Publications — Center for Regulatory and Environmental Analytical Metabolomics

2023

Warner, J. B.; Hardesty, J. E.; Song, Y. L.; Floyd, A. T.; Jebet, A.; He, L.; Zhang, X.; McClain, C. J.; Hammock, B. D., Warner, D. R., Kirpich, I. A. Hepatic transcriptome and its regulation following soluble epoxide hydrolase inhibition in alcohol-associated liver disease. Am. J. Pathol. under revision.
Sarkar, O. S.; Donninger, H.; Rayyan, N. A.; Chew, L. C.; Stamp, B.; Zhang, X.; Whitt, A.; Li, C.; Hall, M.; Mitchell, R. A.; Zippelius, A.; Eaton, J.; Chesney, J. A.; Yaddanapud, K. Monocytic MDSCs exhibit superior immune suppression via adenosine and enzymatic depletion of adenosine improves efficacy of immunotherapy. Sci. Adv. 2023, under revision.
Piell, K. M.; Petri, B. J.; Head, K. Z.; Wahlang, B.; Xu, R.; Zhang, X.; Pan, J.; Rai, S. N.; de Silva, K.; Chariker, J. H.; Rouchka, E. C.; Tan, M.; Li, Y.; Cave, M. C., Kling, C. M. Disruption of the mouse liver epitranscriptome by long-term aroclor 1260. Environ. Toxicol. Phar. 2023. In press
Liu, S.; He, L.; Bannister, O.; Schnegelberger, R.; Vanderpuye, C.; Althouse, A.; Schopfer, F.; Wahlang, B.; Cave, M.; Monga, S. P. S.; Zhang, X.; Arteel, G.; Beier, J. Western diet unmasks transient low-level vinyl chloride-induced tumorigenesis; potential role of the (epi-)transcriptome. Toxicol. Appl. Pharmacol. 2023, 468:116514. https://doi.org/10.1016/j.taap.2023.116514. (PMID: 37061008)
Wise, J. T. F.; Yin, X.; Ma, X.; Zhang, X.; Hein, D. W. Stable isotope tracing reveals an altered fate of glucose in N-acetyltransferase 1 knockout breast cancer cells. Genes, 2023, 14(4), 843. https://doi.org/10.3390/genes14040843.
Zhu, X.; Zhang, X. Discretized skew-t mixture model for deconvoluting liquid chromatograph mass spectrometry data. Statistica Neerlandica2023, 1-20. https://doi.org/10.1111/stan.12285.
Xu, R.; He, L.; Vatsalya, V.; Ma, X.; Kim, S.; Mueller, E. G.; Feng, W.; McClain, C. J.; Zhang, X. Metabolomics analysis of urine from patients with alcohol-associated liver disease reveals dysregulated caffeine metabolism. Am. J. Physiol-Gaster. L. 2023, 324(2), G142-G154. https://doi.org/10.1152/ajpgi.00228.2022. (PMID: 36513601, Journal cover)
Ding, C.; Shrestha, R.; Zhu, X.; Geller, D. A.; Wu, S.; Woeste, M.; Li, W.; Wang, H.; Yuan, F.; Xu, R.; Chariker, J.; Hu, X.; Li, H.; Tieri, D.; Zhang, H-G, Rouchka, E.; Mitchell, R.; Siskind, L.; Zhang, X.; Xu, X.; McMasters, K.; Yu, Y.; Yan, J. Inducing trained immunity in pro-metastatic macrophages to control tumor metastasis. Nat. Immunol.2023, 24, 239-254. https://doi.org/10.1038/s41590-022-01388-8. (PMID: 36604547)

2022 (14)

He, L.; Vatsalya, V.; Ma, X.; Klinge, C.; Cave, M. C.; Feng, W.; McClain, C. J.; Zhang, X. Metabolic analysis of nucleosides/bases in the urine and serum of patients with alcohol-associated liver disease. Metabolites2022, 12, 1187. https://doi.org/10.3390/metabo12121187. (PMID: 36557225)
Miralles-Pérez, B.; Nogués, M. R.; Sánchez-Martos, V.; Fortuño-Mar, À.; Ramos-Romero, S.; Torres, J.; Ponomarenko, J.; Amézqueta, S.; Zhang, X.; Romeu, M. Influence of dietary inulin on fecal microbiota, cardiometabolic risk factors, eicosanoids and oxidative stress in rats fed a high-fat diet. Foods2022,11, 4072. https://doi.org/10.3390/foods11244072. (PMID: 36553814)Kumar, A.; Sundaram, K.; Teng, Y.; Mu, J.; Sriwastva, M. K.; Zhang, L.; Hood, J. L.; Yan, J.; Zhang, X.; Park, J. W.; Merchant, M. L.; Zhang, H-G. Ginger nanoparticles mediated induction of Foxa2 prevents high-fat diet-induced insulin resistance. Theranostics2022, 12(3), 1388-1403. https://doi.org/10.7150/thno.62514. (PMID: 35154496)
Sundaram, K.; Mu, J.; Kumar, A.; Behera, J.; Lei, C.; Sriwastva, M. K.; Xu, F.; Dryden, G. W.; Zhang, L.; Chen, S.; Yan, J.; Zhang, X.; Park, J. W.; Merchant, M. L.; Tyagi, N.; Teng, Y.; Zhang, H-G. Garlic exosome-like nanoparticles reverse high-fat diet induced obesity via the gut/brain axis. Theranostics2022, 12(3), 1220-1246. https://doi.org/10.7150/thno.65427. (PMID: 35154484)
Teng, Y.; Mu, J.; Xu, F.; Zhang, X.; Sriwastva, M. K.; Liu, Q. M.; Li, X.; Lei, C.; Sundaram, K.; Hu, X.; Zhang, L.; Park, J. W.; Hwang, J. Y.; Rouchka, E. C.; Zhang, X.; Yan, J.; Merchant, M. L.; Zhang, H-G. Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death. Cell Host & Microbe2022,30(7), 944–960.e8. https://doi.org/10.1016/j.chom.2022.05.005. (PMID: 35654045)
Kim, S.; Kato, I.; Zhang, X. Comparative analysis of binary similarity measures for compound identification in mass spectrometry-based metabolomics. Metabolites 2022, 12(8), 694. https://doi.org/10.3390/metabo12080694. (PMID: 35893261)
Yan, K.; Mei, Z.; Zhao, J.; Prodhan, Md A. I.; Obal, D.; Katragadda, K.; Doelling, B.; Hoetker, D.; Posa, D. K.; He, L.; Yin, X.; Shah, J.; Pan, J.; Rai, S.; Lorkiewicz, P. K.; Zhang, X.; Liu, S.; Bhatnagar, A.; Baba, S. P. Integrated multilayer omics reveals the genomic, proteomic, and metabolic influences of histidyl dipeptides on the heart. J. Am. Heart Assoc. 2022, 0:e023868. https://doi.org/10.1161/jaha.121.023868. (PMID: 35730646)
Jiang, M.; Li, F.; Liu, Y.; Gu, Z.; Zhang, L.; Lee, J.; He, L.; Vatsalya, V.; Zhang, H-G.; Deng, Z.; Zhang, X.; Chen, S-Y.; Guo, L. G.; Barve, S.; McClain, J. C.; Feng, W. Probiotic-derived nanoparticles inhibit ALD through intestinal miR194 suppression and subsequent FXR activation. Hepatology 2022, Jun 11;10.1002/hep.32608. https://doi.org/10.1002/hep.32608. (PMID: 35689610)
Teng, Y.; Mu, J.; Xu, F.; Zhang, X.; Sriwastva, M. K.; Liu, Q. M.; Li, X.; Lei, C.; Sundaram, K.; Hu, X.; Zhang, L.; Park, J. W.; Hwang, J. Y.; Rouchka, E. C.; Zhang, X.; Yan, J.; Merchant, M. L.; Zhang, H.-G. Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death. Cell Host & Microbe 2022, 30, 1-17. https://doi.org/10.1016/j.chom.2022.05.005. (PMID: 35654045)
Vatsalya, V.; Parthasarathy, R.; Verster, J. C.; Royer, A. C.; Sagaram, M.; Zamani, Z.; Hu, H.; Schwandt, M. L.; Leggio, L.; Kong, M.; Ramchandani, V. A.; Feng, W.; Zhang, X.; McClain, C. J. Illustration of a novel gut-brain axis of alcohol withdrawal, withdrawal-associated depression, craving and alcohol-severity index in alcohol use disorder patients. medRxiv 2022, DOI: 10.1101/2022.05.15.22275115.
Miller, H. A.; Rai, S. N.; Yin, X.; Zhang, X.; Chesney, J. A.; van Berkel, V. H., Frieboes, H. B. Lung cancer metabolomic data from tumor core biopsies enables risk-score calculation for progression-free and overall survival. Metabolomics2022, 14, 18(5):31. https://doi.org/10.1007/s11306-022-01891-x. (PMID: 35567637)
Chen, X.; Cai, Y.; Hu, X.; Ding, C.; Ke, L.; Zhang, X.; Chen, F.; Yan, J. Differential metabolic requirement governed by transcription factor c-Maf dictates γδT17 effector functionality in mice and humans. Sci. Adv.2022, 8(21):eabm9120. https://doi.org/10.1126/sciadv.abm9120. (PMID: 35613277)
Sun, R.; Lei, C.; Chen, L.; He, L.; Guo, H.; Zhang, X.; Feng, W.; Yan, J.; McClain, C. J.; Deng, Z. B. Alcohol-driven metabolic reprogramming promotes development of RORγt-deficient thymic lymphoma. Oncogene 2022, 41(16), 2287-2302. https://doi.org/10.1038/s41388-022-02257-2. (PMID: 35246617)
Sriwastva, M. K.; Deng, Z.; Wang, B.; Teng, Y.; Kumar, A.; Sundaram, K.; Mu, J.; Lei, C.; Dryden, G.W.; Xu, F.; Zhang, L.; Yan, J.; Zhang, X.; Park, J.; Merchant, M.; Egilmez, N.; Zhang, H. Exosome-like nanoparticles from Mulberry bark prevent DSS-induced colitis via the AhR/COPS8 pathway. EMBO Rep. 2022, 23(3):e53365. https://doi.org/10.15252/embr.202153365. (PMID: 34994476)

