Publications

Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer.Lu L, Zhang Q, Aladelokun O, Berardi D, Shen X, Marin A, Garcia-Milian R, Roper J, Khan SA, Johnson CH. Int J Cancer. 2025 Jan 1; 2024 Jul 22. PMID: 39039782.
A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer.van den Driest L, Kelly P, Marshall A, Johnson CH, Lasky-Su J, Lannigan A, Rattray Z, Rattray NJW. Comput Struct Biotechnol J. 2024 Dec; 2024 May 10. PMID: 38817965.
Mapping Pesticide-Induced Metabolic Alterations in Human Gut Bacteria.Chen L, Yan H, Di S, Guo C, Zhang H, Zhang S, Gold A, Wang Y, Hu M, Wu D, Johnson CH, Wang X, Zhu J. bioRxiv. 2024 Nov 16; 2024 Nov 16. PMID: 39605636.
OncoSexome: the landscape of sex-based differences in oncologic diseases.Shen X, Zhang Y, Li J, Zhou Y, Butensky SD, Zhang Y, Cai Z, DeWan AT, Khan SA, Yan H, Johnson CH, Zhu F. Nucleic Acids Res. 2024 Nov 13; 2024 Nov 13. PMID: 39535034.
Longitudinal biomonitoring of mycotoxin exposure during pregnancy in the Yale Pregnancy Outcome Prediction Study.Krausová M, Ayeni KI, Gu Y, Borutzki Y, O'Bryan J, Perley L, Silasi M, Wisgrill L, Johnson CH, Warth B. Environ Int. 2024 Oct 19; 2024 Oct 19. PMID: 39615253.
Charting the metabolic biogeography of the colorectum in cancer: challenging the right sided versus left sided classification.Jain A, Morris MT, Berardi D, Arora T, Domingo-Almenara X, Paty PB, Rattray NJW, Kerekes D, Lu L, Khan SA, Johnson CH. Mol Cancer. 2024 Sep 28; 2024 Sep 28. PMID: 39342363.
Transacylation and hydrolysis of the acyl glucuronides of ibuprofen and its α-methyl-substituted analogues investigated by (1)H NMR spectroscopy and computational chemistry: Implications for drug design.Richards SE, Bradshaw PR, Johnson CH, Stachulski AV, Athersuch TJ, Nicholson JK, Lindon JC, Wilson ID. J Pharm Biomed Anal. 2024 Aug 15; 2024 May 20. PMID: 38805849.
Human AKR1C3 binds agonists of GPR84 and participates in an expanded polyamine pathway.Dudkina N, Park HB, Song D, Jain A, Khan SA, Flavell RA, Johnson CH, Palm NW, Crawford JM. Cell Chem Biol. 2024 Aug 9; 2024 Aug 9. PMID: 39163853.
A machine learning and drug repurposing approach to target ferroptosis in colorectal cancer stratified by sex and KRAS.Yan H, Shen X, Yao Y, Khan SA, Ma S, Johnson CH. bioRxiv. 2024 Jun 28; 2024 Jun 28. PMID: 38979294.
Growth characteristics of HCT116 xenografts lacking asparagine synthetase vary according to sex.Aladelokun O, Lu L, Zheng J, Yan H, Jain A, Gibson J, Khan SA, Johnson CH. Hum Genomics. 2024 Jun 17; 2024 Jun 17. PMID: 38886847.
Perfluorooctanesulfonic Acid and Perfluorooctanoic Acid Promote Migration of Three-Dimensional Colorectal Cancer Spheroids.Zheng J, Sun B, Berardi D, Lu L, Yan H, Zheng S, Aladelokun O, Xie Y, Cai Y, Godri Pollitt KJ, Khan SA, Johnson CH. Environ Sci Technol. 2023 Dec 19; 2023 Dec 8. PMID: 38064429.
Multi-omic analysis reveals metabolic pathways that characterize right-sided colon cancer liver metastasis.Morris MT, Jain A, Sun B, Kurbatov V, Muca E, Zeng Z, Jin Y, Roper J, Lu J, Paty PB, Johnson CH, Khan SA. Cancer Lett. 2023 Oct 10; 2023 Sep 14. PMID: 37716465.
Per- and polyfluoroalkyl substances (PFAS) and thyroid hormone measurements in dried blood spots and neonatal characteristics: a pilot study.Rosen Vollmar AK, Lin EZ, Nason SL, Santiago K, Johnson CH, Ma X, Godri Pollitt KJ, Deziel NC. J Expo Sci Environ Epidemiol. 2023 Sep; 2023 Sep 20. PMID: 37730931.
