Shashank Pritam

You can find my research work here:

• GitHub

• Google Scholar

• Orcid

• LinkedIn

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 alsp 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

Projects

Characterization of Flamenco piRNA Cluster locus in Drosophila Melanogaster

• Duration: February 2025 - Present
• Description: Characterizing the Flamenco piRNA cluster locus in Drosophila melanogaster using computational methods in bioinformatics. This project involves analyzing the genomic and epigenomic features of the Flamenco locus, including its transcriptional regulation and small RNA biogenesis.

Inferring Horizontal Transfer (HT) of Transposable Elements (TEs)

• Duration: January 2025 - Present
• Description: Implementing phylogenetic analysis pipelines to process and visualize large-scale evolutionary tree data to infer the horizontal transfer of transposable elements (TEs) in various species.

Small RNA’s Role in Megachile Rotundata Diapause

• Duration: August 2023 - Present
• Description: Investigating the role of small RNAs in the diapause of Megachile rotundata using computational methods in bioinformatics.

Examining the High Insertion Bias of P-Elements into X-TAS

• Duration: March 2023 - July 2024
• Description: Analyzing the high insertion bias of P-elements into X-TAS using computational methods in bioinformatics.

Prediction of PPII Receptors

• Duration: Jun 2021 – Aug 2022
• Description: Used superimposition-based methods and Monte Carlo simulations to study how protein receptors and PPII peptides interact.

Relevant Courses

Graduate

• Computational Methods in Bioinformatics
• Quantitative Biology
• Statistical Machine Learning

Undergraduate

Presentations

• Examining the High Insertion Bias of P-Elements into X-TAS. [Poster]. Presented at the TAGC, Washington DC, March 2024.
• Investigating the Elevated Insertion Bias of P-elements into X-TAS. [Poster]. Presented at the Northern Plains Biological Symposium, Grand Forks ND, March 2024.

Awards & Recognitions

• Best Poster Presentation, PhD Category. Northern Plains Biological Symposium 2024, University of North Dakota, Grand Forks ND.

Professional Development

Workshops

1. Leadership and Entrepreneurship Workshop. Conducted by the NDSU Research Foundation and NDSU Office of Innovation and Economic Development, January 25, 2024.
2. Poster Preparation and Abstract Writing Workshop. Center for Writers, NDSU, February 29, 2024.

Skills

1. Programming Languages: Python and R for bioinformatics pipelines; familiar with Go and Rust for tool development. Exploring Crystal for specific computational tasks (e.g., scripting).

2. Data Analysis & Visualization: I have been using DuckDB and Polars for efficient in-memory data querying and manipulation. Also, I am experienced with Pandas and NumPy for data analysis, proficient in creating visualizations with Matplotlib, Seaborn, ggplot2, and gnuplot.

3. Machine Learning/Deep Learning: I have used TensorFlow and PyTorch to develop predictive models in genomics and proteomics. I have been using Scikit-learn and JAX for machine learning research.

4. Workflow Management: I have been creating bioinformatics workflows using Just, Snakemake, or Bash for my projects. Experienced in job scheduling with PBS and Slurm for HPC systems.

5. Documentation, and Version Control: LaTeX, Quarto, and Markdown. Also, Git for version control.