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

search .

Papers Published

  1. Curtis, Z; Escudeiro, P; Mallon, J; Leland, O; Rados, T; Dodge, A; Andre, K; Kwak, J; Yun, K; Isaac, B; Martinez Pastor, M; Schmid, AK; Pohlschroder, M; Alva, V; Bisson, A, Halofilins as emerging bactofilin families of archaeal cell shape plasticity orchestrators., Proceedings of the National Academy of Sciences of the United States of America, vol. 121 no. 40 (October, 2024), pp. e2401583121 [doi]  [abs].
  2. Hackley, RK; Hwang, S; Herb, JT; Bhanap, P; Lam, K; Vreugdenhil, A; Darnell, CL; Pastor, MM; Martin, JH; Maupin-Furlow, JA; Schmid, AK, TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii., Molecular microbiology, vol. 121 no. 4 (April, 2024), pp. 742-766 [doi]  [abs].
  3. Hackley, RK; Vreugdenhil-Hayslette, A; Darnell, CL; Schmid, AK, A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities., PLoS genetics, vol. 20 no. 1 (January, 2024), pp. e1011115 [doi]  [abs].
  4. Martinez Pastor, M; Sakrikar, S; Hwang, S; Hackley, RK; Soborowski, AL; Maupin-Furlow, JA; Schmid, AK, TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii., Nucleic acids research, vol. 52 no. 1 (January, 2024), pp. 125-140 [doi]  [abs].
  5. Zheng, J; Mallon, J; Lammers, A; Rados, T; Litschel, T; Moody, ERR; Ramirez-Diaz, DA; Schmid, A; Williams, TA; Bisson-Filho, AW; Garner, E, Salactin, a dynamically unstable actin homolog in Haloarchaea., mBio, vol. 14 no. 6 (December, 2023), pp. e0227223 [doi]  [abs].
  6. M Martinez Pastor, S Sakrikar, S Hwang, RK Hackley, AL Soborowski, JA Maupin-Furlow, AK Schmid, TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii., Nucleic acids research (November, 2023) [doi]  [abs].
  7. Sakrikar, S; Hackley, RK; Martinez-Pastor, M; Darnell, CL; Vreugdenhil, A; Schmid, AK, The Hypersaline Archaeal Histones HpyA and HstA Are DNA Binding Proteins That Defy Categorization According to Commonly Used Functional Criteria., mBio, vol. 14 no. 2 (April, 2023), pp. e0344922 [doi]  [abs].
  8. Mondragon, P; Hwang, S; Schmid, A; Maupin-Furlow, JA, Hypochlorite Stress Assay for Phenotypic Analysis of the Halophilic Archaeon Haloferax volcanii Using an Improved Incubation Method and Growth Monitoring, Bio-protocol, vol. 12 no. 22 (November, 2022) [doi]  [abs].
  9. Mondragon, P; Hwang, S; Kasirajan, L; Oyetoro, R; Nasthas, A; Winters, E; Couto-Rodriguez, RL; Schmid, A; Maupin-Furlow, JA, TrmB Family Transcription Factor as a Thiol-Based Regulator of Oxidative Stress Response., mBio, vol. 13 no. 4 (August, 2022), pp. e0063322 [doi]  [abs].
  10. Pastor, MM; Sakrikar, S; Rodriguez, DN; Schmid, AK, Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea., Biomolecules, vol. 12 no. 5 (May, 2022), pp. 682 [doi]  [abs].
  11. Vogel, C; Balázsi, G; Löwer, A; Jiang, C; Schmid, AK; Sommer, M; Yang, L; Münch, C; Wang, A; Israni-Winger, K; Mühlhaus, T; Des Marais, DL; Oster, H; Socolovsky, M, What differentiates a stress response from responsiveness in general?, Cell systems, vol. 13 no. 3 (March, 2022), pp. 195-200 [doi] .
  12. Sakrikar, S; Schmid, AK, An archaeal histone-like protein regulates gene expression in response to salt stress., Nucleic acids research, vol. 49 no. 22 (December, 2021), pp. 12732-12743 [doi]  [abs].
  13. Tonner, PD; Darnell, CL; Bushell, FML; Lund, PA; Schmid, AK; Schmidler, SC, A Bayesian non-parametric mixed-effects model of microbial growth curves, edited by Papin, JA, PLOS Computational Biology, vol. 16 no. 10 (October, 2020), pp. e1008366-e1008366, Public Library of Science (PLoS) [doi]  [abs].
  14. Darnell, CL; Zheng, J; Wilson, S; Bertoli, RM; Bisson-Filho, AW; Garner, EC; Schmid, AK, The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea., mBio, vol. 11 no. 4 (August, 2020), pp. e01007-e01020 [doi]  [abs].