Urinary Paraben Concentrations and Associations with the Periconceptional Urinary Metabolome: Untargeted and Targeted Metabolomics Analyses of Participants from the Early Pregnancy Study.Rosen Vollmar AK, Rattray NJW, Cai Y, Jain A, Yan H, Deziel NC, Calafat AM, Wilcox AJ, Jukic AMZ, Johnson CH. Environ Health Perspect. 2023 Sep; 2023 Sep 13. PMID: 37702489.
Discovery of decreased ferroptosis in male colorectal cancer patients with KRAS mutations.Yan H, Talty R, Jain A, Cai Y, Zheng J, Shen X, Muca E, Paty PB, Bosenberg MW, Khan SA, Johnson CH. Redox Biol. 2023 Jun; 2023 Apr 14. PMID: 37086630.
Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer.Lu L, Zhang Q, Shen X, Zhen P, Marin A, Garcia-Milian R, Roper J, Khan SA, Johnson CH. bioRxiv. 2023 May 5; 2023 May 5. PMID: 37205388.
Hepatopancreatobiliary malignancies: time to treatment matters.Kerekes DM, Frey AE, Bakkila BF, Johnson CH, Becher RD, Billingsley KG, Khan SA. J Gastrointest Oncol. 2023 Apr 29; 2023 Apr 17. PMID: 37201090.
Ferroptosis in colorectal cancer: a future target?Yan H, Talty R, Aladelokun O, Bosenberg M, Johnson CH. Br J Cancer. 2023 Apr; 2023 Jan 26. PMID: 36703079.
In silico designed mRNA vaccines targeting CA-125 neoantigen in breast and ovarian cancer.Lu L, Ma W, Johnson CH, Khan SA, Irwin ML, Pusztai L. Vaccine. 2023 Mar 17; 2023 Feb 20. PMID: 36813666.
Discovery of decreased ferroptosis in male colorectal cancer patients with KRAS mutations.Yan H, Talty R, Jain A, Cai Y, Zheng J, Shen X, Muca E, Paty PB, Bosenberg MW, Khan SA, Johnson CH. bioRxiv. 2023 Mar 1; 2023 Mar 1. PMID: 36909561.
Early-Onset Colorectal Cancer Somatic Gene Mutations by Population Subgroups.Shen X, DeWan AT, Johnson CH. Cancer Discov. 2023 Mar 1. PMID: 36855917.
Targeting ferroptosis to treat colorectal cancer.Yan H, Talty R, Johnson CH. Trends Cell Biol. 2023 Mar; 2022 Dec 3. PMID: 36473802.
Prenatal Choline Supplement in a Maternal Obesity Model Modulates Offspring Hepatic Lipidomes.Korsmo HW, Kadam I, Reaz A, Bretter R, Saxena A, Johnson CH, Caviglia JM, Jiang X. Nutrients. 2023 Feb 15; 2023 Feb 15. PMID: 36839327.
Urinary phenol concentrations and fecundability and early pregnancy loss.Rosen Vollmar AK, Weinberg CR, Baird DD, Wilcox AJ, Calafat AM, Deziel NC, Johnson CH, Jukic AMZ. Hum Reprod. 2023 Jan 5. PMID: 36346334.
Hemoglobin normalization outperforms other methods for standardizing dried blood spot metabolomics: A comparative study.Jain A, Morris M, Lin EZ, Khan SA, Ma X, Deziel NC, Godri Pollitt KJ, Johnson CH. Sci Total Environ. 2023 Jan 1; 2022 Sep 13. PMID: 36113793.
Bile acid distributions, sex-specificity, and prognosis in colorectal cancer.Cai Y, Shen X, Lu L, Yan H, Huang H, Gaule P, Muca E, Theriot CM, Rattray Z, Rattray NJW, Lu J, Ahuja N, Zhang Y, Paty PB, Khan SA, Johnson CH. Biol Sex Differ. 2022 Oct 23; 2022 Oct 23. PMID: 36274154.
Asparagine, colorectal cancer, and the role of sex, genes, microbes, and diet: A narrative review.Shen X, Jain A, Aladelokun O, Yan H, Gilbride A, Ferrucci LM, Lu L, Khan SA, Johnson CH. Front Mol Biosci. 2022; 2022 Aug 25. PMID: 36090030.
