Research & Innovation

Advancing Bioinformatics Through Computational Innovation

My research focuses on developing cutting-edge computational methods, machine learning models, and bioinformatics tools to analyze complex biological data, particularly in genomics, transcriptomics, epigenomics, and metagenomics. I am passionate about integrating multi-omics data to improve plant and animal health, leveraging AI-driven computational modeling, and exploring host-pathogen interactions through systems biology approaches. With over a decade of experience in bioinformatics, I have developed NGS data analysis pipelines, prediction tools, and databases while collaborating with researchers across institutions. At South Dakota State University, I aim to establish a strong, externally funded research program, foster interdisciplinary collaborations, and mentor students in computational biology and bioinformatics. My work is driven by the goal of bridging the gap between data and discovery, ultimately contributing to advancements in agriculture, medicine, and environmental science. I plan to seek funding from agencies such as NIH, NSF, USDA, DOE, and private foundations to support these initiatives.

30+
Publications
25+
Research Projects
15+
Collaborations
200+
Citations
Research Visualization

Research Focus Areas

Multi-omics Data Integration

Developing cutting-edge computational methods to integrate and analyze diverse biological data types including genomics, transcriptomics, proteomics, and metabolomics. Our research focuses on creating novel algorithms that enable comprehensive understanding of biological systems at multiple levels.

Advanced algorithms for multi-omics data fusion
Machine learning approaches for data integration
Statistical methods for cross-platform analysis
Visualization tools for multi-dimensional data

Technologies & Tools

PythonRTensorFlowPyTorchNext.jsD3.jsAWSDocker

AI in Genomics

Pioneering the application of artificial intelligence and deep learning in genomic research. Our work focuses on developing interpretable AI models that can predict gene function, identify regulatory elements, and understand genetic variations associated with complex traits and diseases.

Deep learning models for genomic prediction
Interpretable AI in genomics
AI-driven drug discovery
Genomic variant analysis

Technologies & Tools

PyTorchTensorFlowscikit-learnCUDAAWSGoogle Cloud

Systems Biology

Investigating complex biological systems through advanced computational modeling. Our research focuses on understanding cellular processes, metabolic pathways, and gene regulatory networks to unravel the complexity of biological systems.

Network analysis of biological systems
Metabolic pathway modeling
Gene regulatory network inference
Systems-level drug target identification

Technologies & Tools

MATLABPythonRCytoscapeDockerAWSMongoDB

Bioinformatics Tools Development

Creating innovative software solutions and databases that empower researchers across disciplines. Our focus is on developing user-friendly, scalable, and efficient tools that facilitate biological data analysis and interpretation.

Development of analysis pipelines
Creation of specialized databases
Implementation of novel algorithms
User interface design for biologists

Technologies & Tools

ReactNode.jsPythonPostgreSQLDockerAWSGraphQL

Featured Research Projects

deepNEC

Deep Learning in Genomics

A deep learning framework for predicting nitrogen metabolism enzymes from protein sequences. The model achieves state-of-the-art performance in enzyme classification and provides interpretable insights into protein structure-function relationships.

PythonTensorFlowKerasBioinformaticsDeep Learning
2022

pySeqRNA

RNA-Seq Analysis Pipeline

A comprehensive Python package for RNA-Seq data analysis, featuring automated workflows for quality control, alignment, quantification, and differential expression analysis. Includes interactive visualizations and detailed reporting.

PythonRNA-SeqNGSBioconductorData Visualization
2021

HuCoPIA

Host-Pathogen Interactions

An interactive atlas of human-coronavirus protein interactions, providing comprehensive insights into viral infection mechanisms. Features include network visualization, pathway analysis, and potential therapeutic target identification.

ProteomicsNetwork AnalysisDatabaseVisualization
2020

miPyRNA

Small RNA Analysis

A Python package for small RNA sequencing data analysis, focusing on microRNA identification, quantification, and target prediction. Includes novel algorithms for miRNA discovery and comprehensive statistical analysis.

PythonSmall RNA-SeqmiRNANGSStatistics
2023

Let's Collaborate

I'm always open to new research collaborations and opportunities to apply computational approaches to solve complex biological problems. Whether you're working on genomics, proteomics, or systems biology, I'd love to discuss how we can work together.