2021 (13)

Morrissey, S.M.; Zhang, F.; Ding, C.; Montoya-Durango, D. E.; Hu, X.; Yang, C.; Wang, Z.; Yuan, F.; Fox, M.; Zhang, H.; Guo, H.; Tieri, D.; Kong, M.; Watson, C. T.; Mitchell, R. A.; Zhang, X.; McMasters, K. M.; Huang, J.; Yan, J. Tumor-derived exosomes drive immunosuppressive macrophages in a pre-metastatic niche through metabolic reprogramming. Cell Metabolism, 2021, 5, 33(10), 2040-2058. (PMID: 34559989) DOI: https://doi.org/10.1016/j.cmet.2021.09.002.
Warner, J.; Hardesty, J.; Song, Y.; Sun, R.; Deng, Z.; Xu, R.; Yin, X.; Zhang, X.; McClain, C. J.; Warner, D.; Kirpich, I. Fat-1 transgenic mice with augmented n3-polyunsaturated fatty acids are protected from liver injury caused by acute-on-chronic ethanol administration. Front. Pharmacol., 2021, 12:711590. DOI: https://doi.org/10.3389/fphar.2021.711590.
Lei, C.; Teng, Y.; He, L.; Sayed, M.; Mu, J.; Xu, F.; Zhang, X.; Kumar, A.; Sundaram, K.; Sriwastva, M.; Zhang, L.; Yan, J.; Park, J.; Merchant, M.; Zhang, X.; Zhang, H-G. Lemon exosome-like nanoparticles enhance stress survival of gut bacteria by RNase P mediated specific tRNA decay. iScience, 2021, 24, 102511.
Teng, Y., Xu, F., Zhang, X., Mu, J., Sayed, M., Hu, X., Lei, C., Sriwastva, M., Kumar, A., Sundaram, K., Zhang, L., Park, J. J. W., Chen, S., Zhang, S., Yan, J., Merchant, M. L., Zhang, X., McClain, C. J., Wolfe, J. K., Adcock, R. S., Chung, D., Palmer, K. E., Zhang, H. Plant-derived exosomal microRNAs inhibit lung inflammation induced by exosomes SARS-CoV-2 Nsp12. Molecular Therapy, 2021, 29 (8), 2424-2440. DOI: https://doi.org/10.1016/j.ymthe.2021.05.005 (PMID: 33984520)
Miller, H.A.; Yin, X.; Smith, S.A.; Hu, X.; Zhang, X.; Yan, J.; Miller, D.M.; van Berkel, V.H.; Frieboes, H.B. Evaluation of disease staging and chemotherapeutic response in non-small cell lung cancer from patient tumor-derived metabolomic data. Lung Cancer, 2021. 156, 20-30. (PMID: 33882406)
Gu, Z.; Li, F.; Liu, Y.; Jiang, M.; Zhang, L.; He, L.; Wilkey, D. W.; Merchant, M.; Zhang, X.; Deng, Z.; Chen, S.; Barve, S.; McClain, C. J.; Feng, W. Exosome-like nanoparticles from Lactobacillus rhamnosus GG protect against alcoholic liver disease through intestinal AhR in mice. Hepatology Commun.2021, 5(5), 846-864.
He, L.; Vatsalya, V.; Ma, X.; Zhang, J.; Yin, X.; Kim, S.; McClain, C. J.; Zhang, X. Metabolic profiling of bile acids in urine of patients with alcohol associated liver disease. Hepatology Commun.2021, 5(5), 798-811. (PMID: 34027270)
Vatsalya, V.; Li, F.; Frimodig, J.; Gala, K. S.; Srivastava, S.; Kong, M.; Ramchandani, V. A.; Feng, W.; Zhang, X.; McClain, C. J. Therapeutic prospects for Th-17 cell immune storm syndrome and neurological symptoms in COVID-19: thiamine efficacy and safety, in-vitro evidence and pharmacokinetic profile. Front. Pharmacol. 2021, 11:598128. (PMID: 32869036)
Kumar, A.; Sundaram, K.; Mu, J.; Dryde, G.; Sriwastva, M.; Lei, C.; Zhang, L.; Qiu, X.; Xu, F.; Yan, J.; Zhang, X.; Park, J.; Merchant, M.; Bohler, H.; Wang, B.; Zhang, S.; Qin, C.; Xu, Z.; Han, X.; McClain, C. J.; Teng, Y.; Zhang, H-G. High-fat diet-induced upregulation of exosomal phosphatidylcholine contributes to insulin resistance. Nat. Commun. 2021, 12(1):213. (PMID: 33431899)
Prodhan, M. A. I.; McClain, C. J.; Zhang, X. Comprehensive two-dimensional gas chromatography mass spectrometry-based metabolomics. In: Hu S. (eds) Cancer Metabolomics. Advances in Experimental Medicine and Biology, 2021, 1280, 57-67. Springer, Cham. https://doi.org/10.1007/978-3-030-51652-9_4. (PMID: 33791974)
Ren, D.; He, Z.; Fedorova, J.; Zhang, J.; Wood, E.; Zhang, X.; Kang, D. E.; Ji, L. Sestrin2 maintains OXPHOS integrity to modulate cardiac substrate metabolism during ischemia and reperfusion. Redox Biol.2021, 28, 1010824. (PMID: 33316744)
Chen, K.; Tsai, S.; Zhang, X.; Zeng, C.; Yang, H. The investigation of the volatile metabolites of lung cancer from the microenvironment of malignant pleural effusion. Sci. Rep.2021, 11, 13585. DOI: https://doi.org/10.1038/s41598-021-93032-y.
Klinge, C.; Piell, K.; Petri, B.; He, L.; Zhang , X.; Pan, J.; Rai, S.; Andreeva, K.; Rouchka, E.; Wahlang, B.; Beier, J.; Cave, M. Polychlorinated biphenyls and high fat diet modify the global epitranscriptomic landscape in mouse liver. Environ. Epigenet.2021, 7(1), 1-12. DOI: https://doi.org/10.1093/eep/dvab008 (PMID: 34548932)

