Johannes F. Fahrmann, Ph.D.

Peer-Reviewed Articles

1. Katayama H, Fahrmann JF, Olsen C, Irajizad E, Cai Y, Hsiao F, Dennison JB, Perrier ND, Hanash SM. Blood-Based Immunoglobulin-Bound Neoantigen Signatures Associated with MEN Type 1-Related Duodenopancreatic Neuroendocrine Tumor Progression. J Am Coll Surg 242(4):834-842, 2026. e-Pub 2026. PMID: 41562477.
2. Vykoukal J, Chen Y, Zuo M, Ballaro R, Hong MJ, Krishna H, Rodriquez-Perera DB, Katayama H, Irajizad E, Wu R, Leon-Letelier RA, Dennison JB, Gutierrez AM, Paulucci-Holthauzen A, Thompson TC, Rusling L, Cai Y, Hsiao FC, Park S, Arun B, Hanash S, Fahrmann JF. Vesicle-mediated mitochondrial clearance presents an actionable metabolic vulnerability in triple-negative breast cancer. Cell Rep Med 6(12), 2025. e-Pub 2025. PMID: 41406946.
3. Chen Y, Dou R, Hong MJ, Xu H, Vykoukal J, Leon-Letelier RA, Cai Y, Park S, Irajizad E, Hsiao FC, Dennison JB, Ostrin EJ, Fahrmann JF, Katayama H, Hanash SM. Lung adenocarcinoma surfaceome remodeling with EGFR inhibitors uncovers placental alkaline phosphatase as a target for combination therapy. Cell Rep Med 6(12), 2025. e-Pub 2025. PMID: 41406940.
4. Deol, P, Fahrmann, JF, Grapov, D, Yang, J, Evans, JR, Fiehn, O, Phinney, B, Hammock, B, Sladek, FM. P2-HNF4α alters linoleic acid metabolism and mitigates soybean oil-induced obesity. Journal of lipid research 66(12), 2025. e-Pub 2025. PMID: 41167395.
5. Fahrmann JF, Irajizad E, Rudsari H, Vykoukal J, Toumazis I, Khorami-Sarvestani S, Ansari S, Yang J, Kettner N, Dennison JB, Ostrin E, Hanash S. Validation of a blood test for multi-cancer risk stratification in a lung cancer screening cohort. medRxiv, 2025. e-Pub 2025. PMID: 41332848.
6. Song, L, Rudsari, HK, Fahrmann, JF, Vykoukal, JV, Hanash, S, Long, JP, Do, K, Irajizad, E. Rank-based learning. Briefings in bioinformatics 26(6), 2025. e-Pub 2025. PMID: 41705520.
7. Khoshfekr Rudsari H, Khorami-Sarvestani S, Fahrmann JF, Long JP, Hanash S, Do KA, Irajizad E. SMAGS-LASSO: A Novel Feature Selection Method for Sensitivity Maximization in Early Cancer Detection. Cancer Epidemiol Biomarkers Prev 34(12):2259-2266, 2025. e-Pub 2025. PMID: 40996315.
8. Velasco WV, Grimaldo MT, Karimi N, Clowers MJ, Krishna A, Wu R, Ejaz R, Yuan B, Aguila SD, Bouchelkia I, Barragan JEM, Larsen KE, Rezai Y, Khalaj F, Mitra K, Rodriguez CR, Millares R, de Anda AB, Castro-Pando S, Karandikar UC, Petrosino JF, McAllister F, Kadara H, Ostrin EJ, Fahrmann JF, Hoffman KL, Moghaddam SJ. Comparative effects of combustible cigarette versus electronic cigarette exposures on KRAS mutant lung cancer promotion. Neoplasia 67:101185, 2025. e-Pub 2025. PMID: 40516145.
9. Liu, C, Mosley, A, Irajizad, E, Yip-Schneider, MT, Wu, H, Smith-Kinnaman, WR, Tran, T, Long, JP, Do, K, Fahrmann, JF, Dewitt, J, Hanash, S, Schmidt, CM, Zhang, J. Cyst fluid proteins stratify malignant risk of intraductal papillary mucinous neoplasm of the pancreas. Cancer Letters 624, 2025. e-Pub 2025. PMID: 40300662.
10. Leon Letelier, R, Sevillano-Mantas, AM, Chen, Y, Park, S, Vykoukal, JV, Fahrmann, JF, Ostrin, EJ, Garrett, C, Dou, R, Cai, Y, Hsiao, FC, Dennison, JB, Vilar Sanchez, E, Arun, BK, Hanash, S, Katayama, H. Citrullinated ENO1 Vaccine Enhances PD-1 Blockade in Mice Implanted with Murine Triple-Negative Breast Cancer Cells. Vaccines 13(6), 2025. e-Pub 2025. PMID: 40573960.
11. Cai L, Rogers TJ, Mousavi Jafarabad R, Vu H, Yang C, Novaresi N, Galan-Cobo A, Girard L, Ostrin EJ, Fahrmann JF, Kim J, Heymach JV, O'Donnell KA, Xiao G, Xie Y, DeBerardinis RJ, Minna JD. High KYNU Expression Is Associated with Poor Prognosis, KEAP1/STK11 Mutations, and Immunosuppressive Metabolism in Patient-Derived but Not Murine Lung Adenocarcinomas. Cancers (Basel) 17(10), 2025. e-Pub 2025. PMID: 40427178.
12. Chen Y, Ballaro R, Sans M, Thege FI, Zuo M, Dou R, Min J, Yip-Schneider M, Zhang J, Wu R, Irajizad E, Makino Y, Rajapakshe KI, Rudsari HK, Hurd MW, Leon-Letelier RA, Katayama H, Ostrin E, Vykoukal J, Dennison JB, Do KA, Hanash SM, Wolff RA, Guerrero PA, Kim M, Schmidt CM, Maitra A, Fahrmann JF. Long-chain sulfatide enrichment is an actionable metabolic vulnerability in intraductal papillary mucinous neoplasm (IPMN)-associated pancreatic cancers. Gut 74(10):1638-1652, 2025. e-Pub 2025. PMID: 40268349.
13. Jhaveri K, Thapa R, Ercan D, Saha A, Noble J, Singh P, Fahrmann J, Saini N, Wu R, Dennison JB, Hanash S, Jenq RR, Modi K, Figura N, Chavez J, Shah B, Nishihori T, Lazaryan A, Khimani F, Bachmeier C, Gage K, Mishra A, Perna F, Davila ML, Spiegel J, Rejeski K, Subklewe M, Locke FL, Freeman C, Parker N, Jain MD. Sarcopenia and Skeletal Muscle Loss after CAR T-cell Therapy in Diffuse Large B cell Lymphoma. Clin Cancer Res 31(13):2756-2766, 2025. e-Pub 2025. PMID: 40238583.
14. Leon-Letelier RA, Chen Y, Dou R, Irajizad E, Yip-Schneider MT, Wu R, Ejaz R, Rudsari HK, Li Y, Spencer R, Ballaro R, Vykoukal J, Hurd M, Dennison JB, Do KA, Maitra A, Zhang J, Hanash S, Schmidt CM, Fahrmann JF. Integrated metabolomics and spatial transcriptomics of cystic pancreatic cancer precursors reveals dysregulated polyamine metabolism as a biomarker of progression. Clin Cancer Res, 2025. e-Pub 2025. PMID: 40184234.
15. Ballaro R, Wasylishen AR, Pieterman CRC, Olsen C, Irajizad E, Wu R, Katayama H, Liu H, Cai Y, Leon-Letelier RA, Dennison JB, Waguespack S, Do KA, Agarwal SK, Walter M, Welch J, Weinstein L, Blau JE, Jha S, Nilubol N, Vriens MR, van Leeuwaarde RS, van Treijen MJC, Valk GD, Perrier ND, Hanash SM, Fahrmann JF. Elevated levels of circulating microbial-associated uremic toxins are associated with metastatic duodenopancreatic neuroendocrine tumors in patients with Multiple Endocrine Neoplasia Type 1. Cancer Lett 614:217537, 2025. e-Pub 2025. PMID: 39924079.
