Publications

    Total Publications: 45

    Total Citations: ~3,000

    Publications with >100 citations: 13

    Data from Google Scholar (update on Oct 2018) Web Link

  • 1. MetFlow: An Interactive and Integrated Workflow for Metabolomics Data Cleaning and Differential Metabolite Discovery

        X. Shen, and Z.-J. Zhu*(Corresponding author), Submitted. Web Server Link



  • 2. Development of A Correlative Strategy to Discover Colorectal Tumor Tissue Derived Metabolite Biomarkers in Plasma Using Untargeted Metabolomics

        Z. Wang†, B. Cui†, F. Zhang, Y. Yang, X. Shen, Z. Li, W. Zhao, Y. Zhang, K. Deng, Z. Rong, K. Yang, X. Yu, K. Li*, P. Han*, and Z.-J. Zhu*, Submitted



  • 3. Metabolic Reaction Network-based Recursive Metabolite Identification for Untargeted Metabolomics

        X. Shen, X. Xiong, R. Wang, Y. Yin, Y. Cai, Z. Ma, N. Liu, and Z.-J. Zhu* (Corresponding Author)

        Preprint at BioRxiv (doi.org/10.1101/305201)

  • 4. A High-Throughput Targeted Metabolomics Workflow for the Detection of 200 Polar Metabolites in Central Carbon Metabolism

        Y. Cai, and Z.-J. Zhu* (Corresponding author)

        Methods in Molecular Biology, 2019, 1859,263-274. Web Link   An invited book chapter for Microbial Metabolomics

  • 5. Stable-isotope Labeled Metabolic Analysis in Drosophila melanogaster: From Experimental Setup to Data Analysis.

         Y. Cai, N. Liu*, and Z. J. Zhu* (Co-Corresponding Author)

         Bio-protocol, 2018, 8(18): e3015.Web Link

  • 6. LipidIMMS Analyzer: Integrating Multi-dimensional Information to Support Lipid Identification in Ion Mobility–Mass Spectrometry based Lipidomics

        Z. Zhou, X. Shen, X. Chen, J. Tu, X. Xiong, and Z.-J. Zhu* (Corresponding Author)

        Bioinformatics, 2018, In Press. Web Link LipidIMMS Web Server Link


  • 7. Predicting the Pathological Response to Neoadjuvant Chemoradiation Using Untargeted Metabolomics in Locally Advanced Rectal Cancer

         H. Jia†, X. Shen†, Y. Guan, M. Xu, J. Tu, M. Mo, L. Xie, J. Yuan, J. Zhu*, and Z.J. Zhu*(†, Co-first authors; *, Co-Corresponding authors)

         Radiotherapy and Oncology, 2018, 128, 548-556. Web Link

  • 8. Epigenetic Drift of H3K27me3 in Aging Links Glycolysis to Healthy Longevity in Drosophila

        Z. Ma†, H. Wang†, Y. Cai†, H. Wang†, K. Niu, X. Wu, H. Ma, Y. Yang, W. Tong, F. Liu, Z. Liu, Y. Zhang, R. Liu, Z.-J. Zhu*, and N. Liu*

        eLife, 2018, 7: e35368 Web Link (†, Co-first authors; *, Co-Corresponding authors)Preprint at BioRxiv (doi.org/10.1101/247726

        --- This paper is highlighted by Science: "Epigenetics, aging, and glycolysis" Web Link

  • 9. SWATHtoMRM: Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery

        H. Zha†, Y. Cai†, Y. Yin†, Z. Wang, K. Li, and Z.-J. Zhu* (†, Co-first authors; *, Corresponding author)

        Analytical Chemistry, 2018, 90, 4062-4070. Web Link


  • 10. Absolute Quantitative Lipidomics Reveals Lipidome-Wide Alterations in Aging Brain

        J. Tu, Y. Yin, M. Xu, R. Wang, and Z.-J. Zhu*(Corresponding author)

        Metabolomics, 2018,14: 5. Web Link

  • 11. Advancing the Large-Scale CCS Database for Metabolomics and Lipidomics at the Machine-Learning Era