2020 (12)

Lei, C., Mu, J., Teng, Y., He, L., Xu, F., Zhang, X., Sundaram, K., Kumar, A., Sriwastva, M.K., Lawrenz, M.B., Zhang, L., Yan, J., Feng, W., McClain, C.J., Zhang, X., Zhang, H. Lemon Exosome-like Nanoparticles-Manipulated Probiotics Protect Mice from C. d iff Infection. iScience 2020, 23(10):101571 (PMID: 33083738 PMCID: PMC7530291)
Yuan, F.; He, L.; Feng, W.; McClain, C.J.; Zhang, X. High-throughput profiling of long chain fatty acids and oxylipins by LC-MS. Current Trends in Mass Spectrometry2020, 18(4), 28-34.
Yuan, F.; Kim, S.; Yin, X.; Zhang, X.; Kato, I. Integrating two-dimensional gas and liquid chromatography mass spectrometry for untargeted colorectal cancer metabolomics: a proof of principle study. Metabolites2020, 10(9), e343.
Fleissig, E.; Appenbrick, E.; Zhang, X.; Barr, C.C. Vitamin analysis comparison study. Am. J. Ophthalmol.2020, 222, 202-205.
Conroy, L.; Lorkiewicz, P.; He, L.; Yin, X.; Zhang, X.; Rai, S.; Clem, B. Palbociclib treatment alters nucleotide biosynthesis and glutamine dependency in A549 cells. Cancer Cell Int. 2020, 20:280. (PMID: 32624705)
Zhao, J.; Conklin, D.; Guo, Y.; Zhang, X.; Obal, D.; Guo, L.; Jagatheesan, G.; Katragadda, K.; He, L.; Yin, X.; Prodhan, A. M.; Shah, J.; Hoetker, D.; Kumar, A.; Kumar, V.; Wempe, M.; Bhatnagar, A.; Baba, S. Cardiospecific overexpression of ATPGD1 increases histidine dipeptide levels and prevents myocardial ischemia-reperfusion injury. J. Am. Heart Assoc.2020, 9:e015222. (PMID: 32515247)
Liu, Y.; Chen, K.; Li, F.; Gu, Z.; Liu, Q.; He, L.; Shao, T.; Song, Q.; Zhu, F.; Zhang, L.; Jiang, M.; Zhou, Y.; Barve, S.; Zhang, X.; McClain, C.J.; Feng, W. Probiotic LGG prevents liver fibrosis through inhibiting hepatic bile acid synthesis and enhancing bile acid excretion in mice. Hepatol. 2020, 71(6), 2050-2066. (PMID: 31571251)
Liu, M.; Tong, Z.; Ding, C.; Luo, F.; Wu, S.; Albeituni, S.; He, L.; Hu, X.; Tieri, D.; Rouchka, E.C.; Hamada, M.; Takahashi, S.; Gibb, A.G.; Kloecker, G.; Zhang, H.; Bousamra II, M.; Hill, B.G.; Zhang, X.; Yan, J. Transcription factor c-Maf is a molecular checkpoint that controls immune suppression by programing macrophages in lung cancer. J. Clin. Invest.2020, 130(4), 2081-2096. (PMID: 31945018)
Reynolds, L.; Dougherty, S.; Kruer, T.; Metcalf, S.; Lorkiewicz, P.; He, L.; Yin, X.; Zhang, X.; Arumugam, S.; Young, L.; Sun, R.; Clem, B. Loss of Rb1 enhances glycolytic metabolism in Kras-driven lung tumors in vivo. Cancers2020, 12(1), 237-253. (PMID: 31963621)
Li, Z.; Kim, S.; Zhong, S.; Zhong, Z.; Kato, I.; Zhang, X. Coherent point drift peak alignment algorithms using distance and similarity measures for analysis of comprehensive two-dimensional gas chromatography mass spectrometry data. J. Chemometrics2020, e3236.
Yuan, F.; Harder, J.; Yin, X.; Zhang, X.; Kosiewicz, M.M. Effects of androgen depletion in mouse feces analyzed using multiple metabolic platforms. J. Proteome Res. 2020, 19, 667-676. (Selected as a journal cover page)
Liu, Q.; Liu, Y,; Li, F.; Gu, Z.; Liu, M.; Shao, T.; Zhang, L.; Zhou, G.; Pan, C.; He, L.; Cai, J.; Zhang, X.; Barve, S.; McClain, C.J.; Chen, Y.; Feng, W. Probiotic culture supernatant improves metabolic function through FGF21-adiponectin pathway in mice. J.Nutr. Biochem. 2020, 75, 108256. (PMID: 31760308)

2019 (12)

Sundaram, K.; Miller, D.P.; Kumar, A.; Teng, Y.; Sayed, M.; Mu, J.; Lei, C.; Sriwastva, M.K.; Zhang, L.; Jun, Y.; Merchant, M.L.; He, L.; Yuan, F.; Zhang, X.; Park, J.W.; Lamont, R.J.; Zhang, H. Plant-derived exosomal nanoparticles inhibit pathogenicity of Porphyromonas gingivalis. iScience 2019, 21, 308-327. (PMID: 31678913; PMCID: PMC6838522)
Warner, D.R.; Warner, J.B.; Hardesty, J.E.; Song, Y.L.; King, T.N.; Kang, J.X.; Chen, C.; Xie, S.; Yuan, F.; Prodhan, A.; Ma, X.; Zhang, X.; Rouchka, E.C.; Whitlock, J.; Li, E.C.; Wang, G.P.; McClain, C.J.; Kirpich, I.A. Decreased ω6/ω3 PUFA ratio attenuates ethanol-induced alterations in intestinal homeostasis, microbiota and liver injury. J. Lipid Res.2019, 60, 2034-2049. (PMID: 31586017)
Lorkiewicz1, P.K.; Gibb, A.A.; Rood, B.R.; He, L.; Zheng, Y.; Clem, B.F.; Zhang, X.; Hill, B.G. Integration of flux measurements and pharmacological controls to optimize stable isotope-resolved metabolomics workflows and interpretation. Sci. Rep-UK2019, 9:13750. (PMID: 31548575; PMCID: PMC6757038)
Young, J. L.; Yan, X.; Xu, J.; Yin, X.; Zhang, X.; Arteel, G.E.; Barnes, G.N.; States, C.J.; Watson, W.; Kong, M.; Cai, L.; Freedman, J.H. Cadmium and high-fat diet disrupt renal, cardiac and hepatic essential metals. Sci. Rep-UK. 2019, 9:14675. (PMID: 31604971; PMCID: PMC6789035)
He, L.; Li, F.; Yin, X.; Bohman, P.; Kim, S.; McClain, C.J.; Feng, W.; Zhang, X. Profiling of Polar Metabolites in Mouse Feces Using Four Analytical Platforms to Study the Effects Of Cathelicidin-Related Antimicrobial Peptide in Alcoholic Liver Disease. J. Proteome. Res.2019, 18, 7, 2875-2884. (PMID: 31188604; PMCID: N/A)
Prodhan, A.I.; Shi, B.; Song, M.; He, L.; Yuan, F.; Yin, X.; Bohman, P.; McClain, C.J.; Zhang, X. Integrating comprehensive two-dimensional gas chromatography mass spectrometry and two-dimensional liquid chromatography mass spectrometry for untargeted metabolomics. Analyst2019, 144, 4331-4341. (PMID: 31192319; PMCID: PMC6677244)
He, L.; Wei, X.; Ma, X.; Yin, X.; Song, M.; Donninger, H.; Yaddanapudi, K.; McClain, C.J.; Zhang, X. Simultaneous quantification of nucleosides and nucleotides from biological samples. J. Am. Soc. Mass Spectrom.2019, 30(6), 987-1000. (PMID: 30847833; PMCID: PMC6520184)
Chakravarty, S.; Mandal, R. K.; Duff, M. L.; Yuan, F.; Zhang, X.; Schmidt, N. W. Intestinal short-chain fatty acid composition does not explain gut microbiota-mediated effects on malaria severity. PLoS ONE2019, 14(2):e0214449. (PMID: 30917184; PMCID: PMC6436795)
Kim, S.; Yin, X.; Prodhan, A.I.; Zhang, X.; Zhong, Z.; Kato, I. Global plasma profiling for colorectal cancer associated volatile organic compounds: a proof of principle study. J. Chromatogr. Sci.2019, 57, 385-396. (PMID: 30796770: PMCID: PMC6478127)
Roumani, A.; Madkour, A.; Ouzzani, M.; McGrew, T.; Omran, E.; Zhang, X. BioNetApp: an interactive visual data analysis platform for molecular expressions. PLoS ONE 2019, 14(2):e0211277. (PMID: 30794548; PMCID: PMC6386483)
Shahrajooihaghighi, A.; Hichem, F.; Zhang, X.; Wei, X.; Shi, B.; McClain, C.J. Ensemble feature selectin for biomarker discovery in mass spectrometry-based metabolomics. Proceedings of the 34th ACM/SIGAPP Symposium on Applied Computing (SAC’19). Page 19-24. April 8-12, 2019. Limassol, Cyprus. https://dl.acm.org/citation.cfm?id=3297283 [Peer-reviewed conference paper]
Trabelsi, A.; Shi, B.; Wei, X.; Frigui, H.; Zhang, X.; McClain, C.J.; Shahrjooihaghighi, A. Molecule specific normalization for protein and metabolite biomarker discovery. Proceedings of the 34th ACM/SIGAPP Symposium on Applied Computing (SAC’19). Pages 25-31. April 8-12, 2019. Limassol, Cyprus. https://dl.acm.org/citation.cfm?id=3297284 [Peer-reviewed conference paper]

