Publications
  1. McDowell, I.C., Manandhar, D., Vockley, C.M., Schmid, A.K., Reddy, T.E.*, Engelhardt, B.E.E.* Clustering gene expression time series data using an infinite Gaussian process mixture model. PLOS Comp Biol. In press. *Equal contributions
  2. Eun, Y-J., Ho, P-Y., Kim, M., Renner, L., LaRussa, S., Robert, L., Schmid, A.K.*, Garner, E.*, Amir, A.* Archaeal cells share common size control with bacteria despite noisier growth and division. Nature Micro. doi:10.1038/s41564-017-0082-6. *Equal contributions.
  3. Martinez-Pastor, M.M., Tonner, P.D., Darnell, C.L., Schmid, A.K. Transcriptional regulation in archaea: from individual genes to global networks. Ann Rev Genet. 51:143-70.
  4. Darnell, C.L.*, Tonner, P.D.*, Gulli, J.G., Schmidler, S., Schmid, A.K. 2017. Systematic discovery of archaeal transcription factor functions in regulatory networks through quantitative phenotyping analysis. mSystems. 19;2(5). pii: e00032-17. *Equal contributions
  5. Martinez-Pastor, M., Lancaster, W.A., Tonner, P.D., Adams, M.W.W., Schmid, A.K. 2017. A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea.Nucleic Acids Research, 45(17):9990-10001.
  6. Tonner, P.D., Darnell, C.L., Engelhardt, B.E., Schmid, A.K. 2017. Detecting differential growth of microbial populations with Gaussian process regression. Genome Research,27:230-333.
  7. Kulp, A.J., Sun, B., Ai, T., Manning, A.J., Orench-Rivera, N., Schmid, A.K., Keuhn, M.J. 2015. Genome-wide assessment of outer membrane vesicle production in Escherichia coli. PLoS ONE.,10(9): e0139200.
  8. Dulmage, K.A., Todor, H., Schmid, A.K. 2015. Growth-phase-specific modulation of cell morphology and gene expression by an archaeal histone protein. mBio, 6(5):e00649-15.
  9. Todor, H., Gooding, J., Ilkayeva, O., Schmid, A.K. 2015. Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences. PLoS ONE.,0(8):e0135693.
  10. Darnell, C.L. and Schmid, A.K. 2015. Systems biology approaches to defining transcription regulatory networks in halophilic Archaea.Methods, 86:102-14.
  11. 27(2):320-333.
  12. Tonner, P.D., Pittman, A.M.C., Gulli, J.G., Sharma, K., Schmid, A.K. 2015. A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea. PLoS Genetics.,11(1):e1004912.
  13. Todor, H., Dulmage, K., Gillum, N., Bain, J.R., Muehlbauer, M.J., Schmid, A.K. 2014. A transcription factor links growth rate and metabolism in the hypersaline adapted archaeon Halobacterium salinarum. Mol Microbiol., 93(6):1172-82.
  14. Todor, H., Sharma, K., Pittman, A.M.C., Schmid, A.K. 2013. Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea. Nucleic Acids Res., 41(18):8546-58.
  15. Sharma, K., Gillum, N., Boyd, J.L., and Schmid, A.K. 2012. The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon. BMC Genomics, 13:351.
  16. Schmid A.K., Pan M., Sharma K., and Baliga N.S., 2011. Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res., 39(7): 2519-33. Supplemental data.
  17. Koide , T., Reiss, D.J., Bare, C.J., Facciotti , M., Schmid , A.K., Pan, M., Marzolf, B., Van , P., Lo , F-Y., Pratap, A., Deutsch , E., Peterson , A., Martin, D., Pang, W.L., Baliga, N.S. 2009. Prevalence of transcription promoters within archaeal operons and coding sequences. Nature Mol Sys Biol., 5:285.
  18. Schmid, A.K. Reiss, D.J., Pan, M., Koide, T., and Baliga, N.S. 2009. A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Nature Mol Sys Biol., 5:282.
  19. Van, P.T., Schmid, A.K., King, N., Kaur, A., Pan, M., Whitehead, K., Koide, T., Facciotti, M., Reiss, D.J., and Baliga, N.S. 2007. The Halobacterium salinarum NRC-1 peptide atlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res. 7(9):3755-64.
  20. Schmid, A.K., Reiss, D.J., Kaur, A., Pan, M., King, N., Van, P., Hohmann, L., Martin, D.B., and Baliga, N.S. 2007. Anatomy of microbial cell state transitions in response to oxygen. Genome Research. 17(10):1399-413.
  21. Bonneau, R., Facciotti, M.T., Reiss, D.J., Schmid, A.K., Pan, M., Kaur, A., Thorsson, V., Shannon, P., Johnson, M., Bare, C.J., Longabaugh, W., Vuthoori, M., Whitehead, K., DiRuggiero, J., Johnson, C., Hood L., and Baliga, N.S. 2007. A predictive model for transcriptional control of physiology in a free-living cell. Cell. 131(7):1354-65 (cover article).
  22. Bare, C.J., Shannon, P.T., Schmid, A.K., Baliga, N.S. 2007. The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics. 8:456.
  23. Rothfuss, H.M., Lara, J.C., Schmid, A.K., and Lidstrom, M.E. 2006. Involvement of the S-layer proteins Hpi and SlpA in the maintenance of cell envelope integrity in Deinococcus radiodurans R1. Microbiology. 152(9): 2779-2787.
  24. Schmid, A.K. and Baliga, N.S. 2006. Prokaryotic Systems Biology, p395-423. In M. Al-Rubeai and M. Fussenegger (ed.), Cell Engineering Vol. 5: Systems Biology. Springer Press, New York, NY.
  25. Schmid, A.K., Howell, H.H., Battista, J.R., Peterson, S.N., and Lidstrom, M.E. 2005. HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans. Mol Microbiol. 55(5):1579-1590.
  26. Schmid, A.K., Howell, H.H., Battista, J.R., Peterson, S.N., and Lidstrom, M.E. 2005. Global transcriptional and proteomic analysis of the Sig1 heat shock regulon of Deinococcus radiodurans. J Bacteriol. 187(10):3339-3351.
  27. Schmid, A.K., Lipton, M.S., Mottaz, H., Monroe, M.E., Smith, R.D., and Lidstrom, M.E. 2005. Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans. J. Proteome Res. 4(3):709-718.
  28. Schmid, A.K. and Lidstrom, M.E., 2002. Involvement of two putative alternative sigma factors in stress response of the radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 184(22):6182-6189.