16. Ghasemi SM, Gu C, Fahrmann JF, Hanash S, Do KA, Long JP, Irajizad E. A Novel Sensitivity Maximization at a Given Specificity Method for Binary Classifications. Cancer Prev Res (Phila) 18(3):117-123, 2025. e-Pub 2025. PMID: 39618306.
17. Fahrmann, JF, Yip-Schneider, MT, Vykoukal, JV, Spencer, R, Dennison, JB, Do, K, Long, JP, Maitra, A, Zhang, J, Schmidt, CM, Hanash, S, Irajizad, E. Lead time trajectory of blood-based protein biomarkers for detection of pancreatic cancer based on repeat testing. Cancer Letters 612, 2025. e-Pub 2025. PMID: 39793753.
18. Prasad R, Rehman A, Rehman L, Darbaniyan F, Blumenberg V, Schubert ML, Mor U, Zamir E, Schmidt S, Hayase T, Chang CC, McDaniel L, Flores I, Strati P, Nair R, Chihara D, Fayad LE, Ahmed S, Iyer SP, Wang M, Jain P, Nastoupil LJ, Westin J, Arora R, Turner J, Khawaja F, Wu R, Dennison JB, Menges M, Hidalgo-Vargas M, Reid K, Davila ML, Dreger P, Korell F, Schmitt A, Tanner MR, Champlin RE, Flowers CR, Shpall EJ, Hanash S, Neelapu SS, Schmitt M, Subklewe M, Francois-Fahrmann J, Stein-Thoeringer CK, Elinav E, Jain MD, Hayase E, Jenq RR, Saini NY. Antibiotic-induced loss of gut microbiome metabolic output correlates with clinical responses to CAR T-cell therapy. Blood 145(8):823-839, 2025. e-Pub 2025. PMID: 39441941.
19. Gendarme S, Irajizad E, Long JP, Fahrmann JF, Dennison JB, Ghasemi SM, Dou R, Volk RJ, Meza R, Toumazis I, Canoui-Poitrine F, Hanash SM, Ostrin EJ. Impact of Comorbidities on the Mortality Benefits of Lung Cancer Screening: A Post-Hoc Analysis of the PLCO and NLST Trials. J Thorac Oncol, 2025. e-Pub 2025. PMID: 39798695.
20. Gu C, Ghasemi SM, Cai Y, Fahrmann JF, Long JP, Katayama H, Wu C, Vykoukal J, Dennison JB, Hanash S, Do KA, Irajizad E. Grape-Pi: graph-based neural networks for enhanced protein identification in proteomics pipelines. Bioinform Adv 5(1):vbaf095, 2025. e-Pub 2025. PMID: 40406669.
21. Gregg, JR, Newcomb, LF, Wu, R, Dennison, JB, Davis, JW, Pettaway, CA, Pisters, L, Ward, JF, Chapin, BF, Chery, LJ, Urkmez, A, Fang, A, Higgason, N, Troncoso, P, Daniel-MacDougall, CR, Logothetis, CJ, Thompson, TC, Hahn, AW, Liu, M, Zheng, Y, Lin, DW, Hanash, SM, Irajizad, E, Fahrmann, JF. Validation of a prognostic blood-based sphingolipid panel for men with localized prostate cancer followed on active surveillance. Biomarker Research 12(1), 2024. e-Pub 2024. PMID: 39522029.
22. Haab, BB, Qian, L, Staal, B, Jain, M, Fahrmann, JF, Worthington, C, Prosser, D, Velokokhatnaya, L, Lopez, C, Tang, R, Hurd, MW, Natarajan, G, Kumar, S, Smith, L, Hanash, S, Batra, SK, Maitra, A, Lokshin, A, Huang, Y, Brand, RE. A rigorous multi-laboratory study of known PDAC biomarkers identifies increased sensitivity and specificity over CA19-9 alone. Cancer Letters 604, 2024. e-Pub 2024. PMID: 39276915.
23. Irajizad, E, Fahrmann, JF, Toumazis, I, Vykoukal, JV, Dennison, JB, Shen, Y, Do, K, Ostrin, EJ, Feng, Z, Hanash, SM. Biomarker trajectory for earlier detection of lung cancer. EBioMedicine 108, 2024. e-Pub 2024. PMID: 39353277.
24. Song, L, Irajizad, E, Rundle, A, Sesso, HD, Gaziano, JM, Vykoukal, JV, Do, K, Dennison, JB, Ostrin, EJ, Fahrmann, JF, Perera, F, Hanash, S. Validation of a Blood-Based Protein Biomarker Panel for a Risk Assessment of Lethal Lung Cancer in the Physicians’ Health Study. Cancers 16(11), 2024. e-Pub 2024. PMID: 38893188.
25. Ghasem SM, Fahrmann JF, Hanash S, Do KA, Long JP, Irajizad E. A novel method to guide biomarker combinations to optimize the sensitivity. bioRxiv, 2024. e-Pub 2024. PMID: 38659773.
26. Faramand, R, Lee, SB, Jain, MD, Cao, B, Wang, X, Rejeski, K, Subklewe, M, Fahrmann, JF, Saini, N, Hanash, S, Kang, YP, Chang, D, Rodriguez, PC, Dean, EA, Nishihori, T, Shah, BD, Lazaryan, A, Chavez, JC, Khimani, F, Pinilla-Ibarz, J, Dam, M, Reid, K, Corallo, SA, Menges, M, Vargas, MH, Mandula, JK, Holliday, BA, Bachmeier, CA, Speth, K, Song, Q, Mattie, M, Locke, FL, Davila, ML. Baseline Serum Inflammatory Proteins Predict Poor CAR T Outcomes in Diffuse Large B-cell Lymphoma. Blood Cancer Discovery 5(2):106-113, 2024. e-Pub 2024. PMID: 38194367.
27. Tai, MC, Bantis, LE, Parhy, G, Kato, T, Tanaka, I, Chow, CW, Fujimoto, J, Behrens, MC, Hase, T, Kawaguchi, K, Fahrmann, JF, Ostrin, EJ, Yokoi, K, Chen-Yoshikawa, TF, Hasegawa, Y, Hanash, S, Wistuba, II, Taguchi, A. Circulating microRNA Panel for Prediction of Recurrence and Survival in Early-Stage Lung Adenocarcinoma. International journal of molecular sciences 25(4), 2024. e-Pub 2024. PMID: 38397007.
28. Leon-Letelier RA, Chen Y, Ballaro R, Irajizad E, Do KA, Maitra A, Zhang J, Schmidt CM, Fahrmann JF. A Blood-based Metabolite Signature for Personalized Risk Assessment of Pancreatic Cancer. J Cancer Immunol (Wilmington) 6(4):148-153, 2024. e-Pub 2024. PMID: 39713022.
29. Ben-Ami R, Wang QL, Zhang J, Supplee JG, Fahrmann JF, Lehmann-Werman R, Brais LK, Nowak J, Yuan C, Loftus M, Babic A, Irajizad E, Davidi T, Zick A, Hubert A, Neiman D, Piyanzin S, Gal-Rosenberg O, Horn A, Shemer R, Glaser B, Boos N, Jajoo K, Lee L, Clancy TE, Rubinson DA, Ng K, Chabot JA, Kastrinos F, Kluger M, Aguirre AJ, Jänne PA, Bardeesy N, Stanger B, O'Hara MH, Till J, Maitra A, Carpenter EL, Bullock AJ, Genkinger J, Hanash SM, Paweletz CP, Dor Y, Wolpin BM. Protein biomarkers and alternatively methylated cell-free DNA detect early stage pancreatic cancer. Gut 73(4):639-648, 2023. e-Pub 2023. PMID: 38123998.