2018 (9)

Shao, T.; Zhao, C.; Li, F.; Gu, Z.; Liu, L.; Zhang, L.; Wang, Y.; He, L.; Liu, Y.; Liu, Q.; Chen, Y.; Donde, H.; Wang, R.; Jala, R.J.; Barve, S.; Chen, S-Y.; Zhang, X.; Chen, Y.; McClain, C.J.; Feng, W. Intestinal HIF-1α deletion exacerbates alcoholic liver disease through inducing intestinal dysbiosis and barrier dysfunction. J. Hepatol. 2018, 69(4), 886-895. (PMID: 29803899; PMCID: PMC6615474)
Prodhan, A.I.; Yin, X.; Kim, S.; McClain, C.J.; Zhang, X. Surface fitting for calculating the second dimension retention index in comprehensive two-dimensional gas chromatography mass spectrometry. J. Chromatogr. A. 2018, 1539, 62-70. (PMID: 29395161; PMCID: PMC5826898)
Warner, D.R.; Liu, H.; Dastidar, S.G.; Warner, J.B.; Prodhan, A.I.; Yin, X.; Zhang, X.; Feldstein, A.E.; Gao, B.; Prough, R.A.; McClain, C.J.; Kirpich, I.A. Ethanol and unsaturated dietary fat induce unique patterns of hepatic ω-6 and ω-3 PUFA oxylipins in a mouse model of alcoholic liver disease. PLoS ONE2018, 13(9): e0204119. (PMID: 30256818; PMCID: PMC6157879)
Song, M.; Li, X.; Zhang, X.; Shi, H.; Vos, M.; Wei, X.; Wang, Y.; Gao, H.; Rouchka, E.C.; Yin, X.; Zhou, Z.; Prough, R.; Cave, M.; McClain, C.J. Dietary copper-fructose interactions alter gut microbial activity in male rats. Am. J. Physiol. –Gastr. L.2018, 314, G119-G130. (PMID: 29025734; PMCID: PMC5866377)
He, L.; Prodhan, A.I.; Yuan, F.; Yin, X.; Lorkiewicz, P.K.; Wei, X.; Feng, W.; McClain, C.; Zhang, X. Simultaneous quantification of straight-chain and branched-chain short fatty acids by gas chromatography mass spectrometry. J. Chromatogr. B. 2018, 1092, 359-367. (PMID: 29936372; PMCID: PMC6190712)
Prodhan, A.I.; Sleman, A.A.; Kim, S.; McClain, C.J.; Zhang, X. Generalization of reference system for calculating the second dimension retention index in GC×GC-MS. J. Anal. Test.2018, 2018, 3, 263-273.
Gao, Y.; Gao, L.; Tian, J.; Qin, X.; Zhang, X. A network pharmacology approach to decipher the mechanisms of anti-depression of Xiaoyaosan formula. World J. Tradit. Chin. Med.2018, 4, 147-162.
Zhao, F.; Chang, Y.; Gao, L.; Qin, X.; Du, G.; Zhang, X.; Zhou, Y. Protective effects of Scutellaria baicalensis Georgi extract on D-galactose induced aging rats. Metab. Brain Dis.2018, 33(5), 1401-1412 (PMID: 29855978; PMCID: N/A)
Gao, X.; Liang, M.; Fang, Y.; Zhao, F.; Tian, J.; Zhang, X.; Qin, X. Deciphering the differential effective and toxic responses of Bupleuri Radix following the induction of chronic unpredictable mild stress and in healthy rats based on serum metabolic profiles. Front. Pharmacol.2018, 8:995. (PMID: 29379441; PMCID: PMC5775221)

2017 (11)

Wei, X.; Shi, B.; Koo, I.; Yin, X.; Lorkiewicz, P.; Suhail, H.; Rattan, R.; Giri, S.; McClain, C.J.; Zhang, X. Analysis of stable isotope assisted metabolomics data acquired by GC-MS. Analytica Chimica Acta2017, 980, 25-32. (PMID: 28622800; PMCID: PMC5541907).
Kim, S.; Jang, H.; Koo, I.; Lee, J.; Zhang, X. Normal-Gamma-Bernoulli peak detection for analysis of comprehensive two-dimensional gas chromatography mass spectrometry data. Comput. Stat. Data Anal.2017, 105, 96-111. (PMID: 27667882; PMCID: PMC5029791)
Wei, X.; Lorkiewicz, P.; Salabei, J.K.; Shi, B.; Hill, B.G.; Kim, S.; McClain, C.J.; Zhang, X. Analysis of stable isotope assisted metabolomics data acquired by high resolution mass spectrometry. Anal. Methods2017, 9, 2275-2283. (PMID: 28622800; PMCID: PMC5541907)
Gibb, A.A.; Lorkiewicz, P.K.; Zheng, Y.; Zhang, X.; Epstein, P.N.; Jones, S.P.; Bhatnagar, A.; Hill, B.G. Integration of flux measurements to resolve changes in anabolic and catabolic metabolism in cardiac myocytes. Biochem. J.2017, 474(16), 2785-2801. (PMID: 28706006; PMCID: PMC554592)
Zhou, Y.; Zhao, F.; Gao, L.; Du, G.; Zhang, X.; Qin, X. Licorice extract attenuates brain aging of D-galactose induced rats through inhibition of oxidative stress and attenuation of neuronal apoptosis. RSC Advances2017, 7, 47758-47766.
Zhou, Y.; Yan, M.; Gao, L.; Zhang, Q.; Qin, X.; Zhang, X.; Du, G. Metabonomics approach to assessing the metabolism variation and gender gap of Drosophila melanogaster in aging process. Experimental Gerontology2017, 98, 110-119. (PMID: 28811139)
Li, J.; Gao, W.; Gao, J.; Li, H.; Zhang, X.; Qin, X.; Li, Z. Metabolomics reveal the protective effect of Farfarae Flos against asthma using an OVA-induced rat model. RSC Adv. 2017, 7 (63), 39929-39939.
Ma, K.; Miao, Y.; Li, X.; Zhou, Y.; Gao, X.; Zhang, X.; Chao, J.; Qin, X. Discovery of 1,3-diyne compounds as novel and potent antidepressant agents: synthesis, cell-based assay and behavioral studies. RSC Adv.2017, 7, 16005-16014.
Zhou, Y.; Li, X.; Gong, W.; Tian, J.; Gao, X.; Gao, L.; Zhang, X.; Du, G.; Qin, X. Protective effect of isoliquiritin against corticosterone-induced neurotoxicity in PC12 cells. Food & Function, 2017, 8, 1235-1244. (PMID: 28229156)
Ma, K.; Miao, Y.; Gao, X.; Chao, J.; Zhang, X.; Qin, X. Total syntheses of bupleurynol and its analog. Chin. Chem. Lett.2017, 28(5), 1035-1038.
Shahrjooihaghighi, A.; Frigui, H.; Zhang, X.; Wei, X.; Shi, B.; Trabelsi, A. An ensemble feature selection method for biomarker discovery. IEEE International Symposium on Signal Processing and Information Technology. University of Deusto – Auditorio Icaza. Dec. 18-20, 2017. Bilbao, Spain. Page 416-421. https://ieeexplore.ieee.org/document/8388679 (PMID: 30887013; PMCID: PMC6420823)

