C-CoMP Publications
Pre-prints
C-CoMP Pub. #070
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. doi: https://doi.org/10.1101/2025.01.15.633187.
C-CoMP Pub. #069
Saito, M. A., & McIlvin, M. R. (2025). Detection of Iron Protein Supercomplexes in Pseudomonas aeruginosa by Native Metalloproteomics. bioRxiv, 2025-01. doi: https://doi.org/10.1101/2025.01.15.633287.
C-CoMP Pub. #065
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. doi: https://doi.org/10.1101/2024.12.23.630198.
C-CoMP Pub. #063
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. doi: https://doi.org/10.1101/2022.09.11.507510.
C-CoMP Pub. #057
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. #054
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. #052
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. #048
Agmon, E. (2024). Foundations of a Compositional Systems Biology. ArXiv, arXiv-2408. doi: https://doi.org/10.48550/arXiv.2408.00942.
C-CoMP Pub. #046
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. #037
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. #031
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.
Peer-reviewed publications
C-CoMP Pub. #071
Howard-Varona, C., Solonenko, N. E., Burris, M., Urvoy, M., Sanderson, C. M., Bolduc, B., & Sullivan, M. B. (2025). Infection and Genomic Properties of Single-and Double-Stranded DNA Cellulophaga Phages. Viruses, 17(3), 365. doi: https://doi.org/10.3390/v17030365.
Open access. Data are available in the Supplementary Materials.
C-CoMP Pub. #061
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. doi: https://doi.org/10.1093/ismeco/ycae131.
Open access, sequencing data is available through NCBI's Gene Expression Omnibus (GEO) using acession number GSE264347. Supplemental Table data are available on Figshare (doi: 10.6084/m9.figshare.25727190.)
C-CoMP Pub. #058
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.
Open access.
C-CoMP Pub. #049
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.
Open access.
C-CoMP Pub. #047
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. #045
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.
Open access.
C-CoMP Pub. #044
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.
Raw sequencing data and metadata are available on the NCBI Sequence Read Archive and available under NCBI BioProject PRJNA1074799. Processed data and analysis and simulation code are available on the Metabolic Complexity Divergence GitHub repository.
C-CoMP Pub. #043
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.
Open access
C-CoMP Pub. #042
Kananen, K., Veseli, I., Quiles Pérez, C. J., Miller, S. E., Eren, A. M., & Bradley, P. H. (2025). Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes. Bioinformatics Advances, 5(1), vbaf039. doi: https://doi.org/10.1093/bioadv/vbaf039.
Open access, scripts and worflow are available on the 2023-anvio-comparison GitHub repository. Anvi'o is available at https://anvio.org. Genome GenBank accessions are available in Supplementary Table S1. High resolution figures are available on Figshare.
C-CoMP Pub. #041
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.
Open access, sequencing data and assemblies are available in NCBI database under the BioProject accession code PRJNA767318. The amplicon raw SRA data are available in NCBI under the BioProject accession code PRJNA769790. Analysis code is available on the AE1712-viromes GitHub repository or on Zenodo. Other data is available within the supplementary materials.
C-CoMP Pub. #040
Clerc, E. E., Schreier, J. E., Słomka, J., Smith, C. B., Fu, H., Seymour, J. R., Raina, J. B., Moran, M. A., & Stocker, R. (2025). Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly. The ISME Journal, wraf101. doi: https://doi.org/10.1093/ismejo/wraf101.
Open access, 16S rRNA gene amplicon sequencing data is available on NCBI's Sequence Read Archive under BioProject PRJNA1234665. Monte Carlo simulation code is available at Zenodo (10.5281/zenodo.12210967).
C-CoMP Pub. #039
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.
Open access, data and code are available on the MASS GitHub repository and within the supplemental methods of the paper.
C-CoMP Pub. #038
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.
Open access
C-CoMP Pub. #036
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.
P. antarctica CCMP1871 mass spectrometry culture proteomics data and transcriptome-derived FASTA files are available on PRIDE under accession number PXD031524. Code for the statistical analysis is available on the Phaeo-Fe-B12 GitHub repository as well as in the paper within relevant figure captions and supporting information.
C-CoMP Pub. #034
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.
Open access, Genomes are available at Joint Genome Institute’s portal for Integrated Microbial Genomes/Virus or GenBank and are listed in the data availability statement of the paper. Supplementary datasets are available on Zenodo.
C-CoMP Pub. #033
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.
Open access, all data are publicly accessible and linked in the materials and methods.
C-CoMP Pub. #032
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.
Open access, targeted metabolomics data are available from MetaboLights (MTBLS567). Code used to find KEGG compound information for Prochlorococcus strains is available on the Pro_mtabs GitHub repository.