30. Zhang X, Irajizad E, Hoffman KL, Fahrmann JF, Li F, Seo YD, Browman GJ, Dennison JB, Vykoukal J, Luna PN, Siu W, Wu R, Murage E, Ajami NJ, McQuade JL, Wargo JA, Long JP, Do KA, Lampe JW, Basen-Engquist KM, Okhuysen PC, Kopetz S, Hanash SM, Petrosino JF, Scheet P, Daniel CR. Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial. EBioMedicine 98:104873, 2023. e-Pub 2023. PMID: 38040541.
31. Fahrmann JF, Wasylishen AR, Pieterman CRC, Irajizad E, Vykoukal J, Wu R, Dennison JB, Peterson CB, Zhao H, Do KA, Halperin DM, Agarwal SK, Blau JE, Jha S, Rivero JD, Nilubol N, Walter MF, Welch JM, Weinstein LS, Vriens MR, van Leeuwaarde RS, van Treijen MJC, Valk GD, Perrier ND, Hanash SM, Katayama H. Blood-based Proteomic Signatures Associated With MEN1-related Duodenopancreatic Neuroendocrine Tumor Progression. J Clin Endocrinol Metab 108(12):3260-3271, 2023. e-Pub 2023. PMID: 37307230.
32. Geng C, Zhang MC, Manyam GC, Vykoukal JV, Fahrmann JF, Peng S, Wu C, Park S, Kondraganti S, Wang D, Robinson BD, Loda M, Barbieri CE, Yap TA, Corn PG, Hanash S, Broom BM, Pilié PG, Thompson TC. SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor-Induced Growth Suppression. Clin Cancer Res 29(21):4464-4478, 2023. e-Pub 2023. PMID: 37581614.
33. Deng N, Reyes-Uribe L, Fahrmann JF, Thoman WS, Munsell MF, Dennison JB, Murage E, Wu R, Hawk ET, Thirumurthi S, Lynch PM, Dieli-Conwright CM, Lazar AJ, Jindal S, Chu K, Chelvanambi M, Basen-Engquist K, Li Y, Wargo JA, McAllister F, Allison JP, Sharma P, Sinha KM, Hanash S, Gilchrist SC, Vilar E. Exercise Training Reduces the Inflammatory Response and Promotes Intestinal Mucosa-Associated Immunity in Lynch Syndrome. Clin Cancer Res 29(21):4361-4372, 2023. e-Pub 2023. PMID: 37724990.
34. Irajizad E, Kenney A, Tang T, Vykoukal J, Wu R, Murage E, Dennison JB, Sans M, Long JP, Loftus M, Chabot JA, Kluger MD, Kastrinos F, Brais L, Babic A, Jajoo K, Lee LS, Clancy TE, Ng K, Bullock A, Genkinger JM, Maitra A, Do KA, Yu B, Wolpin BM, Hanash S, Fahrmann JF. A blood-based metabolomic signature predictive of risk for pancreatic cancer. Cell Rep Med 4(9):101194, 2023. e-Pub 2023. PMID: 37729870.
35. Irajizad E, Fahrmann JF, Marsh T, Vykoukal J, Dennison JB, Long JP, Do KA, Feng Z, Hanash S, Ostrin EJ. Mortality Benefit of a Blood-Based Biomarker Panel for Lung Cancer on the Basis of the Prostate, Lung, Colorectal, and Ovarian Cohort. J Clin Oncol 41(27):4360-4368, 2023. e-Pub 2023. PMID: 37379494.
36. Mukherjee A, Bezwada D, Greco F, Zandbergen M, Shen T, Chiang CY, Tasdemir M, Fahrmann J, Grapov D, La Frano MR, Vu HS, Faubert B, Newman JW, McDonnell LA, Nezi L, Fiehn O, DeBerardinis RJ, Lengyel E. Adipocytes reprogram cancer cell metabolism by diverting glucose towards glycerol-3-phosphate thereby promoting metastasis. Nat Metab 5(9):1563-1577, 2023. e-Pub 2023. PMID: 37653041.
37. Sans M, Chen Y, Thege FI, Dou R, Min J, Yip-Schneider M, Zhang J, Wu R, Irajizad E, Makino Y, Rajapakshe KI, Hurd MW, Leon-Letelier RA, Vykoukal J, Dennison JB, Do KA, Wolff RA, Guerrero PA, Kim MP, Schmidt CM, Maitra A, Hanash S, Fahrmann JF. Integrated spatial transcriptomics and lipidomics of precursor lesions of pancreatic cancer identifies enrichment of long chain sulfatide biosynthesis as an early metabolic alteration. bioRxiv, 2023. e-Pub 2023. PMID: 37645752.
38. Sans M, Makino Y, Min J, Rajapakshe KI, Yip-Schneider M, Schmidt CM, Hurd MW, Burks JK, Gomez JA, Thege FI, Fahrmann JF, Wolff RA, Kim MP, Guerrero PA, Maitra A. Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential. Cancer Discov 13(8):1844-1861, 2023. e-Pub 2023. PMID: 37285225.
39. Kraler S, Wenzl FA, Vykoukal J, Fahrmann JF, Shen MY, Chen DY, Chang KC, Chang CK, von Eckardstein A, Räber L, Mach F, Nanchen D, Matter CM, Liberale L, Camici GG, Akhmedov A, Chen CH, Lüscher TF, investigators S. Low-density lipoprotein electronegativity and risk of death after acute coronary syndromes: A case-cohort analysis. Atherosclerosis 376:43-52, 2023. e-Pub 2023. PMID: 37285778.
40. León-Letelier RA, Abdel Sater AH, Chen Y, Park S, Wu R, Irajizad E, Dennison JB, Katayama H, Vykoukal JV, Hanash S, Ostrin EJ, Fahrmann JF. Kynureninase Upregulation Is a Prominent Feature of NFR2-Activated Cancers and Is Associated with Tumor Immunosuppression and Poor Prognosis. Cancers (Basel) 15(3), 2023. e-Pub 2023. PMID: 36765792.
41. Deans JR, Deol P, Titova N, Radi SH, Vuong LM, Evans JR, Pan S, Fahrmann J, Yang J, Hammock BD, Fiehn O, Fekry B, Eckel-Mahan K, Sladek FM. HNF4α isoforms regulate the circadian balance between carbohydrate and lipid metabolism in the liver. Front Endocrinol (Lausanne) 14:1266527, 2023. e-Pub 2023. PMID: 38111711.
42. Fahrmann JF, Saini NY, Chia-Chi C, Irajizad E, Strati P, Nair R, Fayad LE, Ahmed S, Lee HJ, Iyer S, Steiner R, Vykoukal J, Wu R, Dennison JB, Nastoupil L, Jain P, Wang M, Green M, Westin J, Blumenberg V, Davila M, Champlin R, Shpall EJ, Kebriaei P, Flowers CR, Jain M, Jenq R, Stein-Thoeringer CK, Subklewe M, Neelapu SS, Hanash S. A polyamine-centric, blood-based metabolite panel predictive of poor response to CAR-T cell therapy in large B cell lymphoma. Cell Rep Med 3(11):100720, 2022. e-Pub 2022. PMID: 36384092.
43. Irajizad E, Han CY, Celestino J, Wu R, Murage E, Spencer R, Dennison JB, Vykoukal J, Long JP, Do KA, Drescher C, Lu K, Lu Z, Bast RC, Hanash S, Fahrmann JF. A blood-based metabolite panel for distinguishing ovarian cancer from benign pelvic masses. Clin Cancer Res 28(21):4669-4676, 2022. e-Pub 2022. PMID: 36037307.
