Research Vision • Computational Biology • $2.27M Active Grants

Research Programs & Four Scientific Pillars

My program turns sequencing data into biological understanding. I build NGS and multi-omics pipelines, sequence-based AI models, and systems-level network analyses, and I release them as public web servers and databases. Applications span viral pathogens, crops, livestock, and human disease.

Scientific Domains:#NGS&Transcriptomics#Multi-OmicsIntegration#DeepLearning&AI#ProteinLanguageModels#SystemsBiology#Host-PathogenInteractomes#WebServers&Databases#ViralGenomics#Crop&LivestockGenomics

Core Scientific Architecture

The Four Pillars of My Research Program

Each pillar represents a fundamental thrust of my computational biology research program, operating synergistically while contributing algorithms, datasets, and predictive models to an integrated discovery engine.

PILLAR 01pySeqRNA • MetaNextViro • miPyRNA • SNVguru • PyVirSeq

NGS & Multi-Omics Analytics

From raw reads to biological insight across viruses, crops, livestock, and human disease

Sequencing data is abundant, but turning it into reproducible biological conclusions remains the bottleneck. This pillar develops and applies pipelines for RNA-Seq, small RNA, metagenomic, amplicon, and variant analysis, and integrates these layers into multi-omics views of how genotype shapes phenotype.

Key Research Directions & Methodologies:

All-in-one transcriptomics workflows (pySeqRNA) that move from reads to annotated, publication-ready tables, including two-phase handling of unique and multi-mapped reads.

Viral genomics: targeted amplicon and metagenomic sequencing of avian influenza, avian metapneumovirus, and PRRSV, with quantification of low-frequency intra-host variants (iSNVs) and quasispecies diversity.

Plant and animal genomics: miRNA discovery and classification (miPyRNA), differential expression under drought, salt, heat, and pathogen stress in crops, and microsatellite and variant marker development.

Integrating host and pathogen transcriptomes with variant, small RNA, and epigenomic data (ChIP-seq, Var-seq, dual RNA-seq) for multi-omics interpretation.

PILLAR 02deepNEC 2.0 • PRGminer • MINpred • RSLpred2 • AtSubP-2.0

Artificial Intelligence & Machine Learning

Sequence-based deep learning for annotation, interaction, and risk prediction

Most genomes have far more sequence than experimental annotation. This pillar builds alignment-free deep learning and protein language model approaches that infer function, localization, and interaction properties directly from sequence, with benchmarking designed to avoid homology leakage.

Key Research Directions & Methodologies:

Genome-wide feature annotation: enzyme classification (deepNEC, >95% accuracy), plant disease resistance genes (PRGminer), subcellular localization (AtSubP-2.0, RSLpred2), and mineral transporter prediction (MINpred).

Protein language models and multimodal architectures that combine sequence embeddings, structural interfaces, and host-receptor orthology.

Continuous binding affinity (ΔΔG) and receptor-specificity prediction, for example influenza hemagglutinin against α-2,3 and α-2,6 sialic acid linkages, to prioritize cross-species spillover risk.

Homology-aware train/test partitioning and calibrated uncertainty so that reported performance holds for out-of-distribution sequences.

PILLAR 03deepHPI • HuCoPIA • HuPoxNET • APinet • GreeningDB

Systems Biology & Host–Pathogen Networks

Interactomes, pathways, and regulatory networks across hosts, pathogens, and species

Disease outcomes arise from interacting molecular networks rather than single genes. This pillar models protein-protein interactions within and between species, and integrates them with expression, pathway, and regulatory data to explain susceptibility, resistance, and virulence.

Key Research Directions & Methodologies:

Deep learning prediction of host-pathogen protein-protein interactions (deepHPI) and interactome atlases for human-coronavirus, human-monkeypox, citrus-greening, wheat-Karnal bunt, and cereal-pathogen systems.

Comparative interactomics across reservoir and susceptible species, including host co-factors such as ANP32A/B and innate immune signaling (RIG-I, MDA5, interferon-stimulated genes).

Network-level integration of transcriptomes, metabolic pathways, and gene regulatory networks to identify hub genes and candidate therapeutic or breeding targets.

Prioritizing targets by combining network centrality with functional evidence such as CRISPR screens and mutant lines.

PILLAR 0413 Web Resources • 9 Software Packages • Nextflow DSL2 • Docker / Singularity

Web Servers, Databases & Reproducible Software

Making methods and data usable by the wider research community

A method only has impact if others can run it. This pillar delivers cost-effective prediction servers, curated databases, and containerized workflows, and maintains them for the long term. Public resources have been used by more than 11,000 researchers.

Key Research Directions & Methodologies:

Curated databases: legumeSSRdb, citSATdb, ranchSATdb (microsatellite markers), GreeningDB, TritiKBdb, HuCoPIA, HuPoxNET (host-pathogen interactomes), and covidTracker.

Prediction web servers for deepNEC, deepHPI, PRGminer, MINpred, AtSubP-2.0, and RSLpred2, hosted at kaabil.net and bioinfo.usu.edu.

