Metabolic Ecology, Genomics and Transcriptomics

* graduate student co-author, ** undergraduate student co-author

*Alexander, H, B. Jenkins, T. Rynearson, S. Dyhrman (2015) Metatranscriptome analyses indicate resource partitioning between diatoms in the field. Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1421993112

Keeling, P.J., Burki, F., Wilcox, H.M., Allam, B., Allen, E.E., Amaral-Zettler, L.A., Armbrust, E.V., Archibald, J.M., Bharti, A.K., Bell, C.J., Beszteri, B., Bidle, K.D., Cameron, C.T., Campbell, L., Caron, D.A., Cattolico, R.A., Collier, J.L., Coyne, K., Davy, S.K., Deschamps, P., Dyhrman, S.T., Edvardsen, B., Gates, R.D., Gobler, C.J., Greenwood, S.J., Guida, S.M., Jacobi, J.L., Jakobsen, K.S., James, E.R., Jenkins, B., John, U., Johnson, M.D., Juhl, A.R., Kamp, A., Katz, L.A., Kiene, R., Kudryavtsev, A., Leander, B.S., Lin, S., Lovejoy, C., Lynn, D., Marchetti, A., McManus, G., Nedelcu, A.M., Menden-Deuer, S., Miceli, C., Mock, T., Montresor, M., Moran, M.A., Murray, S., Nadathur, G., Nagai, S., Ngam, P.B., Palenik, B., Pawlowski, J., Petroni, G., Piganeau, G., Posewitz, M.C., Rengefors, K., Romano, G., Rumpho, M.E., Rynearson, T., Schilling, K.B., Schroeder, D.C., Simpson, A.G.B., Slamovits, C.H., Smith, D.R., Smith, G.J., Smith, S.R., Sosik, H.M., Stief, P., Theriot, E., Twary, S.N., Umale, P.E., Vaulot, D., Wawrik, B., Wheeler, G.L., Wilson, W.H., Xu, Y., Zingone, A., Worden, A.Z., 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLoS Biol 12 (6), e1001889.

*Alexander, H., Jenkins, B.D., Rynearson, T.A., Saito, M.A., Mercier, M.L.  Dyhrman, S.T., (2012) Identifying reference genes with stable expression from high throughput sequence data. Frontiers in Aquatic Microbiology. doi: 10.3389/fmicb.2012.00385

#Dyhrman, S., #B. Jenkins, #T. Rynearson, #M. Saito, *M. Mercier, *H. Alexander, *L. Whitney, A. Drzewianowski, V. Bulygin, *E. Bertrand, Z. Wu, C. Benitez-Nelson, and A. Heithoff. (2012) The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse Phosphorus stress response. PLoS One 7:e33768

# Authors contributed equally to the work

Rynearson, T.A. and B. Palenik. (2011) Learning to read the oceans: Genomics of marine phytoplankton. Advances in Marine Biology, Vol 60:1-39

Wu, Z., Jenkins, B. D., Rynearson, T. A., Dyhrman, S. T., Saito, M. A., *Mercier, M. & *Whitney, L.  (2010) Empirical Bayes Analysis of Sequencing-based Transcriptional Profiling Without Replicates. BMC Bioinformatics. 11(1): 564

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Armbrust, E.V., Rynearson, T.A. and Jenkins. (2006) Genomic insights into diatom evolution and metabolism. In Genomics and Evolution of Microbial Eukaryotes, Eds. Katz, L.A. and Bhattacharya, D. 201-213

Armbrust, E. V., J. A. Berges, C. Bowler, B. R. Green, D. Martinez, N. H. Putnam, S. G. Zhou, A. E. Allen, K. E. Apt, M. Bechner, M. A. Brzezinski, B. K. Chaal, A. Chiovitti, A. K. Davis, M. S. Demarest, J. C. Detter, T. Glavina, D. Goodstein, M. Z. Hadi, U. Hellsten, M. Hildebrand, B. D. Jenkins, J. Jurka, V. V. Kapitonov, N. Kroger, W. W. Y. Lau, T. W. Lane, F. W. Larimer, J. C. Lippmeier, S. Lucas, M. Medina, A. Montsant, M. Obornik, M. S. Parker, B. Palenik, G. J. Pazour, P. M. Richardson, T. A. Rynearson, M. A. Saito, D. C. Schwartz, K. Thamatrakoln, K. Valentin, A. Vardi, F. P. Wilkerson, and D. S. Rokhsar. (2004) The genome of the diatom Thalassiosira pseudonana: Ecology, evolution and metabolism. Science 306: 79-86, 10.1126/science.1101156