Harshini Suresha

Stimulation-Resolved Multi-Omics Analysis of Cardiovascular & Immune Cohorts

Multi-Omics & Computational Immunology

Year2026
LocationIISc
TagsCellRanger, scVI, MAST, Harmony

Bulk and single-cell pipelines for CD3, CD28, PMA and P3971 stimulation panels: STARsolo / CellRanger, Harmony and scVI batch correction, DESeq2, limma-voom, MAST and GLMMs, run reproducibly on SLURM with Docker.

Jun 2025 – Jun 2026 at IISc, Bangalore, supervised by Prof. Dipankar Nandi & Dr. Payel Roy.

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Figure for Stimulation-Resolved Multi-Omics Analysis of Cardiovascular & Immune Cohorts
Methods
  1. 01
    Experimental design

    Stimulation-resolved cardiovascular and immune cohorts with CD3, CD28, PMA and P3971 perturbation panels to study T-cell activation and signalling.

    Perturbation panels
  2. 02
    Read processing

    Read-level processing, splice-aware alignment and UMI-aware quantification for bulk and single-cell data.

    fastp, Trimmomatic, STAR, STARsolo, CellRanger
  3. 03
    Quantification

    Gene abundance estimation.

    FeatureCounts, HTSeq, Salmon-Alevin
  4. 04
    QC & correction

    Sequencing and expression QC, batch-aware correction and doublet removal.

    FastQC, MultiQC, Harmony, scVI, Scrublet, DoubletFinder
  5. 05
    Differential analysis

    Gene- and cluster-level differential analysis accounting for between-sample variation.

    DESeq2, edgeR, limma-voom, MAST, GLMMs
  6. 06
    Reproducible compute

    Portable workflows on a SLURM HPC cluster with managed environments and containers.

    Linux & Bash, Conda, SLURM, Docker, Singularity
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