Publications

 

    1. Sakrikar, S. and Schmid, A.K. 2021. An archaeal histone-like protein regulates gene expression in response to salt stress. BioRxiv. https://doi.org/10.1101/2021.10.14.464415
    2. Tonner, P.D., Darnell, C.L., Bushell, F.M.L., Lund, P.A.,Schmid, A.K., Schmidler, S.C. 2020. ABayesian non-parametric mixed-Effects model of microbial growth curves. PLoS Comp Biol.16(10):e1008366. https://doi.org/10.1371/journal.pcbi.100836624.
    3. Darnell, C.L., Zheng, J., Wilson, S., Bertoli, R.M., Bisson-Filho, A.W., Garner, E.C.,*Schmid, A.K.2020. The ribbon-helix-helix domain protein CdrS regulates the tubulin homolog ftsZ2 to control celldivision in archaea. mBio, 11:e01007-20. 10.1128/mBio.01007-20.23.
    4. Schmid, A.K.*, Allers, T.A., and DiRuggiero, J. 2020. SnapShot: Microbial extremophiles. Cell.180(4):818-818.e1. https://doi.org/10.1016/j.cell.2020.01.01822.
    5. Hwang, S., Chavarria, R.K., Schmid, A.K., and Maupin-Furlow, J.A. 2019. Gene expression of Haloferax volcanii on abundant and fixed sources of nitrogen.International Journal of MolecularSciences.20(19):E4784. doi: 10.3390/ijms20194784.21.
    6. Hackley, R. and Schmid, A.K.2019. Global transcriptional programs in archaea share features with eukaryotic environmental stress response. J Mol Biol.S0022-2836(19)30477-2.doi: 10.1016/j.jmb.2019.07.029.20.
    7. Zaretsky, M., Darnell, C.L.,Schmid, A.K., Eichler, J.* 2019. N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility. Frontiers in Microbiology.10:1367. doi: 10.3389/fmicb.2019.01367.19.
    8. Bushell, F.M.L., Tonner, P.D., Jabbari, S.,Schmid, A.K., Lund, P.A.* 2019. Synergistic impacts of organic acids and pH on growth of Pseudomonas aeruginosa: a comparison of parametric and Bayesian non-parametric methods to model growth. Frontiers in Microbiology. 9:3196. doi: 10.3389/fmicb.2018.0319618.
    9. Schmid, A.K.*. 2018. Transcriptional regulatory networks governing metabolic flexibility in archaea. Emerging Topics in Life Sciences. 2(4):659-669.17.
    10. Martin, J.H., Rawls, K.S., Chan, J.C., Hwang, S., Martinez-Pastor, M., McMillan, L.J., Prunetti, L.,Schmid, A.K.*, and Maupin-Furlow, J.A. 2018. GlpR is a direct transcriptional repressor of fructose metabolic genes in Haloferax volcanii. Journal of Bacteriology. 200(17):e00244-18. doi: 10.1128/JB.00244-18.16. Featured article.
    11. Dulmage, K.A., Darnell, C.L., Vreugdenhil, A.,Schmid, A.K.* 2018. Copy number variation is associ-ated with gene expression change in archaea. Microbial Genomics. 4(9). doi: 10.1099/mgen.0.000210
    12. McDowell, I.C., Manandhar, D., Vockley, C.M., Schmid, A.K., Reddy, T.E.*, Engelhardt, B.E.E.* 2019. Clustering gene expression time series data using an infinite Gaussian process mixture model. PLOS Comp Biol. https://doi.org/10.1371/journal.pcbi.1005896 *Equal contributions
    13. Eun, Y-J., Ho, P-Y., Kim, M., Renner, L., LaRussa, S., Robert, L., Schmid, A.K.*, Garner, E.*, Amir, A.* 2018. Archaeal cells share common size control with bacteria despite noisier growth and division. Nature Micro. doi:10.1038/s41564-017-0082-6. *Equal contributions.
    14. Martinez-Pastor, M.M., Tonner, P.D., Darnell, C.L., Schmid, A.K. 2017. Transcriptional regulation in archaea: from individual genes to global networks. Ann Rev Genet. 51:143-70.
    15. 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
    16. 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.
    17. 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.
    18. 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.
    19. 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.
    20. 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.
    21. Darnell, C.L. and Schmid, A.K. 2015. Systems biology approaches to defining transcription regulatory networks in halophilic Archaea.Methods, 86:102-14.27(2):320-333.
    22. 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.
    23. 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.
    24. 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.
    25. 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.
    26. 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.
    27. 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.
    28. 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.
    29. 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.
    30. 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.
    31. 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).
    32. 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.
    33. 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.
    34. 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.
    35. 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.
    36. 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.
    37. 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.
    38. 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.