Research Areas

At PNNL, our biology researchers explore the molecular details of microbiomes, environmental systems, and human health to understand their function and how they respond to change. Then, we make predictions and even manipulate the systems to take steps toward the greater good. Put simply, our goal is to design biological solutions that make the world a better place. 
research bio page

Chemical Biology -- Developing chemical tools based upon principles of synthetic chemistry to address specific knowledge gaps in biology.

Exposure Science & Pathogen Biology -- Understanding exposure to chemicals and pathogens, where they go in human
and biological systems, and how they affect those systems.

Ecosystem Science -- Understanding how the physical and chemical environment influences dynamic living processes.

Microbiome Science -- Addressing fundamental science questions about microbiome evolution, assembly, physiology and function in human, animal, and environmental systems. 

Synthetic Biology -- Collecting and using knowledge about nature’s biological systems to inspire
new, bioengineered systems that scientists can construct or manipulate for other applications.

Data Science & Biostats -- Applying and developing cutting edge mathematical and statistical methods to further biological and chemical research and solve challenges spanning national security, human health, and environmental applications.

Modeling & Simulation -- Advancing the forefront of fundamental biology by integrating complex omics data and prior knowledge with computational models ranging from molecular to cellular scales.

Molecular Analytics -- Building software infrastructure to enable biological and molecular interpretation of high-dimensional experimental datasets.

Systems Biology – Integrating high-dimensional molecular and phenotypic measurements, using statistics and knowledge frameworks, into systems biology models that can be used to drive scientific insight and inquiry.

Biosample Pipeline -- Providing support and expertise to a wide range of projects in the pursuit of high impact omics research using advanced sample processing techniques and cutting-edge high throughput LC-MS instrumentation.

Biostructure & Function – Leveraging cutting-edge instrumentation and methods to resolve the molecular details of complex biological systems. Our goal is to determine how these molecules participate and interact in key biological pathways important in environmental issues, biotechnological applications, and human health.

Instrument Development & Deployment -- Creating next-generation technologies to enhance molecular characterization for environmental and biological multi-omics applications.

Metabolomics -- Identifying and quantifying dynamic changes in hundreds to thousands of small molecule metabolites in cells, tissues, biofluids, and microbiomes in order to identify indicators of chemical exposure, how gut microbes influence health, or how a disease works.

Proteomics -- Developing and applying methods, protocols and workflows that enable robust, spatially resolved quantification of dynamics of proteins and post-translational modifications, as well as integration with other omics and functional measurements, thereby advancing our understanding of the biological systems.

2022 Journal Covers

Analytical Chem_Journalcover2022








Hollerbach AL, RV Norheim, P Kwantwi-Barima, RD Smith, and YM Ibrahim. “A Miniature Multilevel Structures for Lossless Ion Manipulations Ion Mobility Spectrometer with Wide Mobility Range Separation Capabilities.” Analytical Chemistry 2022 94 (4), 2180-2188 DOI: 10.1021/acs.analchem.1c04700

2021 Journal Covers

2021 Journal Covers - BSD






Joshi RP, A McNaughton, DG Thomas, CS Henry, SR Canon, LA McCue, and N Kumar. “Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions.” ACS Omega 2021 6 (14), 9948-9959 DOI: 10.1021/acsomega.1c00997

Stoddard EG, S Nag, J Martin, KJ Tyrrell, T Gibbins, KA Anderson, AK Shukla, R Corley,  AT Wright , JN Smith. “Exposure to an Environmental Mixture of Polycyclic Aromatic Hydrocarbons Induces Hepatic Cytochrome P450 Enzymes in Mice.” Chem Res Toxicol. 2021 Sep 20;34(9):2145-2156. doi: 10.1021/acs.chemrestox.1c00235.

McNaughton AD, EL Bredeweg, J Manzer, J Zucker, N Munoz Munoz, MC Burnet, ES Nakayasu, KR Pomraning, ED Merkley, Z Dai, WB Chrisler, SE Baker, PC St. John, and N Kumar. “Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic.” ACS Synthetic Biology 2021 10 (11), 2968-2981 DOI: 10.1021/acssynbio.1c00267

Joshi RP, NWA Gebauer, M Bontha, M Khazaieli, RM James, JB Brown, N Kumar. “3D-Scaffold: A Deep Learning Framework to Generate 3D Coordinates of Drug-like Molecules with Desired Scaffolds.” J Phys Chem B. 2021 Nov 11;125(44):12166-12176. doi: 10.1021/acs.jpcb.1c06437. Epub 2021 Oct 18. PMID: 34662142.