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Deng, B.; Kim, S.; Li, H.; Heath, E.; Zhang, X. Global peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using point matching algorithms. J. Bioinf. Comput. Biol.2106, 9:1650032. (PMID: 27650662; PMCID: PMC5226864)
Tian, J.; Xia, X.; Wu, Y.; Zhao, L.; Xiang, H.; Du, G.; Zhang, X.; Qin, X. Discovery, screening and evaluation of a plasma biomarker panel for subjects with psychological suboptimal health state using ¹H-NMR-based metabolomics profiles. Sci. Rep-UK2016, 21, 6:33820. (PMID: 27650680; PMCID: PMC5030673)
Salabei, J.K.; Lorkiewicz, P.K.; Mehra, P.; Gibb, A.A.; Haberzettl, P.; Hong, K.U.; Wei, X.; Zhang, X.; Li, Q.; Wysoczynski, M.; Bolli, R.; Bhatnagar, A.; Hill, B.G. Type 2 diabetes dysregulates glucose metabolism in cardiac progenitor cells. J. Biol. Chem.2016, 26, 13634-13648. (PMID: 27151219; PMCID: PMC4919448)
Carlisle, S.M.; Trainor, P.J.; Yin, X.; Doll, M.A.; States, J.C.; Zhang, X.; Hein, D.W.Untargeted polar metabolomics of transformed MDA-MB-231 breast cancer cells expressing varying levels of human arylamine N-acetyltransferase 1. Metabolomics2106, 12:111. (PMID: 27872580; PMCID: PMC5115175)
Wang, S.; Luo, M.; Zhang, Z.; Gu, J.; Chen, J.; Payne, K.M.; Tan, Y.; Wang, Y.; Yin, X.; Zhang, X.; Liu, G.C.; Wintergerst, K.; Liu, Q.; Zheng, Y.; Cai, L. Zinc deficiency exacerbates while zinc supplement attenuates cardiac hypertrophy in high-fat diet-induced obese mice through modulating p38 MAPK-dependent signaling. Toxicol Lett. 2016, 258:134-46. (PMID: 27346292; PMCID: N/A)
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Koo, I.; Kim, S.; Shi, B.; Lorkiewicz, P.; Song, M.; McClain, C.J.; Zhang, X. EIder: a compound identification tool for gas chromatography-mass spectrometry data. J. Chromatogr. A2016, 1448, 107-114. (PMID: 27131963)
Chung, D.; Golden, J.E.; Adcock, R.S.; Chu, Y.; Sotsky, J.B.; Cramer, D.E.; Chilton, P.M.; Song, C.; Anantpadma, M.; Schroeder, C.E.; Prodhan, A.I.; Yin, X.; Zhang, X. Discovery of a broad-spectrum antiviral compound that inhibits pyrimidine biosynthesis and establishes a type 1 interferon-independent antiviral state. Antimicrob. Agents Chemother.2106, 60(8), 4552-4562. (PMID: 27185801; PMCID: PMC4958224)
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Wei, X.; Song, M.; Yin, X.; Schuschke, D.A.; McClain, C.J.; Zhang, X. Effects of dietary different doses of copper and high fructose feeding on rat fecal metabolome. J. Proteome Res.2015, 14(9), 4050-4058. (PMID: 26216400; PMCID: N/A)
Shi, X.; Wei, X.; Yin, X.; Wang, Y.; Zhang, M.; Zhao, C.; Zhao, H.; McClain, CJ.; Feng, W.; Zhang, X. Hepatic and fecal metabolomic analysis of the effects of Lactobacillus rhamnosus GG on alcoholic fatty liver disease in mice. J. Proteome Res.2015, 14, 1174-1182. (PMID: 25592873; PMCID: N/A)
Winnike, J.; Wei, X.; Knagge, K.J.; Colman, S.D.; Gregory, S.G.; Zhang, X. Comparison of GC-MS and GC×GC-MS in the analysis of human serum samples for biomarker discovery. J. Proteome Res.2015, 14, 1810-1817. (PMID: 25735966; PMCID: PMC4849136)
Zhong, W.; Li, Q.; Sun, Q.; Zhang, W.; Zhang, J.; Sun, X.; Yin, X.; Zhang, X.; Zhou, Z. Preventing gut leakiness and endotoxemia contributes to the protective effect of zinc on alcohol-induced steatohepatitis in rats. J. Nutr.2015, 145(12), 2690-2698. (PMID: 26468492; PMCID: PMC4656905)
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Tian, J.; Liu, C.; Xiang, H.; Zheng, X.; Guo-jiang Peng, G.; Xiang Zhang, X.; Du, G.; Qin, X. Investigation on the antidepressant effect of sea buckthorn seed oil through the GC-MS-based metabolomics approach coupled with multivariate analysis. Food Funct.2015, 6, 3585-3592. (PMID: 26328874; PMCID: N/A)
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Wei, X.; Shi, X.; Kim, S.; S, K.; Patrick, J.S.; Binkley, J.; Kong, M.; McClain, C.; Zhang, X. Data dependent chromatographic peak model-based spectrum deconvolution for analysis of LC-MS data. Anal. Chem.2014, 86, 2156−2165. (PMID: 24533635; PMCID: PMC3982975)
Shi, X.; Wei, X.; Koo, I.; Schmidt, R.H.; Yin, X.; Vaughn, A.; Kim, S.H.; McClain, C.J.; Arteel, G.E.; Zhang, X.; Watson, W.H. Metabolomic analysis of the effects of chronic arsenic exposure in a mouse model of diet-induced fatty liver disease. J. Proteome Res.2014, 13, 547−554. (PMID: 24328084; PMCID: PMC3946282)
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Koo. I.; Wei, X.; Shi, X.; Zhou, Z.; Kim, S.; Zhang, X. Constructing metabolic association networks using high-dimensional mass spectrometry data. Chemometri. Intell. Lab. 2014, 138, 193-202. (PMID: 25414536; PMCID: PMC4233464)
Sun, Q.; Li, Q.; Zhong, W.; Zhang, J.; Yin, X.; Sun, X.; Tan, X.; Sun, X.; Zhang, X.; Zhou, X. Dysregulation of hepatic zinc transporters in a mouse model of alcoholic liver disease. Am. J. Physiol. –Gastr. L. 2014, 307(3), 313-322. (PMID: 24924749; PMCID: PMC4121635)
Li, Y.; States, V.A.; Li, S.; Zhang, X.; Martin, R.C. The effect of black raspberry extracts on MnSOD activity in protection against Concanavalin A induced liver injury. Nutri. Cancer, 2014, 9:1-8. (PMID: 24911141; PMCID: PMC4559274)
Koo, I.; Shi, X.; Kim, S.; Zhang, X. iMatch2: compound identification using retention index for analysis of GC-MS data. J. Chromatogr. A2014,1337, 202-210. (PMID: 24630063; PMCID: PMC4106036)
Li, Y.; Shi, X.; Zhang, J.; Zhang, X.; Martin, R. Hepatic protection and anticancer activity of curcuma: A potential chemopreventive strategy against hepatocellular carcinoma. Int. J. Oncol.2014, 44, 505-513. (PMID: 24270742; PMCID: PMC3898719)
Koo, I.; Wei, X.; Zhang, X. Analysis of metabolic profiling data acquired on GC-MS, Methods in Enzymology, Vol 543: Cell-wide metabolic alterations associated with malignancy, Edited byLorenzo Galluzzi and Guido Kramer, UK Burlington: Academic Press, 2014, pp. 315-324. (PMID: 24924140; PMCID: N/A) [Book Chapter]
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Wei, X.; Shi, X.; Koo, I.; Kim, S.; Schmidt, R.H.; Arteel, G.E.; Watson, W.H.; McClain, C.; Zhang, X. MetPP: A computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics. Bioinformatics 2013, 29, 1786-1792.
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Kim, S.; Ouyang, M.; Zhang, X. Compute Spearman correlation coefficient with Matlab/CUDA. IEEE International Symposium on Signal Processing and Information Technology, Dec. 12-15, 2012. Ho Chi Minh City, Vietnam. [Conference paper]
Koo, I.; Zhang, X.; Kim, S. H. Reconstruction of metabolic association networks using high-throughput mass spectrometry data. 2012 International Conference on Intelligent Computing, July 25-29, 2012. Huangsan, Hunan, China. [Conference paper]
Wei, X.; Shi, X.; Kim, S. H.; McClain, C.; Zhang, X. A novel two-stage alignment method for liquid chromatography mass spectrometry-based metabolomics. 2012 International Conference on Intelligent Computing, July 25-29, 2012. Huangsan, Hunan, China. [Conference paper]

