56. Mohiuddin, S.G., et al. The Diverse Phenotypic and Mutational Landscape Induced by Fluoroquinolone Treatment (submitted).

55. Sensenbach, S., et al. The Role of c-Jun Signaling in Cytidine Analog-Induced Cell Death in Melanoma (submitted).

54. Ghosh, S. and Orman, M.A. UV-Induced DNA Repair Mechanisms and Their Effects on Mutagenesis and Culturability in Escherichia coli (submitted).

53. Singh, G., et al. Systematic Design of Pulse Dosing to Eradicate Persister Bacteria: The Case of Fluoroquinolones. Under revision.

52. Zhu, Y., Pei, X., Novaj, A. et al. Large-scale copy number alterations are enriched for synthetic viability in BRCA1/BRCA2 tumors. Genome Med 16, 108 (2024). https://doi.org/10.1186/s13073-024-01371-y

51. Dewangan, N.K., Mohiuddin, S.G., Sensenbach, S. et al. Uncovering bacterial-mammalian cell interactions via single-cell tracking. BMC Biol 22, 256 (2024). https://doi.org/10.1186/s12915-024-02056-z

50. Ngo, H. G., Mohiuddin, S. G., Ananda, A., and Orman, M. A. 2024. Unraveling CRP/cAMP-Mediated Metabolic Regulation In Escherichia coli Persister Cells. eLife, 13:RP99735. https://doi.org/10.7554/eLife.99735.1

49. Kumar, U.R., Nguyen, N.T., Dewangan, N.K., Mohiuddin, S.G., Orman, M.A., Cirino, P.C. and Conrad, J.C., 2024. Co-Expression of type 1 fimbriae and flagella in Escherichia coli: consequences for adhesion at interfaces. Soft Matter. DOI: 10.1039/d4sm00499j

48. Mohiuddin, S.G., Ngo, H. and Orman, M.A., 2024. Unveiling the critical roles of cellular metabolism suppression in antibiotic tolerance. npj Antimicrobials and Resistance, 2(1), p.17.

47. Shiraliyev, R. and Orman, M.A., 2024. Metabolic disruption impairs ribosomal protein levels, resulting in enhanced aminoglycoside tolerance. eLife, 13, p.RP94903.

46. Ghosh, S. and Orman, M.A., 2024. Exploring the links between SOS response, mutagenesis, and resistance during the recovery period. Antimicrobial Agents and Chemotherapy, pp.e01462-23.

45. Singh G, Orman MA, Conrad JC, Nikolaou M. 2023. Systematic design of pulse dosing to eradicate persister bacteria. PLoS Comput Biol 19(1): e1010243.

44. Mafimoghaddam, S., Xu, Y., Sherman, M.B., Orlova, E.V., Karki, P., Orman, M.A. and Vekilov, P.G., 2022. Suppression of amyloid-β fibril growth by drug-engineered polymorph transformation. Journal of Biological Chemistry, 298(12).

43. Mohiuddin, S.G., Ghosh, S., Kavousi, P. and Orman, M.A., 2022. Proton Motive Force Inhibitors Are Detrimental to Methicillin-Resistant Staphylococcus aureus Strains. Microbiology Spectrum, 10(4), pp.e02024-22.

42. Mohiuddin, S.G., Nguyen, T.V. & Orman, M.A., 2022. Pleiotropic actions of phenothiazine drugs are detrimental to Gram-negative bacterial persister cells. Commun Biol 5, 217.

41. Mohiuddin, S.G., Massahi, A. and Orman, M.A., 2022. High-Throughput Screening of a Promoter Library Reveals New Persister Mechanisms in Escherichia Coli. Microbiology Spectrum, 10(1), pp.e02253-21.

40. Mohiuddin, S.G., Massahi, A. and Orman, M.A., 2022. Lon Deletion Impairs Persister Cell Resuscitation in Escherichia coli. Mbio, 13(1), pp. e02187-21.

39. Karki P, Angardi V, Mier JC and Orman MA, 2022. A Transient Metabolic State in Melanoma Persister Cells Mediated by Chemotherapeutic Treatments. Front. Mol. Biosci. 8:780192.

38. Karki, P.; Sensenbach, S.; Angardi, V.; Orman, M.A. 2021. BRAF-Inhibitor-Induced Metabolic Alterations in A375 Melanoma Cells. Metabolites, 11, 777.

