integrating advanced bioinformatics pipelines, including multi-omics signature prediction (DNA/RNA), single-cell RNA sequencing (scRNA-seq), and spatial transcriptomics, to address complex biological questions. Experienced in genomic surveillance and rare disease research, with a current focus on studying congenital melanocytic nevus (CMN) patients with melanoma. Passionate about integrating multi-omics data to identify genetic drivers, biomarkers of treatment response, and pathways of resistance, contributing to precision oncology and the development of innovative therapies.

Journey

My journey into the world of genomics began with a curiosity: How do tiny repetitive sequences called microsatellites drive the evolution of viruses? This curiosity led me to explore microsatellites, or short tandem repeats, and their potential role in shaping viral evolution. I analyzed these patterns to understand how they influence genetic variability and adaptability in viruses.

As the COVID-19 pandemic unfolded, a new challenge emerged: How is SARS-CoV-2 evolving, what mutations drive these changes, and how do they influence clinical outcomes in different patient populations? To address this, I dedicated my Ph.D. research to investigating the genomic landscape of SARS-CoV-2, culminating in the publication of several papers. This work provided significant insights, including the identification of deleterious mutations linked to severe outcomes. Additionally, I constructed phylogeogenomic networks that revealed regional viral evolution patterns, shedding light on how the virus adapts and spreads across populations.

When my country faced the pandemic's challenges, I asked myself: how could I use my expertise to serve my country? Driven by a desire to contribute, I joined the Indian SARS-CoV-2 Genomic Consortium (INSACOG). Here, I analyzed large-scale viral genomes, delivering timely insights and identifying emerging variants like the BA.2.10.1 (link, first reported from India). My detailed reports and visualizations informed government policies, playing a crucial role in mitigating infection waves and preparing for future challenges.

Building on this experience, I expanded my work to the international stage by joining the NGS-BRICS consortium. Here, we tackled a critical question: can we detect emerging variants within hosts before they dominate populations? This challenge required a focus on intra-host variation (iSNV) analysis. Using high-depth NGS data, I developed automated workflows to identify minor variants with precision, enabling the early detection of emerging lineages and strengthening efforts to prevent community transmission.

Seeking to further expand the impact of these techniques, I turned my attention to clinical applications with a new goal: how can these approaches be adapted to improve patient care and advance biomedical research? During my postdoctoral fellowship at The Francis Crick Institute, I extended these workflows to identify mosaic variants in clinical samples. Using similar bioinformatics strategies—such as deep sequencing, sensitive variant detection algorithms, and error correction methods—I collaborated closely with wet lab scientists and clinicians. Together, we uncovered genomic complexities behind disease mechanisms, contributing valuable insights to precision medicine and patient outcomes.

Experience

Post Doctoral Experience

Research Fellow – Bioinformatics

The Francis Crick Institute and University College LondonFeb 2024 – Present

Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, Seconded from UCL Great Ormond Street Institute of Child Health (ICH), Genetics and Genomic Medicine (GGM) Department

  • Directed bioinformatics analysis and processing of genomic data for multiple high-impact lab projects, including large-scale datasets from Genomics England and UK Biobank, focusing on pediatric skin disorders and cancer predispositions.
  • Collaborated with clinicians and wet-lab scientists to identify novel genes, gene fusions, and variants, providing key insights into disease pathways and mechanisms.
  • Designed, developed, and optimized with clinicians and wet-lab scientists to identify novel genes, gene fusions, and variants, providing key insights into disease pathways and mechanisms.
  • Implemented machine learning techniques with clinicians and wet-lab scientists to identify novel genes, gene fusions, and variants, providing key insights into disease pathways and mechanisms.

