*authors contributed equally, ## co-corresponding

35. Prudhomme N, Pastora R, Thomson S, Zheng E, Sproule A, Krieger JR, Murphy JP, Overy DP, McLean MD, Geddes-McAlister J (2024). Bacterial growth-mediated systems remodeling of Nicotiana benthamiana defines unique signatures of target protein production in molecular pharming. Plant biotechnol. 22(8):2248-2266. doi: 10.1111/pbi.14342

35. Sirimuvva T*, Clements DR*, SaravanenS, Ludtke A, Blackmore B, Paulo JA, Chan L, Liu Z, Ginhoux F, Lavine KJ, Murphy JP, Mack M, Graves EE, Idoyaga J (2023). Rapid monocyte recruitment dictates the therapeutic efficacy of focal radiotherapy. Sci. Immunol. 84: DOI: 10.1126/sciimmunol.add744

34. Holay N, Kennedy BE, Murphy JP, Konda P, Giacomantonio M, Brauer-Chapin T, Paulo JA, Kumar V, Kim Y, Elaghil M, Sisson G, Clements D, Richardson C, Gygi SP, Gujar S (2023). After virus exposure, early bystander naïve CD8 T cell activation relies in NAD+ salvage metabolism. Front. Immunol. 13:1047661. https://doi.org/10.3389/fimmu.2022.1047661

33. Young L, Cameron AWR, Springer SSA, PJ Ross, Murray D, Wakelin G, Wolters G, Murphy JP, Arsenault MG, Ng S, Ljubicic V, Johnston A (2022). Muscle injury induces a transient senescence-like state that is required for myofiber growth during muscle regeneration FASEB J. 11:e22587. https://doi.org/10.1096/fj.202200289RR

32. Philips O, Sultonova, Du R, Philips O, Paulo JA, Murphy JP (2022). Understanding emerging bioactive metabolites with putative roles in cancer biology. Front. Oncol. 12:1014748. https://doi.org/10.3389/fonc.2022.1014748

31. Sultonova M, Blackmore B, Du R, Philips O, Paulo JA, Murphy JP (2022). Integrated changes in thermal stability and proteome abundance during altered nutrient states in E.coli and human cells. Proteomics. 22(19-20):e2100254. https://doi.org/10.1002/pmic.202100254

30. Kennedy BE, Giacomantonio M, Murphy JP, Cutler S, Sadek M, Konda P, Paulo JA, Pathak GP,Renkens SHJ, Grieve S, Pol J, Gygi SP, Richardson C, Gaston D, Reiman A, Kroemer G, Elnenaei MO, Gujar SA. (2022). NAD+ depletion enhances reovirus-induced oncolysis in multiple myeloma. Mol. Therapy Oncolytics. 24:695-706. https://doi.org/10.1016/j.omto.2022.02.017

29. Kim Y, Konda P. Murphy JP, Paulo JA, Gygi SP, Gujar S. (2022). Immune checkpoint blockade augments changes within oncolytic virus-induced cancer MHC-I peptidome, creating novel antitumor CD8 T cell reactivities. Mol. Cell. Proteomics. 21(2) 100182. https://pubmed.ncbi.nlm.nih.gov/34922008/

28. Dahn ML, Walsh HR, Dean CA, Giacomantonio M, Fernando W, Murphy JP, Walker OL, Wasson M-C D, Gujar S, Pinto DM, Marcato P. (2022). Metabolite profiling reveals a connection between aldehyde dehydrogenase 1A3 and GABA metabolism in breast cancer metastasis.  Metabolomics.18(1) 10.1007/s11306-021-01864-6

27. Kim Y, Konda P, Murphy JP, Paulo JA, Gygi SP, Gujar S. (2022) Immune checkpoint blockade   augments changes within oncolytic virus-induced cancer MHC-I peptidome, creating novel antitumor CD8 T cell reactivities. Mol. Cell Proteomics. 21(2) 100182 10.1016/j.mcpro.2021.100182

26. Giacomantio MA, Sterea AM, Kim Y, Paulo JA, Clements DR, Kennedy BE, Bydoun MJ, Waisman DM, Gygi SP, Giacomantonio CA, Murphy JP^##, Gujar S^##. (2020). Quantitative proteome responses to oncolytic reovirus in GM-CSF and M-CSF-differentiated bone marrow-derived cells. J. Proteome Res. 19(2):708-718. https://doi.org/10.1021/acs.jproteome.9b00583

