Publications of Amy K. Schmid    :chronological  alphabetical  combined  bibtex listing:

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Papers Published

  1. Martin, JH; Sherwood Rawls, K; Chan, JC; Hwang, S; Martinez-Pastor, M; McMillan, LJ; Prunetti, L; Schmid, AK; Maupin-Furlow, JA, GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii., Journal of Bacteriology, vol. 200 no. 17 (September, 2018) [doi]  [abs].
  2. Dulmage, KA; Darnell, CL; Vreugdenhil, A; Schmid, AK, Copy number variation is associated with gene expression change in archaea., Microbial Genomics, vol. 4 no. 9 (September, 2018) [doi]  [abs].
  3. Eun, Y-J; Ho, P-Y; Kim, M; LaRussa, S; Robert, L; Renner, LD; Schmid, A; Garner, E; Amir, A, Archaeal cells share common size control with bacteria despite noisier growth and division., Nature Microbiology, vol. 3 no. 2 (February, 2018), pp. 148-154, Springer Nature [doi]  [abs].
  4. Bushell, FML; Tonner, PD; Jabbari, S; Schmid, AK; Lund, PA, 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, vol. 9 (January, 2018), pp. 3196 [doi]  [abs].
  5. McDowell, IC; Manandhar, D; Vockley, CM; Schmid, AK; Reddy, TE; Engelhardt, BE, Clustering gene expression time series data using an infinite Gaussian process mixture model., Plos Computational Biology, vol. 14 no. 1 (January, 2018), pp. e1005896 [doi]  [abs].
  6. Martinez-Pastor, M; Tonner, PD; Darnell, CL; Schmid, AK, Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks., Annual Review of Genetics, vol. 51 (November, 2017), pp. 143-170 [doi]  [abs].
  7. Darnell, CL; Tonner, PD; Gulli, JG; Schmidler, SC; Schmid, AK, Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis., Msystems, vol. 2 no. 5 (September, 2017) [doi]  [abs].
  8. Martinez-Pastor, M; Lancaster, WA; Tonner, PD; Adams, MWW; Schmid, AK, A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea., Nucleic Acids Research, vol. 45 no. 17 (September, 2017), pp. 9990-10001 [doi]  [abs].
  9. Tonner, PD; Darnell, CL; Engelhardt, BE; Schmid, AK, Detecting differential growth of microbial populations with Gaussian process regression., Genome Research, vol. 27 no. 2 (February, 2017), pp. 320-333 [doi]  [abs].
  10. Darnell, CL; Schmid, AK, Systems biology approaches to defining transcription regulatory networks in halophilic archaea., Methods (San Diego, Calif.), vol. 86 (September, 2015), pp. 102-114 [doi]  [abs].
  11. Tonner, PD; Pittman, AMC; Gulli, JG; Sharma, K; Schmid, AK, A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea., Plos Genetics, vol. 11 no. 1 (January, 2015), pp. e1004912 [doi]  [abs].
  12. Dulmage, KA; Todor, H; Schmid, AK, Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein., Mbio, vol. 6 no. 5 (January, 2015), pp. e00649-e00615 [doi]  [abs].
  13. Todor, H; Gooding, J; Ilkayeva, OR; Schmid, AK, Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences., Plos One, vol. 10 no. 8 (January, 2015), pp. e0135693 [doi]  [abs].
  14. Kulp, AJ; Sun, B; Ai, T; Manning, AJ; Orench-Rivera, N; Schmid, AK; Kuehn, MJ, Genome-Wide Assessment of Outer Membrane Vesicle Production in Escherichia coli., Plos One, vol. 10 no. 9 (2015), pp. e0139200 [repository], [doi]  [abs].
  15. Todor, H; Dulmage, K; Gillum, N; Bain, JR; Muehlbauer, MJ; Schmid, AK, A transcription factor links growth rate and metabolism in the hypersaline adapted archaeon Halobacterium salinarum., Mol Microbiol, vol. 93 no. 6 (September, 2014), pp. 1172-1182 [doi]  [abs].
  16. Todor, H; Sharma, K; Pittman, AMC; Schmid, AK, Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea., Nucleic Acids Research, vol. 41 no. 18 (October, 2013), pp. 8546-8558 [23892291], [doi]  [abs].
  17. Sharma, K; Gillum, N; Boyd, JL; Schmid, A, The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon., Bmc Genomics, vol. 13 no. 1 (July, 2012), pp. 351 [doi]  [abs].
