Publications

Pre-prints:

  1. MacMullan MA, Dunn ZS, Qu Y, Wang P†, and Graham NA†. Phospho-proteomic analysis of CAR-T cell signaling following activation by antigen-presenting cancer cells. †Co-corresponding authors. Link.
  2. Korsakova E, Morales A, McDaniel T, Lund A, Cooper B, Ma F, Allison TF, Plath K, Graham NA, Bhaduri B, and Lowry WE. Defining dysfunction due to loss of MECP2 in Rett Patient Brain. Link.

Peer-reviewed publications:

  1. Garana BG, Joly JH, Delfarah A, Hong H, and Graham NA (2023). Drug mechanism enrichment analysis improves prioritization of therapeutics for repurposing. BMC Bioinformatics. Link.
  2. Jami SA, Wilkinson BJ, Guglietta R, Hartel N, Babiec WE, Graham NA, Coba MP, and O’Dell TJ (2023). Functional and phosphoproteomic analysis of β-adrenergic receptor signaling at excitatory synapses in the CA1 region of the ventral hippocampus. Scientific Reports. Link.
  3. Gelbach PE, Zheng D, Fraser SE, White KL, Graham NA, and Finley SD (2022). Kinetic and data-driven modeling of pancreatic β-cell central carbon metabolism and insulin secretion. PLoS Computational Biology. Link.
  4. vanLieshout TL, Stouth DW, Hartel NG, Vasam G, Ng SY, Webb EK, Rebalka IA, Mikhail AI, Graham NA, Menzies KJ, Hawke TJ, Ljubicic V (2022). The CARM1 transcriptome and arginine methylproteome mediate skeletal muscle integrative biology. Molecular Metabolism. 64:101555. Link.
  5. MacMullan MA, Wang P, and Graham NA (2022). Phospho-proteomics reveals that RSK signaling is required for proliferation of natural killer cells stimulated with IL-2 or IL-15. Cytokine. 157: 155958. Link.
  6. Qin C, Rao Y, Yuan H, Wang TY, Zhao J, Espinosa B, Liu Y, Zhang S, Savas AC, Liu Q, Zarinfar M, Rice S, Henley J, Comai L, Graham NA, Chen C, Zhang C, Feng P (2022). SARS-CoV-2 couples evasion of inflammatory response to activated nucleotide synthesis. Proceedings of the National Academy of Sciences (USA). 119 (26):e2122897119. Link.
  7. Kilinc M, Arora V, Creson TK, Rojas C, Le AA, Lauterborn J, Wilkinson B, Hartel N, Graham NA, Reich A, Gou G, Araki Y, Bayés A, Coba M, Lynch G, Miller CA, Rumbaugh G (2022). Endogenous Syngap1 alpha splice forms promote cognitive function and seizure protection. eLife, 11:e75707. Link.
  8. Xu T, Junge JA, Delfarah A, Lu YT, Arnesano C, Iqbal M, Delijani K, Hsieh TC, Hodara E, Mehta HH, Cohen P, Graham NA, Fraser SE, and Goldkorn A (2022). Bladder cancer cells shift rapidly and spontaneously to cisplatin-resistant oxidative phosphorylation that is trackable in real time. Scientific Reports, 12:5518. Link.
  9. Garana BB, Graham NA (2022). Metabolomics paves the way for improved drug target identification. Molecular Systems Biology, 18:e10914 (invited News and Views). Link.
  10. Lu V, Roy IJ, Torres Jr. A, Joly JH, Ahsan FM, Graham NA, Teitell MA (2022). Glutamine-dependent signaling controls pluripotent stem cell fate. Developmental Cell, 57(5):610-623. Link.
  11. Wang J, Delfarah A, Gelbach P, Fong E, Macklin P, Mumenthaler S, Graham NA, Finley SD (2022). Elucidating Tumor-stromal Metabolic Crosstalk in Colorectal Cancer through Integration of Constraint-Based Models and LC-MS Metabolomics. Metabolic Engineering, Jan;69:175-187. Link.
