Project Scientist

SKAN Research Trust; Bengaluru; On-site; INR 900,000 - 1,300,000; Full time

Job summary

SKAN Research Trust in Bengaluru is seeking a postdoctoral computational biologist to lead gut microbiome metabolic modelling and host–microbe interaction analyses. The role involves building genome-scale models from multi-omics data and contributing to translational microbiome programs.

The ideal candidate holds a PhD in a relevant field, has strong coding skills in Python, R and MATLAB, and experience with HPC environments and large datasets.

Qualifications

• PhD in computational biology or related field.
• Experience in microbiome bioinformatics and systems biology.
• Strong programming in Python, R, Matlab and Bash.
• Linux/HPC experience and large-scale data handling.
• Metagenomics/metatranscriptomics/metabolomics experience.
• Understanding of microbial ecology and systems biology.
• Ability to work with large datasets and in multidisciplinary teams.

Responsibilities

• Develop and implement genome-scale metabolic models (GEMs).
• Build frameworks for microbiome metabolic network reconstruction.
• Perform systems‑level analyses: shotgun metagenomics, meta‑transcriptomics, metabolomics, metadata.
• Design pipelines using HUMAnN, MetaPhlAn, MICOM, COBRApy, CarveMe, AGORA.
• Conduct microbial interaction analysis.
• Develop workflows using Nextflow, Snakemake, WDL.
• Apply statistical and machine learning methods.
• Support multi‑omics interpretation and manuscript preparation.

Skills

Python

R

Matlab

Bash

Linux

HPC

Microbiome bioinformatics

Education

PhD in Computational Biology / Bioinformatics / Systems Biology / Microbiology / Biotechnology / Genomics

Tools

HUMAnN

MetaPhlAn

MICOM

COBRApy

CarveMe

AGORA

Nextflow

Snakemake

WDL

Job description

Our vision is to advance the frontiers of science to transform the future of medicine and improve thelives of millions

Role (Individual / Team) Postdoctoral Computational Biologist – Gut Microbiome Metabolic Modeling

Qualification PhD Technical Certification (If any): NA

Research Experience 2 years

Relevant Industry/Domain Computational Biology & statistical modelling

Responsibilities

Position Summary

We are seeking a highly motivated postdoctoral computational biologist to lead and support advanced research in gut microbiome metabolic modelling and systems-level interpretation of host–microbe interactions. The candidate will work at the intersection of computational biology, microbial genomics, systems biology, bioinformatics, and translational microbiome science.

The role involves developing computational pipelines and metabolic models from shotgun metagenomics, metatranscriptomics, metabolomics, and associated clinical metadata to understand microbial ecosystem function, metabolic exchange, antimicrobial resistance, and disease-associated dysbiosis.

The successful candidate will contribute to translational microbiome programs spanning population studies, biomarker discovery, precision nutrition, and therapeutic microbiome interventions.

Key Responsibilities

Computational & Scientific Responsibilities

• Develop and implement genome-scale metabolic models (GEMs)
• Build computational frameworks for microbiome metabolic network reconstruction
• Perform systems‑level analyses:
  • Shotgun metagenomics
  • Meta‑transcriptomics
  • Metabolomics
  • Clinical and dietary metadata
• Design pipelines using HUMAnN, MetaPhlAn, MICOM, COBRApy, CarveMe, AGORA
• Conduct microbial interaction analysis
• Develop workflows using Nextflow, Snakemake, WDL
• Apply statistical and machine learning methods
• Support multi‑omics interpretation
• AMR profiling integration

Data Engineering & Infrastructure

• Manage large‑scale microbiome datasets
• Optimize workflows
• Use Git/GitHub/GitLab
• Implement FAIR data practices

Research & Collaboration

• Collaborate with multidisciplinary teams
• Contribute to study design
• Write manuscripts and grants
• Mentor junior staff
• Develop SOPs

Selection criteria Essential

Required Qualifications

• PhD in Computational Biology / Bioinformatics / Systems Biology / Microbiology / Biotechnology / Genomics
• Experience in microbiome bioinformatics
• Strong programming skills (Python, R, Matlab, Bash)
• Linux/HPC experience
• Metagenomics analysis experience
• Understanding of microbial ecology and systems biology
• Experience with large datasets

Selection criteria Desirable

Preferred Qualifications

• Gut microbiome modelling experience
• FBA / Constraint modeling
• Metabolomics integration
• Cloud (AWS/GCP/Azure)
• ML applications
• Docker/Singularity
• Publication record

Desired Competencies

• Analytical thinking
• Scientific writing
• Independent research
• Collaboration

Salary will be based on skills and fitment.