44. Vykoukal J, Fahrmann JF, Patel N, Shimizu M, Ostrin EJ, Dennison JB, Ivan C, Goodman GE, Thornquist MD, Barnett MJ, Feng Z, Calin GA, Hanash SM. Contributions of Circulating microRNAs for Early Detection of Lung Cancer. Cancers (Basel) 14(17), 2022. e-Pub 2022. PMID: 36077759.
45. Park S, Sater AHA, Fahrmann JF, Irajizad E, Cai Y, Katayama H, Vykoukal J, Kobayashi M, Dennison JB, Garcia-Manero G, Mullighan CG, Gu Z, Konopleva M, Hanash S. Novel UHRF1-MYC Axis in Acute Lymphoblastic Leukemia. Cancers (Basel) 14(17), 2022. e-Pub 2022. PMID: 36077796.
46. Irajizad E, Fahrmann JF, Long JP, Vykoukal J, Kobayashi M, Capello M, Yu CY, Cai Y, Hsiao FC, Patel N, Park S, Peng Q, Dennison JB, Kato T, Tai MC, Taguchi A, Kadara H, Wistuba II, Katayama H, Do KA, Hanash SM, Ostrin EJ. A Comprehensive Search of Non-Canonical Proteins in Non-Small Cell Lung Cancer and Their Impact on the Immune Response. Int J Mol Sci 23(16), 2022. e-Pub 2022. PMID: 36012199.
47. Li YJ, Fahrmann JF, Aftabizadeh M, Zhao Q, Tripathi SC, Zhang C, Yuan Y, Ann D, Hanash S, Yu H. Fatty acid oxidation protects cancer cells from apoptosis by increasing mitochondrial membrane lipids. Cell Rep 39(13):111044, 2022. e-Pub 2022. PMID: 35767954.
48. Fahrmann JF, Tanaka I, Irajizad E, Mao X, Dennison JB, Murage E, Casabar J, Mayo J, Peng Q, Celiktas M, Vykoukal JV, Park S, Taguchi A, Delgado O, Tripathi SC, Katayama H, Soto LMS, Rodriguez-Canales J, Behrens C, Wistuba I, Hanash S, Ostrin EJ. Mutational Activation of the NRF2 Pathway Upregulates Kynureninase Resulting in Tumor Immunosuppression and Poor Outcome in Lung Adenocarcinoma. Cancers (Basel) 14(10), 2022. e-Pub 2022. PMID: 35626147.
49. Li YJ, Fahrmann JF, Aftabizadeh M, Zhao Q, Tripathi SC, Zhang C, Yuan Y, Ann D, Hanash S, Yu H. Fatty acid oxidation protects cancer cells from apoptosis by increasing mitochondrial membrane lipids. Cell Rep 39(9):110870, 2022. e-Pub 2022. PMID: 35649368.
50. Fahrmann JF, Marsh T, Irajizad E, Patel N, Murage E, Vykoukal J, Dennison JB, Do KA, Ostrin E, Spitz MR, Lam S, Shete S, Meza R, Tammemägi MC, Feng Z, Hanash SM. Blood-Based Biomarker Panel for Personalized Lung Cancer Risk Assessment. J Clin Oncol 40(8):JCO2101460, 2022. e-Pub 2022. PMID: 34995129.
51. Chen Y, Capello M, Rios Perez MV, Vykoukal JV, Roife D, Kang Y, Prakash LR, Katayama H, Irajizad E, Fleury A, Ferri-Borgogno S, Baluya DL, Dennison JB, Do KA, Fiehn O, Maitra A, Wang H, Chiao PJ, Katz MHG, Fleming JB, Hanash SM, Fahrmann JF. CES2 sustains HNF4α expression to promote pancreatic adenocarcinoma progression through an epoxide hydrolase-dependent regulatory loop. Mol Metab 56:101426, 2022. e-Pub 2022. PMID: 34971802.
52. Tanaka I, Dayde D, Tai MC, Mori H, Solis LM, Tripathi SC, Fahrmann JF, Unver N, Parhy G, Jain R, Parra ER, Murakami Y, Aguilar-Bonavides C, Mino B, Celiktas M, Dhillon D, Casabar JP, Nakatochi M, Stingo F, Baladandayuthapani V, Wang H, Katayama H, Dennison JB, Lorenzi PL, Do KA, Fujimoto J, Behrens C, Ostrin EJ, Rodriguez-Canales J, Hase T, Fukui T, Kajino T, Kato S, Yatabe Y, Hosoda W, Kawaguchi K, Yokoi K, Chen-Yoshikawa TF, Hasegawa Y, Gazdar AF, Wistuba II, Hanash S, Taguchi A. SRGN-Triggered Aggressive and Immunosuppressive Phenotype in a Subset of TTF-1-Negative Lung Adenocarcinomas. J Natl Cancer Inst 114(2):290-301, 2022. e-Pub 2022. PMID: 34524427.
53. Irajizad E, Wu R, Vykoukal J, Murage E, Spencer R, Dennison JB, Moulder S, Ravenberg E, Lim B, Litton J, Tripathym D, Valero V, Damodaran S, Rauch GM, Adrada B, Candelaria R, White JB, Brewster A, Arun B, Long JP, Do KA, Hanash S, Fahrmann JF. Application of Artificial Intelligence to Plasma Metabolomics Profiles to Predict Response to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer. Front Artif Intell 5:876100, 2022. e-Pub 2022. PMID: 36034598.
54. Fahrmann JF, Wasylishen AR, Pieterman CRC, Irajizad E, Vykoukal J, Murage E, Wu R, Dennison JB, Krishna H, Peterson CB, Lozano G, Zhao H, Do KA, Halperin DM, Agarwal SK, Blau JE, Del Rivero J, Nilubol N, Walter MF, Welch JM, Weinstein LS, Vriens MR, van Leeuwaarde RS, van Treijen MJC, Valk GD, Perrier ND, Hanash SM. A Blood-based Polyamine Signature Associated With MEN1 Duodenopancreatic Neuroendocrine Tumor Progression. J Clin Endocrinol Metab 106(12):e4969-e4980, 2021. e-Pub 2021. PMID: 34318891.
55. Fahrmann JF, Katayama H, Irajizad E, Chakraborty A, Kato T, Mao X, Park S, Murage E, Rusling L, Yu CY, Cai Y, Hsiao FC, Dennison JB, Tran H, Ostrin E, Wilson DO, Yuan JM, Vykoukal J, Hanash S. Plasma Based Protein Signatures Associated with Small Cell Lung Cancer. Cancers (Basel) 13(16), 2021. e-Pub 2021. PMID: 34439128.
56. Katayama H, Kobayashi M, Irajizad E, Sevillarno A, Patel N, Mao X, Rusling L, Vykoukal J, Cai Y, Hsiao F, Yu CY, Long J, Liu J, Esteva F, Fahrmann JF, Hanash S. Protein citrullination as a source of cancer neoantigens. J Immunother Cancer 9(6), 2021. e-Pub 2021. PMID: 34112737.
57. Fahrmann JF, Schmidt CM, Mao X, Irajizad E, Loftus M, Zhang J, Patel N, Vykoukal J, Dennison JB, Long JP, Do KA, Zhang J, Chabot JA, Kluger MD, Kastrinos F, Brais L, Babic A, Jajoo K, Lee LS, Clancy TE, Ng K, Bullock A, Genkinger J, Yip-Schneider MT, Maitra A, Wolpin BM, Hanash S. Lead-Time Trajectory of CA19-9 as an Anchor Marker for Pancreatic Cancer Early Detection. Gastroenterology 160(4):1373-1383.e6, 2021. e-Pub 2021. PMID: 33333055.
