Metabolomics data analysis

Publications:

Longnecker, K., M. C. Kido Soule, G. J. Swarr, R. Parsons, S. Liu, W. M. Johnson, B. Widner, R. Curry, C. A. Carlson and E. B. Kujawinski (2024). Seasonal and daily patterns in known dissolved metabolites in the northwestern Sargasso Sea. Limnology and Oceanography. 69(3):449-466  (link to publication)

Kujawinski, E. B., R. Braakman, K. Longnecker, J. W. Becker, S. W. Chisholm, K. Dooley, M. C. Kido Soule, G. J. Swarr and K. Halloran (2023). Metabolite diversity among representatives of divergent Prochlorococcus ecotypes. mSystems. DOI: 10.1128/msystems.01261-22 (link to publication)

Saw, J. H. W., T. Nunoura, M. Hirai, Y. Takaki, R. Parsons, M. Michelsen, K. Longnecker, E. B. Kujawinski, R. Stepanauskas, Z. Landry, C. A. Carlson and S. J. Giovannoni (2020). Pangenomics analysis reveals diversification of enzyme families and niche specification in globally abundant SAR202 bacteria. mBio 11: e02975-02919. (link to publication)

Tolić, N., Y. Liu, A. Liyu, Y. Shen, M. M. Tfaily, E. B. Kujawinski, K. Longnecker, L.-J. Kuo, E. W. Robinson, L. Paša-Tolić and N. J. Hess (2017). Formularity: Software for automated formula assignment of natural and other organic matter from ultrahigh-resolution mass spectra. Analytical Chemistry. 89: 12659-12665. (link to publication)

Longnecker, K. and E. B. Kujawinski (2017). Mining mass spectrometry data: Using new computational tools to find novel organic compounds in complex environmental mixtures. Organic Geochemistry 110:92-99 (link to publication)

Kujawinski, E.B., K. Longnecker, H. Alexander, S.T. Dyhrman, C.L. Fiore, S.T. Haley, and W.M. Johnson (2017). Phosphorus availability regulates intracellular nucleotides in marine eukaryotic phytoplankton. Limnology and Oceanography Letters. (link to publication)

Longnecker, K. and E. B. Kujawinski (2016). Using network analysis to discern compositional patterns in ultrahigh resolution mass spectrometry data of dissolved organic matter. Rapid Communications in Mass Spectrometry 30: 2388-2394. (link to publication)

Post-publication note:

There have been some changes to Cytoscape. In order to use MetaNetter to conduct the analysis we described, you will need to download Cytoscape 2.8 and have Java 8 installed on your computer. Java 6 and 7 will not work with Cytoscape 2.8.

Longnecker, K., J. Futrelle, E. Coburn, M. C. Kido Soule and E. B. Kujawinski (2015). Environmental metabolomics: databases and tools for data analysis. Marine Chemistry 177, Part 2:366-373. (link to publication)

Kido Soule, M. C., K. Longnecker, W. M. Johnson and E. B. Kujawinski (2015). Environmental metabolomics: analytical strategies. Marine Chemistry 177, Part 2: 374-387. (link to publication)

Fiore, C. L., K. Longnecker, M. C. Kido Soule and E. B. Kujawinski (2015). Release of ecologically relevant metabolites by the cyanobacterium, Synechococcus elongatus CCMP 1631. Environmental Microbiology 17:3949-3963. (link to publication)

Longnecker, K., M. C. Kido Soule and E. B. Kujawinski (2015). Dissolved organic matter produced by Thalassiosira pseudonana. Marine Chemistry 168: 114-123. (link to publication)

Kujawinski, E.B., K. Longnecker, N.V. Blough, R. Del Vecchio, L. Finlay, J.B. Kitner, and S.J. Giovannoni (2009). Identification of possible source markers in marine dissolved organic matter using ultrahigh resolution mass spectrometry. Geochimica et Cosmochimica Acta 73: 4384-4399. (link to publication)