Ritupam Sarma

📧 [email protected] | [email protected] Web CV: https://pawnchessmon.github.io/Introduction/ 🔗 LinkedIn

🧬 Profile

I'm a bioinformatician with a classical biology background and strong focus on computational biology. My expertise spans R, Python, and high-throughput data analysis, with special interest in spatial transcriptomics, multi-omics integration, and bioinformatics pipeline automation.

Currently, I work as a Demonstrator at the University of Glasgow, supporting MSc and PhD students with bioinformatics workflows, omics analysis, and statistical modelling. My research contributes to cancer genomics, microbial genomics, and data infrastructure for high-throughput submissions (e.g., ENA).

I’m passionate about inclusive, interdisciplinary science and thrive in collaborative environments where computational methods solve real biological problems.

🔧 Technical Skills

Programming & Workflow Development

• Languages: R, Python, Bash, SQL
• Workflow Automation: RNA-seq, GWAS, WGS, HPC clusters (qsub)
• Database: SQLite, custom data extraction via SQL

Statistical Analysis & Machine Learning

• Tools: DESeq2, scikit-learn, SciPy, enrichment analysis, linear modelling
• Applications: Differential expression, variant enrichment, GWAS interpretation
• Training: PyTorch, TensorFlow, unsupervised learning

Genomic & Transcriptomic Analysis

• RNA-seq (bulk & single-cell), WGS, GWAS, variant annotation
• Tools: PLINK, VEP, PolyPhen-2, SIFT, IGV, Seurat

NGS & Multi-Omics

• E. coli genome assembly & QC
• 10x Visium spatial transcriptomics workflows
• Integrated WGS, metabolomics, and protein modelling in Leishmania

Visualisation & Reporting

• Tools: ggplot2, Matplotlib, Seaborn
• Outputs: PCA, heatmaps, volcano plots, spatial maps

Molecular Visualisation

• PyMOL for protein-ligand interaction and educational graphics
• Familiar with MetaboAnalyst, SnpEff, freebayes, vcffilter, Galaxy platform

🚧 Previous Projects

🔬 Spatial Transcriptomics in Colorectal & Lung Cancer

• Using 10x Visium and Seurat to study tumour microenvironments and metastatic stress responses
• Collaborating with clinicians and academic partners
• 📄 AACR Abstract (2025)

📤 ENA Submission Automation

• Command-line tool for automated data upload to the European Nucleotide Archive (ENA)
• Features: metadata checks, email notifications, and QC logging
• Link

🌍 Independent Projects (Web Apps)

DNA/RNA Sequence Analyser

• Built a Streamlit app in Python for DNA/RNA sequence analysis with GC content, codon usage, and ORF detection.
• 🔗 https://pawnchessmon-dna-rna-sequence-analyzer-app-coddgo.streamlit.app

CSV Interpolation Web App

• Developed a Streamlit app to interpolate missing values in datasets by averaging neighboring values.
• 🔗 https://pawnchessmon-csv-interpolation-app.streamlit.app

🎓 Education

MSc Bioinformatics
University of Glasgow, UK (2022–2023) – Merit

• Thesis: Plasmodium falciparum multigene families (rifin, stevor), network analysis and expression profiling

BSc Zoology
Cotton University, India (2018–2021) – 83.36%

• Focus: molecular biology, biochemistry, genetics, immunology

🛠 Certifications

• Analysing Genomic Data in R – DataCamp, 09/2025
• Introduction to TensorFlow in Python – DataCamp, 06/2025
• Deep Learning with PyTorch – DataCamp, 06/2025
• Unsupervised Learning (Python & R) – DataCamp, 05/2025
• Understanding Machine Learning – DataCamp, 05/2025
• Introduction to the Tidyverse – DataCamp, 10/2024

📄 Publication

Multi-scale multi-omic assessment of matched synchronous colorectal cancer liver metastases using multiple spatial transcriptomic tools
Colin Wood et al. including Ritupam Sarma, AACR Annual Meeting 2025, Abstract #4586
🔗 [DOI] https://doi.org/10.1158/1538-7445.AM2025-4586

Let’s collaborate on data-driven biology, machine learning for genomics, and translational bioinformatics! 🚀