58. Fahrmann JF Irajizad E, Kobayashi M, Vykoukal J, Dennison JB, Murage E, Wu R, Long JP, Do KA, Celestino J, Lu KH, Lu Z, Bast RC, Hanash S. A MYC-Driven Plasma Polyamine Signature for Early Detection of Ovarian Cancer. Cancers (Basel) 13(4), 2021. e-Pub 2021. PMID: 33671595.
59. Ostrin EJ, Bantis LE, Wilson DO, Patel N, Wang R, Kundnani D, Adams-Haduch J, Dennison JB, Fahrmann JF, Chiu HT, Gazdar A, Feng Z, Yuan JM, Hanash SM. Contribution of a blood-based protein biomarker panel to the classification of indeterminate pulmonary nodules. J Thorac Oncol 16(2):228-236, 2021. e-Pub 2021. PMID: 33137463.
60. Abbas A, Witte T, Patterson WL 3rd, Fahrmann JF, Guo K, Hur J, Hardman WE, Georgel PT. Epigenetic Reprogramming Mediated by Maternal Diet Rich in Omega-3 Fatty Acids Protects From Breast Cancer Development in F1 Offspring. Front Cell Dev Biol 9:682593, 2021. e-Pub 2021. PMID: 34179012.
61. Borrego SL, Fahrmann J, Hou J, Lin DW, Tromberg BJ, Fiehn O, Kaiser P. Lipid remodeling in response to methionine stress in MDA-MBA-468 triple-negative breast cancer cells. J Lipid Res 62:100056, 2021. e-Pub 2021. PMID: 33647277.
62. Liu Y, Kaur S, Huang Y, Fahrmann JF, Rinaudo JA, Hanash SM, Batra SK, Singhi AD, Brand RE, Maitra A, Haab BB. Biomarkers and Strategy to Detect Pre-Invasive and Early Pancreatic Cancer: State of the Field and the Impact of the EDRN. Cancer Epidemiol Biomarkers Prev 29(12):2513-2523, 2020. e-Pub 2020. PMID: 32532830.
63. Capello M, Fahrmann JF, Rios Perez MV, Vykoukal JV, Irajizad E, Tripathi SC, Roife D, Bantis LE, Kang Y, Kundnani DL, Xu H, Prakash LR, Long JP, Katayama H, Fleury A, Ferri-Borgogno S, Baluya DL, Dennison JB, Aguilar-Bonavides C, Casabar JP, Celiktas M, Do KA, Fiehn O, Maitra A, Wang H, Feng Z, Chiao PJ, Katz MH, Fleming JB, Hanash SM. CES2 Expression in Pancreatic Adenocarcinoma Is Predictive of Response to Irinotecan and Is Associated With Type 2 Diabetes. JCO Precis Oncol 4:426-436, 2020. e-Pub 2020. PMID: 35050739.
64. Vykoukal J, Fahrmann JF, Gregg JR, Tang Z, Basourakos S, Irajizad E, Park S, Yang G, Creighton CJ, Fleury A, Mayo J, Paulucci-Holthauzen A, Dennison JB, Murage E, Peterson CB, Davis JW, Kim J, Hanash S, Thompson TC. Caveolin-1-mediated sphingolipid oncometabolism underlies a metabolic vulnerability of prostate cancer. Nat Commun 11(1):4279, 2020. e-Pub 2020. PMID: 32855410.
65. Fahrmann JF, Vykoukal J, Fleury A, Tripathi S, Dennison JB, Murage E, Wang P, Yu CY, Capello M, Creighton CJ, Do KA, Long JP, Irajizad E, Peterson C, Katayama H, Disis ML, Arun B, Hanash S. Association between plasma diacetylspermine and tumor spermine synthase with outcome in triple negative breast cancer. J Natl Cancer Inst 112(6):607-616, 2020. e-Pub 2020. PMID: 31503278.
66. Fahrmann JF, Mao X, Irajizad E, Katayama H, Capello M, Tanaka I, Kato T, Wistuba II, Maitra A, Ostrin EJ, Hanash SM, Vykoukal J. Plasma-Derived Extracellular Vesicles Convey Protein Signatures that Reflect Pathophysiology in Lung and Pancreatic Adenocarcinomas. Cancers (Basel) 12(5), 2020. e-Pub 2020. PMID: 32370304.
67. Mukherjee A, Chiang CY, Daifotis HA, Nieman KM, Fahrmann JF, Lastra RR, Romero IL, Fiehn O, Lengyel E. Adipocyte-Induced FABP4 Expression in Ovarian Cancer Cells Promotes Metastasis and Mediates Carboplatin Resistance. Cancer Res 80(8):1748-1761, 2020. e-Pub 2020. PMID: 32054768.
68. Taguchi A, Fahrmann JF, Hanash SM. A Promising CPS1 Inhibitor Keeping Ammonia from Fueling Cancer. Cell Chem Biol 27(3):253-254, 2020. e-Pub 2020. PMID: 32200911.
69. Kobayashi M, Katayama H, Irajizad E, Vykoukal JV, Fahrmann JF, Kundnani DL, Yu CY, Cai Y, Hsiao FC, Yang WL, Lu Z, Celestino J, Long JP, Do KA, Lu KH, Ladd JJ, Urban N, Bast RC, Hanash SM. Proteome Profiling Uncovers an Autoimmune Response Signature That Reflects Ovarian Cancer Pathogenesis. Cancers (Basel) 12(2), 2020. e-Pub 2020. PMID: 32092936.
70. Fahrmann JF, Bantis LE, Capello M, Scelo G, Dennison JB, Patel N, Murage E, Vykoukal J, Kundnani DL, Foretova L, Fabianova E, Holcatova I, Janout V, Feng Z, Yip-Schneider M, Zhang J, Brand R, Taguchi A, Maitra A, Brennan P, Max Schmidt C, Hanash S. A Plasma-Derived Protein-Metabolite Multiplexed Panel for Early-Stage Pancreatic Cancer. J Natl Cancer Inst 111(4):372-379, 2019. e-Pub 2019. PMID: 30137376.
71. Tugizimana F, Djami-Tchatchou AT, Fahrmann JF, Steenkamp PA, Piater LA, Dubery IA. Time-resolved decoding of metabolic signatures of in vitro growth of the hemibiotrophic pathogen Colletotrichum sublineolum. Sci Rep 9(1):3290, 2019. e-Pub 2019. PMID: 30824820.
72. La Frano MR, Fahrmann JF, Grapov D, Pedersen TL, Newman JW, Fiehn O, Underwood MA, Mestan K, Steinhorn RH, Wedgwood S. Umbilical cord blood metabolomics reveal distinct signatures of dyslipidemia prior to bronchopulmonary dysplasia and pulmonary hypertension. Am J Physiol Lung Cell Mol Physiol 315(5):L870-L881, 2018. e-Pub 2018. PMID: 30113229.
73. Wang T, Fahrmann JF, Lee H, Li YJ, Tripathi SC, Yue C, Zhang C, Lifshitz V, Song J, Yuan Y, Somlo G, Jandial R, Ann D, Hanash S, Jove R, Yu H. JAK/STAT3-Regulated Fatty Acid beta-Oxidation Is Critical for Breast Cancer Stem Cell Self-Renewal and Chemoresistance. Cell Metab 27(6):1357, 2018. e-Pub 2018. PMID: 29874570.
74. Wang T, Fahrmann JF, Lee H, Li YJ, Tripathi SC, Yue C, Zhang C, Lifshitz V, Song J, Yuan Y, Somlo G, Jandial R, Ann D, Hanash S, Jove R, Yu H. JAK/STAT3-Regulated Fatty Acid β-Oxidation Is Critical for Breast Cancer Stem Cell Self-Renewal and Chemoresistance. Cell Metab 27(1):136-150.e5, 2018. e-Pub 2018. PMID: 29249690.
