Our Publications

1. Sudipa Maity, Yuanyu Huang, Mitchell D Kilgore, Abbigail N Thurmon, Lee O Vaasjo, Maria J Galazo, Xiaojiang Xu, Jing Cao, Xiaoying Wang, Bo Ning, Ning Liu, Jia Fan. Mapping dynamic molecular changes in hippocampal subregions after traumatic brain injury through spatial proteomics. Clinical Proteomics. 2024. 12, 32.

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2. Duran Bao, Qingbo Shu, Bo Ning, Michael Tang, Yubing Liu, Noel Wong, Zhengming Ding, Zizhan Zheng, Christopher J Lyon, Tony Hu, Jia Fan. Improving Targeted Mass Spectrometry Data Analysis with Nested Active Machine Learning. Advanced Intelligent Systems. 2024.

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3. Alfred Akinlalu, Zachariah Flaten, Komila Rasuleva, Md Saimon Mia, Aaron Bauer, Santhalingam Elamurugan, Nega Ejjigu, Sudipa Maity, Amara Arshad, Min Wu, Wenjie Xia, Jia Fan, Ang Guo, Sijo Mathew, Dali Sun. Integrated proteomic profiling identifies amino acids selectively cytotoxic to pancreatic cancer cells. The Innovation. 2024. 3, 5. ​

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​4.Tianfang Ma, Lianjin Jin, Shanshan Bai, Zhan Liu, Shuo Wang, Beibei Shen, Yeyoung Cho, Subing Cao, Meijuan JS Sun, Ladan Fazli, David Zhang, Chiyaro Wedderburn, Derek Y Zhang, Gavisha Mugon, Nathan Ungerleider, Melody Baddoo, Kun Zhang, Lovisa Holmberg Schiavone, Brant R Burkhardt, Jia Fan, Zongbing You, Erik K Flemington, Xuesen Dong, Yan Dong. Loss of feedback regulation between FAM3B and androgen receptor driving prostate cancer progression. Oxford University Press. 2024. 421-433.​

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5. BAO Duran, Jia Fan, Ye Tony HU, Qingbo Shu, Bo Ning, Christopher J Lyon. Active machine learning model for targeted mass spectrometry data analysis. Patent. 2023.

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6.Sudipa Maity, Meredith G Mayer, Qingbo Shu, Hellmers Linh, Duran Bao, Robert V Blair, Yanlin He, Christopher J Lyon, Tony Y Hu, Tracy Fischer, Jia Fan. Cerebrospinal fluid protein markers indicate neuro-damage in SARS-CoV-2-infected nonhuman primates. Molecular & Cellular Proteomics. 2023. 22, 4. ​

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7.Weiwei Xu, MM Fahd Qadir, Daniela Nasteska, Paula Mota de Sa, Caroline M Gorvin, Manuel Blandino-Rosano, Charles R Evans, Thuong Ho, Evgeniy Potapenko, Rajakrishnan Veluthakal, Fiona B Ashford, Stavroula Bitsi, Jia Fan, Manika Bhondeley, Kejing Song, Venkata N Sure, Siva SVP Sakamuri, Lina Schiffer, Wandy Beatty, Rachael Wyatt, Daniel E Frigo, Xiaowen Liu, Prasad V Katakam, Wiebke Arlt, Jochen Buck, Lonny R Levin, Tony Hu, Jay Kolls, Charles F Burant, Alejandra Tomas, Matthew J Merrins, Debbie C Thurmond, Ernesto Bernal-Mizrachi, David J Hodson, Franck. Architecture of androgen receptor pathways amplifying glucagon-like peptide-1 insulinotropic action in male pancreatic β cells. Cell reports. 2023. 42, 5.

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8.Dora Pungan, Jia Fan, Guixiang Dai, Mst Shamima Khatun, Monika L Dietrich, Kevin J Zwezdaryk, James E Robinson, Samuel J Landry, Jay K Kolls. Novel Pneumocystis Antigens for Seroprevalence Studies. Journal of Fungi. 2023. 9, 6. 

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9.Xingyan Zhou, Jenna C Pucel, Aya Nomura-Kitabayashi, Pallavi Chandakkar, Adella P Guidroz, Nikita L Jhangiani, Duran Bao, Jia Fan, Helen M Arthur, Christoph Ullmer, Christian Klein, Philippe Marambaud, Stryder M Meadows. ANG2 blockade diminishes proangiogenic cerebrovascular defects associated with models of hereditary hemorrhagic telangiectasia. Lippincott Williams & Wilkins. 2023.1384-1403.

