Pre-prints
Agmon, E. (2024). Foundations of a Compositional Systems Biology. ArXiv, arXiv-2408. doi: https://doi.org/10.48550/arXiv.2408.00942. | C-CoMP Pub. #048
Anderson, S. R., Silliman, K., Barbero, L., Gomez, F. A., Stauffer, B. A., Schnetzer, A., Kelble, Cr. R., & Thompson, L. R. (2024). Assessing the effects of warming and carbonate chemistry parameters on marine microbes in the Gulf of Mexico through basin-scale DNA metabarcoding. bioRxiv, 2024-07. doi: https://doi.org/10.1101/2024.07.30.605667. | C-CoMP Pub. #046
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: https://doi.org/10.22541/essoar.170983384.44030316/v1. | C-CoMP Pub. #038
Dukovski, I., Golden, L., Zhang, J., Osborne, M., Segrè, D., & Korolev, K. (2024). Biophysical metabolic modeling of complex bacterial colony morphology. bioRxiv, 2024-03. doi: https://doi.org/10.1101/2024.03.13.584915. | C-CoMP Pub. #057
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: https://doi.org/10.1101/2023.10.16.562604. | C-CoMP Pub. #031
Halloran, K. H., Braakman, R., Coe, A., Swarr, G., Kido Soule, M. C., Chisholm, S. W., & Kujawinski, E. B. (2025). Uptake of Prochlorococcus-derived metabolites by Alteromonas macleodii MIT1002 shows high levels of substrate specificity. bioRxiv, 2025-01. doi: https://doi.org/10.1101/2025.01.10.632383. | C-CoMP Pub. #054
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 ocean. bioRxiv, 2024-03. doi: https://doi.org/10.1101/2024.03.05.583599. | C-CoMP pub. #037
Mejia, C., Trujillo Rodriguez, L., Poudel, R., Ellington, A., Rivers, A. R., & Reisch, C. R. (2022). An arrayed transposon library of Ruegeria pomeroyi DSS-3. bioRxiv, 2022-09. | C-CoMP Pub. #063
Moyer, D. C., Reimertz, J., Segrè, D., & Fuxman Bass, J. I. (2024). Semi-Automatic Detection of Errors in Genome-Scale Metabolic Models. bioRxiv, 2024-06. doi: https://doi.org/10.1101/2024.06.24.600481. | C-CoMP Pub. #052
Schechter, M. S., Trigodet, F., Veseli, I. A., Miller, S. E., Klein, M. L., Sever, M., ... & Eren, A. M. (2025). Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities. bioRxiv, 2025-01. | C-CoMP Pub. #070
Tucker, S. J., Freel, K. C., Murat Eren, A., & Rappé, M. S. (2024). Habitat-specificity in SAR11 is associated with a handful of genes under high selection. bioRxiv, 2024-12. | C-CoMP Pub. #065
Peer-reviewed publications
2025
Braakman, R., Satinsky, B., O’Keefe, T. J., Longnecker, K., Hogle, S. L., Becker, J. W., Li, R. C., Dooley, K., Arellano, A., Kido Soule, M. C., Kujawinski, E. B., & Chisholm, S. W. (2025). Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes. Science Advances, 11(1), eadp1949. doi: https://doi.org/10.1126/sciadv.adp1949. | C-CoMP Pub. #033
Scott, H., & Segrè, D. (2025). Metabolic Flux Modeling in Marine Ecosystems. Annual Review of Marine Science, 17. doi: https://doi.org/10.1146/annurev-marine-032123-033718. | C-CoMP Pub. #043
2024
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 ocean. ISME communications, 4(1), ycae014. doi: https://doi.org/10.1093/ismeco/ycae014. | C-CoMP Pub. #028
Coe, A., Braakman, R., Biller, S. J., Arellano, A., Bliem, C., Vo, N. N., ... & Chisholm, S. W. (2024). Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus. ISME communications, 4(1), ycae131. | C-CoMP Pub/ #061
Doney, S. C., Wolfe, W. H., McKee, D. C., & Fuhrman, J. G. (2024). The science, engineering, and validation of marine carbon dioxide removal and storage. Annual Review of Marine Science, 17. doi: https://doi.org/10.1146/annurev-marine-040523-014702. | C-CoMP Pub. #045
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. Global Biogeochemical Cycles, 38(7), e2024GB008156. doi: https://doi.org/10.1029/2024GB008156. | C-CoMP Pub. #038
Eren, A. M., & Banfield, J. F. (2024). Modern microbiology: Embracing complexity through integration across scales. Cell, 187(19), 5151-5170. doi: https://doi.org/10.1016/j.cell.2024.08.028. | C-CoMP Pub. #049
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 Biology, 7(1), 407. doi: https://doi.org/10.1038/s42003-024-06093-w. | C-CoMP Pub. #039
Hamilton, M., Ferrer‐González, F. X., & Moran, M. A. (2024). Heterotrophic bacteria trigger transcriptome remodelling in the photosynthetic picoeukaryote Micromonas commoda. Environmental Microbiology Reports, 16(3), e13285. doi: https://doi.org/10.1111/1758-2229.13285. | C-CoMP Pub. #030
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: https://doi.org/10.1093/ismejo/wrae055. | 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: https://doi.org/10.1186/s40594-024-00479-2. | C-CoMP Pub. #014