  12. Delfarah A, Hartel NG, Zheng D, Yang J, and Graham NA. Identification of a Proteomic Signature of Senescence in Primary Human Mammary Epithelial Cells (2021). Journal of Proteome Research. Link.
  13. Raveh B, Sun L, White KL, Sanyal T, Tempkin J, Zheng D, Bharat K, Singla J, Wang C, Zhao J, Li A, Graham NA, Kesselman C, Stevens RC, and Sali A (2021). Bayesian metamodeling of complex biological systems across varying representations. Proceedings of the National Academy of Sciences (USA). 118 (35) e2104559118. Link.
  14. Joly JH, Chew BTL, and Graham NA (2021). The landscape of metabolic pathway dependencies in cancer cell lines. PLoS Computational Biology.17(4): e1008942 Link.
  15. Reynolds JC, Lai RW, Woodhead JST, Joly JH, Mitchell CJ, Cameron-Smith D, Lu R, Cohen P, Cohen P, Graham NA, Benayoun BA, Merry TL, and Lee C (2021). MOTS-c is an Exercise-Induced Mitochondrial-Encoded Regulator of Age-Dependent Physical Decline and Muscle Homeostasis. Nature Communications, 12, 470. Link.
  16. Seidel ZP, Zhang X, MacMullan MA, Graham NA, Wang P, and Lee Jr CT (2020). Photo-Triggered Delivery of siRNA and Paclitaxel into Breast Cancer Cells Using Catanionic Vesicles. ACS Applied Bio Materials. 3(11), 7388-7398. Link.
  17. Joly JH, Lowry WE, and Graham NA (2020). Differential Gene Set Enrichment Analysis: A statistical approach to quantify the relative enrichment of two gene sets. Bioinformatics, btaa658. Link.
  18. Hartel NG, Liu CZ, Graham NA (2020). Improved discrimination of asymmetric and symmetric arginine dimethylation by optimization of the normalized collision energy in LC-MS proteomics (2020). Journal of Proteome Research. 19(8):3123-3129. Link.
  19. Zhao J, Tian M, Zhang S, Delfarah A, Gao R, Rao Y, Can Savas A, Lu A, Bubb L, Lei X, Moshirian R, Zhu W, Peng C, Jiang T, Chen L, Graham NA, and Feng P (2020). Deamidation Shunts RelA from Mediating Inflammation to Aerobic Glycolysis. Cell Metabolism. May 5;31(5):937-955.e7. Link.
  20. Zheng D, Sussman JH, Jeon MP, Parrish S, Delfarah A, and Graham NA (2020). AKT but not MYC promotes reactive oxygen species-mediated cell death in oxidative culture. Journal of Cell Science. Link.
  21. Wang L, Hartel NG, Ren K, Graham NA, Malmstadt N (2020). Effect of protein corona on nanoparticle-plasma membrane and nanoparticle-biomimetic membrane interactions. Environmental Science: Nano. Link.
  22. Joly JH, Delfarah A, Phung PS, Parrish S, and Graham NA (2020). A synthetic lethal drug combination mimics glucose deprivation-induced cancer cell death in the presence of glucose. Journal of Biological Chemistry. 295 (5), 1359-1365. Link.
  23. MacMullan MA, Dunn ZS, Graham NA, Yang L, Wang P. Quantitative Proteomics and Metabolomics Reveal Biomarkers of Disease as Potential Immunotherapy Targets and Indicators of Therapeutic Efficacy (2019). Theranostics, Oct 15;9(25): 7872-7888. Link.
  24. Hartel NG, Chew B, Qin J, Xu J, and Graham NA (2019). Deep protein methylation profiling by combined chemical and immunoaffinity approaches reveals novel PRMT1 targets. Molecular and Cellular Proteomics, 18(11):2149-2164. Link.
  25. Delfarah A, Parrish S, Junge JA, Yang J, Seo F, Li S, Mac J, Wang P, Fraser SE, and Graham NA (2019). Inhibition of nucleotide synthesis promotes replicative senescence of human mammary epithelial cells. Journal of Biological Chemistry, 294 (27), 10564-10578. Link.
