Publications

91. Covalent Inhibitors for Bacterial Histidine Kinases

Rodriguez, P. D.;† Fihn, C. A.;† Goswami, M.; Carlson, E. E. Chem. Comm., 2026, 62, 5482-5486.

https://pubs.rsc.org/en/content/articlelanding/2026/cc/d5cc06657c

89. Decoding the Penicillin-Binding Proteins with Activity-Based Probes

Carlson, E. E.; Sparks, N.;† Diwakar, S.† Acc. Chem. Res, 2025, 58, 1754–1763.

 https://doi.org/10.1021/acs.accounts.5c00113

87. Recent Advances in High-Throughput Screening Methods for Bacteria

Addis, H. A. and Carlson, E. E. Curr. Opin. Chem. Biol. 2025, 85, 102571.

https://doi.org/10.1016/j.cbpa.2025.102571

86. Challenges of Biological Complexity in the Study of Nanotoxicology

Northwick, A. B. and Carlson, E. E. Chem. Res. Toxicol. 2025, 38, 7–14.

 https://doi.org/10.1021/acs.chemrestox.4c00220

Included in special issue “Chemical Biology Approaches for Investigating Toxicological Mechanisms.”

84. β-Lactam Titration Assays to Evaluate Penicillin-Binding Protein Selectivity

Sharan, D. and Carlson, E. E. ChemRxiv, 2025, DOI: 10.26434/chemrxiv-2025-qb9jl. Methods Mol. Biol. In Press.

https://doi.org/10.26434/chemrxiv-2025-qb9jl

81. Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock

Mitchell, S. M., Kearns, D. B. and Carlson, E. E. bioRxiv, 2023, 533529v1. Appl. Environ. Microbiol., 2024, 90, e0054823.

 https://doi.org/10.1128/aem.00548-23

80. Molecular-Level Characterization of Protein-Nanoparticle Interactions: Orientation, Deformation and Matrix Effects

Northwick, A. B.; Wang, Y.; Tuga, B.; Haynes, C. L.; Hernandez, R.; Carlson, E. E. ChemRxiv, 2024, DOI: 10.26434/chemrxiv-2025-s3f6v. Under Review.

 https://doi.org/10.26434/chemrxiv-2025-s3f6v

75. Metabolomics Reveals a "Trimeric" γ-Actinorhodin from Streptomyces coelicolor M145

Marshall, A. P.; Carlson, E. E. ChemBioChem 2023, 24, e202200757.

http://dx.doi.org/10.1002/cbic.202200757

74. Live-cell Profiling of Penicillin-Binding Protein Inhibitors in Escherichia coli MG1655

Shirley, J. D.; Nauta, K.; Carlson, E. E. ACS Infect. Dis. 2022, 8, 1241-1252.

https://doi.org/10.1021/acsinfecdis.2c00004

73. Combined Structural Analysis and Molecular Dynamics Reveal Novel Penicillin-Binding Protein Inhibition Mode with β-Lactones

Flanders, P. L.; Contreras-Martel, C.; Brown, N. W.;† Shirley, J. D.;† Martins, A.; Nauta, K. M.; Dessen, A.; Carlson, E. E.;* Ambrose. E. A.* ACS Chem. Biol. 2022, 17, 3110-3120.

https://doi.org/10.1021/acschembio.2c00503 

69. High-level carbapenem tolerance requires antibiotic-induced outer membrane modifications

Murtha, A. N.;  Kazi, M. I.; Schargel, R. D.; Cross, T.; Fihn, C. A.; Cottoir, V.; Carlson, E. E.; Boll, J. M.; Dörr, T. PLoS Pathogens, 2022, 18, e1010307.

https://dx.doi.org/10.1371/journal.ppat.1010307

55. Chronic Exposure to Complex Metal Oxide Nanoparticles Elicits Rapid Resistance in Shewanella oneidensis MR-1

Mitchell, S. L.; Hudson-Smith, N. V.; Cahill, M. S.; Reynolds, B. N.; Frand, S. D.; Green, C. M.; Wang, C.; Hang, M. N.; Tapia Hernandez, R.; Hamers, R. J.; Feng, Z. V.; Haynes, C. L.; Carlson, E. E. Chem. Sci. 2019, 10, 9768-9781.

