Research Publications

*These publications are especially helpful for prospective trainees to get a sense for the research

 

​1. Angela R.S. Kruse, Roy Lardenoije, Lukasz G. Migas, Claire F. Scott, Cody Marshall, Morad C. Malek, Adel Eskaros, Thai Pham, Kristie Aamodt, Madeline Colley, Lissa Ventura-Antunes, Melissa A. Farrow, Raf Van de Plas, Joana Goncalves, Matthew Schrag, Alvin C. Powers, Jeffrey M. Spraggins. Integrative Spatial Omics for Systems-Level Mapping of Pathological Niches. *bioRxiv 2025.09.12.675904; doi: https://doi.org/10.1101/2025.09.12.675904 

 

*​This paper provides an analytical and computational workflow to integrate spatial transcriptomics, imaging mass spectrometry, and microscopy. We present a method to perform Xenium spatial transcriptomics and CODEX multiplexed immunofluorescence on the same tissue samples and provide an integrated analysis of lipid and gene biomarkers for amyloid plaques in the type 2 diabetic pancreas and Alzheimer’s brain.

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2. Nicholson RJ, Cedeno-Rosario L, Maschek JA, Lonergan T, Van Vranken JG, Kruse ARS, Stubben CJ, Wang L, Stuart D, Alcantara QA, Revelop MP, Rutter K, Pahulu M, Taloa J, Wu X, Kim J, Hall I, Clark AJ, Parikh S, Spraggins J, Romero D, Blitzer JT, Gygi SP, Rutter J, Holland WL, Nirupama R, Summers S. (2025) Therapeutic Remodeling of the Ceramide Backbone Prevents Kidney Injury. Cell Metabolism. In Press.

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3. Kruse ARS, Judd A, Gutierrez D, Allen J, Dufresne M, Farrow M, Norris J, Caprioli RM, Spraggins JM. (2024) Thermal denaturation of fresh frozen tissue enhances mass spectrometry detection of peptides. Analytical Chemistry. DOI: 10.1021/acs.analchem.4c03625.* 

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*This work compares the effect of thermal treatment on in situ mass spectrometry proteomics in human pancreas, colon, and ovary tissues, providing a recommended spatial workflow for each organ.

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4. Jain S, HuBMAP Consortium. (2023) Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol. 2023 August; 25(8): 1089–1100. doi:10.1038/s41556-023-01194-w.

 

5. Pi H, Sun R, McBride JR, Kruse ARS, Gibson-Corley KN, Krystofiak ES, Nicholson MR, Spraggins JM, Zhou Q, Skaar EP. (2023) Clostridioides difficile ferrosome organelles resist nutritional immunity. Nature. https://doi.org/10.1038/s41586-023-06719-9.

 

6. Weiss A, Murdoch CC, Edmonds KA, Jordan MR, Monteith AJ, Perera YR, Rodríguez Nassif AM, Petoletti AM, Beavers WN, Munneke MJ, Drury SL, Krystofiak ES, Thalluri K, Wu H, Kruse ARS, DiMarchi RD, Caprioli RM, Spraggins JM, Chazin WJ, Giedroc DP, Skaar EP. (2022) Zn-regulated GTPase metalloprotein activator 1 modulates vertebrate zinc homeostasis. Cell. 185(12):2148-2163.

 

7. Shippy T…Kruse ARS…Saha S. (2022) Diaci v3.0: Chromosome-level assembly, de novo transcriptome and manual annotation of Diaphorina citri, insect vector of Huanglongbing. bioRxiv 869685; doi: https://doi.org/10.1101/869685.

 

8. Kruse ARS. and Spraggins JM. (2022) Uncovering Molecular Heterogeneity in the Kidney with Spatially Targeted Mass Spectrometry. Front. Physiol. 13:837773.

 

9. Djambazova K., Dufresne M., Migas L., Kruse ARS., Van De Plas R., Caprioli R., Spraggins JM. (2022) MALDI TIMS IMS of Disialoganglioside Isomers – GD1a and GD1b in Murine Brain Tissue. Analytical Chemistry. 10.1021/acs.analchem.2c03939.

 

10. Ray J±. and Kruse A±, Ozer A., Kajitani T., Johnson R., MacCoss M., Heck M., Lis J. (2020) RNA aptamer capture of macromolecular complexes for mass spectrometry analysis. Nucleic Acids Research. 48(15). ±Denotes co-first authorship.

 

11. Kruse A, Fleites LA, Heck M. (2019) Lessons from one fastidious bacterium to another: What can we learn about Liberibacter species from Xylella fastidiosa. Insects. 10(9).

 

12. Kruse A, Ramsey J, Johnson R, Hall D, MacCoss M, Heck M. (2018) Candidatus Liberibacter asiaticus Minimally Alters Expression of Immunity and Metabolism Proteins in Hemolymph of Diaphorina citri, the Insect Vector of Huanglongbing. Journal of Proteome Research 17 (9): 2995-3011.

 

13. Kruse A, Fattah-Hosseini S, Saha S, Johnson R, Warwick ER, Sturgeon K, Mueller L, MacCoss M, Shatters R, Cilia M. (2017) Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut. PLoS One 12(6): e0179531

 

14. Fleites LA, Johnson R, Kruse A, Nachman RJ, Hall DG, MacCoss M, Heck M. (2019) Peptidomics-driven insights into Diaphorina citri physiology. Journal of Proteome Research 19(4).

 

15. Pinheiro PV, Wilson JR, Xu Y, Zheng Y, Rebelo AR, Fattah-Hosseini S, Kruse A, Santos Dos Silva R, Xu Y, Kramer M, Giovannoni J, Fei Z, Gray S, Heck M. (2019) Plant viruses transmitted in two different modes produce differing effects on small RNA-mediated processes in their aphid vector. Phytobiomes 3(1).

 

16. Heck M, Ramsey J, Kruse A. (2018) The Asian citrus psyllid: A proteomics perspective. Citrograph 9(1).

 

17. Chen Wenbo C, Hasegawa DK, Kaur N, Kliot A, Pinheiro PV, Luan J, Stensmyr MC, Zheng Y, Liu W, Sun H, Xu Y, Luo Y, Kruse A, Yang X, et al. (2016). "The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance." BMC Biology 14(1): 110.

 

18. Ramsey JS, Johnson RS, Hoki JS, Kruse A, Mahoney J, et al. (2015) Metabolic interplay between the Asian Citrus Psyllid and its Profftella symbiont: An Achilles’ heel of the citrus greening insect vector. PLoS One 10(11): e0140826.