       Z. Zhou†, J. Tu†, and Z.-J. Zhu* (†, Co-first authors; *,Corresponding author)

       Current Opinion in Chemical Biology, 2018, 42, 34-41. (Invited Review) Web Link Recommended by F1000

  • 12. R. Lin*, Y. Mo, H. H. Zha, Z. Qu, P. Xie, Z.-J. Zhu, Y. Xu, Y. Xiong*, K.-L.Guan*,CLOCK Acetylates ASS1 to Drive Circadian Rhythm of Ureagenesis, Molecular Cell, 2017, 68, 198–209.
  • 13. X.Yang, Z. Wang, L. Guo, Z.-J. Zhu, and Y. Zhang*, Proteome-Wide Analysis of N-Glycosylation Stoichiometry Using SWATH Technology, Journal of Proteome Research, 2017, 16, 3830–3840.
  • 14. Z. Zhou, J. Tu, X. Xiong, X. Shen, and Z.-J. Zhu*(Corresponding author), LipidCCS: Prediction of Collision Cross-Section Values for Lipids with High Precision to Support Ion Mobility-Mass Spectrometry based Lipidomics, Analytical Chemistry, 2017, 89, 9559–9566. Web Link for Publication Web Link for LipidCCS Server


  • 15. Z. Zhou, X. Xiong, and Z.-J. Zhu* (Corresponding author), MetCCS Predictor: A Web Server for Predicting Collision Cross-Section Values of Metabolites in Metabolomics, Bioinformatics, 2017, 33, 2235-2237. Web Link for Publication Web Link for MetCCS Server




  • 16. J. Lu, B. Chen, T. T. Chen, S. Guo, X. Xue, Q. Chen, M. Zhao, L. Xia, Z. J. Zhu, L. Zheng*,  H. Yin*,Comprehensive Metabolomics Identified Lipid Peroxidation as A Prominent Feature in Human Plasma of Patients with Coronary Heart Diseases, Redoxy Biology,2017,12,899-907. Web Link
  • 17. M. Wang, Y. Fang, S. Gu, F. F. Chen, Z. J. Zhu, X. Sun*, J. Zhu*, Discovery of novel 1,2,3,4-tetrahydrobenzo[4, 5]thieno[2, 3-c]pyridine derivatives as potent and selective CYP17 inhibitors, European Journal of Medicinal Chemistry, 2017, 132, 157-172.
  • 18. Z. Zhou, X. Shen, J. Tu, and Z.-J. Zhu* (Corresponding author), Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility - Mass Spectrometry, Analytical Chemistry, 2016, 88, 11084-11091. Web Link





  • 19. H. Li, Y. Cai, Y. Guo, F. Chen, and Z.-J. Zhu*(Corresponding author), MetDIA: Targeted Metabolite Extraction of Multiplexed MS/MS Spectra Generated by Data-Independent Acquisition, Analytical Chemistry, 2016, 88, 8757-8764. Web Link





