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Rishika-Madhanagopal/README.md

RISHIKA
MADHANAGOPAL

BIOINFORMATICS ENGINEER   •   SCIENTIFIC SOFTWARE   •   MULTI-OMICS SYSTEMS

⌜                                                                                    ⌝
From Data To Diagnosis: Powering Precision Medicine
⌞                                                                                    ⌟


BIOLOGY
Understanding systems at molecular resolution
DATA
Turning noisy data into structured information
ENGINEERING
Building reproducible, scalable pipelines
IMPACT
Translating insights into real-world outcomes

01 FEATURED WORK

Multi-Omic Drug Sensitivity

Integrated TCGA, DepMap & scRNA-seq to predict drug response in breast cancer.

  • IGKV1-5 & ALPL identified via SHAP
  • Pathway & Network Analysis
  • XAI for Biomarker Discovery
View Project →

Genomics Pipeline on AWS

End-to-end NGS workflow on AWS for scalable variant discovery and analysis.

  • FastQC . BWA . GATK . Samtools
  • Automated with Nextflow, Docker
  • S3 . EC2 . Batch . Lambda
View Project →

Immune Cell Clustering in RA

Density-based clustering of cytometry data to identify immune cell populations.

  • OPTICS clustering
  • UMAP & t-SNE visualisation
  • Biomarker discovery for RA states
View Project →

02 PIPELINE AT A GLANCE

03 TECH STACK

PROGRAMMING & DATA
BIOINFORMATICS
MACHINE LEARNING
DEVOPS & CLOUD
VISUALISATION

04 PHILOSOPHY

Important

Bioinformatics isn't just about analysing data. It's about building systems that keep working when the data doesn't behave.

🛡️ Robust by Design: Anticipate failures. Engineer reliability.

🔍 Explainable Always: Interpretability builds trust in science.

🚀 Impact Driven: Insights should translate to real-world value.

05 LET'S CONNECT

📧   Email: rishikamadhanagopal@outlook.com

🔗   LinkedIn: linkedin.com/in/rishikam

📍   Location: Newcastle Upon Tyne, UK

Pinned Loading

  1. Genomics-Pipeline-on-AWS Genomics-Pipeline-on-AWS Public

    Scalable end-to-end NGS workflow for variant discovery using AWS (EC2, S3, Lambda, Batch), GATK, and BWA.

    Shell 1

  2. Precision-Oncology-XAI Precision-Oncology-XAI Public

    End-to-end Precision Oncology pipeline integrating scRNA-seq, TCGA, and DepMap to predict drug sensitivity via Explainable AI (SHAP).

    Python

  3. Rheumatoid-Arthritis Rheumatoid-Arthritis Public

    Identification of immune cell populations in Rheumatoid Arthritis using OPTICS density-based clustering, UMAP, and t-SNE on BioFlare cytometry data.

    Python

  4. Mycobacterium_tuberculosis_WGS_Analysis Mycobacterium_tuberculosis_WGS_Analysis Public

    NGS-based variant calling pipeline for M. tuberculosis H37Rv - quality control, alignment, variant filtering and functional annotation.

    HTML