Research

A central focus of our laboratory is the development of rapid, sensitive, quantitative, and field-deployable CRISPR-based biosensors for environmental monitoring. This research has been supported by the National Science Foundation and the NYS Center of Excellence in Healthy Water Solutions.

Unlike biomedical samples, environmental samples often contain low target concentrations, complex matrices, and substances that interfere with molecular reactions. Our group develops CRISPR sensing systems specifically designed to address these challenges and enable reliable analysis of natural waters and wastewater. 

Current research includes:

• RPA-aided and preamplification-free CRISPR sensing

• Quantitative assay design and kinetic modeling

• Detection of harmful algal blooms and microbial water-quality markers

• Simplified sample preparation for environmental samples

• Lyophilized and portable sensing platforms

Our current molecular targets include genes associated with toxin-producing cyanobacteria and microbial contamination, such as mcyE, cyrJ, and uidA. Our long-term goal is to translate CRISPR sensing from laboratory demonstrations into practical tools for environmental surveillance and decision-making.

Selected Publications:

• "CRISPR Biosensing for Environmental Monitoring: Workflow Design and Performance Benchmarking". Environmental Science & Technology, 2026. https://pubs.acs.org/doi/10.1021/acs.est.6c02006 

• "A Portable RPA-CRISPR/Cas12a-Based Biosensing Platform for On-Site Detection of the Microcystin Synthetase E Gene in Lake Water". ACS ES&T Engineering, 2025. https://pubs.acs.org/doi/10.1021/acsestengg.5c00604

Our group conducts field- and laboratory-based research on harmful algal blooms, water quality, nutrient cycling, and aquatic ecosystem health, with a major focus on Hyde Lake, NY. This work is conducted in collaboration with the Preservation Alliance of Hyde Lake (PAHL), Jefferson County Soil and Water Conservation District, Clarkson University’s Center for Air and Aquatic Resources Engineering and Sciences (CAARES), academic collaborators, and other community and technical partners. The research has been supported by the NYS Center of Excellence in Healthy Water Solutions and Finger Lakes-Lake Ontario Watershed Protection Alliance (FLLOWPA) program. Our research activities include:

• Seasonal monitoring of harmful algal blooms and water quality

• Evaluation of nutrient loading from lake sediments

• Monitoring of chlorophyll, dissolved oxygen, nutrients, transparency, and other water-quality indicators

• Assessment of microcystins and related biomarkers in fish

• Integration of field observations with laboratory analysis

• Community presentations and citizen-science engagement

By studying both water and fish, we aim to develop a more complete understanding of harmful algal bloom impacts on aquatic ecosystems and local communities. The resulting data are intended to support science-based lake management, restoration planning, and public communication.

Selected Publications:

• "Emerging investigator series: mitigation of harmful algal blooms by electrochemical ozonation: from bench-scale studies to field applications". Environmental Science: Water Research & Technology, 2024. https://pubs.rsc.org/ew/article-abstract/10/10/2381/850093/Emerging-investigator-series-mitigation-of-harmful

Building on our current work in CRISPR sensing, environmental microbiology, and molecular analysis, our laboratory is interested in developing integrated molecular platforms for more comprehensive environmental monitoring. Our long-term vision is to combine efficient sample preparation, nucleic acid amplification, quantitative analysis, and multiplexed detection into portable and user-friendly systems that can support timely environmental and water-management decisions.

Potential future directions include electrochemical nucleic acid sensors, integrated sample-to-answer platforms, multiplexed detection of biological contaminants, and automated or autonomous monitoring systems. We welcome interdisciplinary collaborations that connect molecular biology, electrochemistry, materials science, microfluidics, data analysis, and environmental engineering.