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Dr. Nachiket Shankar

Nachiket Shankar

Position: Postdoctoral Fellow, Center for Personalized Cancer Therapy
Secondary Appointment: Hon. Assistant Professorship at the Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India Role: Computational Biologist and Molecular Geneticist

Education:

  • Ph.D. in Molecular, Cellular, and Organismal Biology from the University of Massachusetts Boston in 2023.
  • B.Tech. in Biotechnology from Visvesvaraya Technological University in 2012.

Research Interests:

  • Genomics and next-generation sequencing (NGS) data analysis
  • Epigenomics
  • Single-cell and bulk RNA-sequencing
  • Metagenomics (16S rRNA and complete metagenomic workflows)
  • Computational pipelines (Snakemake, Docker, HPC)
  • Statistical genetics and hypothesis testing
  • Molecular approaches to plant–microbe interactions
  • Genome assembly and microbial evolution

Email: (protected)

Links:
GitHub | ORCID | ResearchGate | Twitter

Biography

I am a Postdoctoral Fellow at the Center for Personalized Cancer Therapy, University of Massachusetts Boston, where my research focuses on understanding cell division plasticity in Apicomplexan parasites using single-cell RNA-sequencing, chromatin accessibility data, and other high-throughput genomics approaches. I work closely with experimental biologists to develop and maintain robust pipelines for data processing and analysis, employing statistical genetics and advanced bioinformatics tools to uncover new insights into parasite biology.

In addition to my postdoctoral role, I serve as an Honorary Assistant Professor at the Trans-Disciplinary Health Sciences and Technology (TDU) in Bangalore. Through this appointment, I collaborate on research projects in molecular genetics and computational biology, as well as mentor students in these fields.

Before starting my postdoctoral work, I completed my Ph.D. in Molecular, Cellular, and Organismal Biology at UMass Boston. My doctoral research centered on plant–microbe interactions, where I utilized metagenomic selection studies in the rhizosphere of Arabidopsis thaliana to explore how specific plant genotypes influence soil microbial communities. I also have research experience in bacterial evolutionary genomics from my time at the National Centre for Biological Sciences (NCBS) in Bangalore.

Research Focus

My work combines genomics, metagenomics, and computational biology to tackle fundamental questions in both plant and parasite systems:

  • Apicomplexan Parasitology
    I employ single-cell transcriptomic and epigenomic data to explore how Toxoplasma gondii and other Apicomplexan parasites regulate cell division and differentiation.

  • Plant–Microbe Interactions
    I investigate the ways in which plant genotypes influence rhizosphere microbial communities, using large-scale metagenomic analyses and statistical genetics approaches.

  • High-Performance Computing & Pipelines
    I develop reproducible workflows for large-scale sequencing projects, leveraging Docker, Snakemake, and HPC clusters to efficiently handle massive datasets.

  • Statistical & Evolutionary Genetics
    I utilize quantitative methods to study host–microbe co-evolution, bacterial genome evolution, and selection-driven shifts in microbial consortia.

Current Projects

1. Single-Cell Omics in Toxoplasma gondii

  • Objective: I seek to integrate single-cell RNA-seq and CUT&RUN data to create a detailed map of chromatin accessibility and transcriptional regulation during the parasite’s lytic cycle.
  • Approach: I build high-throughput pipelines on HPC clusters and apply downstream analytics to pinpoint key regulatory mechanisms involved in parasite replication and development.

Past Projects

2. Multi-Generation Rhizosphere Selection in Arabidopsis thaliana

  • Objective: I aimed to determine which plant genomic regions mediated soil microbiota composition and ultimately impacted plant biomass.
  • Approach: I combined near-isogenic line (NIL) mapping with 16S rRNA/complete metagenomics to identify specific genetic factors that shaped root-associated microbial communities.

3. Collaborative Initiatives in Plant Growth & Metagenomics

  • Objective: I collaborated with international institutions (e.g., Seqomics Ltd. in Hungary) to broaden high-throughput sequencing projects investigating plant–microbe systems.
  • Approach: I led multi-institutional research efforts, secured grants, and mentored undergraduate and graduate students in advanced molecular and computational techniques.

Selected Publications

  1. Lou, J., Rezvani, Y., Arriojas, A., Shankar, N., et al. (2024). “Single-cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver.” Nature Communications, 15(1):7419.

  2. Shankar, N., Shetty, P., Kesseli, R. (2023). “Multi-Generation Selection of Rhizosphere Ecosystem Associated with Plant Genotype and Biomass in Arabidopsis thaliana.” Microorganisms, 11(12):2932.

  3. Woodhams, D.C., Bletz, M.C., Becker, C.G., Bender, H.A., Buitrago-Rosas, D., Shankar, N., Diebboll, H., et al. (2020). “Publisher Correction: Host-associated microbiomes are predicted by immune system complexity and climate.” Genome Biology, 21.

  4. Agashe, D., Shankar, N. (2014). “The evolution of bacterial DNA base composition.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 322(2).

  5. Shankar, N., Shetty, P., Maroti, G. (Manuscript). “Complete metagenomic analysis of multi-generation ecosystem selection of microbial community associated with plant biomass in Arabidopsis thaliana Cvi and Ler.”

  6. Shankar, N., Morey, S., Rosenwald, J., Rawal, M., Kesseli, R. (Manuscript). “Traditional mapping approach using Near Isogenic Lines (NILs) and 16S rRNA metagenomic data to identify plant genomic regions that modulate rhizosphere microbiome in Arabidopsis thaliana Cvi and Ler.”

Software and Resources

I rely on various pipelines and tools for high-throughput sequencing data processing, although I have not yet released standalone software packages:

  • Docker for reproducible bioinformatics environments
  • Snakemake for scalable, automated workflow management
  • HPC Clusters for efficiently handling large NGS datasets
  • Python/R for robust statistical analyses and data visualization

Honors and Awards

  • Nancy Goranson Graduate Research Grant (UMass Boston)
  • Herbert Lipke Graduate Travel Research Grant (UMass Boston)
  • UMass Beacon Student Success Fellowship Grants
  • I secured these grants to mentor four undergraduate researchers, guiding their development in both molecular and computational biology.

Conferences and Presentations

  • Northeastern American Society for Plant Biology Conference (UMass Amherst, 2018) – Presented a poster on my metagenomics research
  • American Society for Plant Biology (ASPB) International Conference (San Jose, California, 2019) – Delivered an e-poster presentation
  • ASPB International Virtual Conference (2020) – Presented a poster highlighting further advances in plant–microbe interaction research

Mentoring and Community Engagement

  • Undergraduate Research Mentorship: I have supervised multiple REU and Bridges scholarship students, helping secure research funding and guiding them toward advanced degrees.
  • International Collaboration: I led large-scale metagenomic sequencing projects in partnership with Seqomics Ltd. (Hungary).
  • Teaching: Over the past eight years, I served as a Teaching Assistant and guest lecturer in Genetics, which allowed me to sharpen my pedagogical skills.
  • Avniraksha Environmental Initiative: I co-founded Avniraksha, a student organization in Bangalore, India, focusing on environmental sustainability and city-wide waste segregation campaigns.