Evaluation of the role of KPNA2 mutations in breast cancer prognosis using bioinformatics datasets.Alnoumas L, van den Driest L, Apczynski Z, Lannigan A, Johnson CH, Rattray NJW, Rattray Z. BMC Cancer. 2022 Aug 10; 2022 Aug 10. PMID: 35948941.
TidyMass an object-oriented reproducible analysis framework for LC-MS data.Shen X, Yan H, Wang C, Gao P, Johnson CH, Snyder MP. Nat Commun. 2022 Jul 28; 2022 Jul 28. PMID: 35902589.
Development of an Accessible Gene Expression Bioinformatics Pipeline to Study Driver Mutations of Colorectal Cancer.van den Driest L, Johnson CH, Rattray NJW, Rattray Z. Altern Lab Anim. 2022 Jul; 2022 Jun 28. PMID: 35765262.
Evaluation of Racial Disparities in Quality of Care for Patients With Gastrointestinal Tract Cancer Treated With Surgery.Bakkila BF, Kerekes D, Nunez-Smith M, Billingsley KG, Ahuja N, Wang K, Oladele C, Johnson CH, Khan SA. JAMA Netw Open. 2022 Apr 1; 2022 Apr 1. PMID: 35377425.
Non-targeted metabolomics and associations with per- and polyfluoroalkyl substances (PFAS) exposure in humans: A scoping review.Guo P, Furnary T, Vasiliou V, Yan Q, Nyhan K, Jones DP, Johnson CH, Liew Z. Environ Int. 2022 Apr; 2022 Feb 26. PMID: 35231839.
Asparagine Metabolism in Tumors Is Linked to Poor Survival in Females with Colorectal Cancer: A Cohort Study.Shen X, Cai Y, Lu L, Huang H, Yan H, Paty PB, Muca E, Ahuja N, Zhang Y, Johnson CH, Khan SA. Metabolites. 2022 Feb 9; 2022 Feb 9. PMID: 35208238.
Identification of Dose-Dependent DNA Damage and Repair Responses From Subchronic Exposure to 1,4-Dioxane in Mice Using a Systems Analysis Approach.Charkoftaki G, Golla JP, Santos-Neto A, Orlicky DJ, Garcia-Milian R, Chen Y, Rattray NJW, Cai Y, Wang Y, Shearn CT, Mironova V, Wang Y, Johnson CH, Thompson DC, Vasiliou V. Toxicol Sci. 2021 Sep 28. PMID: 33693819.
Molecular Mechanisms of Alcohol-Induced Colorectal Carcinogenesis.Johnson CH, Golla JP, Dioletis E, Singh S, Ishii M, Charkoftaki G, Thompson DC, Vasiliou V. Cancers (Basel). 2021 Aug 31; 2021 Aug 31. PMID: 34503214.
ENT2 facilitates brain endothelial cell penetration and blood-brain barrier transport by a tumor-targeting anti-DNA autoantibody.Rattray Z, Deng G, Zhang S, Shirali A, May CK, Chen X, Cuffari BJ, Liu J, Zou P, Rattray NJ, Johnson CH, Dubljevic V, Campbell JA, Huttner A, Baehring JM, Zhou J, Hansen JE. JCI Insight. 2021 Jul 22; 2021 Jul 22. PMID: 34128837.
Kynurenic acid may underlie sex-specific immune responses to COVID-19.Cai Y, Kim DJ, Takahashi T, Broadhurst DI, Yan H, Ma S, Rattray NJW, Casanovas-Massana A, Israelow B, Klein J, Lucas C, Mao T, Moore AJ, Muenker MC, Oh JE, Silva J, Wong P, Ko AI, Khan SA, Iwasaki A, Johnson CH. Sci Signal. 2021 Jul 6; 2021 Jul 6. PMID: 34230210.
Intratumour microbiome associated with the infiltration of cytotoxic CD8+ T cells and patient survival in cutaneous melanoma.Zhu G, Su H, Johnson CH, Khan SA, Kluger H, Lu L. Eur J Cancer. 2021 Jul; 2021 May 4. PMID: 33962358.
YIV-906 potentiated anti-PD1 action against hepatocellular carcinoma by enhancing adaptive and innate immunity in the tumor microenvironment.Yang X, Lam W, Jiang Z, Guan F, Han X, Hu R, Cai W, Cheng W, Liu SH, Cheng P, Cai Y, Rattray NJW, Johnson CH, Chen L, Cheng YC. Sci Rep. 2021 Jun 29; 2021 Jun 29. PMID: 34188068.