75. Vykoukal J, Sun N, Aguilar-Bonavides C, Katayama H, Tanaka I, Fahrmann JF, Capello M, Fujimoto J, Aguilar M, Wistuba II, Taguchi A, Ostrin EJ, Hanash SM. Plasma-derived extracellular vesicle proteins as a source of biomarkers for lung adenocarcinoma. Oncotarget 8(56):95466-95480, 2017. e-Pub 2017. PMID: 29221141.
76. Brito A, Grapov D, Fahrmann J, Harvey D, Green R, Miller JW, Fedosov SN, Shahab-Ferdows S, Hampel D, Pedersen TL, Fiehn O, Newman JW, Uauy R, Allen LH. The Human Serum Metabolome of Vitamin B-12 Deficiency and Repletion, and Associations with Neurological Function in Elderly Adults. J Nutr 147(10):1839-1849, 2017. e-Pub 2017. PMID: 28794205.
77. Deol P, Fahrmann J, Yang J, Evans JR, Rizo A, Grapov D, Salemi M, Wanichthanarak K, Fiehn O, Phinney B, Hammock BD, Sladek FM. Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice. Sci Rep 7(1):12488, 2017. e-Pub 2017. PMID: 28970503.
78. Fong LY, Jing R, Smalley KJ, Taccioli C, Fahrmann J, Barupal DK, Alder H, Farber JL, Fiehn O, Croce CM. Integration of metabolomics, transcriptomics, and microRNA expression profiling reveals a miR-143-HK2-glucose network underlying zinc-deficiency-associated esophageal neoplasia. Oncotarget 8(47):81910-81925, 2017. e-Pub 2017. PMID: 29137232.
79. Tripathi SC, Fahrmann JF, Celiktas M, Aguilar M, Marini KD, Jolly MK, Katayama H, Wang H, Murage EN, Dennison JB, Watkins DN, Levine H, Ostrin EJ, Taguchi A, Hanash SM. MCAM Mediates Chemoresistance in Small-Cell Lung Cancer via the PI3K/AKT/SOX2 Signaling Pathway. Cancer Res 77(16):4414-4425, 2017. e-Pub 2017. PMID: 28646020.
80. Olmstead KI, La Frano MR, Fahrmann J, Grapov D, Viscarra JA, Newman JW, Fiehn O, Crocker DE, Filipp FV, Ortiz RM. Insulin induces a shift in lipid and primary carbon metabolites in a model of fasting-induced insulin resistance. Metabolomics 13(5), 2017. e-Pub 2017. PMID: 28757815.
81. DeFelice BC, Mehta SS, Samra S, Cajka T, Wancewicz B, Fahrmann JF, Fiehn O. Mass Spectral Feature List Optimizer (MS-FLO): A Tool To Minimize False Positive Peak Reports in Untargeted Liquid Chromatography-Mass Spectroscopy (LC-MS) Data Processing. Anal Chem 89(6):3250-3255, 2017. e-Pub 2017. PMID: 28225594.
82. Çeliktas M, Tanaka I, Tripathi SC, Fahrmann JF, Aguilar-Bonavides C, Villalobos P, Delgado O, Dhillon D, Dennison JB, Ostrin EJ, Wang H, Behrens C, Do KA, Gazdar AF, Hanash SM, Taguchi A. Role of CPS1 in Cell Growth, Metabolism and Prognosis in LKB1-Inactivated Lung Adenocarcinoma. J Natl Cancer Inst 109(3):1-9, 2017. e-Pub 2017. PMID: 28376202.
83. Lam WY, Becker AM, Kennerly KM, Wong R, Curtis JD, Llufrio EM, McCommis KS, Fahrmann J, Pizzato HA, Nunley RM, Lee J, Wolfgang MJ, Patti GJ, Finck BN, Pearce EL, Bhattacharya D. Mitochondrial Pyruvate Import Promotes Long-Term Survival of Antibody-Secreting Plasma Cells. Immunity 45(1):60-73, 2016. e-Pub 2016. PMID: 27396958.
84. Fahrmann JF, Grapov D, DeFelice BC, Taylor S, Kim K, Kelly K, Wikoff WR, Pass H, Rom WN, Fiehn O, Miyamoto S. Serum phosphatidylethanolamine levels distinguish benign from malignant solitary pulmonary nodules and represent a potential diagnostic biomarker for lung cancer. Cancer Biomark 16(4):609-17, 2016. e-Pub 2016. PMID: 27002763.
85. Borrego SL, Fahrmann J, Datta R, Stringari C, Grapov D, Zeller M, Chen Y, Wang P, Baldi P, Gratton E, Fiehn O, Kaiser P. Metabolic changes associated with methionine stress sensitivity in MDA-MB-468 breast cancer cells. Cancer Metab 4:9, 2016. e-Pub 2016. PMID: 27141305.
86. Fahrmann JF, Grapov D, Phinney BS, Stroble C, DeFelice BC, Rom W, Gandara DR, Zhang Y, Fiehn O, Pass H, Miyamoto S. Proteomic profiling of lung adenocarcinoma indicates heightened DNA repair, antioxidant mechanisms and identifies LASP1 as a potential negative predictor of survival. Clin Proteomics 13:31, 2016. e-Pub 2016. PMID: 27799870.
87. Fahrmann JF, Kim K, DeFelice BC, Taylor SL, Gandara DR, Yoneda KY, Cooke DT, Fiehn O, Kelly K, Miyamoto S. Investigation of metabolomic blood biomarkers for detection of adenocarcinoma lung cancer. Cancer Epidemiol Biomarkers Prev 24(11):1716-23, 2015. e-Pub 2015. PMID: 26282632.
88. Zeng H, Grapov D, Jackson MI, Fahrmann J, Fiehn O, Combs GF. Integrating Multiple Analytical Datasets to Compare Metabolite Profiles of Mouse Colonic-Cecal Contents and Feces. Metabolites 5(3):489-501, 2015. e-Pub 2015. PMID: 26378591.
89. Liesenfeld DB, Grapov D, Fahrmann JF, Salou M, Scherer D, Toth R, Habermann N, Böhm J, Schrotz-King P, Gigic B, Schneider M, Ulrich A, Herpel E, Schirmacher P, Fiehn O, Lampe JW, Ulrich CM. Metabolomics and transcriptomics identify pathway differences between visceral and subcutaneous adipose tissue in colorectal cancer patients: the ColoCare study. Am J Clin Nutr 102(2):433-43, 2015. e-Pub 2015. PMID: 26156741.
90. Fahrmann J, Grapov D, Yang J, Hammock B, Fiehn O, Bell GI, Hara M. Systemic alterations in the metabolome of diabetic NOD mice delineate increased oxidative stress accompanied by reduced inflammation and hypertriglyceremia. Am J Physiol Endocrinol Metab 308(11):E978-89, 2015. e-Pub 2015. PMID: 25852003.
91. Wikoff WR, Grapov D, Fahrmann JF, DeFelice B, Rom WN, Pass HI, Kim K, Nguyen U, Taylor SL, Gandara DR, Kelly K, Fiehn O, Miyamoto S. Metabolomic markers of altered nucleotide metabolism in early stage adenocarcinoma. Cancer Prev Res (Phila) 8(5):410-8, 2015. e-Pub 2015. PMID: 25657018.
92. Grapov D, Fahrmann J, Hwang J, Poudel A, Jo J, Periwal V, Fiehn O, Hara M. Diabetes Associated Metabolomic Perturbations in NOD Mice. Metabolomics 11(2):425-437, 2015. e-Pub 2015. PMID: 25755629.
93. Ray K, Fahrmann J, Mitchell B, Paul D, King H, Crain C, Cook C, Golovko M, Brose S, Golovko S, Santanam N. Oxidation-sensitive nociception involved in endometriosis-associated pain. Pain 156(3):528-39, 2015. e-Pub 2015. PMID: 25599233.