C-CoMP Pub. #030
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.
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.5822680)
C-CoMP Pub. #029
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.
Open access, mass spectrometry and protein sequence files from Saunders et al. (2022) are deposited in ProteomeXchange (PRIDE) (dataset ID PXD030684) as well as through the Ocean Protein Portal under expedition FK160115. Metagenomic sequences can be accessed on JGI's IMG database (IDs: Gp0055157, Gp0055156, Gp0055136, Gp0055135, Gp0055134, and Gp0055133). Supporting Information includes seed sequences and tree files.
C-CoMP Pub. #028
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.
Open access, all files and code can be found on the BATS-parasites GitHub repository. 18S rRNA sequences are deposited under BioProject PRJNA769790 on the Sequence Read Archive.
C-CoMP Pub. #027
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.
Open access, code for making the pipeline is available on the MiCoNE repository on GitHub. Documentation is provided on the MiCoNE - Microbial Co-occurrence Network Explorer Read the Docs webpage. Data and scripts are available on the MiCoNE pipeline-paper repository on GitHub. Synthetic data and scripts are available on the MiCoNE-synthetic-data repository on GitHub.
C-CoMP Pub. #026
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.
Open access
C-CoMP Pub. #025
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.
Open access, full source code is available on the vivarium-ecoli repository on GitHub. Results can be reproduced by running on the version of the code archived at Zenodo (DOI 10.5281/zenodo.7709618). The data files used to generate all figures are deposited at Zenodo (DOI 10.5281/zenodo.7709450).
C-CoMP Pub. #024
Veseli, I., DeMers, M. A., Cooper, Z. S., 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, M. A., Moran, M. A., & Braakman, R. (2024). Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms. Scientific Data, 11(1), 967. doi: https://doi.org/10.1038/s41597-024-03778-z.
Open access, Reproducible workflows for the generation and analyses of the Digital Microbes can be accessed at on the digital-microbe repository on GitHub. The R pomeroyi and Alteromonas Digital Microbes are available on Zenodo (https://doi.org/10.5281/zenodo.7304959 and https://doi.org/10.5281/zenodo.7430118, respectively). The R. pomeroyi raw proteomics data is available on PRIDE under project PXD045824 with accompanying metadata and processed data available in BCO-DMO dataset 927507. The accompanying raw transcriptomic expression data is available under the NCBI BioProject PRJNA972985 with metadata available in BCO-DMO dataset 916134.
C-CoMP Pub. #023
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.
Open access
C-CoMP Pub. #022
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.
Open access, all growth and RB-TnSeq data are available on BCO-DMO (Project 884792). All raw NMR data, processing scripts, and processed files are available on Metabolomics Workbench (Study ID ST002381).
C-CoMP Pub. #021
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.
Open access, all data and code are available on GitHub.
C-CoMP Pub. #020
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.
Open access
C-CoMP Pub. #019
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.
Open access, datasets can be found using this CMIP6 Data Search tool in the Earth System Grid Federation website. Please use the experimental IDs listed in the first supplementary table (within supplementary materials) to search for the datasets.
C-CoMP Pub. #018
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.
Open access, data are uploaded to the NCBI Sequence Read Archive and available under the Umbrella BioProject PRJNA533622 and BioProject and PRJNA505827. Biological and chemical data are available at BCO-DMO (Dataset CTD 2016 and Dataset NIskin 2016).
C-CoMP Pub. #017
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.
Open access, original data, processing scripts, and processed files are available at Metabolomics Workbench with Study Identification ST002321 (Project ID: PR001487).
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. #015
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.
Open access, analysis code is available on the TnSeq Phycosphere Interactions GitHub repository and TnSeq Phycosphere Interactions Zenodo webpage. Other code, data, and files are linked here: FASTQ Transposon sequencing files, and the Wig formatted file. All other data are included in the article or SI Appendix.
C-CoMP Pub. #014
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.
Open access, interview questions and codebook are available in additional file one.
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.
Open access
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 the Cyano_phage_grazer_omics Cyverse folder. Metabolomics analysis scripts are located on the Metabolomics_CyanophageGrazer GitHub repository.
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 the marine_heterotrophs GitHub repository.
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: Resource Partitioning of Diatom Metabolites that Support Bacterial Heterotrophy in the Ocean 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. 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 the coenzymes GitHub repository.
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 is available on the Labile_DOC_supply_chain GitHub repository.
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.
Names of C-CoMP members are emboldened. Publications are ordered numerically by their C-CoMP Publication number (C-CoMP Pub. ###).