Research Domain

Diseases:

COVID-19, Rare Diseases (e.g., Congenital Melanocytic Nevus), Cancer (e.g., Skin Cancer)

Core Domain:

Genomics, Molecular Evolution, Bioinformatics, Pathogen Surveillance, Artificial Intelligence (AI) in Multi-Omics Analysis

Extended Domain:

Proteomics, Molecular Dynamics, Computational Drug Discovery, Vaccine Design, and Genome-Scale Data Analysis

Technical Expertise

  • Programming & Scripting: Python | Bash | R
  • Local HPC System & Cloud: HPC (Slurm) | AWS
  • Workflow Management: Conda | Mamba | Snakemake | Nextflow
  • Containerization Installation: Docker | Singularity
  • Version Control: GitHub
  • Data Visualization: Tableau | PowerBI
  • Data & Image Analysis Libraries: Pandas | Numpy | Matplotlib | Seaborn | Fiji
  • Machine Learning Frameworks: Sklearn | PyTorch | TensorFlow

Domain-Specific Expertise

  • Next-Generation Sequencing (NGS) & Bioinformatics Data: Illumina | ONT
  • Genomic Databases: Genomics England | TCGA | UK-BioBank | GISAID | NCBI | RCSB | IEDB
  • Human Genomics: DNA & RNA | Somatic & Germline | Gene fusion | Variant calling (SNV, CNV, SV, Alternative Splicing, Mosaic variant) | Bulk RNA-seq | scRNA-seq (Seurat, Scanpy) | Spatial Transcriptomics (Xenium) | Hyperplex ICC
  • Microbial Genomics: Recombination Detection | Intra-Host Single Nucleotide Variation
  • Pipeline Development

Publications

Journal Articles

  1. Rezwanuzzaman Laskar, M. Hoque, and Safdar Ali. (2024), Phylogeogenomic analysis of the earliest reported sequences of SARS-CoV-2 from 161 countries. APMIS. https://doi.org/10.1111/apm.13499. IF: 2.2
  2. Animesh K Singh*, Rezwanuzzaman Laskar* et al. Contrasting Distribution of SARS-CoV-2 Lineages across Multiple Rounds of Pandemic Waves in West Bengal, the Gateway of East and North-East States of India. Microbiol Spectr. 2022;10(4):e0091422. doi:10.1128/spectrum.00914-22; PMCID: PMC9430150. IF: 9.043 *Equally contributed.
  3. Rezwanuzzaman Laskar, Md Gulam Jilani, Taslima Nasrin, Safdar Ali. Microsatellite Signature of Reference Genome Sequence of SARS-CoV-2 and 32 Species of Coronaviridae Family. Int J Infect. 2022;9(2):e122019. https://doi.org/10.5812/iji-122019.
  4. Rezwanuzzaman Laskar and Safdar Ali. Differential mutation profile of SARS-CoV-2 proteins across deceased and asymptomatic patients. Chem Biol Interact. 2021;347:109598. Published online 2021 Jul 23. doi:10.1016/j.cbi.2021.109598; PMCID: PMC8299203. IF: 5.168
  5. Rezwanuzzaman Laskar and Safdar Ali. Phylo-geo-network and haplogroup analysis of 611 novel coronavirus (SARS-CoV-2) genomes from India. Life Sci Alliance. 2021;4(5):e202000925. doi:10.26508/lsa.202000925. IF: 5.781
  6. Rezwanuzzaman Laskar and Safdar Ali. Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India. Gene. 2021;778:145470. doi:10.1016/j.gene.2021.145470. IF: 3.913
  7. Rezwanuzzaman Laskar, Md Gulam Jilani, Safdar Ali. Implications of genome simple sequence repeats signature in 98 Polyomaviridae species. 3 Biotech. 2021;11(1):35. doi:10.1007/s13205-020-02583-w. IF: 2.893