94. Ma Y, Kind T, Vaniya A, Gennity I, Fahrmann JF, Fiehn O. An in silico MS/MS library for automatic annotation of novel FAHFA lipids. J Cheminform 7:53, 2015. e-Pub 2015. PMID: 26579213.
95. Fahrmann JF, Hardman WE. Omega 3 fatty acids increase the chemo-sensitivity of B-CLL-derived cell lines EHEB and MEC-2 and of B-PLL-derived cell line JVM-2 to anti-cancer drugs doxorubicin, vincristine and fludarabine. Lipids Health Dis 12:36, 2013. e-Pub 2013. PMID: 23497075.
96. Fahrmann JF, Ballester OF, Ballester G, Witte TR, Salazar AJ, Kordusky B, Cowen KG, Ion G, Primerano DA, Boskovic G, Denvir J, Hardman WE. Inhibition of nuclear factor kappa B activation in early-stage chronic lymphocytic leukemia by omega-3 fatty acids. Cancer Invest 31(1):24-38, 2013. e-Pub 2013. PMID: 23193970.

Review Articles

1. Khorami-Sarvestani, S, Hanash, S, Fahrmann, JF, Leon Letelier, R, Katayama, H. Glycosylation in cancer as a source of biomarkers. Expert Review of Proteomics 21(9-10):345-365, 2024. e-Pub 2024. PMID: 39376081.
2. León-Letelier, RA, Dou, R, Vykoukal, JV, Yip-Schneider, MT, Maitra, A, Irajizad, E, Wu, R, Dennison, JB, Do, KA, Zhang, J, Schmidt, CM, Hanash, S, Fahrmann, JF. Contributions of the Microbiome-Derived Metabolome for Risk Assessment and Prognostication of Pancreatic Cancer. Clinical chemistry 70(1):102-115, 2024. e-Pub 2024. PMID: 38175578.
3. Chuchueva N, Carta F, Nguyen HN, Luevano J, Lewis IA, Rios-Castillo I, Fanos V, King E, Swistushkin V, Reshetov I, Rusetsky Y, Shestakova K, Moskaleva N, Mariani C, Castillo-Carniglia A, Grapov D, Fahrmann J, La Frano MR, Puxeddu R, Appolonova SA, Brito A. Metabolomics of head and neck cancer in biofluids: an integrative systematic review. Metabolomics 19(9):77, 2023. e-Pub 2023. PMID: 37644353.
4. Chen Y, León-Letelier RA, Abdel Sater AH, Vykoukal J, Dennison JB, Hanash S, Fahrmann JF. c-MYC-Driven Polyamine Metabolism in Ovarian Cancer: From Pathogenesis to Early Detection and Therapy. Cancers (Basel) 15(3), 2023. e-Pub 2023. PMID: 36765581.
5. León-Letelier RA, Dou R, Vykoukal J, Sater AHA, Ostrin E, Hanash S, Fahrmann JF. The kynurenine pathway presents multi-faceted metabolic vulnerabilities in cancer. Front Oncol 13:1256769, 2023. e-Pub 2023. PMID: 37876966.
6. Kato T, Vykoukal JV, Fahrmann JF, Hanash S. Extracellular Vesicles in Lung Cancer: Prospects for Diagnostic and Therapeutic Applications. Cancers (Basel) 13(18), 2021. e-Pub 2021. PMID: 34572829.
7. Kobayashi M, Katayama H, Fahrmann JF, Hanash SM. Development of autoantibody signatures for common cancers. Semin Immunol 47:101388, 2020. e-Pub 2020. PMID: 31924500.
8. Pomyen Y, Wanichthanarak K, Poungsombat P, Fahrmann J, Grapov D, Khoomrung S. Deep metabolome: Applications of deep learning in metabolomics. Comput Struct Biotechnol J 18:2818-2825, 2020. e-Pub 2020. PMID: 33133423.
9. Fahrmann JF, Vykoukal JV, Ostrin EJ. Amino Acid Oncometabolism and Immunomodulation of the Tumor Microenvironment in Lung Cancer. Front Oncol 10:276, 2020. e-Pub 2020. PMID: 32266129.
10. Tripathi SC, Fahrmann JF, Vykoukal JV, Dennison JB, Hanash SM. Targeting metabolic vulnerabilities of cancer: Small molecule inhibitors in clinic. Cancer Rep (Hoboken) 2(1):e1131, 2019. e-Pub 2019. PMID: 32721114.
11. Grapov D, Fahrmann J, Wanichthanarak K, Khoomrung S. Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integration in Precision Medicine. OMICS 22(10):630-636, 2018. e-Pub 2018. PMID: 30124358.
12. Hanash SM, Ostrin EJ, Fahrmann JF. Blood based biomarkers beyond genomics for lung cancer screening. Transl Lung Cancer Res 7(3):327-335, 2018. e-Pub 2018. PMID: 30050770.
13. Fahrmann JF, Grapov DD, Wanichthanarak K, DeFelice BC, Salemi MR, Rom WN, Gandara DR, Phinney BS, Fiehn O, Pass H, Miyamoto S. Integrated Metabolomics and Proteomics Highlight Altered Nicotinamide- and Polyamine Pathways in Lung Adenocarcinoma. Carcinogenesis 38(3):271-280, 2017. e-Pub 2017. PMID: 28049629.
14. Wanichthanarak K, Fahrmann JF, Grapov D. Genomic, Proteomic, and Metabolomic Data Integration Strategies. Biomark Insights 10(Suppl 4):1-6, 2015. e-Pub 2015. PMID: 26396492.

Editorials

1. Vykoukal JV, Fahrmann JF, Thompson TC. Caveolin and lipid domains-close companions in managing cellular pathways. Cancer Metastasis Rev 39(2):341-342, 2020. PMID: 32417992.
2. Kato T, Fahrmann JF, Hanash SM, Vykoukal J. Extracellular Vesicles Mediate B Cell Immune Response and Are a Potential Target for Cancer Therapy. Cells 9(6), 2020. PMID: 32580358.
3. Misra BB, Fahrmann JF, Grapov D. Review of emerging metabolomic tools and resources: 2015-2016. Electrophoresis 38(18):2257-2274, 2017. PMID: 28621886.

Abstracts

1. Fahrmann JF. CES2 expression in pancreatic adenocarcinoma is predictive of response to irinotecan and is associated with type 2 diabetes. AACR 2020, 2020. e-Pub 2020.
2. Fahrmann JF, Bantis LE, Capello M, Scelo G, Dennison JB, Patel N, Murage E, Vykoukal J, Kundnani DL, Foretova L, Fabianova E, Holcatova I, Janout V, Feng Z, Yip-Schneider M, Zhang J, Brand R, Taguchi A, Maitra A, Brennan P, Schmidt MC, Hanash S. A Plasma-derived Protein-Metabolite Multiplexed Panel for Early Stage Pancreatic Cancer. Keystone Cancer Metabolism Symposia, Keystone, CO,, 2019. e-Pub 2019.
3. Fahrmann JF, Bantis LE, Capello M, Scelo G, Dennison JB, Patel N, Murage E, Vykoukal J, Kundnani DL, Foretova L, Fabianova E, Holcatova I, Janout V, Feng Z, Yip-Schneider M, Zhang J, Brand R, Taguchi A, Maitra A, Brennan P, Schmidt MC, Hanash S. A Plasma-derived Protein-Metabolite Multiplexed Panel for Early Stage Pancreatic Cancer. Pancreatic Cancer Collective Symposium, 2019. e-Pub 2019.
