Bhavya Kaushal
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Assembly · RNA-seq · Evolution · Algorithms · Databases
MSc Bioinformatics · Edinburgh · graduating Aug 2026
I work right across the bioinformatics pipeline, from building genomes and reading RNA-seq to tracing evolutionary history and writing the software and databases that make an analysis hold up.
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01 / About
I'm a bioinformatician finishing my MSc at Edinburgh, and I like the problems that start with messy data and end with an actual biological answer. My work spans the whole pipeline, from assembling genomes and quantifying gene expression to tracing evolutionary history and writing the software and databases that hold an analysis together.
What I enjoy most is the variety. Across my projects I've put genomes together from raw reads, dug through RNA-seq for the pathways that shift in a mutant, tested where an animal really sits on the tree of life, hardened an alignment toolkit until it stopped falling over, and pulled three databases into a single answer. What ties it together is curiosity about the biology and a bit of stubbornness about getting the method right.
Day to day I work in Python, R and Bash, mostly on HPC clusters, and I'm fussy about pipelines someone else can actually re-run without me in the room.
02 / Skills
03 / Selected work
Each project as a short story: what I set out to do, and what I actually found.
MSc dissertation
Working on a highly penetrant infertility variant in a cattle breed. Using Oxford Nanopore and Illumina reads, I first built a high-quality genome, polished it into a clean assembly, and then ran the downstream analysis from there. Details kept brief, as this is ongoing work under non-disclosure.
Took a published mouse dataset (healthy vs Isl1-mutant tissue) and asked what the mutation changes in gene expression. The real story was at the pathway level: hypoxia, EMT and angiogenesis lit up, fitting the placental blood-vessel defects reported for this gene. Ranked pathways on the directional statistic rather than raw p-values for a cleaner signal.
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Where do horseshoe crabs sit in the arachnid tree? Tested with a mitochondrial and a nuclear marker under many models, and the instability itself was the result, showing how much a single-marker phylogeny hinges on the marker. Separately, used presence/absence of the key nitrogen-fixation gene across 10 cyanobacteria to predict others: 81% already had documented roles.
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Using Darwin Tree of Life data for a rare Scottish montane willow, ran two assembly approaches head to head, and one clearly won on completeness and contiguity. Cross-species reads then mapped almost as well (only a 5% drop), so one good reference can realistically serve a group of closely related willows.
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Turned an existing alignment codebase into a usable tool with one clean interface over BLAST, Smith-Waterman, statistics and testing. Much of the effort went into trust: a validation layer catching bad input, configurable scoring, and a 32-test suite. Careful reading turned up five genuine bugs, fixed and documented.
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For a set of mouse genes, built something that queries three major databases at once, works out functional similarity, and stores the combined result in a proper relational database. Went further with a design essay taking apart STRING's structure and proposing a cleaner schema with provenance tracking and a modern API layer.
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First prize
In a hackathon my team built a tool that automatically detects short-lived protein filaments in microscopy footage of living yeast, which is tricky because the filaments flicker in and out of view. We wrapped it in a working website so others could run it on their own images. It won first prize.
View code04 / Publications
Review
Conference
Abstract
Abstract
05 / Experience & education
Jun 2024
Structural bioinformatics: homology modelling, docking, GROMACS MD; Python/R automation of virtual high-throughput screening.
Sep 2023 to Jun 2024
Co-developed a milk-adulteration detection device (EEE Dept.); assays, microcontrollers, instrumentation.
2022 to 2023
Genomics/biostatistics, molecular docking; pathology-lab routines; BSL-2 (COVID-19) testing.
2025 to 2026
1st Prize PRIMED Bio-hackathon; Digital Skills Specialist Edinburgh Award. Core: genome assembly, RNA-seq, comparative & evolutionary genomics, NGS, databases, R/stats.
2021 to 2025
CGPA 8.016. IIT Roorkee R&D (Chanakya UG) Fellowship. Certifications: Google, IIT Madras/Guwahati/Roorkee/Kharagpur.
Design Lead, Google Developer Student Club (led team of 5; 600-student Google Crowdsource campaign) · Organising Committee, Kotlin Conference 2023 · Drafting Team Lead, TechBiome.