**Press releases from NSF, AAAS, Chemistry World, UMN, and Star Tribune.

https://dx.doi.org/10.1039/C9SC01942A

53. Structure Elucidation of Macrolide Antibiotics Using MSn Analysis and Deuterium Labelling

Johnson, A. R.; Carlson, E. E. J. Am. Soc. Mass Spectrom., 2019, 30, 1464-1480.

https://dx.doi.org/10.1007/s13361-019-02210-w

52. Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2

Gehrke, E. J.; Zhang, X., Pimentel-Elardo, S. M.; Johnson, A. R.; Rees, C. A.; Jones S. E.; Hindra; Gehrke, S. S.; Turvey S.; Boursalie, S.; Hill, J. E.; Carlson, E. E.; Nodwell, J. R.; Elliot M. A. Elife, 2019, 8, e47691.

https://elifesciences.org/articles/47691

50. Activity-Based Protein Profiling Methods to Study Bacteria: The Power of Small Molecule Electrophiles

Sharifzadeh, S.; Shirley, J. D.; Carlson, E. E. In: Curr. Top. Microbiol. and Immunol. Springer, Berlin, Heidelberg. Edited Cravatt, B. F.; Hsu, K-L.; Weerapana, E. 2019. Invited Book Chapter.

https://dx.doi.org/10.1007/82_2018_135

47. Disarming the virulence arsenal of Pseudomonas aeruginosa by blocking two-component system signaling

Goswami, M.; Espinasse, A.; Carlson, E. E. Chem. Sci., 2018, 10, 7332-7337.

Selected as part of the 2018 Chemical Science HOT Article Collection 

https://dx.doi.org/10.1039/C8SC02496K

46. Tiny Things with Enormous Impact: Nanotechnology in the Fight Against Infectious Disease

Mitchell, S. L. and Carlson, E. E. ACS Infect. Dis. 2018, 12, 1432-1435. Invited View Point.

https://dx.doi.org/10.1021/acsinfecdis.8b00138

45. Real-Time Visualization of In Vitro Transcription of a Fluorescent RNA Aptamer: An Experiment for the Upper-Division Undergraduate or First-Year Graduate Laboratory

Heili, J. M.; Gomez-Garcia, J.; Gaut, N. J.; Cash, B. W.; Aufdembrink, L. M.; Heffron, B. A.; Shirley, J. S.; Carlson, E. E.; Admala, K. P.; Engelhart, A. E. J. Chem. Ed. 2018, 95, 1867–1871.

https://dx.doi.org/10.1021/acs.jchemed.7b00735

44. Exploration of the effects of γ-phosphate modified ATP analogs on histidine kinase autophosphorylation

Chase, O. M.; Espinasse, A.; Carlson, E. E. Biochemistry 2018, 57, 4368–4373.

https://dx.doi.org/10.1021/acs.biochem.8b00485

43. Screening Serine/Threonine and Tyrosine Kinase Inhibitors for Histidine Kinase Inhibition

Wilke, K. E.; Fihn, C. A.; Carlson, E. E. Bioorg. Med. Chem. 2018, 26, 5322-5326.

https://dx.doi.org/10.1016/j.bmc.2018.04.047

42. Rational Design Of Selective Adenine-Based Scaffolds For Inactivation Of Bacterial Histidine Kinases

Goswami, M.; Wilke, K. E.; Carlson, E. E. J. Med. Chem., 2017, 60, 8170-8182.

https://dx.doi.org/10.1021/acs.jmedchem.7b01066

41. Novel Electrophilic Scaffold for Imaging of Essential Penicillin-Binding Proteins in Streptococcus pneumoniae

Sharifzadeh, S.; Boersma, M. J.; Kocaoglu, O.;† Shokri, A.;† Brown, C. L.; Shirley, J. D.; Winkler, M. E. and Carlson, E. E. ACS Chem. Biol. 2017, 12, 2849-2857.

