Shashank Pritam
You can find my research work here:
OBJECTIVE
Hello! I am a Ph.D. student at North Dakota State University (NDSU), enrolled in the Department of Biological Sciences. My research interests lie in the field of computational biology, particularly in bioinformatics and genomics. Biology is a domain that provides me with intellectual satisfaction and also enables me to help society in a way that I can. Currently, the biological domain I am working on involves small RNAs (such as piRNA and miRNA) and Transposable Elements. I also enjoy working with different programming languages and learning new programming paradigms. I am interested in the intersection of computational biology and software engineering, where I can apply my skills to solve complex biological problems.
EDUCATION
| Degree | Institution | Location | Duration |
|---|---|---|---|
| Ph.D., Biological Sciences | North Dakota State University | Fargo, ND, USA | Aug 2022 – Apr 2026 |
| BS-MS, Biological Sciences | Indian Institutes of Science Education and Research | Pune, MH, India | Aug 2017 – May 2022 |
PUBLICATIONS
- Pritam, S., Signor, S. (2024). Evolution of piRNA-guided defense against transposable elements. Trends in Genetics.
- Pritam, S., Scarpa, A., Kofler, R., Signor, S. (2025). The impact of insertion bias into piRNA clusters on the invasion of transposable elements. BMC Biology.
WORK EXPERIENCE
Graduate Research Assistant Signor Lab, NDSU | Aug 2022 – Present
Graduate Teaching Assistant Biological Sciences, NDSU | Spring 2024, Fall 2024
Masters Research Student COSPI Lab, IISER Pune | Jun 2021 – Aug 2022
RESEARCH PROJECTS
Insertion Bias of Transposons into piRNA Clusters
Duration: Feb 2023 – Jul 2025
- Developed computational models and population genetics simulations to study transposon invasion and host defense mechanisms
- Built scalable data processing workflows using Python, R, and DuckDB with HPC optimization
Horizontal Transfer of Transposons in Drosophila
Duration: Jan 2025 – Aug 2025
- Engineered computational methods to detect horizontal transfer events across 300+ Drosophila genome assemblies and 200+ transposable elements
- Implemented phylogenetic analysis pipelines using Bash, R, and Python with machine learning prediction models (scikit-learn)
PPII Receptor Prediction
Duration: Jun 2021 – Aug 2022
- Developed receptor prediction software for PPII peptides using superimposition-based methods and Monte Carlo simulations
- Built comprehensive prediction software suite with automated molecular simulation workflows
Flamenco Locus Duplication in Drosophila melanogaster
Duration: Dec 2024 – Present
- Analyzed D. melanogaster genome sequences to identify flamenco piRNA cluster duplication across different strains
- Developed custom tools for large-scale transposable element analysis and syntenic gene mapping
Small RNA Regulation in Megachile rotundata Diapause
Duration: Aug 2023 – Present
- Analyzed small RNA (piRNA and miRNA) expression patterns across diapause stages using miRDeep2, ShortStack, and custom Python/Raku pipelines
- Built small RNA sequencing workflows for non-model organism analysis
TECHNICAL SKILLS
Programming Languages: Python, R, Bash/Shell, Odin
Machine Learning & AI: scikit-learn, TensorFlow, PyTorch, JAX, DNABert
Bioinformatics Tools: DESeq, miRDeep2, ShortStack, GROMACS, BioPython
Systems & Development: Linux/Unix, Git version control, server administration
Analysis Methods: Evolutionary Biology, Population Genetics, Comparative Genomics, Network Analysis
AWARDS & HONORS
- Best Poster Presentation (Ph.D. Category), Northern Plains Biological Symposium 2024
- Infosys Foundation Scholar, IISER Pune (2017-2018)
RELEVANT COURSES
Graduate: Computational Methods in Bioinformatics, Quantitative Biology, Statistical Machine Learning
Undergraduate: Linear Algebra, Statistical Inference, Combinatorics, Graph Theory, Operations Research, Algorithms, Mathematical & Computational Biology, Data Science, Microbiology, Genome Biology, Bioinformatics
PRESENTATIONS
Conference Presentations
Insertion Bias of Transposons into piRNA Clusters
- The Allied Genetics Conference (TAGC), Washington DC | March 2024
- Northern Plains Biological Symposium, Grand Forks, ND | March 2024
- 66th Annual Drosophila Research Conference, San Diego, CA | March 2025