Use of Untargeted Metabolomics to Explore the Air Pollution-Related Disease Continuum.Jin L, Godri Pollitt KJ, Liew Z, Rosen Vollmar AK, Vasiliou V, Johnson CH, Zhang Y. Curr Environ Health Rep. 2021 Mar; 2021 Jan 9. PMID: 33420964.
Accounting for urinary dilution in peri-implantation samples: implications for creatinine adjustment and specimen pooling.Rosen Vollmar AK, Johnson CH, Weinberg CR, Deziel NC, Baird DD, Wilcox AJ, Jukic AMZ. J Expo Sci Environ Epidemiol. 2021 Mar; 2020 May 18. PMID: 32424331.
Immune landscape and prognostic immune-related genes in KRAS-mutant colorectal cancer patients.Liu J, Huang X, Liu H, Wei C, Ru H, Qin H, Lai H, Meng Y, Wu G, Xie W, Mo X, Johnson CH, Zhang Y, Tang W. J Transl Med. 2021 Jan 7; 2021 Jan 7. PMID: 33413474.
Gene Alterations of N6-Methyladenosine (m(6)A) Regulators in Colorectal Cancer: A TCGA Database Study.Zhang Q, Cai Y, Kurbatov V, Khan SA, Lu L, Zhang Y, Johnson CH. Biomed Res Int. 2020; 2020 Dec 19. PMID: 33415160.
Kynurenic acid underlies sex-specific immune responses to COVID-19.Cai Y, Kim DJ, Takahashi T, Broadhurst DI, Ma S, Rattray NJW, Casanovas-Massana A, Israelow B, Klein J, Lucas C, Mao T, Moore AJ, Muenker MC, Oh J, Silva J, Wong P, Ko AI, Khan SA, Iwasaki A, Johnson CH. medRxiv. 2020 Sep 8; 2020 Sep 8. PMID: 32935119.
Tumor Tissue-Specific Biomarkers of Colorectal Cancer by Anatomic Location and Stage.Cai Y, Rattray NJW, Zhang Q, Mironova V, Santos-Neto A, Muca E, Vollmar AKR, Hsu KS, Rattray Z, Cross JR, Zhang Y, Paty PB, Khan SA, Johnson CH. Metabolites. 2020 Jun 19; 2020 Jun 19. PMID: 32575361.
Joint effect of pre-operative anemia and perioperative blood transfusion on outcomes of colon-cancer patients undergoing colectomy.Liu Z, Luo JJ, Pei KY, Khan SA, Wang XX, Zhao ZX, Yang M, Johnson CH, Wang XS, Zhang Y. Gastroenterol Rep (Oxf). 2020 Apr; 2019 Aug 9. PMID: 32280475.
Sex Differences in Colon Cancer Metabolism Reveal A Novel Subphenotype.Cai Y, Rattray NJW, Zhang Q, Mironova V, Santos-Neto A, Hsu KS, Rattray Z, Cross JR, Zhang Y, Paty PB, Khan SA, Johnson CH. Sci Rep. 2020 Mar 17; 2020 Mar 17. PMID: 32184446.
Analyzing Metabolomics Data for Environmental Health and Exposome Research.Cai Y, Rosen Vollmar AK, Johnson CH. Methods Mol Biol. 2020. PMID: 31953830.
Molecular Pathway Analysis Indicates a Distinct Metabolic Phenotype in Women With Right-Sided Colon Cancer.Sun Y, Mironova V, Chen Y, Lundh EPF, Zhang Q, Cai Y, Vasiliou V, Zhang Y, Garcia-Milian R, Khan SA, Johnson CH. Transl Oncol. 2020 Jan; 2019 Nov 21. PMID: 31760268.
1,4-Dioxane as an emerging water contaminant: State of the science and evaluation of research needs.Godri Pollitt KJ, Kim JH, Peccia J, Elimelech M, Zhang Y, Charkoftaki G, Hodges B, Zucker I, Huang H, Deziel NC, Murphy K, Ishii M, Johnson CH, Boissevain A, O'Keefe E, Anastas PT, Orlicky D, Thompson DC, Vasiliou V. Sci Total Environ. 2019 Nov 10; 2019 Jun 28. PMID: 31302550.
Metabolic dysregulation in vitamin E and carnitine shuttle energy mechanisms associate with human frailty.Rattray NJW, Trivedi DK, Xu Y, Chandola T, Johnson CH, Marshall AD, Mekli K, Rattray Z, Tampubolon G, Vanhoutte B, White IR, Wu FCW, Pendleton N, Nazroo J, Goodacre R. Nat Commun. 2019 Nov 5; 2019 Nov 5. PMID: 31690722.
