Ali Marhon
in gh @
Data Science Portfolio

Building intelligence
from biology.

I'm a data scientist working at the intersection of machine learning and biology. Graph deep learning for drug discovery; reproducible single-cell pipelines for cardiovascular genomics.

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[ 02 / ABOUT ]

About.

Data scientist working at the intersection of machine learning and biology. My focus is on turning raw biological signal — single-cell transcriptomes, molecular graphs, sequence data — into reproducible, statistically defensible insight: pipelines that re-run end-to-end from raw archives, models that hold up under held-out evaluation, and analyses that respect the hierarchy of the experiment (patient, not cell).

Recent work spans graph deep learning for drug–target interaction prediction and sex-stratified differential expression in cardiovascular disease. The throughline: small, well-instrumented experiments whose conclusions you can actually defend.

[ 03 / RESEARCH & EXPERIENCE ]

Research
& experience.

  1. Mar 2025 — Mar 2026 · Current

    Data Scientist / Bioinformatics Analyst

    Lawson Health Research Institute · Western University affiliate · London, ON

    Building end-to-end RNA-seq and single-cell ML pipelines (STAR, Salmon, DESeq2, Scanpy) for translational oncology — processing 1,200+ patient samples through a Docker-containerized, Snakemake/Airflow-orchestrated, MLflow-tracked stack on Compute Canada HPC.

    Recent work includes a random-forest oncology classifier (transcriptomic + clinical, n=480) reaching AUROC 0.87 / PR-AUC 0.71 on a held-out cohort, and a LIMS-to-warehouse ETL (Python + REST + PostgreSQL + dbt) connecting STARLIMS to internal analytics that eliminated ~12 hours/week of manual extraction for the pathology team. Plus gene-set enrichment pipelines (Fisher's exact, BH-FDR, GSEA) and internal R/Python workshops for wet-lab scientists.

    • PYTHON
    • R
    • SCANPY
    • DESEQ2
    • SNAKEMAKE
    • AIRFLOW
    • MLFLOW
    • DOCKER
    • POSTGRES
    • DBT

  2. M.Sc. Biochemistry · Robarts Research Institute

    Age- & Sex-dependent Profiling of Angiotensin II–Induced Thoracic Aortic Degeneration in Mice

    Pickering Lab · Robarts Research Institute · Western University

    Thesis: Age- and Sex-dependent Profiling of Angiotensin II–Induced Thoracic Aortic Degeneration in Mice. Investigated sex- and age-dependent protective mechanisms in murine TAA through integrated wet-lab and computational workflows — in situ aortic measurements, histology, RNA isolation, and transcriptomic profiling on the NanoString nCounter platform.

    Built reproducible R pipelines for differential expression, pathway enrichment, and multi-group transcriptomic integration. Identified metabolic and inflammatory programs associated with vascular protection — including altered branched-chain amino acid catabolism and vascular smooth muscle cell remodeling.

    • R
    • NANOSTRING
    • DESEQ2
    • FGSEA
    • HISTOLOGY
    • RNA-SEQ

  3. 2019 — 2021

    Undergraduate Research Assistant

    Western University · London, ON

    Functional analysis of ATAD5 — a gene central to DNA replication, repair, and genome maintenance with implications for cancer biology. Generated wild-type and mutant constructs via PIPE cloning, performed site-directed mutagenesis and Sanger sequencing for downstream functional assays.

    Day-to-day molecular biology stack: plasmid preparation, bacterial transformation, colony PCR for insertion verification, midi/miniprep extractions, and maintenance of E. coli cultures + competent cells for cloning workflows.

    • MOLECULAR BIOLOGY
    • PIPE CLONING
    • SANGER
    • SITE-DIRECTED MUTAGENESIS
    • PCR
    • E. COLI

  4. 2018 — 2020

    Clinical Research Assistant · Cardiovascular

    University Hospital · London Health Sciences Centre · London, ON

    Supported a minimally-invasive cardiovascular outcomes study — patient data collection and database maintenance in close collaboration with physicians, nurses, and PIs to ensure accurate documentation and regulatory compliance. Generated anonymized visual reports for internal review and external presentations; handled patient recruitment and follow-up with strict confidentiality.

    Worked daily with Cerner and Kroll pharmacy management systems alongside clinical pharmacists on medication documentation, workflow optimization, and EMR integration.

    • CLINICAL RESEARCH
    • CERNER
    • KROLL
    • REGULATORY COMPLIANCE
    • EMR

[ 05 / CONTACT ]

Let’s
talk.

alimarhon786@gmail.com LinkedIn  /  in/alimarhon GitHub  /  @amarhon786