プロフィール詳細

プロジェクトを作成

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Maria N.に依頼

Canada

Microbial Genomics & Bioinformatics Expert — NGS Assembly, Annotation & Comparative Genomics

プロフィール概要

I'm a Ph.D. candidate in Microbiology at McGill University, where my research centers on bacterial genomics — specifically the evolution and population structure of Legionella pneumophila and related species, using whole-genome sequencing, comparative genomics, and phylogenomics. Over the past four years I've assembled, annotated, and analyzed dozens of bacterial genomes from both short-read (Illumina) and long-read (Oxford Nanopore) sequencing data, including hybrid assemblies, and I regularly build and run the pipelines behind that work myself rather than relying on black-box tools. I offer end-to-end NGS genome assembly and annotation services for bacterial and phage genomes: raw read QC and trimming, assembly (SPAdes, Flye, hybrid approaches), annotation (Prokka), pangenome and comparative genomics (Roary/Panaroo), phylogenetic reconstruction (IQ-TREE), variant calling (Snippy), and taxonomic/metagenomic profiling (Kraken2, Kaiju, MetaBAT2, GTDB-Tk, CheckM) when a project needs it. I work comfortably in Linux/HPC environments and use Python and R for downstream analysis and visualization. Because I come from a wet-lab microbiology background as well, I don't just hand back an assembly — I sanity-check it: contamination screening, expected genome size and GC content, completeness (CheckM/BUSCO-style checks), and biologically meaningful annotation review, not just default tool output. I've also trained and supervised multiple students (MITACS interns, Honours project students) through exactly this kind of analysis, so I'm used to explaining results clearly to people who aren't bioinformaticians themselves. Recent published and in-review work includes comparative genomic analyses of Legionella pneumophila and Legionella anisa population structure, detection of plasmid-borne resistance genes via WGS, and comparative genomics/secretome proteomics in Bacillus. I'm looking to take on freelance projects in bacterial or phage genome assembly, annotation, comparative genomics, and related NGS data analysis. Core services: Bacterial/phage genome assembly (short-read, long-read, and hybrid) Genome annotation and quality control/completeness assessment Comparative genomics and pangenome analysis Phylogenetic and phylogenomic reconstruction Metagenome assembly, binning, and taxonomic profiling Variant calling and outbreak/strain-tracking analysis Clear, non-specialist-friendly reporting of results Tools & environment: SPAdes, Flye, Prokka, Roary/Panaroo, IQ-TREE, Snippy, Kraken2, Kaiju, MetaBAT2, GTDB-Tk, CheckM, Python, R, Linux/HPC

専門分野

• ☆ Microbiology
• ☆ Microbiome Research
• ☆ Bioinformatics
• ☆ Pathogenesis
• ☆ Clinical Microbiology
• ☆ Python

サービス

• Research

Research Scientific and Technical Research, Systematic Literature Review

職務経験

PhD Candidate

McGill University

- 現在

PhD Candidate; Microbial Genomics & Bioinformatics

McGill University (Faucher Lab, Department of Natural Resource Sciences)

9月 2022 - 現在

Teaching Assisstant

McGill University

1月 2026 - 4月 2026

Teaching Assisstant

McGill University

9月 2025 - 12月 2025

Teaching Asistant

McGill University

1月 2025 - 4月 2025

Teaching Assisstant

McGill University

9月 2024 - 12月 2024

Teaching Assisstant

McGill University

1月 2024 - 4月 2024

COVID-19 Diagnostic Lab Intern

University of Veterinary and Animal Sciences, Lahore, Pakistan

8月 2021 - 8月 2022

Content Writer

Healthwire, Lahore, Pakistan

9月 2020 - 2月 2021

学歴

Ph.D in Microbiology

McGill University

9月 2022 - 現在

M.Phil. in Microbiology

GC University, Lahore, Pakistan

1月 2017 - 8月 2019

B.Sc. (Hons.) in Microbiology

GC University, Lahore, Pakistan

1月 2013 - 8月 2017

認定資格

• Python for Data Science, AI and Development

  coursera

  12月 2025 - 現在

• Introduction to Biosafety

  Environmenatal Health and Safety, McGill University

  12月 2025 - 現在

• Safe Use of Biological Safety Cabinet

  Environmental Health and Safety, McGill University

  12月 2025 - 現在

• Hazardous Waste Management for Laboratory

  Environmental Health and Safety, McGill University

  12月 2025 - 現在

• Safe Use of Biosafety Cabinet

  Environmental Health and Safety, McGill University

  12月 2025 - 現在

出版物

JOURNAL ARTICLE

Maria Najeeb, Gillian Cameron, Marianne Grimard-Conea, Sara Matthews, Julie Brodeur, Geneviève Cadieux, Pierre A. Pilon, Xavier Marchand-Senécal, Cindy Lalancette, Martin Smith, et al. (2025). Comparative genome analysis investigation of nosocomial and community-acquired cases of Legionnaires’ disease caused by ST2858 and ST378 . Microbiology Spectrum.

Zeshan M.Q. (2023). Antimicrobial activity of essential oils of Curcuma longa and Syzygium aromaticum against multiple drug-resistant pathogenic bacteria . Tropical Biomedicine.

Mughis, Z., Ali, M. A., Anjum, A. A., Omer, M. O., Abbas, M., Najeeb, M. (2022). Molecular characterization of mycotoxin-producing Aspergillus parasiticus and sensitivity pattern to different disinfectants . Malaysian Journal of Microbiology.

Maria Najeeb, Saadia Ijaz, Masood Afzal, Tahir Naeem, Nayab Zaid, Syed Faraz Gillani, Aqib Saeed, Kashif Ur Rehman, Shafay Haseeb (2021). Knowledge, Attitude, Practices (KAP) and Psychological Impact of COVID-19 among Pakistani Population: A Quick Cross-Sectional Online Study . Advancements in Life Sciences.

REVIEW

Maria Najeeb, Sikander Ali, Aiman Tahir Laghari, Maryam Salahuddin, Atia Majeed (2018). Production of microbial metabolites and optimization of key factors involving their hyperproduction in batch culture. Eur. J. Pharma. Med. Res.,.

Maria Najeeb, Sikander Alia, Aiman Tahir Laghari, Nimra Zafar (2017). Monoamine oxidase and its inhibitors correlating to neurodegenerative disorders. Eur. J. Pharma. Med. Res.,.