https://doi.org/10.1021/acschembio.7b00614

40. Mass Spectrometry-Based Assay for the Rapid Detection of Thiol-Containing Natural Products

Capehart, S. L. and Carlson, E. E. Chem. Commun. 2016, 52, 13229-13232.

https://doi.org/10.1039/C6CC07111B

39. Progress and Prospects for Small-Molecule Probes of Bacterial Imaging. 

Kocaoglu, O. and Carlson, E. E. Nat. Chem. Biol. 2016, 12, 472-478. Invited Perspective.

https://doi.org/10.1038/nchembio.2109

38. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Wang, M.; Carver, J. J.; Phelan, V. V.; Sanchez, L. M.; Garg, N.; Peng, Y.; Nguyen, D. D.; Watrous, J.; Kapono, C. A.; Luzzatto-Knaan, T.; Porto, C.; Bouslimani, A.; Melnik, A. V.; Meehan, M. J.; Liu, W.T.; Crüsemann, M.; Boudreau, P. D.; Esquenazi, E.; Sandoval-Calderón, M.; Kersten, R. D.; Pace, L. A.; Quinn, R. A.; Duncan, K. R.; Hsu, C. C.; Floros, D. J.; Gavilan, R. G.; Kleigrewe, K.; Northen, T.; Dutton, R. J.; Parrot, D.; Carlson, E. E.; Aigle, B.; Michelsen, C. F.; Jelsbak, L.; Sohlenkamp, C.; Pevzner, P.; Edlund, A.; McLean, J.; Piel, J.; Murphy, B. T.; Gerwick, L.; Liaw, C. C.; Yang, Y. L.; Humpf, H. U.; Maansson, M.; Keyzers, R. A; Sims, A. C.; Johnson, A. R.; Sidebottom, A. M.; Sedio, B. E.; Klitgaard, A.; Larson, C. B.; Boya, P. C. A.; Torres-Mendoza, D.; Gonzalez, D. J.; Silva, D. B.; Marques, L. M.; Demarque, D. P.; Pociute, E.; O'Neill, E. C.; Briand, E.; Helfrich, E. J.; Granatosky, E. A.; Glukhov, E.; Ryffel, F.; Houson, H.; Mohimani, H.; Kharbush, J. J.; Zeng, Y.; Vorholt, J. A.; Kurita, K. L.; Charusanti, P.; McPhail, K. L.; Nielsen, K. F.; Vuong, L.; Elfeki, M.; Traxler, M. F.; Engene, N.; Koyama, N.; Vining, O. B.; Baric, R.; Silva, R. R.; Mascuch, S. J.; Tomasi, S.; Jenkins, S.; Macherla, V.; Hoffman, T.; Agarwal, V.; Williams, P. G.; Dai, J.; Neupane, R.; Gurr, J.; Rodríguez, A. M.; Lamsa, A.; Zhang, C.; Dorrestein, K.; Duggan, B. M.; Almaliti, J.; Allard, P. M.; Phapale, P.; Nothias, L. F.; Alexandrov, T.; Litaudon, M.; Wolfender, J. L.; Kyle, J. E.; Metz, T. O.; Peryea, T.; Nguyen, D. T.; VanLeer, D.; Shinn, P.; Jadhav, A.; Müller, R.; Waters, K. M.; Shi, W.; Liu, X.; Zhang, L.; Knight, R.; Jensen, P. R.; Palsson, B. Ø.; Pogliano, K.; Linington, R. G.; Gutiérrez, M.; Lopes, N. P.; Gerwick, W. H.; Moore, B. S.; Dorrestein, P. C.; Bandeira, N. Nat. Biotechnol. 2016, 34, 828-837.

https://doi.org/10.1038/nbt.3597

37. Thiol-ene Enabled Detection of Thiophosphorylation as a Labeling Strategy for Phosphoproteins

Wilke, K. E. and Carlson, E. E. Methods Mol. Biol. 2016, 1355, 3-15. Invited.

