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
Open Access, MSPACMAM (Model of Sinking Particles and Cycling of Marine Aggregated Matter) code.
C-CoMP Pub. #012
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. ###).