Publications

Students and postdocs are indicated with a §.

(2024). sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets. Journal of Open Source Software.

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(2024). The Dawn of the BioGeoSCAPES Program. Oceanography.

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(2024). Molecular forecasting of toxic bloom events. Proceedings of the National Academy of Sciences.

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(2024). Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling. Nature Communications.

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(2023). Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. BMC Bioinformatics.

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(2022). Microbiomes of bloom-forming Phaeocystis algae are stable and consistently recruited, with both symbiotic and opportunistic modes. The ISME Journal.

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(2022). Marine microeukaryote metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications. Frontiers in Marine Science.

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(2022). Bio-GO-SHIP: The Time Is Right to Establish Global Repeat Sections of Ocean Biology. Frontiers in Marine Science.

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(2021). The osmolyte ties that bind: genomic insights into synthesis and breakdown of organic osmolytes in marine microbes. Frontiers in Microbiology.

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(2021). EUKulele: Taxonomic annotation of the unsung eukaryotic microbes. The Journal of Open Source Software.

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(2021). DMSP synthesis genes distinguish two types of DMSP producer phenotypes. Environmental Microbiology.

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(2020). Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities?. FEMS Microbiology Ecology.

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(2020). Transcriptional response of Emiliania huxleyi under changing nutrient environments in the North Pacific Subtropical Gyre. Environmental Microbiology.

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(2018). Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. GigaScience.

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(2018). Keeping it light: (Re)analyzing community-wide datasets without major infrastructure. GigaScience.

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(2018). QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science.

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(2018). Transcriptional patterns identify resource controls on the diazotroph Trichodesmium in the Atlantic and Pacific oceans. The ISME Journal.

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(2018). Shifting metabolic priorities among key protistan taxa within and below the euphotic zone. Environmental Microbiology.

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(2017). What are the type, direction, and strength of species, community, and ecosystem responses to warming in aquatic mesocosm studies and their dependency on experimental characteristics? A systematic review protocol. Environmental Evidence.

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(2017). Transcriptional response of the harmful raphidophyte Heterosigma akashiwo to nitrate and phosphate stress. Harmful Algae.

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(2017). Conserved transcriptional responses to nutrient stress in bloom-forming algae. Frontiers in Microbiology.

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(2017). Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics. Nature Communications.

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(2017). Phosphorus availability regulates intracellular nucleotides in marine eukaryotic phytoplankton. Limnology and Oceanography Letters.

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(2017). Integrating 'big data' into aquatic ecology: Challenges and opportunities. Limnology and Oceanography Bulletin.

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(2016). Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nature Reviews Microbiology.

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(2016). Variable depth distribution of Trichodesmium clades in the North Pacific Ocean. Environmental Microbiology Reports.

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(2015). Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean. Proceedings of the National Academy of Sciences.

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(2015). Metatranscriptome analyses indicate resource partitioning between diatoms in the field. Proceedings of the National Academy of Sciences.

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(2014). Sixty Years of Sverdrup: A Retrospective of Progress in the Study of Phytoplankton Blooms. Oceanography.

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(2012). The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response. PloS one.

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(2012). Identifying reference genes with stable expression from high throughput sequence data. Frontiers in Microbiology.

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