Conference Papers

  1. Md Gulam Jilani, Rezwanuzzaman Laskar and Safdar Ali (2020): Genome-wide scans for analysis of simple and imperfect microsatellites in diverse Lyssavirus. Abstract published in the Proceedings of International Conference on Innovations in Biotechnology and Life Sciences. AB-088. PP:128. ISBN: 978-93-88647-33-5; DOI: 10.6084/m9.figshare.13947833
  2. Rezwanuzzaman Laskar, Md Gulam Gilani and Safdar Ali (2020): Microsatellite Mining and Protein Dynamics of 43 Species of Alphapolyomavirus. Abstract published online in the International Conference on Drug Discovery organised by Schrodinger, USA and BITS Pilani, Hyderabad, 29th Feb – 2nd March 2020. Link
  3. Rezwanuzzaman Laskar, Md Gulam Gilani and Safdar Ali (2019): Microsatellite elicitation and investigation of 30 Betapolyomavirus: In-silico approach. Abstract published online in the Young Scientists’ Conference as a part of India International Science Festival – 2019 organised by DST, GoI and Vijnana Bharati, 5th – 8th November, 2019.
  4. Rezwanuzzaman Laskar and Safdar Ali (2018): In-silico Extraction and Analysis of Imperfect microsatellites Across 37 Species of Polyomaviridae. Abstract published in the abstract volume of 3rd Regional Science and Technology Congress, Southern region 18th and 19th December, 2018.
  5. N.C. Halder and Rezwanuzzaman Laskar (2017): Studies on Production of Nitrogen Fixing Cyanoprokaryota (BGA) starter Culture of Nostoc sp. In open and Laboratory Culture Condition. Full paper published in the proceedings of the UGC-Sponsored National Seminar on Mission Sustainability: Through Environmental Education, 1st - 2nd March in Dept. of B.Ed., Uluberia College, Uluberia, Howrah. ISBN: 978-81-928627-5-0.
  6. Rezwanuzzaman Laskar and N.C. Halder (2016): Biodiversity of Nitrogen fixing unicellular and filamentous Cyanobacteria in different rice fields of Howrah district in West Bengal, India. Abstract published in the abstract volume of the International Conference on ‘The Green Planet: Past, Present and Future’, 21st – 23rd December, 2016 in Dept. of Botany, University of Calcutta, Kolkata.

Projects

Exploring Microsatellites in Genomic Evolution

Microsatellites play a vital role in genomic evolution and adaptability. I explored their patterns across viral and host genomes, shedding light on how these simple sequences influence evolutionary dynamics of viruses.

Decoding SARS-CoV-2: Evolutionary Trajectories and Clinical Impacts

My work focused on understanding how SARS-CoV-2 evolved over time and its link to clinical outcomes. By analyzing mutations and their effects on disease progression and transmission, I contributed to uncovering genomic drivers that shaped the pandemic’s trajectory.

Intra-Host Variation: Identifying Early Signs of Viral Evolution

I investigated intra-host Single Nucleotide Variants (iSNVs) to detect early signs of variant emergence within individual hosts. Through high-depth sequencing, I developed workflows that identify these minor changes, offering a deeper understanding of how new variants arise.

Understanding the Molecular Basis of Rare Diseases

Rare diseases, like congenital melanocytic nevus (CMN), often lack clear genetic explanations. My research combines multi-omics data to identify key genetic drivers and pathways, offering insights that bring us closer to personalized treatments for these challenging conditions.

Resources

BioTools

For tools designed for biological data analysis and research, visit my GitHub repository below:

  • GitHub: Click here

    • Blog

    This page is currently under construction. Please check back soon for links to blogs and articles on bioinformatics, genomics, and AI-driven research insights.

    Recognitions

    Fellowships

    • Research Fellow, The Francis Crick Institute and University College London
    • Project Associate II (Bioinformatic Analysis), Indian SARS-CoV-2 Genomic Consortia (INSACOG)
    • Senior Project Associate (Bioinformatics), SARS-CoV-2 network for Genomic Surveillance in Brazil, Russia, India, China, and South Africa (NGS-BRICS)

    Professional Memberships

    • American Chemical Society
    • World Society for Virology

    Best Poster Award

    International Conference on Drug Discovery, organised by Schrodinger, USA and BITS Pilani, Hyderabad

    Instructor

    Hands-on Training Workshop on SARS-CoV-2 Genome Sequencing and Surveillance, NIBMG, Kalyani, West Bengal, India

    Journal Reviewer

    • Scientific Reports
    • Infection, Genetics and Evolution
    • BMC Genomics

    Mentor

    This page is currently under construction.

    Contact

    I’m open to collaborations, research partnerships, and consultancy in bioinformatics, genomics, and AI-driven insights. Reach out to discuss ideas or explore opportunities to advance science together. Use the form below or contact me directly: