I am a Bioinformatician and Demonstrator at the University of Glasgow with expertise in cancer genomics, infection biology, and computational genomics. I specialize in analyzing complex multi-omic datasets, including cutting-edge spatial transcriptomics, to uncover biological insights in cancer and infectious diseases.
flowchart TD
Q[Biological question] --> D[Study design and data collection]
D --> T{Data type}
T --> R1[Bulk or scRNA-seq]
T --> R2[WGS or variant data]
T --> R3[Spatial transcriptomics]
%% RNA-seq branch
R1 --> QC1[QC and trimming]
QC1 --> ALN1[Alignment and quantification]
ALN1 --> DE[Differential expression analysis]
DE --> VIS1[Dimensionality reduction and plots]
%% WGS / variant branch
R2 --> QC2[QC and alignment]
QC2 --> VAR[Variant calling and annotation]
VAR --> VIS2[Variant summaries and burden plots]
%% Spatial branch
R3 --> QC3[Image and spot QC]
QC3 --> MAP[Map spots to tissue]
MAP --> VIS3[Spatial feature plots and region stats]
%% Integration & interpretation
VIS1 --> INT[Multi-omics integration and ML]
VIS2 --> INT
VIS3 --> INT
INT --> BIO[Biological interpretation]
BIO --> REP[Reports, figures and pipelines]
Learn more about my background, skills, and research on my Online Portfolio.
- Proficient in NGS data analysis, variant filtering, and multi-omics integration using R, Python, and UNIX/Linux environments.
- Skilled in developing robust bioinformatics pipelines with Nextflow and managing HPC workflows.
- Experienced in spatial transcriptomics platforms such as 10x Genomics Visium, CosMx, and GeoMx DSP.
- Passionate about applying computational biology techniques to understand cancer progression, pathogen biology, and host–pathogen interactions.
- Interested in machine learning and deep learning applications in bioinformatics using PyTorch and TensorFlow.
- Genomics & Transcriptomics: RNA-seq (bulk & single-cell), WGS, GWAS, variant annotation, spatial transcriptomics
- Programming & Tools: R (Seurat, DESeq2), Python (scikit-learn, PyTorch), SQL, Git, Nextflow, UNIX/Linux
- Data Analysis & Visualization: ggplot2, Matplotlib, Seaborn, PCA, heatmaps, spatial feature plots
- Molecular Visualization: PyMOL, UCSF Chimera
- Investigated the role of chronic stress on lung cancer spatial transcriptomics.
- Developed pipelines for colorectal cancer liver metastasis multi-omic studies, identifying therapeutic targets.
- MSc project on Plasmodium falciparum gene family networks to reveal immune evasion mechanisms.
Feel free to explore my repositories for pipelines, analysis scripts, and projects related to cancer genomics, spatial transcriptomics, and infection biology.
📫 You can reach me at ritupam.sarma@gmail.com
🔗 Connect on LinkedIn | GitHub: @PawnChessmon