37. Mohiuddin, S.G.; Ghosh, S.; Ngo, H.G.; Sensenbach, S.; Karki, P.; Dewangan, N.K.; Angardi, V.; Orman, M.A. 2021. Cellular Self-Digestion and Persistence in Bacteria. Microorganisms, 9, 2269.

36. Mohiuddin, S.G. and Orman, M.A., 2021. Monitoring Persister Resuscitation with Flow Cytometry. In Bacterial Persistence (pp. 209-222). Humana, New York, NY. (invited).

35. Karki, P. and Orman, M.A., 2021. High-throughput Screening of Chemical Compounds to Elucidate Their Effects on Bacterial Persistence. JoVE (Journal of Visualized Experiments), (168), p.e61597 (invited).

34. Karki, P. and Orman, M.A., 2020. Cancer Persisters: How Playing Dead Helps Cancer Cells Survive Treatment. Frontiers Young Minds. 8:549100 (outreach for kids).

33. Mohiuddin, S.G., Kavousi, P. and Orman, M.A., 2020. Flow-cytometry Analysis Reveals Persister Resuscitation Characteristics. BMC Microbiology, 20:202.

32. Mohiuddin, S.G., Hoang, T., Saba, A., Karki, P. and Orman, M.A., 2020. Identifying Metabolic Inhibitors to Reduce Bacterial Persistence. Frontiers in Microbiology, 11, p.472.

31. Karki, P., Mohiuddin, S.G., Kavousi, P. and Orman, M.A., 2020. Investigating the Effects of Osmolytes and Environmental pH on Bacterial Persisters. Antimicrobial Agents and Chemotherapy, 64(5).

30. Aedo SJ, Orman MA, Brynildsen MP, 2019. Stationary phase persister formation in Escherichia coli can be suppressed by piperacillin and PBP3 inhibition. BMC Microbiology, 19:140.

29. Rao R, Yang Q, Orman MA, Berthiaume F, Ierapetritou MG, Androulakis IP. Burn trauma disrupts circadian rhythms in rat liver. International journal of burns and trauma. 2016; 6(2):12-25.

28. Orman MA, Brynildsen MP. Persister formation in Escherichia coli can be inhibited by treatment with nitric oxide. Free radical biology & medicine. 2016; 93:145-54.

27. Orman MA, Henry TC, DeCoste CJ, Brynildsen MP. Analyzing Persister Physiology with Fluorescence-Activated Cell Sorting. Methods in molecular biology (Clifton, N.J.). 2016; 1333:83-100.

26. Orman MA, Brynildsen MP. Inhibition of stationary phase respiration impairs persister formation in E. coli. Nature communications. 2015; 6:7983.

25. Rao R, Orman MA, Berthiaume F, Androulakis IP. Dynamics of hepatic gene expression and serum cytokine profiles in single and double-hit burn and sepsis animal models. Data in brief. 2015; 3:229-33.

24. Mok WW*, Orman MA*, Brynildsen MP. Impacts of global transcriptional regulators on persister metabolism. Antimicrobial agents and chemotherapy. 2015; 59(5):2713-9. * Contributed equally.

23. Orman MA, Mok WW, Brynildsen MP. Aminoglycoside-enabled elucidation of bacterial persister metabolism. Current protocols in microbiology. 2015; 36:17.9.1-14.

22. Nguyen TT, Mattick JS, Yang Q, Orman MA, Ierapetritou MG, Berthiaume F, Androulakis IP. Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver. BMC bioinformatics. 2014; 15:83.

21. Amato SM*, Fazen CH*, Henry TC*, Mok WW*, Orman MA*, Sandvik EL*, Volzing KG*, Brynildsen MP. The role of metabolism in bacterial persistence. Frontiers in microbiology. 2014; 5:70. * Contributed equally.

20. Orman MA, Brynildsen MP. Establishment of a method to rapidly assay bacterial persister metabolism. Antimicrobial agents and chemotherapy. 2013; 57(9):4398-409.

19. Orman MA, Brynildsen MP. Dormancy is not necessary or sufficient for bacterial persistence. Antimicrobial agents and chemotherapy. 2013; 57(7):3230-9.

18. Amato SM, Orman MA, Brynildsen MP. Metabolic control of persister formation in Escherichia coli. Molecular cell. 2013; 50(4):475-87.

