Jojy John

I am a researcher in microbial ecology and ecophysiology, studying how microbial communities respond, adapt, and recover under environmental stress and extreme conditions. My work integrates metagenomics, metatranscriptomics, genome-resolved analysis, whole genome analysis and statistical modeling to link microbial diversity with ecosystem function.

I am currently affiliated with the Department of Biological Sciences, Clemson University, where my research spans estuarine, marine, and soil ecosystem.

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🔬 Research Focus

I am currently working on several research projects that integrate metagenomics, metatranscriptomics, and whole-genome sequencing across a wide range of environmental systems. These projects span marine, estuarine, and terrestrial, with the goal of linking microbial diversity to ecosystem-level processes.

My research broadly focuses on:

• How microbial communities maintain ecosystem function under environmental disturbance
• The balance between functional potential and expressed activity in complex microbiomes
• Microbial recovery and adaptation following stress or extreme conditions
• Resource partitioning, co-occurrence, and metabolic interactions across ecological niches

These questions are addressed using multi-omics datasets, genome-resolved analyses, and reproducible bioinformatics workflows designed for large-scale and high-performance computing environments.

👉 For detailed descriptions of individual studies, Explore my Projects page for more details.

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🛠 Core Expertise

• Microbial Ecology
  Community structure, ecosystem function, and disturbance response

• Multi-Omics Integration
  Metagenomics, metatranscriptomics, MAGs, Whole Genomics, viromics

• Bioinformatics & Data Science
  Custom pipelines, HPC workflows, statistical modeling

• Molecular & Environmental Microbiology
  Broad wet-lab experience supporting computational analyses

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🧠 Open Research, Code & Writing

In addition to peer-reviewed publications Publications, I actively share my research workflows, analyses, and troubleshooting experiences through open platforms. These serve as a living record of my scientific thinking, methods development, and day-to-day bioinformatics work.

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✍️ Blog — Daily Bioinformatics from Jojy’s Desk

🔗 https://jojyjohn28.github.io/blog/

My blog functions as an open laboratory notebook, where I document real-world bioinformatics challenges and solutions encountered in microbial ecology research.

Topics include:

• Metagenome and metatranscriptome analysis
• MAGs, viromes, CAZymes, and energy metabolism markers
• Functional redundancy (FRed) modeling
• Hybrid assembly and whole-genome workflows
• Machine-learning–assisted MAG binning (CPU/GPU)
• HPC troubleshooting, R/Python tips, and figure generation

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💻 GitHub — Reproducible Research & Pipelines

🔗 https://github.com/jojyjohn28

My GitHub repositories host reproducible pipelines, workflows, and analysis frameworks used across my research projects and student mentoring. These repositories are designed for HPC environments and emphasize transparency, scalability, and long-term reuse.

Highlighted areas include:

• Amplicon sequencing workflows
• Metagenomics and metatranscriptomics pipelines
• Genome-resolved metagenomics and hybrid assembly
• Functional redundancy and ecological modeling

🤝 Mentorship & Collaboration

In addition to research, I actively mentor graduate students and interns, develop reproducible workflows, and collaborate across disciplines including microbial ecology, bioengineering, viromics, and environmental biotechnology.

👉 See Mentoring and Collaboration page for more details.