Hi, I'm Pratibha, PhD

I'm a Bioinformatician.

I'm passionate about RNA, technology development, biotech, business, and art.

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About Me

Background & Interests

I’m a scientist, bioinformatician, and biotech enthusiast with a background that spans academic research, venture capital, and technology development. My work centers on decoding RNA biology using next-generation sequencing, high-throughput screening, and machine learning—driven by a passion for transforming complex data into actionable insights. Beyond science, I’m deeply connected to the arts. Trained in Indian classical music and dance for over 15 years, I now enjoy social dancing, jazz, and curating the perfect R&B playlist.

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Skills

My technical level

Computational Biology & Bioinformatics

Expertise in the construction and implementation of analysis pipelines and integrative analysis.
  • Transcriptome assembly and quantification
  • Alternative splicing and polyadenylation analysis
  • Long-read and short-read sequencing analysis (bulk and single-cell)
  • RNA-protein and Protein-Protein interaction and network analysis
  • Multi-omics integration
  • Statistical testing and enrichment analysis

Tools, Programming, & Automation

Proficient in widely used programming languages, workflow tools, and high-performance computing resources.
  • Python, R, Jupyter
  • Linux, Bash
  • Data visualization
  • GitHub
  • HPC Cluster Computing
  • Snakemake
  • AWS

AI / Machine Learning

Expertise in applying AI/ML to biological data and therapeutic discovery.
  • Deep learning (standard Python packages)
  • Predictive modeling
  • Feature engineering for biological sequence
  • HPC Cluster Computing
  • Model interpretation and validation

Data Generation & Experimental Design

Proficient in experimental techniques and design.
  • High-throughput screening
  • Molecular biology techniques
  • Cell culture
  • Library preparation

Leadership, Communication, & Strategy

Expertise in effective project management, leadership, and communication across cross-disciplinary teams.
  • Scientific due dilligence
  • Project planning
  • Public speaking
  • Collaboration

Research

Publications, Topics, and Themes
  1. Jagannatha, P., Yoon, Y., Landry, S., Naritomi, J.T., Zhan, L., Olson, S., Wei, X., Street, L. A., Jovanovic, M., Graveley, B. R., Yeo, G.W., Large-scale discovery of RNA-binding proteins that directly modulate poly(A) site selection (in preparation)
  2. Zampa, F., Sison, L. S., Kofman, E. R., Choi, S. Y., Jagannatha, P., Nguyen, G. G., Naritomi, J. T., Shin, A., Khorgade, A., Jin, W., Chen, C., Sievert, D. M., Mukhopadhyay, S., Mizrahi, O., Blue, S. M., Marina, R. J., Yang, D., Wang, C. C., Pang, Z., Brannan, K. W., Ye, Li., Stowers, L., Al’ Khafaji, A. M., Lippi, G., Yeo, G. W. Single cell and isoform-specific translational profiling of the mouse brain. (submitted)
  3. Liang, Q., Yu, T., Kofman, E., Jagannatha, P., Rhine, K., Yee, B. A., Corbett, K. D., Yeo, G. W.. High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. Nat Commun 15, 7067 (2024). https://doi.org/10.1038/s41467-024-50363-4
  4. Jagannatha, P., Tankka, A. T., Lorenz, D. A., Yu, T., Yee, B. A., Brannan, K. W., Zhou, C. J., Underwood, J. G., & Yeo, G. W. (2024). Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution. Genome research, gr.279176.124. Advance online publication. https://doi.org/10.1101/gr.279176.124
  5. Medina-Munoz, H. C., Kofman, E., Jagannatha, P., Boyle, E. A., Yu, T., Jones, K. L., Mueller, J. R., Lykins, G. D., Doudna, A. T., Park, S. S., Blue, S. M., Ranzau, B. L., Kohli, R. M., Komor, A. C., & Yeo, G. W. (2024). Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. Nature communications, 15(1), 875. https://doi.org/10.1038/s41467-024-45009-4
  6. Schmok, J. C., Jain, M., Street, L. A., Tankka, A. T., Schafer, D., Her, H. L., Elmsaouri, S., Gosztyla, M. L., Boyle, E. A., Jagannatha, P., Luo, E. C., Kwon, E. J., Jovanovic, M., & Yeo, G. W. (2024). Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. Nature biotechnology, 10.1038/s41587-023-02014-0. Advance online publication. https://doi.org/10.1038/s41587-023-02014-0
  7. Boyle, E. A., Goldberg, G., Schmok, J. C., Burgado, J., Izidro Layng, F., Grunwald, H. A., Balotin, K. M., Cuoco, M. S., Chang, K. C., Ecklu-Mensah, G., Arakaki, A. K. S., Ahmed, N., Garcia Arceo, X., Jagannatha, P., Pekar, J., Iyer, M., DASL Alliance, & Yeo, G. W. (2023). Junior scientists spotlight social bonds in seminars for diversity, equity, and inclusion in STEM. PloS one, 18(11), e0293322. https://doi.org/10.1371/journal.pone.0293322
  8. Brannan K. W., Chaim I. A., Marina R. J., Yee B. A., Kofman E. R., Lorenz D. A., Jagannatha, P., Dong K. D.,Madrigal A. A., Underwood J. G. & Yeo G. W. (2021). Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. Nat Methods 18, 507–519. https://doi.org/10.1038/s41592-021-01128-0
  9. Robinson, E. K.*, Jagannatha, P.*, Covarrubias, S., Cattle, M., Smaliy, V., Safavi, R., Shapleigh, B., Abu-Shumays, R., Jain, M., Cloonan, S. M., Akeson, M., Brooks, A. N., & Carpenter, S. (2021). Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2. eLife, 10, e69431. https://doi.org/10.7554/eLife.69431

Contact Me

Get in touch

Email

hi@pratibhajagannatha.com

LinkedIn

https://www.linkedin.com/in/pratibha-jagannatha/