https://doi.org/10.1007/978-1-4939-3049-4_1

36. New Approaches to Understanding Bacterial Histidine Kinase Activity and Inhibition

Wilke, K. E. and Carlson, E. E. In Kinomics: Approaches and Applications, Kraatz, H.B.; Martic, S., Eds.; WILEY-VCH: Weinheim, 2015, pp 233-254. Invited Book Chapter.

https://doi.org/10.1002/9783527683031.ch10

35. Profiling of Beta-Lactam Selectivity for Penicillin-Binding Proteins in Streptococcus pneumoniae D39

Kocaoglu, O.;† Tsui, H-C. T.;† Winkler, M. E; Carlson, E. E. Antimicrob. Agents Chemother. 2015, 59, 3548-3555.

† Co-first authors

https://doi.org/10.1128/aac.05142-14

34. Inactivation of Multiple Bacterial Histidine Kinases by Targeting the ATP-Binding Domain

Wilke, K. E.; Francis, S.; Carlson, E. E. ACS Chem. Biol. 2015, 10, 328-335.

https://doi.org/10.1021/cb5008019

33. Profiling of Beta-Lactam Selectivity for Penicillin-Binding Proteins in Escherichia coli DC2

 Kocaoglu, O. and Carlson, E. E. Antimicrob. Agents Chemother. 2015, 59, 2785-2790.

https://doi.org/10.1128/aac.04552-14

32. Chemoselective Enrichment as a Tool to Increase Access to Bioactive Natural Products: Case Study Borrelidin

Trader, D. J. and Carlson, E. E. Bioorg. Med. Chem. Lett. 2015, 25, 4767-4769. 25th Anniversary Issue Entitled, "Recent Advances in Medicinal Chemistry and Chemical Biology.”

https://doi.org/10.1016/j.bmcl.2015.07.062

31. Accurate Mass MS/MS/MS Analysis of Siderophores Ferrioxamine B and E1 by Collision-Induced Dissociation Electrospray Mass Spectrometry

Sidebottom, A. M; Karty, J. A.; Carlson, E. E. J. Am. Soc. Mass Spectrom. 2015, 26, 1899-1902.

https://doi.org/10.1007/s13361-015-1242-7

30. Collision-Induced Dissociation Mass Spectrometry: A Powerful Tool for Natural Product Structure Elucidation

Johnson, A. J. and Carlson, E. E. Anal. Chem. 2015, 87, 10668-10678. Invited Feature.

Selected for virtual issue of Analytical Chemistry to “Highlight Selected Women Analytical Chemists.”

https://doi.org/10.1021/acs.analchem.5b01543

29. A Reinvigorated Era of Bacterial Secondary Metabolite Discovery

Sidebottom, A. M. and Carlson, E. E. Curr. Opin. Chem. Biol. 2015, 24, 104-111. Invited Review in –Omics Themed Issue.

https://doi.org/10.1016/j.cbpa.2014.10.014

28. Biological Responses to Engineered Nanomaterials: Needs for the Next Decade

Murphy, C. J.; Vartanian, A. M.; Geiger, F. M.; Hamers, R. J.; Pedersen, J.; Cui, Q.; Haynes, C. L.; Carlson, E. E.; Hernandez, R.; Klaper, R. D.; Orr, G.; Rosenzweig, Z. ACS Cent. Sci. 2015, 1, 117-123.

https://doi.org/10.1021/acscentsci.5b00182

27. Negatively-Charged Helices in the Gas Phase

Johnson, A. R.; Dilger, J. M.; Glover, M. S.; Clemmer, D. E.; Carlson, E. E. Chem. Commun. 2014, 50, 8849-8851. Invited article in 2015 Emerging Investigators Issue.

https://doi.org/10.1039/C4CC03257H

26. PBP2x localizes separately from PBP2b and other peptidoglycan synthesis proteins during later stages of cell division of Streptococcus pneumoniae D39

Tsui, H-C. T.;†  Boesma, M. J.;†  Vella, S. A.; Kocaoglu, O.; Kuru, E.; Perceny, J. K.; Carlson, E. E.; VanNieuwenhze, M. S.; Brun. Y. V.; Shaw, S. L.; Winkler, M. E. Mol. Microbiol. 2014, 94, 21-40.