  26. Flores A, Sandoval-Gonzalez S, Takahashi R, Krall A, Sathe L, Wei L, Radu C, Joly JH, Graham NA, Christofk HR, Lowry WE (2019). Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin. Nature Communications. Link.
  27. Wilkinson B, Evgrafov O, Zheng D, Hartel H, Knowles J, Graham NA, Ichida J, and Coba MP (2019). Endogenous Cell Type-Specific DISC1 Interactomes Reveal Protein Networks Associated to Neurodevelopmental Disorders. Biological Psychiatry. Link.
  28. Rohrs JA, Zheng D, Graham NA, Wang P, Finley S (2018). Computational model of chimeric antigen receptors explains site-specific phosphorylation kinetics. Biophysical Journal, 115(6):1116-1129. Link.
  29. Cheng LC, Li Z., Graeber TG, Graham NA, and Drake JM (2018). Phosphopeptide enrichment coupled with label-free quantitative mass spectrometry to investigate the phosphoproteome in prostate cancer. Journal of Visualized Experiments. Link.
  30. Flores A, Schell J, Krall A, Jelinek D, Miranda M, Grigorian M, Braas D, White A, Zhou J, Graham NA, Graeber TG, Seth P, Evseenko D, Coller H, Rutter J, Christofk HR, and Lowry WE (2017). Lactate production drives hair follicle stem cell activation. Nature Cell Biology, 19(9), 1017-1026. Link.
  31. Graham NA*, Minasyan A*, Lomova A, Cass A, Balanis N, Friedman M, Chan S, Zhao S, Delgado A, Go J, Beck, L, Hurtz C, Ng C, Qiao R, ten Hoeve J, Palaskas N, Wu H, Muschen M, Port E, Larson S, Schultz N, Brass D, Christofk HR, Mellinghoff IK and Graeber TG (2017). Recurrent aneuploidy patterns enable fitness gains in tumor metabolism. Molecular Systems Biology. PMCID: PMC5327725 (*denotes equal contribution). Link.
  32. Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM, Uzunangelov V, Carlin DE, Fleming DT, Wong CK, Newton Y, Sudha S, Vashisht AA, Huang J, Wohlschlegel JA, Graeber TG, Witte ON and Stuart JM (2016). Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. Cell, 166(4), 1041-54. PMCID: PMC4985183. Link.
  33. Hong CS, Graham NA, Gu W, Camacho CE, Mah V, Maresh EL, Alavi M, Bagryanova L, Krotee PAL, Gardner BK, Behbahan IS, Horvath S, Chia D, Mellinghoff IK, Hurvitz SA, Dubinett SM, Critchlow SE, Kurdistani SK, Goodglick L, Braas D, Graeber TG, Christofk HR (2016). MCT1 modulates cancer cell pyruvate export and growth of tumors that co-express MCT1 and MCT4. Cell Reports, 14(7), 1590-601. PMCID: PMC4816454. Link.
  34. Goodwin JF, Kothari V, Drake JM, Zhao S, Dylgjeri E, Dean JL, Schiewer MJ, McNair C, Jones JK, Aytes A, Magee MS, Snook AE, Zhu Z, Den RB, Birbe RC, Gomella LG, Graham NA, Vashisht AA, Wohlschlegel JA, Graeber TG, Karnes RJ, Takhar M, Davicioni E, Tomlins SA, Abate-Shen C, Sharifi N, Witte ON, Feng FY, and Knudsen KE (2015). DNA-PKcs mediated transcriptional regulation drives prostate cancer progression and metastasis. Cancer Cell, 28(1), 97-113. PMCID: PMC4531387. Link.
  35. Thai M, Graham NA, Braas D, Nehil M, Komisopoulou E, Kurdistani SK, McCormick F, Graeber TG and Christofk HR (2014). Adenovirus E4ORF1-induced MYC activation promotes host cell anabolic glucose metabolism and virus replication.Cell Metabolism, 19(4), 694-701.