4. Fahrmann JF, Bantis LE, Capello M, Scelo G, Dennison JB, Patel N, Murage E, Vykoukal J, Kundnani DL, Foretova L, Fabianova E, Holcatova I, Janout V, Feng Z, Yip-Schneider M, Zhang J, Brand R, Taguchi A, Maitra A, Brennan P, Schmidt MC, Hanash S. A Plasma-derived Protein-Metabolite Multiplexed Panel for Early Stage Pancreatic Cancer. EDRN Scientific Workshop, Bethesda, MD, 2019. e-Pub 2019.
5. Fahrmann JF, Wang T, Lee H, Li YJ, Tripathi SC, Yue C, Zhang C, Lifshitz V, Song J, Yuan Y, Somlo G, Jandial R, Ann D, Hanash S, Jove R, Yu H. AK/STAT3-Regulated Fatty Acid ß-Oxidation is Critical for Breast Cancer Stem Cell Self-Renewal and Chemoresistance. Keystone Cancer Metabolism Symposia, Snowbird, Salt Lake City, UT, 2018. e-Pub 2018.
6. Fahrmann JF, Bantis LE, Capello M, Scelo G, Dennison JB, Patel N, Murage E, Vykoukal J, Kundnani DL, Foretova L, Fabianova E, Holcatova I, Janout V, Feng Z, Yip-Schneider M, Zhang J, Brand R, Taguchi A, Maitra A, Brennan P, Schmidt MC, Hanash S. Plasma-derived Metabolite and Protein Biomarker Panels Have Additive Performance for Early Stage Pancreatic Cancer. Annual Metabolomics Conference, Seattle, WA, 2018. e-Pub 2018.
7. Fahrmann JF. Applied Metabolomics for Risk Assessment of Cancer. Cancer Metabolism Symposium. MD Anderson, Houston, TX, 2017. e-Pub 2017.
8. Fahrmann JF, Tanaka I, Celiktas M, Aguilar M, Aguilar-Bonavides C, Dennison JB, Murage E, Wang H, Rodriguez J, Behrens C, Ostrin EJ, Wistuba I, Taguchi A, Hanash S. Kynureninase is Predictive of Poor Survival in Lung Adenocarcinoma and its Immunosuppressive Effects are Mediated through an Altered Metabolic Phenotype. 3rd Annual Immuno-Oncology Young Investigator’s Forum. Houston, TX, 2017. e-Pub 2017.
9. Fahrmann JF, Vykoukal J, Basourakos S, Wang J, Dennison JB, Murage M, Peterson CB, Kim J, Thompson TC, Hanash S. Metabolomics Identifies a Caveolin-1-associated Plasma Glycosphingolipid and Sphingomyelin Signature that Differentiates Aggressive from Indolent Prostate Cancer in an Active Surveillance Cohort. AACR Annual Meeting, Washington D.C., MD, 2017. e-Pub 2017.
10. Fahrmann JF, Muge C, Delgado O, Aguilar-Bonavides C, Aguilar M, Dennison JB, Murage E, Wang H, Ostring EJ, Taguchi A, Hanash S. Elevated Kynureninase Protein Expression is Associated with KEAP1 mutant Non-Small Cell Lung Cancer Adenocarcinoma and is Predictive of Poor Overall Survival. AACR Annual Meeting, New Orleans, 2016. e-Pub 2016.
11. Brito A, Grapov D, Fahrmann JF, Green R, Miller J, Fedosov S, Shahab-Ferdows S, Hampel D, Pederson T, Fiehn O, Newman J, Uauy R, Allen L. Metabolomics reveals new pathways and candidate biomarkers of vitamin B12 status and effects of B12 on myelinated peripheral nerve conduction. 11th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
12. DeFelice BC, Mehta S, Samra S, Fahrmann JF, Fiehn O. Untargeted LC-MS data post-processing: Look at only the peaks that matter!. 11th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
13. Fahrmann JF, Kim K, DeFelice BC, Taylor SL, Gandara D, Yoneda KY, Cooke DT, Fiehn O, Kelly K, Miyamoto S. Blood metabolites for diagnosis of adenocarcinoma lung cancer to complement low dose CT scans. 11th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
14. Liesenfeld DB, Grapov D, Fahrmann JF, Salou M, Scherer D, Toth R, Habermann N, Bohm J, Schrotz-King P, Schneider M, Ulrich A, Herpel E, Schirmacher P, Fiehn O, Lampe J, Ulrich C. Metabolomics and transcriptomics identify pathway differences between visceral and subcutaneous adipose tissue in colorectal cancer patients-the ColoCare study. 11th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
15. Borrego S, Fahrmann JF, Stringari C, Datta R, Zeller M, Baldi P, Gratton E, Fiehn O, Kaiser P. Metabolite Changes Associated with Methionine Stress Sensitivity in Cancer. 11th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
16. Deol P, Fahrmann JF, Yan J, Evans J, Briancon N, Weiss M, Fiehn OF. Metabolomics Approach to Determine the Roles of Soybean Oil and HNF4α in Obesity. 1th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
17. Fahrmann JF, Kyoungmi K, DeFelice BC, Taylor SL, Gandara D, Yoneda YK, Cooke D, Fiehn O, Kelly K, Miyamoto S. Investigation of Metabolomic Blood Biomarkers for Detection of Adenocarinoma Lung Cancer. Early Cancer Detection Symposium, Canary Foundation. Standford, CA, 2015. e-Pub 2015.
18. Olmstead K, Fahrmann JF, La Frano M, Grapov D, Viscarra J, Fiehn O, Newman J, Crocker D, Filipp F, Ortiz R. Metabolic shift in response to fasting and insulin infusion. 11th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
19. Mukherjee A, Ladanyi A, Fahrmann JF, La Frano M, Grapov D, Newman J, Fiehn O, and Lengyel E. A Systemic Analysis of Bidirectional Metabolomics Changes upon Interaction of Cancer Cells with Adipocytes. 11th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
20. Osborn O, Hernandez-Carretero A, Fahrmann JF, La Frano M, Fiehn O, Newman J. Metabolite Changes Associated with Obesity and Weight Loss. 11th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
21. Wickoff W, DeFelice BC, Fahrmann JF, Rom W, Miyamoto S, Pass H, Taguchi A, Hanash S, Fiehn O. Pre-diagnostic Biomarkers and Clinical Biochemistry of Lung Cancer in Blood and Tumor Tissue. 11th International Conference of the Metabolomics Society, Burlingame, CA, 2015. e-Pub 2015.
22. Fahrmann JF. The Imbalance that Persists: Application of Omega-3 Fatty Acids as Therapeutic Options for Cancers. Medical Oncology Fellowship Program, Marshall University School of Medicine, WV, 2013. e-Pub 2013.
23. Fahrmann JF, Hardman WE. Omega-3 Fatty Acids Are Potential Chemo-sensitizing Agents for the Treatment of B-Cell Chronic Lymphocytic Leukemia. Research Day, Marshall University School of Medicine, WV, 2013. e-Pub 2013.
24. Fahrmann JF. Lead-time trajectory of CA19-9 as an anchor marker for pancreatic cancer early detection. EDRN Virtual Symposium.

Book Chapters

1. Tripathi, SC, Fahrmann, JF, Amle, D. Targeting the Immuno-Oncology Metabolism in Cancer, 117-152, 2022.
2. Fahrmann JF, Witte TR, Hardman WE. Cancer Therapy May be Improved if Diet Contains Omega 3 Fatty Acids. In: Cutting Edge Therapies for Cancer in the 21st Century. Bentham eBooks, Bentham Science Publishers Ltd, 387-424, 2014.

Letters to the Editor

1. Fahrmann, JF, Ghasemi, SM, Han, CY, Wu, R, Dennison, JB, Vykoukal, JV, Celestino, J, Lu, KH, Lu, Z, Drescher, CW, Do, K, Hanash, SM, Bast Jr, RC, Irajizad, E. A metabolite-based liquid biopsy for detection of ovarian cancer. Biomarker Research 12, 2024.