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    Doney, S. C., Mitchell, K. A., Henson, S. A., Cavan, E. L., DeVries, T., Gruber, N., Hauck, J., Mouw, C. B., Müller, J. D., & Primeau, F. W. (2024). Observational and numerical modeling constraints on the global ocean biological carbon pump. Authorea Preprints. doi: | C-CoMP Pub. #038

    McParland, E. L., Wittmers, F., Bolanos, L. M., Carlson, C. A., Giovannoni, S. J., Michelsen, M. Parsons, R. J., Kido Soule, M. C., Swarr, G. J., Temperton, B., Vergin, K. Worden, A. Z., Longnecker, K. & Kujawinski, E. B. (2024). Seasonal exometabolites are regulated by essential microbial metabolisms in the oligotrophic oceanbioRxiv, 2024-03. doi: | C-CoMP pub. #037

    Gregor, R., Szabo, R. E., Vercelli, G. T., Gralka, M., Reynolds, R., Qu, E. B., Levine, N. M., & Cordero, O. X. (2023). Widespread B-vitamin auxotrophy in marine particle-associated bacteria. bioRxiv, 2023-10. doi: | C-CoMP Pub. #031

    Veseli, I., Cooper, Z. S., DeMers, M. A., Schechter, M. S., Miller, S., Weber, L., Smith, C. B., Rodriguez, L. T., Schroer, W. F., McIlvin, M. R., Lopez, P. Z., Saito, M., Dyhrman, S., Eren, A. M., Moran, M. A., & Braakman, R. (2024). Digital Microbe: A Genome-Informed Data Integration Framework for Collaborative Research on Emerging Model Organisms. bioRxiv, 2024-01. doi: | C-CoMP Pub. #024


    Peer-reviewed publications


    Anderson, S. R., Blanco-Bercial, L., Carlson, C. A., & Harvey, E. L. (2024). Role of Syndiniales parasites in depth-specific networks and carbon flux in the oligotrophic oceanISME communications4(1), ycae014. doi: | C-CoMP Pub. #028

    Herbst, K., Wang, T., Forchielli, E. J., Thommes, M., Paschalidis, I. C., & Segrè, D. (2024). Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations. Communications Biology7(1), 407. doi: | C-CoMP Pub. #039

    Howard-Varona, C., Lindback, M. M., Fudyma, J. D., Krongauz, A., Solonenko, N. E., Zayed, A. A. Andreopoulos, W. B., Olsen, H. M., Kim, Y., Kyle, J. E., Glavina del Rio, T., Adkins, J. N., Tfaily, M. M., Paul, S., Sullivan, M. B., & Duhaime, M. B. (2024). Environment-specific virocell metabolic reprogramming. The ISME Journal, wrae055. doi: | C-CoMP Pub. #034

    Pfeifer, M. A., Zajic, C. J., Isaacs, J. M., Erickson, O. A., & Dolan, E. L. (2024). Beyond performance, competence, and recognition: forging a science researcher identity in the context of research training. International Journal of STEM Education, 11(1), 19. doi:  | C-CoMP Pub. #014


    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: | C-CoMP Pub. #016

    Gregor, R., Johnson, J., Coe L. S. Y., Evans, N. Forsythe, D., Jones, R., Muratore, D., Rodrigues de Oliveira, B. F., Szabo, R., Wan, Y., Williams, J., Chappell, C. R., Matsuda, S. B., Alvarez de la Campa, M. O., Queer and Trans in Microbiology Consortium, Weismann, J. L. (2023). Building a queer- and trans-inclusive microbiology conference. mSystems. doi: | C-CoMP Pub. #023

    Jo, C., Bernstein, D. B., Vaisman, N., Frydman H. M., & Segrè, D. (2023). Construction and modeling of a coculture microplate for real-time measurement of microbial interactions. mSystems. doi: | C-CoMP Pub. #021

    Kim, H. H., Laufkötter, C., Lovato, T., Doney, S. C., & Ducklow, H. W. (2023). Projected 21st-Century Changes in Marine Heterotrophic Bacteria Under Climate ChangeFrontiers in Microbiology14, 233. doi: | C-CoMP Pub. #019

    Kishore, D., Birzu, G., Hu, Z., DeLisi, C., Korolev, K. S., & Segrè, D. (2023). Inferring microbial co-occurrence networks from amplicon data: a systematic evaluationMsystems, e00961-22. doi: | C-CoMP Pub. #027