  • 20. J. Wang*,†, T. Zhang†, X. Shen†, J. Liu, D. Zhao, Y. Sun, L. Wang, Y. Liu, X. Gong, Y. Liu, Z.-J. Zhu* (Co-corresponding author), F. Xue,*  Serum Metabolomics for Early Diagnosis of Esophageal Squamous Cell Carcinoma by UHPLC-QTOF/MS, Metabolomics, 2016, 12: 116 (*, Co-corresponding authors; †, Co-first authors) Web Link
  • 21. X. Shen, X. Gong, Y. Cai, Y. Guo, J. Tu, H. Li, T.Zhang, J. Wang, F. Xue, and Z.-J. Zhu* (Corresponding author),Normalization and Integration of Large-Scale Metabolomics Data Using Support Vector Regression, Metabolomics, 2016, 12: 89 Web Link
  • 22. Y. Cai, K. Weng, Y. Guo, J. Peng, and Z.-J. Zhu* (Corresponding author), An Integrated Targeted Metabolomic Platform for High-Throughput Metabolite Profiling and Automated Data Processing, Metabolomics, 2015,11,1575-1586. Web Link
  • 23. H.- G. Xia, A. Najafov,. J.Geng,. L. Galan-Acosta, X. Han,. Y. Guo, B. Shan, Y. Zhang, E. Norberg, T. Zhang, L.Pan, J.Liu, J. L. Coloff, D. Ofengeim, H. Zhu, K. Wu, Y. Cai, J. R. Yates, Z.- J. Zhu, J. Yuan, and H. Vakifahmetoglu-Norberg, Degradation of HK2 by Chaperone-Mediated Autophagy Promotes Metabolic Catastrophe and Cell Death, Journal of Cell Biology, 2015, 210,705-716.
  • 24. M. E. Kurczy, Z.-J. Zhu, ... 20 other authors..., G. Siuzdak*, Comprehensive Bioimaging with Fluorinated Nanoparticles Using Breathable Liquids, Nature Communications, 2015, 6, 5998.
  • 25. J. Ivanisevic, D. Elias, H. Deguchi, P.M. Averell, M. Kurczy, C. H. Johnson, R. Tautenhahn, Z.-J. Zhu, J. Watrous, M.Jain, J.Griffin, G.J. Patti  and G. Siuzdak*, Arteriovenous Blood Metabolomics: A Readout of Intra-Tissue Metabostasis, Scientific Reports, 2015, 5, 12757.
  • 26. C. Kim, G. Y. Tonga,B. Yan, C. S. Kim,S. T. Kim, M. H. Park,Z.-J. Zhu, B. Duncan,B. Creran, and V. M. Rotello*, Regulating Exocytosis of Nanoparticles via Host-guest Chemistry,Organic and Biomolecular Chemistry, 2015,13, 2474-2479.
  • 27. J. Ivanisevic, Z.-J. Zhu (Co-first author), L. Plate, R. Tautenhahn, S. Chen, P.J. O’Brien, C.H. Johnson, M. A. Marletta, G.J. Patti, and G. Siuzdak*, Toward 'Omic' Scale Metabolite Profiling: A Dual Separation – Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism, Analytical Chemistry, 2013, 85, 6876–6884.
  • 28. Z.-J. Zhu, A.W. Schultz, J. Wang, C. H. Johnson, G. J. Patti, and G. Siuzdak*, Liquid Chromatography Quadrupole Time-of-Flight Characterization of Metabolites Guided by the METLIN Database, Nature Protocols, 2013, 8, 451-460.
  • 29. R. Tang, C. S. Kim, D. J. Solfiell, S. Rana, R. Mout, E. M. Velazquez-Delgado, A. Chompoosor, Y. Jeong, B. Yan, Z.-J. Zhu, C. Kim, J. A. Hardy, and V. M. Rotello*, Direct Delivery of Functional Proteins and Enzymes to the Cytosol Using Nanoparticle-Stabilized Nanocapsules, ACS Nano, 2013, 7, 6667-6673.
  • 30. B. Yan, Y. Jeong, L. A. Mercante, G. Y. Tonga, C. Kim, Z.-J. Zhu, R. W. Vachet*, and V. M. Rotello*, Characterization of surface ligands on functionalized magnetic nanoparticles using laser desorption/ionization mass spectrometry (LDI-MS), Nanoscale, 2013, 5, 5063-5066.
  • 31. R. Tautenhahn, K. Cho, W. Uritboonthai, Z.-J. Zhu, G. J. Patti, and G. Siuzdak*, An Accelerated Workflow for Untargeted Metabolomics Using the METLIN Database, Nature Biotechnology, 2012, 30, 826-828.
