About

Nicole Avalon is an Assistant Professor in the Department of Pharmaceutical Sciences at the School of Pharmacy & Pharmaceutical Sciences at UC Irvine. She holds a B.S. in Biomedical Sciences from the University of South Florida, a Master's of Physician Assistant Studies from the University of Florida, and a Ph.D. in Chemistry from the University of South Florida. Her research interests encompass natural product chemistry, biosynthesis, drug discovery, integrated omics, and neuroscience. Her professional background includes a postdoctoral fellowship at the Scripps Institution of Oceanography, UC San Diego, from 2021 to 2024, and experience as a Physician Assistant at Mayo Clinic, Jacksonville. Her work involves the discovery and analysis of marine natural products, biosynthetic pathways, and the development of metabolomics tools for drug discovery. She has contributed to advancing understanding of microbial and marine natural products, including cytotoxic metallophores, linear lipodepsipeptides, and bioactive compounds from cyanobacteria, with a focus on their biosynthesis, structural elucidation, and potential therapeutic applications.

Selected publications

• Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-29

  articleOpen access

  Microbial metabolites play a critical role in regulating ecosystems, including the human body and its microbiota. However, understanding the physiologically relevant role of these molecules, especially through liquid chromatography tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomics, poses significant challenges and often requires manual parsing of a large amount of literature, databases, and webpages. To address this gap, we established the Collaborative Microbial Metabolite Center knowledgebase (CMMC-KB), a platform that fosters collaborative efforts within the scientific community to curate knowledge about microbial metabolites. The CMMC-KB aims to collect comprehensive information about microbial molecules originating from microbial biosynthesis, drug metabolism, exposure-related molecules, food, host-derived molecules, and, whenever available, their known activities. Molecules from other sources, including host-produced, dietary, and pharmaceutical compounds, are also included. By enabling direct integration of this knowledgebase with downstream analytical tools, including molecular networking, we can deepen insights into microbiota and their metabolites, ultimately advancing our understanding of microbial ecosystems.

  PublisherOA PDFDOI

• Diversity in Structure and Function: How Cyanobacterial Metallophores Reveal a Broadening Perspective of Microbial Metal-Chelators

  Journal of Natural Products · 2026-02-20

  articleSenior authorCorresponding

  Cyanobacteria are known for their rich secondary metabolome with a long history of research directed toward the industrial and pharmaceutical applications of their natural products. Cyanobacterial metallophores (metal-chelating molecules), however, are understudied relative to metallophores from other phyla despite evidence suggesting that genes for metallophore biosynthesis are well-represented in cyanobacterial genomes. Many of the characterized cyanobacterial metallophores are formed from hybrid biosynthetic pathways and feature mixed coordinating functional groups, leading to enhanced structural and functional diversity. The few characterized metallophore families have intriguing properties including promiscuity of metal binding, photoreactivity, and amphiphilicity that are yet to be fully explored. Research suggests that these compounds are ecologically relevant and could guide community dynamics by controlling the availability of iron, detoxifying copper, and allelopathically inhibiting certain organisms. Cyanobacterial metallophores also have potential in the fields of therapeutic design, bioremediation, technology, and agriculture. In the past five years, the number of characterized metallophores from cyanobacteria has doubled, pointing to the great promise for future discoveries.

  PublisherDOI

• A resource to empirically establish drug exposure records directly from untargeted metabolomics data

  Nature Communications · 2025-12-09 · 3 citations

  articleOpen access

  Despite extensive efforts, extracting medication exposure information from clinical records remains challenging. To complement this approach, here we show the Global Natural Product Social Molecular Networking (GNPS) Drug Library, a tandem mass spectrometry (MS/MS) based resource designed for drug screening with untargeted metabolomics. This resource integrates MS/MS references of drugs and their metabolites/analogs with standardized vocabularies on their exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data, supporting flexible summarization at multiple ontology levels to align with different research goals. We demonstrate its application by stratifying participants in a human immunodeficiency virus (HIV) cohort based on detected drug exposures. We uncover drug-associated alterations in microbiota-derived N-acyl lipids that are not captured when stratifying by self-reported medication use. Overall, GNPS Drug Library provides a scalable resource for empirical drug screening in clinical, nutritional, environmental, and other research disciplines, facilitating insights into the ecological and health consequences of drug exposures. While not intended for immediate clinical decision-making, it supports data-driven exploration of drug exposures where traditional records are limited or unreliable.

  PublisherDOI

• Molecules to medicine: advances in metabolomics for natural product drug discovery

  Current Opinion in Biotechnology · 2025-10-31 · 2 citations

  reviewOpen accessSenior authorCorresponding

  Recent advances in metabolomics are accelerating natural product (NP) drug discovery. NPs possess diverse biological relevance and comprise a significant portion of our modern pharmacopeia. We highlight studies from the past two years with innovative discovery techniques, ranging from small sample analyses to large-scale data-driven approaches. We focus on nuclear magnetic resonance- and mass spectrometry-based metabolomics for their broad use and greatest advancements in the field. We highlight strategies that utilize computational tools to enable prioritization of samples based on structural novelty, cross-referencing structural data with bioactivity, and the development of innovative annotation techniques that surpass common library matching methods. We also look at the trajectory of metabolomic discovery of NPs over the last decade to inform how these platforms may further evolve. The goal is to enhance the likelihood and improve the efficiency of discovering NPs with pharmaceutical potential, while strategically harnessing data in order to reduce rediscovery and methodological redundancy.