Containerized, portable pipelines (Nextflow DSL2, Slurm HPC, Docker, Singularity) such as MetaNextViro.

Open-source Python packages on PyPI, GitHub, and Zenodo with versioned models, documentation, and regression tests, with results published in venues such as Nucleic Acids Research web server and database issues.

Active Funding Portfolio • $2,269,435 in Awarded Grants

Awarded & Active Research Grants

Federal and foundation awards supporting pathogen genomic surveillance, host-pathogen interactomics, and rapid outbreak diagnostic intervention across agricultural and biological systems.

AWARDED • 2025 – Present • USDA-APHIS

Decoding the Poultry-HPAI Interactome: An Integrative Pipeline for Targeted Therapeutics Against Highly Pathogenic Avian Influenza

Investigator Role: Co-PI

$1,969,435

$799,443 SDSU Subaward

Decoding the poultry-HPAI interactome to develop an integrative pipeline for targeted therapeutics against Highly Pathogenic Avian Influenza. Incorporates multi-omics sequencing, structural interactomics, and viral surveillance.

USDA-APHISCo-PIHPAI H5N1Host-Pathogen InteractomeStructural Interactomics

ACTIVE • 2024 – Present • Foundation for Food & Agriculture Research (FFAR)

Emerging avian metapneumovirus subgroup A and B in US poultry: development of diagnostic assays and control strategies

Investigator Role: Co-PI

$150,000

Development of high-sensitivity diagnostic assays and control strategies for emerging avian metapneumovirus (aMPV) subgroups A and B causing outbreaks in US poultry flocks.

FFARCo-PIAvian MetapneumovirusDiagnostic AssaysControl Strategies

ACTIVE • 2024 – Present • Foundation for Food & Agriculture Research (FFAR) ROAR

Broad-spectrum live recombinant vaccine and improved diagnostics for emerging avian metapneumovirus subgroups A and B causing severe outbreaks in US poultry

Investigator Role: Co-I

$150,000

Rapid outbreak response for evaluating broad-spectrum live recombinant vaccines and improved diagnostics for emerging aMPV subgroups A and B.

FFAR ROARCo-IRecombinant VaccineDiagnosticsRapid Outbreak Response

Proposals in Pipeline • $2,100,500 Under Review

Submitted Proposals & Grants Under Review

Competitive research proposals submitted as Principal Investigator (PI) and Co-Investigator to USDA-AFRI and NIH R21 programs.

USDA-AFRI • PI$300,000

AI-Driven Genomic Surveillance and Control Strategies for Emerging Turkey Reoviruses (TRV)

AI-driven computational genomic surveillance, molecular evolution modeling, and intervention strategies for emerging turkey reoviruses.

USDA-AFRIPIAI SurveillanceTurkey ReovirusMolecular Evolution

USDA-AFRI • PI$300,000

BRIDGE: A host-pathogen interactome and machine learning platform to predict zoonotic risk of livestock and poultry viruses

Developing a host-pathogen interactome and deep learning platform to forecast cross-species transmission and zoonotic spillover risk.

USDA-AFRIPIMachine LearningHost-Pathogen InteractomeZoonotic Risk

DHHS / National Institutes of Health (NIH) • Co-I$400,500

Innovative approaches for early detection and control of zoonotic influenza viruses in poultry

Innovative computational and experimental approaches for early detection, variant characterization, and control of zoonotic influenza viruses.

NIH R21Co-IZoonotic InfluenzaEarly DetectionSurveillance

USDA-AFRI • Co-PI$300,000

Novel mass administration vaccine for humoral and cellular immunity using mRNA plus virus like particle

Computational design and evaluation of mass-administration mRNA and virus-like particle (VLP) vaccine platforms for agricultural livestock.

USDA-AFRICo-PImRNA VaccineVLPComputational Design

USDA-AFRI • Co-PI$800,000

Systems-Level Host Interactome Framework for Avian Metapneumovirus Mitigation: Advancing Therapeutics to Strengthen US Agricultural Biosecurity

Systems-level host interactome framework modeling host-pathogen protein networks to advance antiviral discovery and biosecurity defenses.

USDA-AFRICo-PISystems BiologyInteractomeAgricultural Biosecurity

Collaborative Horizons • Computational Biology Direction

Bridging High-Performance Computing with Diagnostic Reality

Computational biology is at its best when algorithms are continually calibrated against real diagnostic samples and biological reality. By anchoring our computational pipelines directly in high-throughput sequencing workflows and active pathogen outbreak surveillance, our tools are tested against real-world biological complexity rather than idealized theoretical datasets.

Whether uncovering novel zoonotic spillover markers, building containerized Nextflow pipelines for high-performance clusters, or deploying accessible web servers for global scientists, my program is committed to open, reproducible, and interdisciplinary computational science.

Explore 9 Packages & 13 Web Resources →Read 34 Peer-Reviewed Publications →