Kinnari Zala | Bioinformatics

Introduction

About Me

Bioinformatics MSc student at Deggendorf Institute of Technology with hands-on experience in NGS data analysis, omics pipelines (transcriptomics, proteomics, metagenomics), and reproducible workflow development using Python, R, and Snakemake. Skilled in interpreting complex multi-condition biological datasets and building interactive visualization and data-tracking tools.

Recently built SeqTrace — a DSI reuse tracking tool that traces plant DNA sequences from ENA submission through scientific literature and patents worldwide, integrating the ENA, NCBI Entrez, and EuropePMC APIs into a live Streamlit dashboard deployed on a Linux server. Built as a prototype directly relevant to biodiversity benefit-sharing policy under the Kunming-Montreal Global Biodiversity Framework.

Published researcher with a broad interest in computational biology — from microbial community dynamics and environmental genomics to molecular adaptations in human systems. Seeking a Master's thesis position where bioinformatics meets cutting-edge biological questions.

Technical Skills

Programming & Analysis

Python (Pandas, NumPy, SciPy, gseapy), R (limma, DESeq2, ggplot2), Bash/Linux, SQLite

Proteomics & Bioinformatics

MaxQuant LFQ, Perseus-style imputation, FastQC, Cutadapt, STAR, featureCounts, Snakemake

Omics Analysis

Differential expression, pathway enrichment (GO, KEGG, Reactome), PPI networks, FDR correction, PCA

Visualization & Apps

Matplotlib, Seaborn, Plotly, Streamlit · REST APIs (ENA, NCBI Entrez, EuropePMC)

Software & Deployment

Git/GitHub, VS Code, Linux server deployment, nginx, Oracle Cloud, Let's Encrypt SSL

Languages

English (C1) · German (B1)

Portfolio

My Projects

SeqTrace — DSI Reuse Tracker

Bioinformatics · Python · Streamlit

Tracks the downstream journey of plant DNA sequences from ENA submission through scientific literature and patents — directly relevant to biodiversity benefit-sharing policy under the Kunming-Montreal Global Biodiversity Framework
Integrates three public REST APIs (ENA Portal, NCBI Entrez, EuropePMC) with a SQLite database; analysed 500 sequences across 299 organisms from 29 countries (1999–2018)
Found 54.4% traceability gap — 272 of 500 sequences leave no recoverable downstream footprint despite originating from well-documented biodiversity collections
Interactive 6-tab Streamlit dashboard with world map, taxonomy sunburst, patent office breakdown, and live filters; deployed on Oracle Cloud VM with nginx and HTTPS

View on GitHub → Live Demo →

Proteomics DIA Analysis Pipeline

Proteomics · Python · R

End-to-end LFQ proteomics pipeline (MaxQuant output → pathway enrichment) using a public SH-SY5Y neuronal dataset (PRIDE: PXD031054)
Perseus-style imputation, empirical Bayes differential expression with limma, BH-FDR correction across two differentiation conditions (n=6 per group)
Pathway enrichment via GO, KEGG, and Reactome identified cytoskeletal remodeling, axon guidance, and synaptic pathways relevant to neurodegeneration research

View on GitHub →

RNA_Snakemake_Workflow – Automated RNA-Seq Pipeline

RNA-Seq · Snakemake

End-to-end reproducible workflow (FASTQ → Differentially Expressed Genes)
Tools: Snakemake, STAR, Cutadapt, featureCounts, DESeq2
Isolated Conda environments per rule for HPC reproducibility

View on GitHub →

GeneScope – Interactive Transcriptomic Visualization App

Streamlit · Python

Streamlit-based tool for PCA, KMeans clustering, and interactive gene expression visualization
Backend with Pandas, NumPy; interactive heatmaps and boxplots using Plotly
Designed for non-bioinformatic researchers to explore expression data without coding

View on GitHub →

Genomic Visualization Series

Visualization · Python

Four-part coursework project covering a broad range of genomic visualization techniques using Python (Matplotlib, Seaborn)
RNA-binding protein signal visualization across genomic coordinates with transcript annotation integration
K-mer frequency analysis, motif detection, spectral mapping for DNA sequences, and comparative/longitudinal multi-panel frameworks

RBP → Part 2 → Part 3 → Part 4 →

Background

Education

MSc Life Science Informatics (Bioinformatics)

Deggendorf Institute of Technology, Bavaria, Germany · Expected 2026

Focus: RNA-Seq analysis, NGS data processing, R & Python programming, workflow automation

Postgraduate Research Experience, Biological Sciences

University of Reading, UK · 2017–2019, 2021

Laboratory and genomics-related research in microbiology, cytogenetics, and evolutionary biology

MSc Forensic Science

Gujarat University, Ahmedabad, India · 2013

Thesis published as a scientific book

BSc Microbiology

Gujarat University, Ahmedabad, India · 2011

Diploma in Computer Applications

SITD, Ahmedabad, India · 2009

Scholarships & Achievements

Qualified UGC-NET (India) National Eligibility Test for Lectureship – 2012, 2013, 2014
Rajiv Gandhi National Fellowship from UGC, India – 2014
National Overseas Scholarship, Government of India – 2015, 2016

Interests & Hobbies

Cooking Bird Watching Rifle Shooting Travelling

Live Demo

Bioinformatics Tools

GeneScope is an interactive Streamlit application designed to enable non-bioinformatic researchers to explore gene expression data without writing code. Users can upload CSV datasets and generate boxplots, heatmaps, and PCA visualizations with integrated KMeans clustering. The app includes log2 transformation options, top variable gene selection, and fully interactive Plotly charts. All plots and clustering results can be downloaded as PNG and CSV files.

SeqTrace — DSI Reuse Tracker. Tracks the downstream journey of plant DNA sequences from ENA submission through scientific literature and patents worldwide. Built as a prototype for DSI reuse analysis under the Kunming-Montreal Global Biodiversity Framework. Dataset: 500 plant sequences (1999–2018) · 299 organisms · 134 patents · 5 patent offices.

About Me

Technical Skills

My Projects

SeqTrace — DSI Reuse Tracker

Proteomics DIA Analysis Pipeline

RNA_Snakemake_Workflow – Automated RNA-Seq Pipeline

GeneScope – Interactive Transcriptomic Visualization App

Genomic Visualization Series

Education

Scholarships & Achievements

Interests & Hobbies

Bioinformatics Tools

Contact Me