C-CoMP Publications

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.

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.

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: 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: 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: 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: 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: 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: 10.1038/s41564-022-01090-3.

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