Normalizing Untargeted Periconceptional Urinary Metabolomics Data: A Comparison of Approaches.Rosen Vollmar AK, Rattray NJW, Cai Y, Santos-Neto ÁJ, Deziel NC, Jukic AMZ, Johnson CH. Metabolites. 2019 Sep 21; 2019 Sep 21. PMID: 31546636.
Evaluation of potential carcinogenicity of organic chemicals in synthetic turf crumb rubber.Perkins AN, Inayat-Hussain SH, Deziel NC, Johnson CH, Ferguson SS, Garcia-Milian R, Thompson DC, Vasiliou V. Environ Res. 2019 Feb; 2018 Oct 24. PMID: 30458352.
Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells.Warth B, Palermo A, Rattray NJW, Lee NV, Zhu Z, Hoang LT, Cai Y, Mazurek A, Dann S, VanArsdale T, Fantin VR, Shields D, Siuzdak G, Johnson CH. Metabolites. 2019 Jan 2; 2019 Jan 2. PMID: 30609717.
Defining Early-Onset Colon and Rectal Cancers.Jacobs D, Zhu R, Luo J, Grisotti G, Heller DR, Kurbatov V, Johnson CH, Zhang Y, Khan SA. Front Oncol. 2018; 2018 Nov 6. PMID: 30460196.
Spontaneous DNA damage to the nuclear genome promotes senescence, redox imbalance and aging.Robinson AR, Yousefzadeh MJ, Rozgaja TA, Wang J, Li X, Tilstra JS, Feldman CH, Gregg SQ, Johnson CH, Skoda EM, Frantz MC, Bell-Temin H, Pope-Varsalona H, Gurkar AU, Nasto LA, Robinson RAS, Fuhrmann-Stroissnigg H, Czerwinska J, McGowan SJ, Cantu-Medellin N, Harris JB, Maniar S, Ross MA, Trussoni CE, LaRusso NF, Cifuentes-Pagano E, Pagano PJ, Tudek B, Vo NV, Rigatti LH, Opresko PL, Stolz DB, Watkins SC, Burd CE, Croix CMS, Siuzdak G, Yates NA, Robbins PD, Wang Y, Wipf P, Kelley EE, Niedernhofer LJ. Redox Biol. 2018 Jul; 2018 Apr 13. PMID: 29747066.
Distinctive features of gastrointestinal stromal tumors arising from the colon and rectum.Zhu R, Liu F, Grisotti G, Pérez-Irizarry J, Cha CH, Johnson CH, Boffa DJ, Han D, Johung KL, Zhang Y, Khan SA. J Gastrointest Oncol. 2018 Apr. PMID: 29755761.
Metabolomics Reveals that Dietary Xenoestrogens Alter Cellular Metabolism Induced by Palbociclib/Letrozole Combination Cancer Therapy.Warth B, Raffeiner P, Granados A, Huan T, Fang M, Forsberg EM, Benton HP, Goetz L, Johnson CH, Siuzdak G. Cell Chem Biol. 2018 Mar 15; 2018 Jan 11. PMID: 29337187.
Carnitine palmitoyltransferase 1C regulates cancer cell senescence through mitochondria-associated metabolic reprograming.Wang Y, Chen Y, Guan L, Zhang H, Huang Y, Johnson CH, Wu Z, Gonzalez FJ, Yu A, Huang P, Wang Y, Yang S, Chen P, Fan X, Huang M, Bi H. Cell Death Differ. 2018 Mar; 2018 Jan 9. PMID: 29317762.
Yale School of Public Health Symposium on tissue imaging mass spectrometry: illuminating phenotypic heterogeneity and drug disposition at the molecular level.Charkoftaki G, Rattray NJW, Andrén PE, Caprioli RM, Castellino S, Duncan MW, Goodwin RJA, Schey KL, Shahidi-Latham SK, Veselkov KA, Johnson CH, Vasiliou V. Hum Genomics. 2018 Feb 27; 2018 Feb 27. PMID: 29482659.
Re-engineering and evaluation of anti-DNA autoantibody 3E10 for therapeutic applications.Rattray Z, Dubljevic V, Rattray NJW, Greenwood DL, Johnson CH, Campbell JA, Hansen JE. Biochem Biophys Res Commun. 2018 Feb 12; 2018 Jan 31. PMID: 29374508.
