// computational biology · AI · virology

Kritika
Prasai

Ph.D. Candidate in Computer Science University of Missouri — Columbia

I develop AI-driven approaches and computational frameworks for protein interaction prediction, genomics and multi-omics data integration, antigenic and viral evolution, and infectious disease modeling.

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Kritika Prasai Mizzou · CS

01 — About

AI methods for computational biology

I am a Ph.D. candidate in Computer Science at the University of Missouri-Columbia. My research develops AI-driven computational methods for understanding and predicting complex biological systems, with research focused in viral evolution, infectious disease modeling, and large-scale biological discovery.

My work integrates protein language models, graph neural networks, multi-omics analysis, and genomic modeling to study protein interactions and pathogen evolution. Previously, I developed 3D deep learning models for medical image segmentation as an AI engineer.

02 — Research

Highlighted work

Three threads — each pairing a hard biological question with a tailored ML method.

CompatNet model architecture

Deep Learning · PLMs

Protein Binding Prediction

A multi-task framework using ESM-2 protein language models and transformer-based gated cross-attention to model residue-level viral–host interactions.

Epistasis-aware model architecture

Graph Neural Networks

Antigenic Escape Modeling

Graph neural networks that capture higher-order mutational interactions driving influenza antigenic evolution, enabling early detection of escape variants.

Viral genomics and vaccine analysis figure

Genomics · Vaccines

Viral Genomics & Vaccines

Large-scale polymorphism and entropy-based diversity analysis, integrated with scRNA-seq, to inform influenza vaccine breadth and durability.

03 — Publications

Selected publications

Full and up-to-date list on Google Scholar.

  1. P4

    Intrahost HA polymorphisms and culture adaptation shape antigenic profiles of H3N2 influenza viruses.

    Prasai, K., Yang, Z., Guan, M., Li, T., Ware, D., Hang, J., Wan, X.-F.

    Journal of Virology · 2026 · DOI

  2. P3

    Epitope-spanning antigenic variation reprograms immunodominance and broadens immunity in sequential influenza vaccination.

    Guan, M., Balamalaliyage, P., Prasai, K., Alcala, A., Driver, J., et al., Wan, X.-F.

    Nature Communications · 2026 · DOI

  3. P2

    Species- and variant-specific ACE2 compatibility shapes SARS-CoV-2 spillover potential in North American cervids.

    Espada, C., Long, Y., Prasai, K., Wiese, R., Yang, Q., Zhou, M., DeLiberto, T.J., Chandler, J.C., Tao, Y.J., Wan, X.-F.

    Nature Communications · 2026 · DOI

  4. P1

    Prediction models for COVID-19 disease outcomes.

    Tang, C.Y., Gao, C., Prasai, K., Li, T., Dash, S., McElroy, J.A., Hang, J., Wan, X.-F.

    Emerging Microbes & Infections · 2024 · DOI

View all on Google Scholar →

04 — Path

Experience & education

Professional Experience

Aug 2022 – Present

Research Assistant

University of Missouri-Columbia

Develop AI-driven computational methods for predictive modeling of viral evolution, host adaptation, antigenic phenotypes, and transmission risk through machine learning, protein modeling, and large-scale genomic analysis.

Feb 2020 – May 2022

AI Engineer

PSP Corporation — Nepal

Developed advanced computer vision methods for voxel-level segmentation of medical DICOM images, enabling automated analysis of abdominal CT scans, kidney volumetrics, tumor detection, and lung lobe segmentation for clinical imaging applications.

Education

Aug 2022 – Present

Ph.D. in Computer Science

University of Missouri-Columbia

2015 – 2020

B.E. in Computer Engineering

Tribhuvan University, Nepal

GPA 3.5 / 4.0

05 — Recognition

Awards & leadership

Outstanding PhD Student Award ceremony

2026

Outstanding PhD Student Award

EECS Department, University of Missouri

April 2026

Rising Stars in Computational and Data Sciences 2026, Santa Fe Institute

2026

Rising Stars in Computational & Data Sciences

Santa Fe Institute

Selected Research Talk

Team Everest, winners of the GPC Interdisciplinary Case Competition

2024

Interdisciplinary Case Competition Winner

Graduate Professional Council, University of Missouri

January 2024 · Team Everest

Presiding as EECS Graduate Student Association President

2025

President, EECS Graduate Student Association

University of Missouri

2025–2026

Leadership & service

2025

President, EECS Graduate Student Association

University of Missouri · 2025–2026

Led the Tiger Internship Seminar, ShowMe Course Project Showcase, and a college-wide ARC-AGI hackathon.

2024

Director of Communication, EECS GSA

University of Missouri · 2024–2025

2024

Department Representative, Graduate Professional Council

University of Missouri · 2024–Present

Student affairs initiatives supporting graduate mental health and well-being.

2024

Vice Secretary, MUNSA

Missouri University Nepali Student Association · 2024–2025

06 — Talks

Conference & workshop presentations

Click any card to read what I presented.

ISMB 2026

ISMB 2026 — Oral

Intelligent Systems for Molecular Biology

CompatNet: predicting virus–host receptor compatibility.

Read more →
ISMB 2026 poster session

ISMB 2026 — Poster

ISMB 2026

Receptor compatibility landscapes across sarbecoviruses.

Read more →
Rising Stars Workshop

Rising Stars Workshop

Santa Fe Institute

Predicting pandemic risk from virus–host protein interactions.

Read more →
Epidemics 2025 poster

Epidemics 2025 — Poster

Epidemics Conference

Culture adaptation reshapes H3N2 antigenic profiles.

Read more →
ASV 2024 Conference

ASV 2024 — Oral

American Society for Virology

Innate immune responses to influenza A vs. influenza D.

Read more →

07 — Contact

Let's build something at the edge of AI and biology.

Open to research collaborations, talks, and postdoctoral opportunities in computational biology and machine learning for the life sciences.

Email kpvwx@missouri.edu Resume Download PDF ↓ Scholar Google Scholar profile LinkedIn kritikaprasai397 ORCID 0009-0004-8749-5719
Location Columbia, Missouri, USA
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