Rao, D., Füssy, Z., Brisbin, M. M., McIlvin, M. R., Moran, D. M., Allen, A. E., Follows, M. J. & Saito, M. A. (2024). Flexible B12 ecophysiology of Phaeocystis antarctica due to a fusion B12–independent methionine synthase with widespread homologues. Proceedings of the National Academy of Sciences, 121(6), e2204075121. doi: https://doi.org/10.1073/pnas.2204075121. | C-CoMP Pub. #036
Sher, D., Segrè, D., & Follows, M. J. (2024). Quantitative principles of microbial metabolism shared across scales. Nature Microbiology, 1-14. doi: https://doi.org/10.1038/s41564-024-01764-0. | C-CoMP Pub. #047
Silverstein, M. R., Bhatnagar, J. M., & Segrè, D. (2024). Metabolic complexity drives divergence in microbial communities. Nature Ecology & Evolution, 1-12. doi: https://doi.org/10.1038/s41559-024-02440-6. | C-CoMP Pub. #044
Warwick-Dugdale, J., Tian, F., Michelsen, M. L., Cronin, D. R., Moore, K., Farbos, A., ... & Temperton, B. (2024). Long-read powered viral metagenomics in the oligotrophic Sargasso Sea. Nature Communications, 15(1), 4089. doi: https://doi.org/10.1038/s41467-024-48300-6. | C-CoMP Pub. #041
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. Scientific Data, 11, 967. doi: https://doi.org/10.1038/s41597-024-03778-z. | C-CoMP Pub. #024
2023
DeVries, T., Yamamoto, K., Wanninkhof, R., Gruber, N., Hauck, J., Müller, J. D., ... & Zeng, J. (2023). Magnitude, trends, and variability of the global ocean carbon sink from 1985 to 2018. Global Biogeochemical Cycles, 37(10), e2023GB007780. doi: https://doi.org/10.1029/2023GB007780. | C-CoMP Pub. #058
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. | 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: https://doi.org/10.1128/msystems.00433-23. | 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: https://doi.org/10.1128/msystems.00017-21. | 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 Change. Frontiers in Microbiology, 14, 233. doi: https://doi.org/10.3389/fmicb.2023.1049579. | 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 evaluation. Msystems, e00961-22. doi: https://doi.org/10.1128/msystems.00961-22. | 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 ecotypes. Msystems, 8(5), e01261-22. doi: https://doi.org/10.1128/msystems.01261-22. | 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: https://doi.org/10.1038/s41396-023-01390-4. | 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 Portal. Journal of Proteome Research, 22(9),2775-3102. doi: https://doi.org/10.1021/acs.jproteome.3c00152. | C-CoMP Pub. #029
Pfeifer, M. A., & Dolan, E. L. (2023). Venturing into Qualitative Research: A Practical Guide to Getting Started. Scholarship and Practice of Undergraduate Research, 7(1), 10-20. doi: https://doi.org/10.18833/spur/7/1/2. | 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: https://doi.org/10.1073/pnas.2217200120. | 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 exometabolites. ISME communications, 3(1), 37. doi: https://doi.org/10.1038/s43705-023-00244-6. | C-CoMP Pub. #022
Silverstein, M. R., Segrè, D., & Bhatnagar, J. M. (2023). Environmental microbiome engineering for the mitigation of climate change. Global Change Biology. doi: https://doi.org/10.1111/gcb.16609. | 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 Biology, 19(6), e1011232. doi: https://doi.org/10.1371/journal.pcbi.1011232. | 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 INADEQUATE. Journal of Magnetic Resonance, 347, 107365. doi: https://doi.org/10.1016/j.jmr.2022.107365. | C-CoMP Pub. #017
2022
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. | C-CoMP Pub. #009
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. | 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 Communications, 2(1), 1-14. doi: https://doi.org/10.1038/s43705-022-00169-6. | 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 media. NMR in Biomedicine, e4797. doi: https://doi.org/10.1002/nbm.4797. | 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: https://doi.org/10.1002/lno.12053. | 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 Microbiology, 7(4), 508-523. doi: https://doi.org/10.1038/s41564-022-01090-3. | 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 Communications, 2(1), 1-9. doi: https://doi.org/10.1038/s43705-022-00116-5. | C-CoMP Pub. #004
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. #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-aminophenylalanine. iScience, 104562. doi: https://doi.org/10.1016/j.isci.2022.104562. | C-CoMP Pub. #006
2021
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. | 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 Research, 21(1), 77-89. doi: https://doi.org/10.1021/acs.jproteome.1c00517. | C-CoMP Pub. #007