  18. Schmid, AK; Pan, M; Sharma, K; Baliga, NS, Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon., Nucleic Acids Research, vol. 39 no. 7 (April, 2011), pp. 2519-2533 [21109526], [doi]  [abs].
  19. Koide, T; Reiss, DJ; Bare, JC; Pang, WL; Facciotti, MT; Schmid, AK; Pan, M; Marzolf, B; Van, PT; Lo, F-Y; Pratap, A; Deutsch, EW; Peterson, A; Martin, D; Baliga, NS, Prevalence of transcription promoters within archaeal operons and coding sequences., Molecular Systems Biology, vol. 5 (January, 2009), pp. 285 [doi]  [abs].
  20. Schmid, AK; Reiss, DJ; Pan, M; Koide, T; Baliga, NS, A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability., Molecular Systems Biology, vol. 5 (January, 2009), pp. 282 [doi]  [abs].
  21. Van, PT; Schmid, AK; King, NL; Kaur, A; Pan, M; Whitehead, K; Koide, T; Facciotti, MT; Goo, YA; Deutsch, EW; Reiss, DJ; Mallick, P; Baliga, NS, Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage., Journal of Proteome Research, vol. 7 no. 9 (September, 2008), pp. 3755-3764 [doi]  [abs].
  22. Bonneau, R; Facciotti, MT; Reiss, DJ; Schmid, AK; Pan, M; Kaur, A; Thorsson, V; Shannon, P; Johnson, MH; Bare, JC; Longabaugh, W; Vuthoori, M; Whitehead, K; Madar, A; Suzuki, L; Mori, T; Chang, D-E; Diruggiero, J; Johnson, CH; Hood, L; Baliga, NS, A predictive model for transcriptional control of physiology in a free living cell., Cell, vol. 131 no. 7 (December, 2007), pp. 1354-1365 [doi]  [abs].
  23. Bare, JC; Shannon, PT; Schmid, AK; Baliga, NS, The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications., Bmc Bioinformatics, vol. 8 (November, 2007), pp. 456 [doi]  [abs].
  24. Schmid, AK; Reiss, DJ; Kaur, A; Pan, M; King, N; Van, PT; Hohmann, L; Martin, DB; Baliga, NS, The anatomy of microbial cell state transitions in response to oxygen., Genome Research, vol. 17 no. 10 (October, 2007), pp. 1399-1413 [doi]  [abs].
  25. Schmid, AK; Baliga, NS, Prokaryotic Systems Biology, in Systems Biology, Cell Engineering, edited by Al-Rubeai, M; Fussenegger, M, vol. 5 (December, 2006), pp. 395-423, SPRINGER [1-4020-5252-9_12]  [abs].
  26. Rothfuss, H; Lara, JC; Schmid, AK; Lidstrom, ME, Involvement of the S-layer proteins Hpi and SlpA in the maintenance of cell envelope integrity in Deinococcus radiodurans R1., Microbiology, vol. 152 no. Pt 9 (September, 2006), pp. 2779-2787 [doi]  [abs].
  27. Rothfuss, H; Lara, JC; Schmid, AK; Lidstrom, ME, Involvement of the S-layer proteins Hpi and SlpA in the maintenance of cell envelope integrity in Deinococcus radiodurans R1, Microbiology, vol. 152 no. 9 (2006), pp. 2779-2787 [doi]  [abs].
  28. Schmid, AK; Lipton, MS; Mottaz, H; Monroe, ME; Smith, RD; Lidstrom, ME, Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans., Journal of Proteome Research, vol. 4 no. 3 (May, 2005), pp. 709-718 [doi]  [abs].
  29. Schmid, AK; Howell, HA; Battista, JR; Peterson, SN; Lidstrom, ME, Global transcriptional and proteomic analysis of the Sig1 heat shock regulon of Deinococcus radiodurans., Journal of Bacteriology, vol. 187 no. 10 (May, 2005), pp. 3339-3351 [doi]  [abs].
  30. Schmid, AK; Howell, HA; Battista, JR; Peterson, SN; Lidstrom, ME, HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans., Molecular Microbiology, vol. 55 no. 5 (March, 2005), pp. 1579-1590 [doi]  [abs].
  31. Schmid, AK; Lidstrom, ME, Involvement of two putative alternative sigma factors in stress response of the radioresistant bacterium Deinococcus radiodurans., Journal of Bacteriology, vol. 184 no. 22 (November, 2002), pp. 6182-6189 [doi]  [abs].