Saifur Rahman Jony

Saifur Rahman Jony

PhD student | WashU Medicine

Saifur Rahman Jony

Computational biology | cancer genomics | AI & Machine Learning

I am a PhD student in Computational & Systems Biology at Washington University School of Medicine, working in the Wang Lab in the Department of Genetics.

My research focuses on the intersection of cancer (epi-)genomics, transposable elements, and deep learning based predictive models to infer treatment-induced changes from pre-treatment genomic and epigenomic state.

Epigenetic therapy Transposable elements Single-cell multi-omics Deep learning Sequence2Function Models

Research Focus

Predictive cancer epigenomics

Designing predictive models to estimate epigenetic treatment-induced changes in transposable element expression from pre-treatment genomic and epigenomic data in glioblastoma.

Genomic Analysis

Studying open chromatin regions, 3D conformation, DNA methylation and hydroxymethylation in various cellular context including natural killer cells, hepatocytes, neurons and glias in both development and disease context.

Single-cell biology

Building cellular dynamics models based on single cell assays to understand gene regulatory networks in development and disease context.

Current Position

Aug 2024 - present

Graduate Research Assistant, Wang Lab

Department of Genetics, WashU Medicine

  • Developing predictive models for epigenetic drug-induced transposable element expression changes in glioblastoma.
  • Analyzing methylation and sequencing data across cancer, immune, developmental, and prenatal epigenomics collaborations.
  • Integrating genomic, epigenomic, and machine learning methods to identify regulatory changes with therapeutic relevance.

Background

  • 2024 - present
    PhD, Computational & Systems Biology, WashU Medicine
    Doctoral advisor: Ting Wang, PhD, FAIMBE
    Precision Medicine Pathway Fellow (2025-2027)
  • 2023
    BS, Computer Science & Engineering, BUET
    Thesis: Modeling single-cell time series for cell trajectory inference. Supervisor: M. Sohel Rahman, PhD

Selected Highlights

  • Associate Member, American Association for Cancer Research.
  • Graduate Teaching Assistant for BIOL 5495: Computational Molecular Biology at WashU Medicine.
  • Graduate mentor for the IEEE VIP CUP 2023 winning team in Kuala Lumpur, Malaysia.
  • Contributor to COVID-19 forecasting, geospatial public-health analytics, and ICT labor-market analyses used in policy-facing projects.

For collaboration or research inquiries, contact saifur at wustl.edu