C-CoMP Publications

C-CoMP Pub. #016

Ferrer-González, F. X., Hamilton, M., Smith, C. B., Schreier, J. E., Olofsson, M., & Moran, M. A. (2023). Bacterial transcriptional response to labile exometabolites from photosynthetic picoeukaryote Micromonas commoda. ISME Communications, 3(5). doi:https://doi.org/10.1038/s43705-023-00212-0.

Open Access, raw transcript sequences are uploaded to the NCBI Sequence Read Archive and available under NCBI BioProject PRJNA787291. Data products are available on Zenodo (DOI: 10.5281/zenodo.6812122).

C-CoMP Pub. #013

Dinauer, A., Laufkötter, C., Doney, S. C., & Joos, F. 2022: What controls the large-scale efficiency of carbon transfer through the ocean’s mesopelagic zone? Insights from a new, mechanistic model (MSPACMAM), Global Biogeochemical Cycles, 36, e2021GB007131. doi:https://doi.org/10.1029/2021GB007131.

Open Access, MSPACMAM (Model of Sinking Particles and Cycling of Marine Aggregated Matter) code.

C-CoMP Pub. #012

Fennel, K., Mattern, J. P., Doney, S. C., Bopp, L., Moore, A. M., Wang, B., & Yu, L. 2022: Ocean biogeochemical modelling, Nature Reviews Methods Primers, 2(76). doi: https://doi.org/10.1038/s43586-022-00154-2.

Paper is available from the authors. Example code is available on Zenodo and linked here for the nutrient–phytoplankton–zooplankton–detritus (NPZD) model, parameter optimization and state estimation, and the ensemble Kalman filter application for an ocean biogeochemical model in an idealized 3-dimensional channel.

C-CoMP Pub. #011

Pacheco, A. R., Pauvert, C., Kishore, D., & Segrè, D. (2022). Toward FAIR Representations of Microbial Interactions. mSystems, e00659-22. doi:https://doi.org/10.1128/msystems.00659-22.

C-CoMP Pub. #010

Howard-Varona, C., Roux, S., Bowen, B. P., Silva, L. P., Lau, R., Schwenck, S. M., Schwartz, S., Woyke, T., Northen, T. Sullivan, M. B., & Floge, S. A. (2022). Protist impacts on marine cyanovirocell metabolism. ISME Communications, 2(1), 1-14. doi:https://doi.org/10.1038/s43705-022-00169-6.

Open Access, Raw data, calculations, scripts, & statistical tests are deposited in Cyverse. Metabolomics analysis scripts are located on GitHub.

C-CoMP Pub. #009

Forchielli, E., Sher, D., & Segrè, D. (2022). Metabolic phenotyping of marine heterotrophs on refactored media reveals diverse metabolic adaptations and lifestyle strategies. mSystems, e00070-22. doi:https://doi.org/10.1128/msystems.00070-22.

Open Access, Raw data and code are available on GitHub.

C-CoMP Pub. #008

Holderman, N. R., Ferrer‐Gonzalez, F., Glushka, J., Moran, M. A., & Edison, A. S. (2022). Dissolved organic metabolite extraction from high salt media. NMR in Biomedicine, e4797. doi:https://doi.org/10.1002/nbm.4797.

Open Access, Data are linked here: NMR data.

C-CoMP Pub. #007

Walworth, N. G., Saito, M. A., Lee, M. D., McIlvin, M. R., Moran, D. M., Kellogg, R. M., Fu, F. X., Hutchins, D. A., & Webb, E. A. (2021). Why Environmental Biomarkers Work: Transcriptome–Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium. Journal of proteome research, 21(1), 77-89. doi:https://doi.org/10.1021/acs.jproteome.1c00517.

Open Access on PubMed here. Data and code are linked here: RNA-seq data, Protein Spectral Count data, Raw mass spectra, RNA-protein model code.

C-CoMP Pub. #006

Zomorrodi, A. R., Hemez, C., Arranz-Gibert, P., Wu, T., Isaacs, F. J., & Segrè, D. (2022). Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine. iScience, 104562. doi: https://doi.org/10.1016/j.isci.2022.104562.

Open Access, Data and Code available on Zenodo (DOI: 10.5281/zenodo.6569900).

C-CoMP Pub. #005

Goldford, J. E., George, A. B., Flamholz, A. I., & Segrè, D. (2022). Protein cost minimization promotes the emergence of coenzyme redundancy. Proceedings of the National Academy of Sciences, 119(14), e2110787119. doi:https://doi.org/10.1073/pnas.2110787119.

Open Access, Data and Code available on GitHub.

C-CoMP Pub. #004

Olofsson, M., Ferrer-González, F. X., Uchimiya, M., Schreier, J. E., Holderman, N. R., Smith, C. B., Edison, A. S., & Moran, M. A. (2022). Growth-stage-related shifts in diatom endometabolome composition set the stage for bacterial heterotrophy. ISME Communications, 2(1), 1-9. doi:https://doi.org/10.1038/s43705-022-00116-5.

Open Access. Data are linked here: Transcriptome Data, Metabolomics Data, Additional Data Products and Metadata.

C-CoMP Pub. #003

Moran, M. A., Ferrer‐González, F. X., Fu, H., Nowinski, B., Olofsson, M., Powers, M. A., Schreier, J. E., Schroer, W. F., Smith, C. B., & Uchimiya, M. (2022). The Ocean's labile DOC supply chain. Limnology and Oceanography, 9999, 1-15. doi:https://doi.org/10.1002/lno.12053.

Open Access. Model Code.

C-CoMP Pub. #002

Uchimiya, M., Schroer, W., Olofsson, M., Edison, A. S., & Moran, M. A. (2021). Diel investments in metabolite production and consumption in a model microbial system. The ISME journal, 1-12. doi:https://doi.org/10.1038/s41396-021-01172-w.

Open Access. Data are linked here: Sequencing Data, Metabolomics Data.

C-CoMP Pub. #001

Moran, M. A., Kujawinski, E. B., Schroer, W. F., Amin, S. A., Bates, N. R., Bertrand, E. M., Braakman, R., Brown, C. T., Covert, M. W., Doney, S. C., Dyhrman, S. T., Edison, A. S., Eren, A. M., Levine, N. M., Li, L., Ross, A. C., Saito, M. A., Santoro, A. E., Segré, D., Shade, A., Sullivan, M. B., & Vardi, A. (2022). Microbial metabolites in the marine carbon cycle. Nature Microbiology, 7(4), 508-523. doi:https://doi.org/10.1038/s41564-022-01090-3.

A read-only version is available at here. A pre-print version is available for download here.

Names of C-CoMP members are emboldened. Publications are ordered numerically by their C-CoMP Publication number (C-CoMP Pub. ###).