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Simran Krishnakant Kushwaha

Computational Biologist | Bacterial Genomics & Phage Biology | PhD in Biological Sciences | BRC Postdoctoral Fellow

Bengaluru

3+ years of work experience

Mandrake Bio
Feb 20268 mosPresent

Bengaluru, Karnataka, India

Leading the metagenomics workflow to identify next-generation genome-editing enzymes. Building and analysing a multi-billion protein sequence library sourced from millions of microbial, viral, and eukaryotic genomes to uncover novel DNA-modification systems with therapeutic and biotechnological potential.
University of Southampton
Dec 20241 yr 2 mosJan 2026

Southampton, England, United Kingdom

Awarded the BRC Postdoctoral Fellowship. Conducted large-scale computational genomics across multiple bacterial pathogens, including Salmonella, E. coli, and Klebsiella. Key projects included the discovery of novel defence systems across thousands of Salmonella and E. coli genomes, identifying new DNA mimics using sequence and structural analysis, and profiling phage-associated mucin-degrading proteins across millions of gut phage genomes.
University of Liverpool
Feb 20241 yrJan 2025

Liverpool, England, United Kingdom

Developed Bactowise, a computational tool for unified bacterial genome annotation, streamlining cross-tool comparison and improving annotation accuracy for downstream genomic analyses.
University of Southampton
Jun 20226 mosNov 2022

City Of Southampton, England, United Kingdom

Awarded the prestigious Newton-Bhabha PhD Placement grant for a 6-month research visit to the UK, where I investigated phage-host interactions and defence systems in Enterobacteriaceae, combining experimental and computational approaches.
Central Institute of Fisheries Education
Dec 20174 mosMar 2018

Mumbai Metropolitan Region

Generated a DNA barcode library of chosen species of Barnacles and fish from the Indian coastal region and submitted the DNA Barcode sequences to Barcode of Life Data System, Centre for Biodiversity Genomics, Canada.

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Education

Birla Institute of Technology and Science, Pilani

Ph.D. Candidate, Biological Sciences

Birla Institute of Technology and Science, Pilani

20194 yrs2023
University of Mumbai

Bachelor of Engineering - BE, Biotechnology

University of Mumbai

20144 yrs2018

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Headline

Computational Biologist | Bacterial Genomics & Phage Biology | PhD in Biological Sciences | BRC Postdoctoral Fellow

About

I'm a computational biologist with a PhD in Biological Sciences, specialising in bacterial pathogenesis, CRISPR-Cas systems, and phage-host interactions. My work spans large-scale genomic analysis, defence system discovery, and building tools for bacterial genome annotation. During my PhD and postdoctoral research, I worked extensively with Salmonella, E. coli, and Klebsiella, analysing thousands of genomes to uncover novel defence systems, DNA mimics, and phage-encoded proteins. I also developed Bactowise, a unified bacterial genome annotation tool. Currently in the industry, bridging genomics research with real-world applications.

Location

Bengaluru

AI stack

claude code

claude

deepmind

gemini

hugging face

Work experience

Member of Technical Staff (Founding Team) at Mandrake Bio, Feb 2026 - Present · 8 mos, Bengaluru, Karnataka, India, Leading the metagenomics workflow to identify next-generation genome-editing enzymes. Building and analysing a multi-billion protein sequence library sourced from millions of microbial, viral, and eukaryotic genomes to uncover novel DNA-modification systems with therapeutic and biotechnological potential.

Postdoctoral Researcher at University of Southampton, Dec 2024 - Jan 2026 · 1 yr 2 mos, Southampton, England, United Kingdom, Awarded the BRC Postdoctoral Fellowship. Conducted large-scale computational genomics across multiple bacterial pathogens, including Salmonella, E. coli, and Klebsiella. Key projects included the discovery of novel defence systems across thousands of Salmonella and E. coli genomes, identifying new DNA mimics using sequence and structural analysis, and profiling phage-associated mucin-degrading proteins across millions of gut phage genomes.

Computational Biologist at University of Liverpool, Feb 2024 - Jan 2025 · 1 yr, Liverpool, England, United Kingdom, Developed Bactowise, a computational tool for unified bacterial genome annotation, streamlining cross-tool comparison and improving annotation accuracy for downstream genomic analyses.

Visiting Researcher at University of Southampton, Jun 2022 - Nov 2022 · 6 mos, City Of Southampton, England, United Kingdom, Awarded the prestigious Newton-Bhabha PhD Placement grant for a 6-month research visit to the UK, where I investigated phage-host interactions and defence systems in Enterobacteriaceae, combining experimental and computational approaches.

Intern at Central Institute of Fisheries Education, Dec 2017 - Mar 2018 · 4 mos, Mumbai Metropolitan Region, Generated a DNA barcode library of chosen species of Barnacles and fish from the Indian coastal region and submitted the DNA Barcode sequences to Barcode of Life Data System, Centre for Biodiversity Genomics, Canada.

Education

Ph.D. Candidate, Biological Sciences, Birla Institute of Technology and Science, Pilani

Bachelor of Engineering - BE, Biotechnology, University of Mumbai