† Co-first authors

**Highlighted in: Cadby, I. T. and Lovering, A. L. Molecular surveillance of the subtle septum: discovering a new mode of peptidoglycan synthesis in streptococci. Mol. Microbiol. 2014, 94, 1-4.

https://doi.org/10.1111/mmi.12745

**Selected for Journal Cover Image

25. Towards the Development of Solid Supported Reagents for Separation of Alcohol-Containing Compounds by Steric Environment

Trader, D. J. and Carlson, E. E. Tetrahedron, 2014, 70, 4191-4196. Invited article in Special Issue to honor Sarah Reisman for receipt of the Tetrahedron Young Investigator Award.

https://doi.org/10.1016/j.tet.2014.03.040

24. Requirement of Essential Pbp2x and GpsB for Septal Ring Closure in Streptococcus pneumoniae D39

Land, A. D.;† Tsui, H-C. T.;† Kocaoglu, O.; Vella, S. A.; Shaw, S. L.; Keen, S. K.; Sham, L. T.; Carlson, E. E.; Winkler, M. E. Mol. Microbiol. 2013, 90, 939-955.

† Co-first authors

https://doi.org/10.1111/mmi.12408

**Selected for Journal Cover Image

23. Integrated Metabolomics Approach Facilitates Discovery of an Unpredicted Natural Product Suite from Streptomyces coelicolor M145

Sidebottom, A. M.; Johnson, A. R.; Karty, J. A.; Trader, D. J.; Carlson, E. E. ACS Chem. Biol. 2013, 8, 2009-2016.

https://doi.org/10.1021/cb4002798

22. Taming of a Superbase for Selective Phenol Desilylation and Natural Product Isolation

Trader, D. J. and Carlson, E. E. J. Org. Chem. 2013, 78, 7349-7355.

https://doi.org/10.1021/jo4010298

21. Thiol-ene Enabled Detection of Thiophosphorylated Kinase Substrates

Garber, K. C. A. and Carlson, E. E. ACS Chem. Biol. 2013, 8, 1671-1676.

https://doi.org/10.1021/cb400184v

20. Plant Pigment Identification: A Classroom and Outreach Activity

Garber, K. C. A.;† Odendaal, A. Y.;† Carlson, E. E. J. Chem. Ed. 2013, 90, 755-759.

† Co-first authors

https://doi.org/10.1021/ed200823t

19. Mechanistic Insight into Inhibition of Two-Component System Signaling

Francis, S.; Wilke, K. E.; Brown, D. E.; Carlson, E. E. Med. Chem. Commun. 2013, 4, 269-277. Invited Article in the New Talent Themed Issue.

https://doi.org/10.1039/C2MD20308A

18. All Signals Lost

Wilke, K. E. and Carlson, E. E. Sci. Transl. Med. 2013, 5, 203ps12. Invited Perspective.

https://doi.org/10.1126/scitranslmed.3006670

17. Penicillin-Binding Protein Imaging Probes

Kocaoglu, O. and Carlson, E. E. Curr. Prot. Chem. Bio. 2013, 5, 239-250. Invited.

https://doi.org/10.1002/9780470559277.ch130102

16. Chemoselective Hydroxyl Group Transformation: An Elusive Target

Trader, D. J. and Carlson, E. E. Mol. BioSyst. 2012, 8, 2484-2493. Invited Review in Emerging Investigators Themed Issue. 

