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arunviswanathan91/README.md

Arun (Geetha) Viswanathan

Wet lab scientist who somehow ended up writing Python at 2am.

I'm a PhD candidate at BRIC-RGCB Thiruvananthapuram, working on obesity-driven pancreatic cancer. My actual job is raising mice, doing immunostaining, and kicking cytometers till it run for real. The bioinformatics happened gradually, then all at once.

It will take days to write a simple code for me and often can't write a single code without googling and AI'ing. All code still ircks me. But i somehow cross the bridge at the end. Fake it till you make it! (I guess)


What I work on

Currently working on pancreatic ductal adenocarcinoma (PDAC) - specifically how STAT3 loss reshapes the tumour microenvironment in obese mice. The short version: I planned, then i failed so i resort to omics data(only to fail again).

  • LC-MS/MS proteomics
  • Untargeted serum metabolomics (no code thanks to MetaboAnalyst.ca)
  • Computational pathology (WSI/DICOM pipeline — this one was not in the plan)
  • Bayesian hierarchical modelling (this one really was not in the plan)
  • Single cell RNA analysis (this one was in the plan but did not happen, but learned to do it for the plan above this)
  • Bulk RNA seq analysis
  • Metagenomics (no code thanks to Microbiomeanalyst.ca)
  • An andoid app for my very crafty entrepreneur friend sofi <3
  • Silly stuffs for my great boyfriend <3

Lab: Cancer Research Program -7, RGCB - Dr. K.B. Harikumar's group (KBH lab)


Publications

  • Journal of Advanced Research, 2023
  • Progress in Lipid Research, 2023
  • Chemico-Biological Interactions, 2017
  • loading ....

Awards

  • GCC Best Oral Presentation, 2nd place (2025) at Noida, Delhi, IN
  • BRIC-RGCB Best Poster, Top 5 (2025) (this was at our own lobby but still counts)
  • FCS Singapore 🇸🇬 Travel Award (2025) (this is my first ever visit outside IN | 🇮🇳 🛺 ᯓ ✈︎ 🇸🇬 🦁)

Before the PhD

Taught biology, ocular biochemistry to optometrists in Kozhikode, KL, IN. Coached students for CSIR-NET and GATE. That version of me would be surprised by the GitHub account.


Pinned Loading

  1. cell-analysis-viewer cell-analysis-viewer Public

    Streamlit App for paper "Obesity-Driven Pancreatic Cancer: A Machine Learning Based Bayesian Model and Interactome analysis by Arun Viswanthan, Justin Seby, K.B.Harikumar"

    Python

  2. FIJI-imagej FIJI-imagej Public

    Contains FIJI-imageJ macros and plugins for everyday use

    ImageJ Macro

  3. Sofie-dream Sofie-dream Public

    A free android business studio built for handmade creators

    TypeScript

  4. StreamFlow StreamFlow Public

    R

  5. MetaboMatch MetaboMatch Public

    MetaboMatch is a Python package and command-line interface (CLI) tool designed to match metabolomics compound names against the Human Metabolome Database (HMDB)

    Python

  6. msigdb-signature-generator msigdb-signature-generator Public

    Python