  36. Graham NA, Graeber TG (2014). Complexity of metastasis-associated SDF-1 ligand signaling in breast cancer stem cells. Proceedings of the National Academy of Sciences (USA), Epub May 14. (Invited News and Views)
  37. Drake JM, Graham NA, Lee JK, Stoyanova T, Faltermeier CM, Sudha S, Titz B, Huang J, Pienta, KJ, Graeber TG and Witte ON (2013). Metastatic castration-resistant prostate cancer reveals intrapatient similarity and interpatient heterogeneity of therapeutic kinases. Proceedings of the National Academy of Sciences (USA), 110(49), E4762-9.
  38. Graham NA, Tahmasian M, Kohli B, Komisopoulou E, Zhu M, Vivanco I, Teitell MA, Wu H, Ribas A, Lo RS, Mellinghoff IK, Mischel PS, and Graeber TG (2012).  Glucose deprivation activates a metabolic and signaling amplification loop leading to cell death.  Molecular Systems Biology, 8:589. PMCID: PMC3397414 (profiled in accompanying News & Views)
  39. Koya RC, Mok S, Otte N, Blacketor KJ, Comin-Anduix B, Tumeh PC, Minasyan A, Graham NA, Graeber TG, Chodon T, Ribas A (2012).  BRAF Inhibitor Vemurafenib Improves the Antitumor Activity of Adoptive Cell Immunotherapy.  Cancer Research, 72(16), 3928-37.  PMCID: PMC3422880
  40. Drake JM, Graham NA, Stoyanova T, Sedghi A, Goldstein AS, Cai H, Smith DA, Zhang H, Komisopoulou E, Huang J, Graeber TG, and Witte ON (2012).  Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression.  Proceedings of the National Academy of Sciences (USA), 109(5), 1643-8.  PMCID:  PMC3277127
  41. Tumeh PD, Koya RC, Chodon T, Graham NA, Graeber TG, Comin-Anduix B, and Ribas A (2010).  The impact of ex vivo clinical grade activation protocols on human T-cell phenotype and function for the generation of genetically modified cells for adoptive cell transfer therapy.  The Journal of Immunotherapy, 33(8), 759-68.  PMCID:  PMC3114626
  42. Sun J*, Masterman-Smith M*, Graham NA*, Jiao J*, Mottahedeh J, Laks DR, Ohashi M, DeJesus J, Kamei K, Lee KB, Wang H, Yu ZT,Lu YT, Hou S, Li K, Liu M, Zhang N, Wang S, Angenieux B, Panosyan E, Samuels ER, Park J, Williams D, Konkankit V, Nathanson D, van Dam RM, Phelps ME, Wu H, Liau LM, Mischel PS, Lazareff JA, Kornblum HI, Yong WH, Graeber TG and Tseng HR (2010).  A microfluidic platform for systems pathology: multiparameter single-cell signaling measurements of clinical brain tumor specimens.  Cancer Research, 70(15), 6128-38.  PMCID: PMC3163840 (*denotes equal contribution)
  43. Kim JH, Kushiro K, Graham NA, Asthagiri AR (2009).  Tunable Interplay between epidermal growth factor and cell-cell contact governs the spatial dynamics of epithelial growth.  Proceedings of the National Academy of Sciences (USA), 106(27), 11149-53.  PMCID:  PMC2708686
  44. Pope MD, Graham NA, Huang BK, and Asthagiri AR (2008).  Automated quantitative analysis of epithelial cell scatter.  Cell Adhesion & Migration, 2(2), 110-6.  PMCID:  PMC2634994
  45. Graham NA, Pope MD, Rimchala T, Huang BK, and Asthagiri AR (2007).  A microtiter assay for quantifying protein-protein interactions associated with cell-cell adhesion.  The Journal of Biomolecular Screening, 12(5), 683-93.
  46. Graham NA and Asthagiri AR (2004).  EGF-mediated Tcf/Lef transcriptional activity is essential, but not sufficient, for cell cycle progression in non-transformed mammary epithelial cells.  The Journal of Biological Chemistry,279(22), 23517-24.