Beyond genomics: understanding exposotypes through metabolomics.Rattray NJW, Deziel NC, Wallach JD, Khan SA, Vasiliou V, Ioannidis JPA, Johnson CH. Hum Genomics. 2018 Jan 26; 2018 Jan 26. PMID: 29373992.
Yale school of public health symposium on lifetime exposures and human health: the exposome; summary and future reflections.Johnson CH, Athersuch TJ, Collman GW, Dhungana S, Grant DF, Jones DP, Patel CJ, Vasiliou V. Hum Genomics. 2017 Dec 8; 2017 Dec 8. PMID: 29221465.
Exposome-Scale Investigations Guided by Global Metabolomics, Pathway Analysis, and Cognitive Computing.Warth B, Spangler S, Fang M, Johnson CH, Forsberg EM, Granados A, Martin RL, Domingo-Almenara X, Huan T, Rinehart D, Montenegro-Burke JR, Hilmers B, Aisporna A, Hoang LT, Uritboonthai W, Benton HP, Richardson SD, Williams AJ, Siuzdak G. Anal Chem. 2017 Nov 7; 2017 Oct 9. PMID: 28945073.
Metabolomics guided pathway analysis reveals link between cancer metastasis, cholesterol sulfate, and phospholipids.Johnson CH, Santidrian AF, LeBoeuf SE, Kurczy ME, Rattray NJW, Rattray Z, Warth B, Ritland M, Hoang LT, Loriot C, Higa J, Hansen JE, Felding BH, Siuzdak G. Cancer Metab. 2017; 2017 Oct 31. PMID: 29093815.
Environmental influences in the etiology of colorectal cancer: the premise of metabolomics.Rattray NJW, Charkoftaki G, Rattray Z, Hansen JE, Vasiliou V, Johnson CH. Curr Pharmacol Rep. 2017 Jun; 2017 Apr 7. PMID: 28642837.
Systems biology guided by XCMS Online metabolomics.Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G. Nat Methods. 2017 Apr 27. PMID: 28448069.
PPARα regulates tumor cell proliferation and senescence via a novel target gene carnitine palmitoyltransferase 1C.Chen Y, Wang Y, Huang Y, Zeng H, Hu B, Guan L, Zhang H, Yu AM, Johnson CH, Gonzalez FJ, Huang M, Bi H. Carcinogenesis. 2017 Apr 1. PMID: 28334197.
Metabolite and Microbiome Interplay in Cancer Immunotherapy.Johnson CH, Spilker ME, Goetz L, Peterson SN, Siuzdak G. Cancer Res. 2016 Nov 1; 2016 Oct 11. PMID: 27729325.
Metabolomics: beyond biomarkers and towards mechanisms.Johnson CH, Ivanisevic J, Siuzdak G. Nat Rev Mol Cell Biol. 2016 Jul; 2016 Mar 16. PMID: 26979502.
Metabolomics reveals mycoplasma contamination interferes with the metabolism of PANC-1 cells.Yu T, Wang Y, Zhang H, Johnson CH, Jiang Y, Li X, Wu Z, Liu T, Krausz KW, Yu A, Gonzalez FJ, Huang M, Bi H. Anal Bioanal Chem. 2016 Jun; 2016 Apr 13. PMID: 27074779.
Global metabolomics reveals metabolic dysregulation in ischemic retinopathy.Paris LP, Johnson CH, Aguilar E, Usui Y, Cho K, Hoang LT, Feitelberg D, Benton HP, Westenskow PD, Kurihara T, Trombley J, Tsubota K, Ueda S, Wakabayashi Y, Patti GJ, Ivanisevic J, Siuzdak G, Friedlander M. Metabolomics. 2016; 2015 Nov 18. PMID: 26617478.
Determining conserved metabolic biomarkers from a million database queries.Kurczy ME, Ivanisevic J, Johnson CH, Uritboonthai W, Hoang L, Fang M, Hicks M, Aldebot A, Rinehart D, Mellander LJ, Tautenhahn R, Patti GJ, Spilker ME, Benton HP, Siuzdak G. Bioinformatics. 2015 Dec 1; 2015 Aug 13. PMID: 26275895.
Thermal Degradation of Small Molecules: A Global Metabolomic Investigation.Fang M, Ivanisevic J, Benton HP, Johnson CH, Patti GJ, Hoang LT, Uritboonthai W, Kurczy ME, Siuzdak G. Anal Chem. 2015 Nov 3; 2015 Oct 14. PMID: 26434689.