**Selected as Molecular BioSystems HOT Article and highlighted on their blog, http://blogs.rsc.org/mb/ (7/17/2012).

https://doi.org/10.1039/C2MB25122A

15. Selective Penicillin-Binding Protein Imaging Probes Reveal Substructure in Bacterial Cell Division

Kocaoglu, O.; Calvo, R. A.; Sham, L. T.; Cozy, L. M.;† Lanning, B. R.;† Francis, S.; Winkler, M. E.; Kearns, D. B.; Carlson, E. E. ACS Chem. Biol. 2012, 7, 1746-1753. 

**Highlighted by: Walker, S. and Pasquina, L., Faculty of 1000, 05 Nov 2012; DOI: 10.3410/f.717960899.793463846.

https://doi.org/10.1021/cb300329r

14. Activity-Based Probe for Histidine Kinase Signaling

Wilke, K. E.; Francis, S.; Carlson, E. E. J. Am. Chem. Soc. 2012, 134, 9150-9153. 

**Highlighted in: J. Am. Chem. Soc. 2012, 134, 10715-10716.

https://doi.org/10.1021/ja3041702

13. Siloxyl Ether Functionalized Resins for Chemoselective Enrichment of Carboxylic Acids

Trader, D.J. and Carlson, E. E. Org. Lett. 2011, 13, 5652-5655.

https://doi.org/10.1021/ol202376m

12. Chemoselective Enrichment for Natural Products Discovery

Odendaal, A. Y.;† Trader, D. J.;† Carlson, E. E. Chem. Sci. 2011, 2, 760-764. 

† Co-first authors

**Highlighted in: Chem. & Eng. News, 2011, 89, Feb 14, 34-35 and Chemistry World

https://doi.org/10.1039/C0SC00620C

11. Mass Spectrometry for Systems-Level Biological Analysis

Carlson, E. E. Nat. Chem. Biol. 2010, DOI: 10.1038/nchembio.490. Invited.

10. Natural Products as Chemical Probes

Carlson, E. E. ACS Chem. Biol. 2010, 5, 639-653. Invited.

https://doi.org/10.1021/cb100105c

9. A General Glycomimetic Strategy Yields Non-Carbohydrate Inhibitors of DC-SIGN

Garber, K. C. A.; Wangkanont, K.; Carlson, E. E.; Kiessling, L. L. Chem. Commun. 2010, 46, 6747-6749.

https://doi.org/10.1039/C0CC00830C

8. Enrichment Tags for Enhanced-Resolution Profiling of Hydrophilic Metabolites

Carlson, E. E. and Cravatt, B. F. J. Am. Chem. Soc. 2007, 129, 15780-15782.

https://doi.org/10.1021/ja0779506

7. Chemoselective Probes for Metabolite Enrichment and Profiling

Carlson, E. E. and Cravatt, B. F. Nat. Methods, 2007, 4, 429-435. 

**Highlighted in: J. Prot. Res. 2007, 6, 2049 and Anal. Chem. 2007, 79, 3957.

https://doi.org/10.1038/nmeth1038

6. The Search for Chemical Probes to Illuminate Carbohydrate Function

Kiessling, L. L. and Carlson, E. E. In Chemical Biology. From Small Molecules to System Biology and Drug Design. Schreiber, S. L., Kapoor, T. M., Wess, G., Eds.; WILEY-VCH: Weinheim, 2007, pp 635-667. Invited Book Chapter.

 https://doi.org/10.1002/9783527619375.ch11a

5. Chemical Probes of UDP-Galactopyranose Mutase

Carlson, E. E.; May, J. F.; Kiessling, L. L. Chem. Biol. 2006, 13, 825-837.

https://doi.org/10.1016/j.chembiol.2006.06.007

3. Identification of Inhibitors for UDP-Galactopyranose Mutase

Soltero-Higgin, M.; Carlson E. E.; Phillips, J. H.; Kiessling, L. L. J. Am. Chem. Soc. 2004, 126, 10532-10533.

https://doi.org/10.1021/ja048017v

1. Improved Chemical Syntheses of 1- and 5-Deazariboflavin

Carlson, E. E. and Kiessling, L. L. J. Org. Chem. 2004, 69, 2614-2617.

https://doi.org/10.1021/jo049859f