17. Orman MA, Ierapetritou MG, Androulakis IP, Berthiaume F. Effect of fasting on the metabolic response of liver to experimental burn injury. PloS one. 2013; 8(2):e54825.

16. Mattick JS, Yang Q, Orman MA, Ierapetritou MG, Berthiaume F, Gale SC, Androulakis IP. Impact of burn priming on immune and metabolic functions of whole liver in a rat cecal ligation and puncture model. International journal of burns and trauma. 2013; 3(1):55-65.

15. Calik P, Bozkurt B, Zerze GH, Inankur B, Bayraktar E, Boy E, Orman MA, Acik E, Ozdamar Th. Effect of co-substrate sorbitol different feeding strategies on human growth hormone production by recombinant Pichia pastoris. J. Chem. Technol. Biotechnol. 2013; 88:1631-1640.

14. Mattick JS, Yang Q, Orman MA, Ierapetritou MG, Berthiaume F, Androulakis IP. Long-term gene expression profile dynamics following cecal ligation and puncture in the rat. The Journal of surgical research. 2012; 178(1):431-42.

13. Yang Q, Mattick JS, Orman MA, Nguyen TT, Ierapetritou MG, Berthiaume F, Androulakis IP. Dynamics of hepatic gene expression profile in a rat cecal ligation and puncture model. The Journal of surgical research. 2012; 176(2):583-600.

12. Yang Q, Orman MA, Berthiaume F, Ierapetritou MG, Androulakis IP. Dynamics of short-term gene expression profiling in liver following thermal injury. The Journal of surgical research. 2012; 176(2):549-58.

11. Orman MA, Ierapetritou MG, Berthiaume F, Androulakis IP. Long-term dynamic profiling of inflammatory mediators in double-hit burn and sepsis animal models. Cytokine. 2012; 58(2):307-15.

10. Orman MA, Mattick J, Androulakis IP, Berthiaume F, Ierapetritou MG. Stoichiometry based steady-state hepatic flux analysis: computational and experimental aspects. Metabolites. 2012; 2(1):268-91.

9. Orman MA, Androulakis IP, Berthiaume F, Ierapetritou MG. Metabolic network analysis of perfused livers under fed and fasted states: incorporating thermodynamic and futile-cycle-associated regulatory constraints. Journal of theoretical biology. 2012; 293:101-10.

8. Orman MA, Ierapetritou MG, Androulakis IP, Berthiaume F. Metabolic response of perfused livers to various oxygenation conditions. Biotechnology and bioengineering. 2011; 108(12):2947-57.

7. Orman MA, Ierapetritou MG, Berthiaume F, Androulakis IP. The dynamics of the early inflammatory response in double-hit burn and sepsis animal models. Cytokine. 2011; 56(2):494-502.

6. Orman MA, Nguyen TT, Ierapetritou MG, Berthiaume F, Androulakis IP. Comparison of the cytokine and chemokine dynamics of the early inflammatory response in models of burn injury and infection. Cytokine. 2011; 55(3):362-71.

5. Orman MA, Berthiaume F, Androulakis IP, Ierapetritou MG. Pathway analysis of liver metabolism under stressed condition. Journal of theoretical biology. 2011; 272(1):131-40.

4. Orman MA, Berthiaume F, Androulakis IP, Ierapetritou MG. Advanced stoichiometric analysis of metabolic networks of mammalian systems. Critical reviews in biomedical engineering. 2011; 39(6):511-34.

3. Orman MA, Arai K, Yarmush ML, Androulakis IP, Berthiaume F, Ierapetritou MG. Metabolic flux determination in perfused livers by mass balance analysis: effect of fasting. Biotechnology and bioengineering. 2010; 107(5):825-35.

2. Orman MA, Calik P, Ozdamar TH. The influence of carbon sources on recombinant-human- growth-hormone production by Pichia pastoris is dependent on phenotype: a comparison of Muts and Mut+ strains. Biotechnology and applied biochemistry. 2009; 52(Pt 3):245-55.

1. Calik P, Orman MA, Celik E, Halloran SM, Calik G, Ozdamar TH. Expression system for synthesis and purification of recombinant human growth hormone in Pichia pastoris and structural analysis by MALDI-ToF Mass Spectrometry. Biotechnology progress. 2008; 24(1):221-6.