2011 (29)

Fan, T. W-M., Lane, A.N., Higashi, R.M., Yan, J. (2011) Stable Isotope Resolved Metabolomics of Lung Cancer in a SCID Mouse Model. Metabolomics 7, 257-269.
Lane, A.N., Fan, T. W-M, Bousamra II, M., Higashi, R.M., Yan, J., Miller, D.M. (2011) Clinical Applications of Stable Isotope-Resolved Metabolomics (SIRM) in Non-Small Cell Lung Cancer. Omics 15, 173-182 DOI: 10.1089/omi.2010.0088.
Moseley, H.N.B., Higashi, R.M., Fan, T. W-M., Lane, A.N. (2011) Analysis of Non-Steady State Stable Isotope-Resolve Metabolism of UDP-GlcNAc and UDP-GalNAc. Proceedings of BIOINFORMATICS 2011– Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. (Ed. Marco Pellegrini, Ana Fred, Joaquim Filipe, and Hugo Gamboa). SciTePress, Portugal, pp 108-115.
Fan, T.W-M. & Lane, A.N. (2011) NMR-based Stable Isotope Resolved Metabolomics in Systems Biochemistry. J. Biomolec. NMR Sp. Edn. 49, 267–280.
M. K. McDonald, E. J. Miracco, J. Chen, Y. Xie, and E. G. Mueller (2011) The Handling of the Mechanistic Probe 5-Fluorouridine by the Pseudouridine Synthase TruA and Its Consistency with the Handling of the Same Probe by the Pseudouridine Synthases TruB and RluA. Biochemistry, 50, 426-436.
Wang, X., Altman, B., Eno, C.O., Olberding, K.E., Rathmell, J.C., Li, C. (2011) ER Stress Modulates Cellular Metabolism. Biochem. J. 435, 285-296.
Clem BF, Clem AL, Yalcin A, Goswami U, Arumugam S, Telang S, Trent JO, Chesney J (2011) A novel small molecule antagonist of choline kinase-α that simultaneously suppresses MAPK and PI3K/AKT signaling. Oncogene. 30, 3370-3380.
Moseley, H.N.B., Lane, A.N., Belshoff, A.C, Higashi, R.M. Fan, T. W-M., (2011) Non-Steady State Modeling of UDP-GlcNAc Biosynthesis is Enabled by Stable Isotope Resolved Metabolomics (SIRM). BMC Biology 9, 37.
Fan, T. W-M.,Tan, J., McKinney, M.M. and Lane, A.N. (2011) Stable Isotope Resolved Metabolomics Analysis of Ribonucleotide and RNA Metabolism in Human Lung Cancer Cells. Metabolomics. 8, 517-527 DOI: 10.1007/s11306-011-0337-9.
Lane, A.N. (2011) The stability of intramolecular DNA quadruplexes compared with other macromolecules. Biochimie. 94:277-86.
Gracey AY, Lee TH, Higashi RM, Fan T. (2011) Hypoxia-induced mobilization of stored triglycerides in the euryoxic goby Gillichthys mirabilis. J Exp Biol. 15, 3005-12.
Muenyi CS, States VA, Masters JH, Fan TW-M, Helm CW, States JC. (2011) Sodium arsenite and hyperthermia modulate cisplatin-DNA damage responses and enhance platinum accumulation in murine metastatic ovarian cancer xenograft after hyperthermic intraperitoneal chemotherapy (HIPEC). J Ovarian Res. 4:9.
Song, M.; Zhou, Z.; Chen, T.; Zhang, J.; McClain, C. J. Copper deficiency exacerbates bile duct ligation-induced liver injury and fibrosis in rats. J. Pharmacol. Exp. Ther. 2013 347:80-90. doi:10.1124/jpet.111.184325.
Fu, X., Li, M., Biswas, S., Nantz, M.H., Higashi, R.M. (2011) A novel microreactor approach for analysis of ketones and aldehydes in breath Analyst. 136, 4662-4666.
M. C. Miller, H. Le, W. L. Dean, P. A. Holt, J. B. Chaires, J. O. Trent (2011) Polymorphism and resolution of oncogene promoter quadruplex-forming sequences. Organic & Biomolecular Chemistry 9: 7633-7637.
Wei, X.; Sun, W.; Shi, X.; Koo, I.; Wang, B.; Yin, X.; Tang, Y.; Bogdanov, B.; Kim, S. H.; Zhou, Z., McClain, C. J.; Zhang, X. MetSign: A computational platform for high-resolution mass spectrometry-based metabolomics. Anal. Chem. 2011, 83, 7668–7675.(PMCID: PMC3196362)
Koo, I.; Zhang, X.; Kim, S. Wavelet- and Fourier-Transforms-based spectrum similarity approaches to compound identification in gas chromatography/mass spectrometry. Anal. Chem. 2011, 83, 5631–5638. (PMCID: PMC3136582)
Kim, S.; Fang, A.; Wang, B.; Jeong, J.; Zhang, X. An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure. Bioinformatics 2011, 27, 1660–1666. (PMCID: PMC3106184)
Zhang, J.; Fang, A.; Wang, B.; Bogdanov, B.; Kim, S. H.; Zhou, Z.; McClain, C.; Zhang, X. iMatch, A retention index tool for analysis of gas chromatography mass spectrometry data. J. Chromatogr. A 2011, 1218, 6522–6530. (PMCID: PMC3163042)
Zhao, Y.; Zhang, J.; Wang, B.; Kim, S.; Fang, A.; Bogdanov, B.; Zhou, Z.; McClain, C.; Zhang, X. A method of calculating the second dimension retention index in comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. J. Chromatogr. A 2011, 1218, 2577–2583. (PMCID: PMC3078172)
Jeong, J.; Shi, X.; Zhang, X; Kim, S.; Shen, C. An empirical Bayes model using a competition score for metabolite identification in gas chromatography mass spectrometry. BMC Bioinformatics 2011, 12:392. (PMCID: PMC3228553)
Kim, S.; Koo, I.; Fang, A.; Zhang, X. Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry. BMC Bioinformatics 2011, 12:235.(PMCID: PMC3133553)
Riley, C. P.; Zhang, X.; Nakshatri, H.; Schneider, B.; Regnier, F. E.; Adamec, J.; Buck, C.A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples. J. Transl. Med. 2011, 9:80.
Zhao, Y.; Tan, Y.; Dai, J.; Li,B.; Guo, L.; Cui, J.; Wang, G.; Shi, X.; Zhang, X.; Mellen, N.; Li, W.; Cai, L. Exacerbation of diabetes-induced testicular apoptosis by zinc deficiency is most likely associated with oxidative stress; p38 MAPK activation; and p53 activation in mice. Toxicol. Lett.2011, 200, 100–106.
Wang, B.; Fang, A.; Shi, X.; Kim, S.; Zhang, X. A comprehensive peak alignment algorithm for two-dimensional gas chromatography time-of-flight mass spectrometry. 2011 International Conference on Intelligent Computing, Aug 11-14, 2011. Zhengzhou, Henan, China. [Conference paper]
Koo, I.; Zhang, X.; Kim, S. Comparison of spectral similarity measures for compound identification. The 5th International Conference on Bioinformatics and Biomedical Engineering, May 10-12, 2011. Wuhan, Hubei, China. [Conference paper]
Chen, Y.T.; Zhang, J.; Zhang, X.; Kim, S. Statistical analysis of gas chromatography retention index database. The 5th International Conference Bioinformatics and Biomedical Engineering, May 10-12, 2011. Wuhan, Hubei, China.[Conference paper]
Chen, J; Canales, L ; Neal, RE. (2011) Multi-Segment Direct Inject nano-ESI-LTQ-FT-ICRMS/MS For Protein Identification Proteome Science 9:38.