Alterations in Spinal Cord Metabolism during Treatment of Neuropathic Pain.Johnson CH, Patti GJ, Courade JP, Shriver LP, Hoang LT, Manchester M, Siuzdak G. J Neuroimmune Pharmacol. 2015 Sep; 2015 Aug 2. PMID: 26232265.
Arteriovenous Blood Metabolomics: A Readout of Intra-Tissue Metabostasis.Ivanisevic J, Elias D, Deguchi H, Averell PM, Kurczy M, Johnson CH, Tautenhahn R, Zhu Z, Watrous J, Jain M, Griffin J, Patti GJ, Siuzdak G. Sci Rep. 2015 Aug 5; 2015 Aug 5. PMID: 26244428.
Metabolism links bacterial biofilms and colon carcinogenesis.Johnson CH, Dejea CM, Edler D, Hoang LT, Santidrian AF, Felding BH, Ivanisevic J, Cho K, Wick EC, Hechenbleikner EM, Uritboonthai W, Goetz L, Casero RA Jr, Pardoll DM, White JR, Patti GJ, Sears CL, Siuzdak G. Cell Metab. 2015 Jun 2; 2015 May 7. PMID: 25959674.
Comprehensive bioimaging with fluorinated nanoparticles using breathable liquids.Kurczy ME, Zhu ZJ, Ivanisevic J, Schuyler AM, Lalwani K, Santidrian AF, David JM, Giddabasappa A, Roberts AJ, Olivos HJ, O'Brien PJ, Franco L, Fields MW, Paris LP, Friedlander M, Johnson CH, Epstein AA, Gendelman HE, Wood MR, Felding BH, Patti GJ, Spilker ME, Siuzdak G. Nat Commun. 2015 Jan 20; 2015 Jan 20. PMID: 25601659.
Autonomous metabolomics for rapid metabolite identification in global profiling.Benton HP, Ivanisevic J, Mahieu NG, Kurczy ME, Johnson CH, Franco L, Rinehart D, Valentine E, Gowda H, Ubhi BK, Tautenhahn R, Gieschen A, Fields MW, Patti GJ, Siuzdak G. Anal Chem. 2015 Jan 20; 2014 Dec 26. PMID: 25496351.
Bioinformatics: the next frontier of metabolomics.Johnson CH, Ivanisevic J, Benton HP, Siuzdak G. Anal Chem. 2015 Jan 6; 2014 Nov 20. PMID: 25389922.
N-methylnicotinamide and nicotinamide N-methyltransferase are associated with microRNA-1291-altered pancreatic carcinoma cell metabolome and suppressed tumorigenesis.Bi HC, Pan YZ, Qiu JX, Krausz KW, Li F, Johnson CH, Jiang CT, Gonzalez FJ, Yu AM. Carcinogenesis. 2014 Oct; 2014 Aug 12. PMID: 25115443.
Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G. Anal Chem. 2014 Jul 15; 2014 Jun 25. PMID: 24934772.
Metabolomic data streaming for biology-dependent data acquisition.Rinehart D, Johnson CH, Nguyen T, Ivanisevic J, Benton HP, Lloyd J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G. Nat Biotechnol. 2014 Jun. PMID: 24911492.
Luciferase does not Alter Metabolism in Cancer Cells.Johnson CH, Fisher TS, Hoang LT, Felding BH, Siuzdak G, O'Brien PJ. Metabolomics. 2014 Jun 1. PMID: 24791164.
Global metabolomics reveals urinary biomarkers of breast cancer in a mcf-7 xenograft mouse model.Johnson CH, Manna SK, Krausz KW, Bonzo JA, Divelbiss RD, Hollingshead MG, Gonzalez FJ. Metabolites. 2013 Aug 7; 2013 Aug 7. PMID: 24958144.
Toward 'omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism.Ivanisevic J, Zhu ZJ, Plate L, Tautenhahn R, Chen S, O'Brien PJ, Johnson CH, Marletta MA, Patti GJ, Siuzdak G. Anal Chem. 2013 Jul 16; 2013 Jul 3. PMID: 23781873.
Optimization of harvesting, extraction, and analytical protocols for UPLC-ESI-MS-based metabolomic analysis of adherent mammalian cancer cells.Bi H, Krausz KW, Manna SK, Li F, Johnson CH, Gonzalez FJ. Anal Bioanal Chem. 2013 Jun; 2013 Apr 19. PMID: 23604415.
Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database.Zhu ZJ, Schultz AW, Wang J, Johnson CH, Yannone SM, Patti GJ, Siuzdak G. Nat Protoc. 2013 Mar; 2013 Feb 7. PMID: 23391889.
Cytochrome P450 regulation by α-tocopherol in Pxr-null and PXR-humanized mice.Johnson CH, Bonzo JA, Cheng J, Krausz KW, Kang DW, Luecke H, Idle JR, Gonzalez FJ. Drug Metab Dispos. 2013 Feb; 2012 Nov 16. PMID: 23160821.
Monitoring metabolic responses to chemotherapy in single cells and tumors using nanostructure-initiator mass spectrometry (NIMS) imaging.O'Brien PJ, Lee M, Spilker ME, Zhang CC, Yan Z, Nichols TC, Li W, Johnson CH, Patti GJ, Siuzdak G. Cancer Metab. 2013 Jan 23; 2013 Jan 23. PMID: 24280026.
A view from above: cloud plots to visualize global metabolomic data.Patti GJ, Tautenhahn R, Rinehart D, Cho K, Shriver LP, Manchester M, Nikolskiy I, Johnson CH, Mahieu NG, Siuzdak G. Anal Chem. 2013 Jan 15; 2012 Dec 26. PMID: 23206250.
Targeted Metabolomics of Serum Acylcarnitines Evaluates Hepatoprotective Effect of Wuzhi Tablet (Schisandra sphenanthera Extract) against Acute Acetaminophen Toxicity.Bi H, Li F, Krausz KW, Qu A, Johnson CH, Gonzalez FJ. Evid Based Complement Alternat Med. 2013; 2013 Feb 4. PMID: 23431354.
Implication of intestinal VDR deficiency in inflammatory bowel disease.Kim JH, Yamaori S, Tanabe T, Johnson CH, Krausz KW, Kato S, Gonzalez FJ. Biochim Biophys Acta. 2013 Jan; 2012 Oct 2. PMID: 23041070.
Radiation metabolomics. 5. Identification of urinary biomarkers of ionizing radiation exposure in nonhuman primates by mass spectrometry-based metabolomics.Johnson CH, Patterson AD, Krausz KW, Kalinich JF, Tyburski JB, Kang DW, Luecke H, Gonzalez FJ, Blakely WF, Idle JR. Radiat Res. 2012 Oct; 2012 Sep 6. PMID: 22954391.
Novel metabolites and roles for α-tocopherol in humans and mice discovered by mass spectrometry-based metabolomics.Johnson CH, Slanař O, Krausz KW, Kang DW, Patterson AD, Kim JH, Luecke H, Gonzalez FJ, Idle JR. Am J Clin Nutr. 2012 Oct; 2012 Sep 5. PMID: 22952181.
Challenges and opportunities of metabolomics.Johnson CH, Gonzalez FJ. J Cell Physiol. 2012 Aug. PMID: 22034100.
Xenobiotic metabolomics: major impact on the metabolome.Johnson CH, Patterson AD, Idle JR, Gonzalez FJ. Annu Rev Pharmacol Toxicol. 2012; 2011 Aug 3. PMID: 21819238.
Radiation metabolomics. 4. UPLC-ESI-QTOFMS-Based metabolomics for urinary biomarker discovery in gamma-irradiated rats.Johnson CH, Patterson AD, Krausz KW, Lanz C, Kang DW, Luecke H, Gonzalez FJ, Idle JR. Radiat Res. 2011 Apr; 2011 Feb 10. PMID: 21309707.
Synthesis of a series of phenylacetic acid 1-β-O-acyl glucosides and comparison of their acyl migration and hydrolysis kinetics with the corresponding acyl glucuronides.Iddon L, Richards SE, Johnson CH, Harding JR, Wilson ID, Nicholson JK, Lindon JC, Stachulski AV. Org Biomol Chem. 2011 Feb 7; 2010 Dec 8. PMID: 21152488.
High-performance liquid chromatography/mass spectrometric and proton nuclear magnetic resonance spectroscopic studies of the transacylation and hydrolysis of the acyl glucuronides of a series of phenylacetic acids in buffer and human plasma.Karlsson ES, Johnson CH, Sarda S, Iddon L, Iqbal M, Meng X, Harding JR, Stachulski AV, Nicholson JK, Wilson ID, Lindon JC. Rapid Commun Mass Spectrom. 2010 Oct 30. PMID: 20872637.