25. Sharif T, Dai C, Martell E, Ghassemi-Rad MS, Hanes MR, Murphy JP, Kennedy BE, Venugopal C, Subapanditha M, Giacomantonio CA, Marcato P, Singh S, Gujar S. (2019). TAp73 modifies metabolism and positively regulates growth of cancer stem-like cells in a redox-sensitive manner. Clin. Cancer Res. 25(6): 2001-2017 https://doi.org/10.1158/1078-0432.ccr-17-3177

24. Murphy JP, Yu Q, Konda P, Paulo JA, Jedrychowski MP, Kowalewski DJ, Schuster H, Kim Y, Clements D, Jain A, Stevanovic S, Gygi SP, Mancias JD, Gujar S. (2019). Multiplexed relative quantitation with isobaric tagging mass spectrometry reveals class I major histocompatibility complex ligand dynamics in response to doxorubicin. Anal. Chem. 91(8): 5106-5115. https://doi.org/10.1021/acs.analchem.8b05616

23. Sharif T, Martell E, Dai C, Ghassemi-Rad MS, Hanes MR, Murphy JP, Margam NN, Parmar HB, Giacomantonio CA, Duncan R, Lee PWK, Gujar S. (2019). HDAC6 differentially regulates autophagy in stem-like versus differentiated cancer cells. Autophagy. 15(4): 686-706. https://doi.org/10.1080/15548627.2018.1548547

22. Murphy JP^*, Kim Y^*, Clements D, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Stevanovic S, Gygi SP, Gujar S. (2019). Therapy-induced MHC I ligands shape neo antitumor CD8 T cell responses during oncolytic virus-based cancer immunotherapy. J. Proteome Res. 18(6): 2666-2675. https://doi.org/10.1021/acs.jproteome.9b00173

21. Konda P*, Murphy JP*, Gujar S. (2019). Improving MHC-I ligand identifications from LC-MS/MS data by incorporating allelic peptide motifs. Proteomics. 19(5): 1800458. https://doi.org/10.1002/pmic.201800458

20. Kennedy BE, Murphy JP, Clements D, Konda P, Holay N, Kim Y, Giacomantonio M, Gujar S. (2019). Inhibition of pyruvate dehydrogenase kinase enhances the antitumor efficacy of oncolytic reovirus. Cancer Res. 79(15): 3824-3836. https://doi.org/10.1158/0008-5472.can-18-2414

19. Pathak GP, Shah R, Kennedy BE, Murphy JP, Clements D, Konda P, Giacomantonio M, Xu Z, Schlaepfer IR, Gujar S. (2018). RTN4 knockdown dysregulates the Akt pathway, destabilizes the cytoskeleton, and enhances paclitaxel-induced cytotoxicity in cancers. Mol. Therapy. 26(8): 2019-2033. https://doi.org/10.1016/j.ymthe.2018.05.026

18. Murphy JP, Giacomantonio M, Paulo JA, Everley RA, Kennedy BE, Pathak GP, Clements DR, Kim Y, Dai C, Sharif T, Gygi SP, Gujar S. (2018). The NAD+ salvage pathway supports PHGDH-driven serine biosynthesis. Cell Reports. 24(9): 2381-2391. https://doi.org/10.1016/j.celrep.2018.07.086

17. Clements D, Murphy JP, Sterea A, Kennedy BE, Kim Y, Helson E, Almasi S, Holay N, Konda P, Paulo JA, Sharif T, Lee PW, Weekes MP, Gygi SP, Gujar S. (2017). Quantitative temporal in vivo proteomics deciphers the transition of virus-driven myeloid cells into M2 macrophages. J. Proteome Res.16(9): 3391-3406. https://doi.org/10.1021/acs.jproteome.7b00425

16. Murphy JP, Konda P, Kowalewski DJ, Schuster H, Clements D, Kim Y, Cohen AM, Sharif T, Nielsen M, Stevanovic S, Lee PW, Gujar SA. (2017). MHC-I ligand discovery using targeted database searches of mass spectrometry data: implications for T-cell immunotherapies. J. Proteome Res.16:1806-1816. https://doi.org/10.1021/acs.jproteome.6b00971

15. Sharif T, Martell E, Dai C, Kennedy BE, Murphy JP, Clements DR, Kim Y, Lee PWK, Gujar SA. (2016). Autophagic homeostasis is required for the pluripotency of cancer stem cells. Autophagy. 13(2): 264-284. https://doi.org/10.1080/15548627.2016.1260808