2010 (23)

A Yalcin, B Clem, S Makoni, A Clem, K Nelson, J Thornburg, D Siow, A N Lane, S E Brock, U Goswami, Eaton, J.W., Telang, S. & Chesney, J. (2010) Selective inhibition of choline kinase simultaneously attenuates MAPK and PI3K/AKT signaling Oncogene 29, 139–149. doi:10.1038/onc.2009.317.
Wang, W.; Jasinski, J.; Hammond, G.B.; Xu, B. Fluorine-Enabled Cationic Gold Catalysis: Functionalized Hydration of Alkynes. Angew. Chem. 2010, 122, 7405 –7410. DOI: 10.1002/ange.201003593.
Liu, L-P.; Malhotra, D.; Paton, R.S.; Houk, K.N.; Hammond, G.B. The [4+2], not [2+2], mechanism occurs in the gold-catalyzed intramolecular oxygen transfer reaction of 2-alkynyl-1,5-diketones. Angew. Chem. Int. Ed. 2010, 49, 9132 –9135. DOI: 10.1002/anie.201005514.
Fan, T. W-M. Yuan, P., Lane, A.N., Higashi, R.M., Wang, Y., Hamidi, A., Zhou, R., Xavier Guitart-Navarro, X., Chen, G., Manji, H.K., Kaddurah-Daouk, R. (2010) Stable Isotope Resolved Metabolomic Analysis of Lithium Effects on Glial-Neuronal Interactions. Metabolomics 6, 165 - 179. DOI 10.1007/s11306-010-0208-9.
Dailey, M.M., Miller, M.C., Bates, P.J., Lane, A.N., Trent, J.O. (2010) Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence. Nucl.Acids Res. 38, 4877-4888 (Featured article).
Moseley, H.N.B. (2010) Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry. BMCBioinformatics 11, 139.
Selivanov, V. A., Vizan, P., Mollinedo, F., Fan, T. W-M., Lee, P. W. N., Cascante, M. (2010) Edelfosine-induced metabolic changes in cancer cells that precede the overproduction of reactive oxygen species and apoptosis. BMC System Biol. Art 135.
Fan, T. W-M. (2010) Metabolomics-Edited Transcriptomics Analysis (Meta) Comprehensive Toxicology vol. 2 (McQueen, C.A., ed) pp 685–706. Academic Press.
Doblin, M., Fan, T. W-M., Foster, S., Garrett, R., Maher, W., Möller, G., Oram, L. L., Roach, A., and Wallschläger, D. (2010) “Sources, Speciation, and Environmental Partitioning”, in: Chapman PM, Adams WJ, Brooks ML, Delos CG, Luoma SN, Maher WA, Ohlendorf HM, Presser TS, Shaw DP (eds). Ecological Assessment of Selenium in the Aquatic Environment. SETAC Press, Pensacola, FL, USA.
Arumugam, S., Miller, M.C., Maliekal, J., Trent, J.O., and Lane, A.N. (2010) NMR Structure Note: Solution structure of the RBD1,2 domains from human nucleolin. J. Biomolec. NMR 47, 79-83. DOI: 10.1007/s10858-010-9412-1.
Miller, M.C., Buscaglia, R., Chaires, J.B., Lane, A.N., Trent, J.O. (2010) Hydration determines the G-quadruplex stability and conformation of the human telomere 3’ sequence d(A(GGGTTA)3GGG)). JACS. 132, 17105-17107. DOI: 10.1021/ja105259m.
Wang, B.; Fang, A.; Heim, J.; Bogdanov, B.; Pugh, S.; Libardoni, M.; Zhang, X. DISCO: distance and spectrum correlation optimization alignment for two dimensional gas chromatography time-of-flight mass spectrometry - based metabolomics. Anal. Chem. 2010, 82, 5069–5081. (PMCID: PMC2891529)
Wang, B.; Valentine, S.; Plasencia, M.; Raghuraman, S.; Zhang, X. Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry. BMC Bioinformatics 2010, 11:182. (PMCID: PMC2874804)
Zhang, X.; Fang, A.; Riley, C. P.; Wang, M.; Regnier, F. E. Buck, C. Multi-dimensional liquid chromatography in quantitative proteomics. Anal. Chimica Acta 2010, 664, 101–113. (PMCID: PMC2852180)
Riley, P. C.; Gough, S. E.; He, J.; Jandhyala, S. S.; Kennedy, B.; Orcun, S.; Ouzzani, M.; Buck, C.; Roumani, A.M.; Zhang, X. The Proteome Discovery Pipeline – A data analysis pipeline for mass spectrometry-based differential proteomics discovery. TheOpen Proteomics Journal 2010, 3, 8–19.
Wang, B.; Valentine, S.; Plasencia, M.; Zhang, X. Prediction of drift time in ion mobility-mass spectrometry based on peptide molecular weight. Protein &Peptide Letters 2010, 17(9), 1143–1147.
Wang, B.; Chen, P.; Zhang, J.; Zhao G.; Zhang, X. Inferring protein-protein interactions using a hybrid GA/SVM method. Protein &Peptide Letters 2010, 17(9), 1079 –1084.
Wang, B.; Chen, P.; Wang, P.; Zhao, G.; Zhang, X. Construction of radial basis function neural networks optimized by expectation maximization algorithm for predicting protein-protein interaction sites. Protein &Peptide Letters 2010, 17(9), 1111–1116.
Wang, B.; Zhang, X. Evolutionary computation applications in current bioinformatics. New Achievement in Evolutionary Computation 2010, 173–180. [Book Chapter]
Zhang, J.; Wang, B.; Zhang, X. Optimal selection of support vector regression parameters and molecular descriptors for retention indices prediction. Advanced Intelligent Computing Theories and Applications with Aspects of Artificial Intelligence. Aug. 18–21, 2010, Changsha, Hunan, China. [Conference paper]
Wang, B.; Zhang, J.; Zhang, X. Multiple linear regression for peptides drift time prediction. The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, July 12–14, 2010. Orlando, FL. [Conference paper]
De-Shuang Huang, Xiang Zhang, Carlos Alberto Reyes Garcia (Eds.): Advanced Intelligent Computing Theories and Applications, 6th International Conference on Intelligent Computing, ICIC 2010, Changsha, China, August 18-21, 2010, Proceedings. Lecture Notes in Computer Science. 6216 Springer 2010, ISBN 978-3-642-14931-3. [Book]