  15. Schmid, AK; Allers, T; DiRuggiero, J, SnapShot: Microbial Extremophiles., Cell, vol. 180 no. 4 (February, 2020), pp. 818-818.e1 [doi]  [abs].
  16. Hackley, RK; Schmid, AK, Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response., Journal of molecular biology, vol. 431 no. 20 (September, 2019), pp. 4147-4166 [doi]  [abs].
  17. Hwang, S; Chavarria, NE; Hackley, RK; Schmid, AK; Maupin-Furlow, JA, Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen., International journal of molecular sciences, vol. 20 no. 19 (September, 2019), pp. E4784 [doi]  [abs].
  18. Zaretsky, M; Darnell, CL; Schmid, AK; Eichler, J, N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility., Frontiers in microbiology, vol. 10 (January, 2019), pp. 1367 [doi]  [abs].
  19. Schmid, AK, Conserved principles of transcriptional networks controlling metabolic flexibility in archaea., Emerging topics in life sciences, vol. 2 no. 4 (December, 2018), pp. 659-669 [doi]  [abs].
  20. 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), pp. e00244-e00218 [doi]  [abs].
  21. 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].
  22. 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].
  23. 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 Comput Biol, vol. 14 no. 1 (January, 2018), pp. e1005896 [doi]  [abs].
  24. 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].
  25. FML Bushell, PD Tonner, S Jabbari, AK Schmid, PA Lund, HASH(0x9429f68), Frontiers in microbiology, vol. 9 (2018), pp. 3196 [doi]  [abs].
  26. FML Bushell, PD Tonner, S Jabbari, AK Schmid, PA Lund, 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 (2018), pp. 3196 [doi]  [abs].
  27. 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].
  28. Darnell, CL; Tonner, PD; Gulli, JG; Schmidler, SC; Schmid, AK, Systematic discovery of Archaeal transcription factor functions in regulatory networks through quantitative phenotyping analysis, edited by Shank, EA, mSystems, vol. 2 no. 5 (October, 2017), pp. e00032-e00017, American Society for Microbiology [doi]  [abs].
  29. 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].
  30. 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].
  31. 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 (September, 2015), pp. e00649-e00615 [doi]  [abs].
  32. 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].
  33. Eun, Y; Kim, M; LaRussa, SA; Dulmage, K; Schmid, AK; Garner, EC, How archaeal cells generate their cell shape, MOLECULAR BIOLOGY OF THE CELL, vol. 26 (January, 2015), pp. 2 pages, AMER SOC CELL BIOLOGY .
  34. 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].
  35. 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].
  36. 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 (2015), pp. e0135693 [doi]  [abs].
  37. 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].
  38. 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].
  39. 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].
  40. 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].
  41. 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].
  42. 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].
  43. 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].
  44. 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].
  45. 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].
  46. 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].
  47. 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].
  48. 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 (Reading, England), vol. 152 no. Pt 9 (September, 2006), pp. 2779-2787 [doi]  [abs].
  49. 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].
  50. 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].
  51. 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].
  52. 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].