    Kujawinski, E. B., Braakman, R., Longnecker, K., Becker, J. W., Chisholm, S. W., Dooley, K., Kido Soule, M. C., Swarr, G. J., & Halloran, K. (2023). Metabolite diversity among representatives of divergent Prochlorococcus ecotypesMsystems8(5), e01261-22. doi: | C-CoMP Pub. #032

    Nowinski, B., Feng, X., Preston, C. M., Birch, J. M., Luo, H., Whitman, W. B., Moran M. A. (2023). Ecological divergence of synoptic marine bacterial species is shaped by gene content and expression. The ISME Journal, 1-10. doi: | C-CoMP Pub. #018

    Paoletti, M. M., Fournier, G. P., Dolan, E. L., & Saito, M. A. (2023). Metaproteogenomic Profile of a Mesopelagic Adenylylsulfate Reductase: Course-Based Discovery Using the Ocean Protein PortalJournal of Proteome Research, 22(9),2775-3102. doi: | C-CoMP Pub. #029

    Pfeifer, M. A., & Dolan, E. L. (2023). Venturing into Qualitative Research: A Practical Guide to Getting StartedScholarship and Practice of Undergraduate Research7(1), 10-20. doi: | C-CoMP Pub. #026

    Schreier, J. E., Smith, C. B., Ioerger, T. R., Moran, M. A. (2023). A mutant fitness assay identifies bacterial interactions in a model ocean hot spot. Proceedings of the National Academy of Sciences, 120(12), 2217200120. doi: | C-CoMP Pub. #015

    Schroer, W. F., Kepner, H. E., Uchimiya, M., Mejia, C., Rodriguez, L. T., Reisch, C. R., & Moran, M. A. (2023). Functional annotation and importance of marine bacterial transporters of plankton exometabolitesISME communications3(1), 37. doi: | C-CoMP Pub. #022

    Silverstein, M. R., Segrè, D., & Bhatnagar, J. M. (2023). Environmental microbiome engineering for the mitigation of climate changeGlobal Change Biology. doi: | C-CoMP Pub. #020

    Skalnik, C. J., Cheah, S. Y., Yang, M. Y., Wolff, M. B., Spangler, R. K., Talman, L., Morrison, J. H., Peirce, S. M., Agmon, E. & Covert, M. W. (2023). Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses. PLOS Computational Biology19(6), e1011232. doi: | C-CoMP Pub. #025

    Uchimiya, M., Olofsson, M., Powers, M. A., Hopkinson, B. M., Moran, M. A., & Edison, A. S. (2023). 13C NMR metabolomics: J-resolved STOCSY meets INADEQUATEJournal of Magnetic Resonance347, 107365. doi: | C-CoMP Pub. #017


    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: | C-CoMP Pub. #013
    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: | C-CoMP Pub. #012 | A read-only version of Ocean Biogeochemical modelling paper.

    Forchielli, E., Sher, D., & Segrè, D. (2022). Metabolic phenotyping of marine heterotrophs on refactored media reveals diverse metabolic adaptations and lifestyle strategiesmSystems, e00070-22. doi: | C-CoMP Pub. #009

    Goldford, J. E., George, A. B., Flamholz, A. I., & Segrè, D. (2022). Protein cost minimization promotes the emergence of coenzyme redundancyProceedings of the National Academy of Sciences119(14), e2110787119. doi: | C-CoMP Pub. #005

    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 Communications2(1), 1-14. doi: | C-CoMP Pub. #010

    Holderman, N. R., Ferrer‐Gonzalez, F., Glushka, J., Moran, M. A., & Edison, A. S. (2022). Dissolved organic metabolite extraction from high salt mediaNMR in Biomedicine, e4797. doi: | C-CoMP Pub. #008

    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: | C-CoMP Pub. #003

    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 Microbiology7(4), 508-523. doi: | C-CoMP Pub. #001 | Read-only version. Pre-print version.

    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 Communications2(1), 1-9. doi: | C-CoMP Pub. #004

    Pacheco, A. R., Pauvert, C., Kishore, D., & Segrè, D. (2022). Toward FAIR Representations of Microbial Interactions. mSystems, e00659-22. doi: | C-CoMP Pub. #011

    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-aminophenylalanineiScience, 104562. doi: | C-CoMP Pub. #006


    Uchimiya, M., Schroer, W., Olofsson, M., Edison, A. S., & Moran, M. A. (2021). Diel investments in metabolite production and consumption in a model microbial systemThe ISME Journal, 1-12. doi: | C-CoMP Pub. #002

    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 Research21(1), 77-89. doi: | C-CoMP Pub. #007