14. Sharif T, Ahn DG, Liu RZ, Pringle E, Martell E, Dai C, Nunokawa A, Kwak M, Clements D, Murphy JP, Dean C, Marcato P, MsCormick C, Godbout R, Gujar SA, Lee PWK. (2016). The NAD+ salvage pathway modulates cancer cell viability via p73. Cell Death Differ. 23(4): 669-680. https://doi.org/10.1038/cdd.2015.134

13. Coyle KM, Murphy JP, Vidovic D, Vaghar-Kashani A, Dean CA, Sultan M, Clements D, Wallace M, Thomas ML, Hundert A, Giacomantonio C, Helyer L, Gujar SA, Lee PWK, Weaver ICG, Marcato P. (2016). Breast cancer subtype dictates DNA methylation and ALDH1A3-mediated expression of tumor suppressor RARRES1. Oncotarget. 7(28): 44096-44112. https://doi.org/10.18632/oncotarget.9858

12. Coloff JL, Murphy JP, Braun CR, Harris IS, Shelton LM, Kami K, Gygi SP, Selfors L, Brugge. (2016). Differential glutamate metabolism in proliferating and quiescent mammary epithelial cells. Cell Metab. 23(5): 867-880. https://doi.org/10.1016/j.cmet.2016.03.016

11. German NJ, Yoon H, Rushdia ZY, Murphy JP, Finley LWS, Laurent G, Haas W, Satterstrom FK, Guarnerio J, Zaganjor E, Santos D, Pandolfi PP, Beck AH, Gygi SP, Scadden DT, Kaelin WG, Haigus MC. (2016). PHD3 loss in cancer enables metabolic reliance on fatty acid oxidation via deactivation of ACC2. Mol. Cell. 63(6): 1006-1020. https://doi.org/10.1016/j.molcel.2016.08.014

10. Murphy JP, Stepanova E, Everley RE, Paulo JA, Gygi SP. (2015). Comprehensive temporal protein dynamics during the diauxic shift in Saccharomyces cerevisiae. Mol. Cell. Proteomics. 14:2454-2465.https://doi.org/10.1074/mcp.m114.045849

9. Jastrab JB, Wong T, Murphy JP, Bai L, Hu K, Merkx R, Huang J, Champak C, Ovaa H, Gygi SP, Darwin KH. (2015). An adenosine triphosphate-independent proteasome activator contributes to the virulence of Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. 112(14): E1763-E1772. https://doi.org/10.1073/pnas.1423319112

8. Liew GM, Fan Y, Nager AR, Murphy JP, Lee JS, Aguiar M, Breslow DK, Gygi SP, Nachury MV. (2014). The intraflagellar transport protein IFT27 promotes BBSome exit from cilia through the GTPase ARL6/BBS3. Dev. Cell. 31(3): 265-278. https://doi.org/10.1016/j.devcel.2014.09.004

7. Murphy JP, Everley RE, Coloff JL, Gygi SP. (2014). Combining amine metabolomics and quantitative proteomics of cancer cells using derivatization with isobaric tags. Anal. Chem.86: 3585-3593. https://doi.org/10.1021/ac500153a

6. Yamada T, Yang Y, Hemberg M, Yoshida T, Cho HY, Murphy JP, Fioravante D, Regehr WG, Gygi SP, Georgopoulos K, Bonni A. (2014). Promoter decommissioning by the NuRD chromatin remodelling complex triggers synaptic connectivity in the mammalian brain. Neuron. 83(1): 122-134. https://doi.org/10.1016/j.neuron.2014.05.039

5.  Murphy JP, Côté PD, Pinto DM. Monitoring the switch: The Warburg effect and targeted proteomic analysis of cancer metabolism. Current Proteomics (2012) 9, 26-39.

4.  Murphy JP, Pinto DM. Targeted proteomic analysis of glycolysis in cancer cells. J. Proteome Res. (2011) 10(2), 604-613. https://doi.org/10.1021/pr100774f

3.  Murphy JP, Pinto DM. Temporal proteomic analysis of IGF-1R signalling in MCF-7 breast adenocarcinoma cells. Proteomics (2010) 10(9), 1847-1860.

2.   Murphy JP, Kong F, Pinto DM, Wang-Pruski G. Relative quantitative proteomic analysis reveals wound response proteins correlated with after-cooking darkening. Proteomics (2010) 10(23), 4258-4269. https://doi.org/10.1002/pmic.200900718

1.  Mataija-Botelho D, Murphy JP, Pinto DM, MacLellan DL, Langois C, Doucette AA. A qualitative proteome investigation of the sediment portion of human urine: Implications in the biomarker discovery process. Proteomics Clin. App., 2009, 3(1), 95-105.