  • 32. Z.-J. Zhu, H. Wang, B. Yan, H. Zheng, Y. Jiang, O. R. Miranda, V. M. Rotello*, B. Xing*, and R. W. Vachet*, Effect of Surface Charge on the Uptake and Distribution of Gold Nanoparticles in Four Plant Species, Environmental Science and Technology, 2012, 22,12391-12398.
  • 33. Z.-J. Zhu, T. Posati, D. F. Moyano, R. Tang, B. Yan, R. W. Vachet*, and V. M. Rotello*, The Interplay of Monolayer Structure and Serum Protein Interactions on the Cellular Uptake of Gold Nanoparticles, Small, 2012, 8, 2659-2663.
  • 34. Z.-J. Zhu, R. Tang, Y.-C. Yeh, O. R. Miranda, V. M. Rotello*, and R. W. Vachet*, Determination of the Intracellular Stability of Gold Nanoparticle Monolayers Using Mass Spectrometry, Anal. Chem., 2012, 84, 4321-4326.
  • 35. Z.-J. Zhu, Y.-C. Yeh, R. Tang, R., B. Yan, Tamayo, J., R. W. Vachet*, and V. M. Rotello*, Stability of Quantum Dots in Live Cells, Nature Chemistry, 2011, 3, 963-968.
  • 36. O. R. Miranda, X. Li, L. Garcia-Gonzalez, Z.-J. Zhu, B. Yan, U. H. F. Bunz, and V. M. Rotello, Colorimetric Bacteria Sensing Using a Supramolecular Enzyme-Nanoparticle Biosensor, J. Am. Chem. Soc., 2011, 133, 9650-9653.
  • 37. X.-C. Yang, B. Samanta, S. S. Agasti, Y. Jeong, Z.-J. Zhu, S. Rana, O. R. Miranda, and V. M. Rotello*, Drug Delivery Using Nanoparticle‐Stabilized Nanocapsules, Angew. Chem., Int. Ed. 2011, 50, 477-481.
  • 38. C. K. Kim, S. S. Agasti, Z.-J. Zhu, L. Isaacs, and V. M. Rotello*, Host-Guest Chemistry inside Living Cells: Recognition-Mediated Activation of Therapeutic Gold Nanoparticles, Nature Chemistry, 2010, 2, 962-966.
  • 39. Z.-J. Zhu, R. Carboni, M. J. Quercio Jr., B. Yan, O. R. Miranda, D. L. Anderton, K. F. Arcaro*, V. M. Rotello*, and R. W. Vachet*, Surface Properties Dictate Uptake, Distribution, Excretion, and Toxicity of Nanoparticles in Fish, Small, 2010, 6, 2261-2265.
  • 40. A. Chompoosor, K. Saha, P. S. Ghosh, O. R. Miranda, Z.-J. Zhu, K. F. Arcaro, and V. M. Rotello*, The Role of Surface Functionality on Acute Cytotoxicity, ROS Generation and DNA Damage by Cationic Gold Nanoparticles, Small, 2010, 6, 2246-2249.
  • 41. P. Ghosh, X. Yang, R. Arvizo, Z.-J. Zhu, H. Mo, and V. M. Rotello*, Intracellular Delivery of a Membrane-Impermeable Enzyme in Active Form Using Functionalized Gold Nanoparticles, J. Am. Chem. Soc., 2010, 132, 2642–2645.
  • 42. B. Yan,Z.-J. Zhu, O. R. Miranda, A. Chompoosor, V. M. Rotello*, and R. W. Vachet*, Laser Desorption/Ionization Mass Spectrometry Analysis of Monolayer-protected Gold Nanoparticles, Anal. Bioanal. Chem., 2010, 396, 1025-1035.
  • 43. Z.-J. Zhu, V. M. Rotello*, and R. W. Vachet*, Engineered Nanoparticle Surfaces for Improved Mass Spectrometric Analyses, Analyst, 2009, 134, 2183-2188.
  • 44. C. K. Kim, P. Ghosh, C. Pagliuca, Z.-J. Zhu, S. Menichetti, and V. M. Rotello*, Entrapment of Hydrophobic Drugs in Nanoparticle Monolayers with Efficient Release into Cancer Cells, J. Am. Chem. Soc., 2009, 131, 1360–1361.
  • 45. Z.-J. Zhu, P. S. Ghosh, O. R. Miranda, R. W. Vachet*, and V. M. Rotello*, Multiplexed Screening of Cellular Uptake of Gold Nanoparticles Using Laser Desorption/Ionization Mass Spectrometry, J. Am. Chem. Soc., 2008, 130, 14139-14143.
  • 46. W.-Z. Jia, K. Wang, Z.-J. Zhu, H.-T. Song, and X.-H. Xia*, One-Step Immobilization of Glucose Oxidase in a Silica Matrix on a Pt Electrode by an Electrochemically Induced Sol-Gel Process, Langmuir, 2007, 23, 11896-11900.