  PublisherDOI

• Green genes from blue greens: challenges and solutions to unlocking the potential of cyanobacteria in drug discovery

  Natural Product Reports · 2025-07-15 · 5 citations

  reviewOpen access

  Cyanobacteria are prolific producers of biologically active compounds that are important in influencing ecology, behavior of interacting organisms, and as leads in drug discovery efforts. Here we discuss the challenges faced by all natural product researchers, especially those that focus on cyanobacteria, and then describe progress that has been made in these areas. We also propose some solutions, paths forward, and thoughts for consideration on these challenges.

  PublisherDOI

• Discovery of a brominated Ahp-containing cyclic depsipeptide from the marine cyanobacterium Moorena sp. collected in Panama

  Phytochemistry Letters · 2025-10-01

  article
  PublisherDOI

• Enabling pan-repository reanalysis for big data science of public metabolomics data

  Nature Communications · 2025-05-24 · 27 citations

  articleOpen access

  Public untargeted metabolomics data is a growing resource for metabolite and phenotype discovery; however, accessing and utilizing these data across repositories pose significant challenges. Therefore, here we develop pan-repository universal identifiers and harmonized cross-repository metadata. This ecosystem facilitates discovery by integrating diverse data sources from public repositories including MetaboLights, Metabolomics Workbench, and GNPS/MassIVE. Our approach simplified data handling and unlocks previously inaccessible reanalysis workflows, fostering unmatched research opportunities.

  PublisherOA PDFDOI

• Cyanobacteria Join the Kahalalide Conversation: Genome and Metabolite Evidence for Structurally Related Peptides

  Journal of the American Chemical Society · 2025-08-19 · 4 citations

  articleOpen access

  Kahalalide F is a cyclic depsipeptide with notable anticancer properties, initially discovered from the green alga Bryopsis sp. and its molluscan predator Elysia rufescens. Recent studies have pinpointed a bacterial endosymbiont of the green alga, Candidatus Endobryopsis kahalalidefaciens, as the true producer of kahalalide F. In the present work, we characterize a closely related kahalalide F analog, kahalalide Z5, from the marine cyanobacterium Limnoraphis sp. collected in the Las Perlas Islands, Panama, and propose the structures of several related compounds by detailed MS analysis. To uncover novel metabolites and prioritize them for targeted isolation from this organism, we employed a robust metabolomics strategy combining LC-MS/MS with SMART NMR and DeepSAT, artificial intelligence platforms trained to infer chemical structures from 1H–13C HSQC NMR data. This integrated approach annotated a compound with structural similarities to kahalalide F, which we subsequently characterized using a suite of spectroscopic techniques and chemical degradation studies. Whole-genome sequencing of the producing strain further revealed a NRPS biosynthetic gene cluster that aligns with the structural features of kahalalide Z5. This study identifies the marine cyanobacterium Limnoraphis sp. as an independent source of kahalalide F-like molecules. This work broadens the phylogenetic spectrum of organisms capable of producing these bioactive compounds, reveals marine cyanobacteria as producers of an increased repertoire of unique natural products, and illustrates the potential of AI-enhanced metabolomic and genomic analyses to streamline the discovery and characterization of complex biomedically relevant natural products.

  PublisherOA PDFDOI

• MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis

  Nucleic Acids Research · 2025-09-11 · 5 citations

  articleOpen access

  Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industrial applications. The biosynthesis of these metabolites usually starts with the assembly of a core 'scaffold', which is subsequently modified by tailoring enzymes to define the molecule's final structure and, in turn, its biological activity profile. Knowledge about reaction and substrate specificity of tailoring enzymes is essential for understanding and computationally predicting metabolite biosynthesis, but this information is usually scattered in the literature. Here, we present MITE, the Minimum Information about a Tailoring Enzyme database. MITE employs a comprehensive set of parameters to annotate tailoring enzymes, defining substrate and reaction specificity by the expressive reaction SMARTS (Simplified Molecular Input Line Entry System Arbitrary Target Specification) chemical pattern language. Both human and machine readable, MITE can be used as a knowledge base, for in silico biosynthesis, or to train machine-learning applications, and tightly integrates with existing resources. Designed as a community-driven and open resource, MITE employs a rolling release model of data curation and expert review. MITE is freely accessible at https://mite.bioinformatics.nl/.

  PublisherOA PDFDOI

• Author response for "Green genes from blue greens: challenges and solutions to unlocking the potential of cyanobacteria in drug discovery"

  2025-06-19

  peer-review
  PublisherDOI