Bioinformatics Analyst

Parth Doshi

Genomics & Multi-Omics · NGS Pipelines · Python / R

MSc Applied Bioinformatics graduate from Cranfield University with 3+ years of freelance bioinformatics experience and prior molecular diagnostics exposure. I turn complex genomic, transcriptomic, metagenomic, epigenomic, and multi-omics datasets into reproducible workflows, clear biological interpretation, and publication-ready reports.

View Projects Get in Touch

Technical Skills

Programming & Data Analysis

  • Python
  • R
  • Bash / Shell
  • PL/SQL
  • MySQL
  • pandas
  • tidyverse
  • Scientific viz

NGS / Genomics

  • WGS / WES
  • FastQC / MultiQC
  • BWA / Bowtie
  • SAMtools / BCFtools
  • GATK
  • nf-core/Sarek
  • VCF processing

Annotation & Databases

  • VEP
  • vcfanno
  • gnomAD
  • dbSNP
  • Ensembl
  • UCSC
  • KEGG
  • GO
  • HPO
  • Exomiser

Transcriptomics / Pathways

  • Bulk RNA-seq
  • scRNA-seq
  • STAR / HISAT2
  • Salmon / Kallisto
  • DESeq2
  • edgeR / limma
  • clusterProfiler

Multi-omics & Biology

  • ChIP-seq
  • EM-seq / DNA methylation
  • 16S metagenomics
  • Proteomics
  • Gene regulation
  • Pathway interpretation

Workflow / Cloud / DevOps

  • Linux / Unix
  • Git
  • Nextflow / nf-core
  • Snakemake
  • Docker
  • Singularity
  • HPC
  • AWS
  • GCP

Selected Projects

Genomics

Rare-Disease Variant Annotation Pipeline

A Nextflow DSL2 pipeline that annotates VCFs with VEP and vcfanno, filters by impact severity, applies inheritance logic via Genmod, and produces prioritized candidate lists for clinical review of family or single-sample genomic data.

  • Nextflow DSL2
  • VEP
  • vcfanno
  • Genmod
View on GitHub →
Transcriptomics

TCGA BRCA RNA-seq & WGCNA

End-to-end analysis of TCGA breast-cancer RNA-seq combining DESeq2 differential expression with WGCNA co-expression networks to identify tumor-associated gene programs and hub genes, with enrichment analysis and module-preservation validation.

  • R / Bioconductor
  • DESeq2
  • WGCNA
  • Enrichment
View on GitHub →
Genomics

VCF Liftover Wrapper

A high-throughput clinical VCF coordinate liftover engine (GRCh37 ⇄ GRCh38 via UCSC chain files) written in Rust — a streaming pipeline covering parsing, normalization, coordinate mapping, and validation for large variant datasets.

  • Rust
  • GRCh37 ⇄ GRCh38
  • UCSC chain
  • Clinical genomics
View on GitHub →
Genomics · AMR

AMR Gene Detection (ResFinder + CARD)

Bash tooling that predicts antimicrobial-resistance genes in genomic data by integrating the ResFinder and CARD databases, with batch processing of multiple inputs for high-throughput analysis of bacterial resistance patterns.

  • Bash
  • ResFinder
  • CARD
  • AMR
View on GitHub →
Machine Learning

Sake Fermentation Predictive Modeling

A predictive-modeling project exploring sake fermentation outcomes from process data, applying machine-learning workflows for feature analysis and outcome prediction.

  • Python
  • Machine Learning
  • Predictive modeling
View on GitHub →
Multi-omics

RAP2.12 Multi-Omics Integration

Integrated ChIP-seq, RNA-seq, and EM-seq/DNA methylation datasets to identify RAP2.12 direct targets, methylation–expression associations, triple-regulated candidate genes, and pathway-level biological insights.

  • ChIP-seq
  • RNA-seq
  • EM-seq
  • Methylation

Experience

Freelance Bioinformatics Consultant

Nov 2023 – Present

Remote · Pune, India

  • End-to-end analysis across genomics, transcriptomics, epigenomics, metagenomics, proteomics, and healthcare datasets, delivering QC summaries, interpretation, visualizations, and report-ready outputs.
  • Built reproducible Python/R/Bash workflows for preprocessing, normalization, statistics, annotation, pathway enrichment, and downstream reporting.
  • Collaborated remotely with academic, biotech, pharma R&D, and healthcare clients, translating complex outputs into clear reports for scientific decision-making.

Bioinformatics Technical Supporter

Dec 2023 – Feb 2024

Dr Geetanjali's HealthCare Centre · Remote, UK

  • Processed large-scale metagenomic and omics datasets into interpretable Python/R reports for research and healthcare teams.
  • Reduced turnaround via automation, reproducible scripting, and HPC-based workflow optimization with clear method documentation.

Scientific Officer

Mar 2021 – May 2022

Metropolis Healthcare · Pune, India

  • Ran high-throughput COVID RT-PCR workflows supporting 1,000+ tests daily with strong QC discipline and turnaround awareness.
  • Optimized DNA/RNA extraction with Thermo Fisher kits, supervised a team of 8–10, and interpreted RT-PCR data from 96-well instruments.

Research Intern

Jun 2019 – Sep 2019

Ion Cure Tech Pvt Ltd · Remote, India

  • Conducted computational docking studies with AI-assisted tools, assessing antibiotic binding affinities with transmembrane proteins for drug design.

Education

MSc, Applied Bioinformatics

Cranfield University, United Kingdom

Oct 2022 – Nov 2023

Advanced Diploma, Bioinformatics

Rajiv Gandhi Institute of IT & Biotechnology, Pune

Aug 2019 – Jan 2021

BSc, Biotechnology

Pune University, India

Aug 2015 – May 2019

Publications & Certifications

Publication

Glycosylated Antibiotics: New Promising Bacterial Efflux Pumps Inhibitors — Microbiology Research Journal International, Apr 2024. DOI: 10.9734/mrji/2024/v34i31435

Certifications

  • Python Analyst Professional
  • Python & MySQL Language
  • Clinical Research Management
  • Evolution Biology and Beyond

Contact

Open to Bioinformatics Analyst roles and collaboration on genomics & multi-omics projects. Feel free to reach out.

✉️ parthdosshi@outlook.com 📞 +91 7350015629 🔗 linkedin.com/in/parth-doshi2219 💼 Hire me on Upwork