2009 (8)

Lane, A.N., Fan, T. W-M. & Higashi, R.M. (2009) Metabolic acidosis and the importance of balanced equations. Metabolomics.5, 163-165 DOI: 10.1007/s11306-008-0142-2.
Fan, T. W-M., Bird, J.A,, Brodie, E.L., Lane, A.N. (2009) 13C-Isotopomer-based Metabolomics of Microbial Groups Isolated from Two Forest Soils. Metabolomics 5, 108-122 DOI:10.1007/s11306-008-0150-2.
Fan, T. W-M; Lane, A. N.; Higashi . M.; Bousamra II, M.; Kloecker, G.;. Miller, D. M. (2009) Erlotinib-sensitive and resistant lung tumors show radically different metabolic Profiles.Exp. Molec. Pathol. 87, 83-86 doi:10.1016/j.yexmp.2009.04.004.
Fan, T.WM., Lane, A.N., Higashi, R.M., Farag, M.A., Gao, H., Bousamra, M. & Miller, D.M. (2009) Altered Regulation of Metabolic Pathways in Human Lung Cancer Discerned by13C Stable Isotope-Resolved Metabolomics (SIRM). Molecular Cancer. 8:41 doi:10.1186/1476-4598-8-41.
Lane, A.N., Fan, T. WM, Higashi, R.M., Tan, J., Bousamra, M. and Miller, D.M (2009) Prospects for clinical cancer metabolomics using stable isotope tracers. Exp. Molec. Pathol. 86,165-173 Sp. Issue. doi:10.1016/j.yexmp.2009.01.005.
Yalcin, A., Clem, B.F., Simmons, S., Lane, A.N, Nelson, K.K., Clem, A.L., Brock, E., Siow, D., Wattenberg, B., Telang, S. & Chesney, J. (2009) Nuclear targeting of 6-phosphofructo-2-kinase (PFKFB3) increases proliferation via cyclin-dependent kinases. J. Biol. Chem. 284: 24223-24232. doi:10.1074/jbc.M109.016816.
Yalcin A, Telang S, Clem B, Chesney, J. (2009) Regulation of glucose metabolism by 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatases in cancer Experimental And MolecularPathology 86, 174-179.
Lane, A.N., Fan, T. W-M., Xie, X. Moseley, H.N. & Higashi, R.M. (2009) Stable isotope analysis of lipid biosynthesis by high resolution mass spectrometry and NMR. Anal. Chim. Acta. 651, 201-208. doi:10.1016/j.aca2009.08.032.

2008 (8)

McNeely, S. C., Belshoff, A. C.. Taylor, B. F.. Fan, T. W. M., McCabe, M. J., Pinhas, A.R., States, J. C. (2008) Sensitivity to sodium arsenite in human melanoma cells depends upon susceptibility to arsenite-induced mitotic arrest. Toxicology and Applied Pharmacology 229, 252-261.
Clem, B.F., Telang, S., Clem, A., Yalcin, A., Meier, J., Simmons, A., Rasku, M..A, Arumugam, S., Dean, W.L., Eaton, J., Lane, A.N., Trent, J.O. and Chesney. J.A. (2008) “Small MoleculeInhibition of 6-Phosphofructo-2-Kinase Activity Suppresses Glycolytic Flux and TumorGrowth” Molecular Cancer Therapeutics. 7, 110-120.
Lane, A.N., Fan, T-WM. & Higashi, R.M. (2008) “Isotopomer-based metabolomic analysis by NMR and mass spectrometry". Methods in Cell Biology, Vol 84. Biophysical Tools forBiologists, Volume 1, edited by Drs. John J. Correia and H. William Detrich. Elsevier Science & Technology Books Ch. 18. pp 541-588. ISBN:9780123725202.
Fan, T.W-M. & Lane, A.N. (2008) Structure-based profiling of Metabolites and Isotopomers by NMR, Prog. NMR Spectrosc. 52, 69-117 doi:10.1016/j.pnmrs.2007.03.002 (invited review)
Lane, A.N., Fan. T. W-M. and Higashi, R.M. (2008) “Stable isotope assisted metabolomics in cancer research”. IUBMB Life. 60, 124-129 DOI:10.1002/iub.00017 (Invited review)
Fan, T. W-M., Kucia M., Jankowski, K., Higashi, R.M., Rataczjak, M.Z., Rataczjak, J., & Lane, A.N. (2008) Proliferating Rhabdomyosarcoma cells shows an energy producing anabolic metabolic phenotype compared with Primary Myocytes Molecular Cancer 7:79.
Thornburg, J.M., Nelson, K.K., Lane, A.N., Arumugam, S., Simmons, A. Eaton, J.W., Telang, S., & Chesney, J. (2008) Targeting Aspartate Aminotransferase in Breast Cancer Breast CancerRes. 10:R84.
Lane, A.N., Fan, T. W-M., Higashi, R.M., Deleeuw, L., and Yang, T.H. (2008) Stable isotope tracing in metabolic pathways in "Modelling Complex Biological Systems In The Context Of The Genome" (Patrick Amar, Francois Kepes, Vic Norris, Bernard Vandenbunder, Eds.). Pp 69-78.

2007 (6)

Lane, A.N. & Fan, T. W-M. (2007) Determination of positional isotopomers in metabolites. Metabolomics 3, 79-86.
Podrabsky JE , Lopez JP, Fan TW-M, Higashi R, Somero GN (2007) Extreme anoxia tolerance in embryos of the annual killifish Austrofundulus limnaeus: insights from a metabolomics analysis J. Exp. Biol. 210, 2253-2266.
Sansone S, Nikolau B, van Ommen B, Kristal B, Taylor C, Robertson D, Lindon J, Griffin J, Sumner L, van der Werf M, Hardy N, Morrison N, Mendes P, Kaddurah-Daouk R, Goodacre R, Fan TW-M, Fiehn O. (2007) The Metabolomics Standards Initiative (MSI). Nature Biotech 25:844-8.
Sumner, L.W., Amberg, A., Barrett, D., Beger, R., Beale, M.H., Daykin, C. Fan, T. W-M., Fiehn, O., Goodacre, R., Griffin, J.L., Hardy, N., Higashi, R.M., Kopka, J., Lindon, J.C., Lane,A.N., Marriott, P., Nicholls, A.W., Reily, M.D., Viant, M. (2007) Proposed Minimum Reporting Standards for Chemical Analysis. Metabolomics. 3, 211-221.
Kurtoglu, M., Gao, N., Maher, J.C., Lehrman, M.A., Wangpaichitr, M.,Savaraj, N., Lane, A.N. and Lampidis, T.J. . (2007) Under normoxia 2-deoxy-D-Glucose, but not 2-fluoro-deoxy-Dglucose,kills select tumor cells by interfering with N-linked glycosylation. Molecular CancerTherapeutics 6: 3049-3058.
Telang, S., Lane, A.N., Nelson, K.K. Arumugam, S. & Chesney, J.A. (2007) The oncoprotein H-RasV12 increases mitochondrial metabolism Molec. Cancer. 6, 77 doi:10.1186/1476-4598-6-77.

2006 (2)

Telang S. Yalcin A., Clem A. L.,Bucala R., Lane A. N., Eaton, J. W., & Chesney J. A. (2006) Ras Transformation Requires Metabolic Control by 6-Phosphofructo-2-Kinase. Oncogene 25:7225-7234.
Fan, T. W-M., Bandura, L.L., Lane, A.N. & Higashi, R.M. (2006) “ Integrating Genomics and Metabolomics for Probing Se Anticancer Mechanisms” Drug Metabolism Reviews 38, 1-25.