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10. Partha K Chandra, Stephen E Braun, Sudipa Maity, Jorge A Castorena-Gonzalez, Hogyoung Kim, Jeffrey G Shaffer, Sinisa Cikic, Ibolya Rutkai, Jia Fan, Jessie J Guidry, David K Worthylake, Chenzhong Li, Asim B Abdel-Mageed, David W Busija. Circulating plasma exosomal proteins of either SHIV-infected rhesus macaque or HIV-infected patient indicates a link to neuropathogenesis. Viruses. 2023. 15, 3.

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11.PK Chandra, SE Braun, S Maity, JA Castorena-Gonzalez, H Kim, JG Shaffer, S Cikic, I Rutkai, J Fan, JJ Guidry. Circulating Plasma Exosomal Proteins of Either SHIV-Infected Rhesus Macaque or HIV-Infected Patient Indicates a Link to Neuropathogenesis. Viruses 2023, 15, 794.

 

12. Shan Liu, Xue Wu, Sutapa Chandra, Christopher Lyon, Bo Ning, Jia Fan, Tony Y Hu. Extracellular vesicles: emerging tools as therapeutic agent carriers. Acta Pharmaceutica Sinica B. 2022. 3822-3842.

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13. Qingbo Shu, Jia Fan, Christopher J Lyon, Tony Hu. MS-based Detection of Pathogen Antigen Through Immunoprecipitation of Its Proteolytic Peptides. MOLECULAR & CELLULAR PROTEOMICS. 2022. 21, 8. S55-S55.

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14. Wenshu Zheng, Sylvia M LaCourse, Bofan Song, Dhiraj Kumar Singh, Mayank Khanna, Juan Olivo, Joshua Stern, Jaclyn N Escudero, Carlos Vergara, Fangfang Zhang, Shaobai Li, Shu Wang, Lisa M Cranmer, Zhen Huang, Christine M Bojanowski, Duran Bao, Irene Njuguna, Yating Xiao, Dalton C Wamalwa, Duc T Nguyen, Li Yang, Elizabeth Maleche-Obimbo, Nhung Nguyen, Lili Zhang, Ha Phan, Jia Fan, Bo Ning, Chenzhong Li, Christopher J Lyon, Edward A Graviss, Grace John-Stewart, Charles D Mitchell, Alistair J Ramsay, Deepak Kaushal, Rongguang Liang, Eddy Pérez-Then, Tony Y Hu. Diagnosis of paediatric tuberculosis by optically detecting two virulence factors on extracellular vesicles in blood samples. Nature biomedical engineering. 2022. 6, 8. 979-991. 

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15.Qingbo Shu, Meena Rajagopal, Jia Fan, Lingpeng Zhan, Xiangxing Kong, Yifan He, Suwatchareeporn Rotcheewaphan, Christopher J Lyon, Wei Sha, Adrian M Zelazny, Tony Hu. Peptidomic analysis of mycobacterial secreted proteins enables species identification. View. 2022. 3, 4. 

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16. D Pungan, J Fan, K Zwezdaryk, M Dietrich, J Robinson, G Dai, JK Kolls. Serum Anti-p Jiroveci Glucanase Responses in a Pediatric Cohort. C61. BREAKING THE MOLD. 2022. A5752-A5752.

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17. Terri J Harford, Fariba Rezaee, Briana R Dye, Jia Fan, Jason R Spence, Giovanni Piedimonte. RSV-induced changes in a 3-dimensional organoid model of human fetal lungs. PLoS One. 2022. 17, 3. 

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18. Lingchen Fu, Jia Fan, Sudipa Maity, Grant McFadden, Yixin Shi, Wei Kong. PD-L1 interacts with Frizzled 6 to activate β-catenin and form a positive feedback loop to promote cancer stem cell expansion. Oncogene. 2022. 41, 8. 1100-1113.

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19. Bing Feng, Jerney Harms, Nirali Patel, Hui Ye, Pei Luo, Valeria Torres Irizarry, Jacob Vidrine, Ann Coulter, Candida J Rebello, Sangho Yu, Jia Fan, Hans-Rudolf Berthoud, Frank Greenway, Heike Münzberg, Christopher Morrison, Pingwen Xu, Yanlin He. Targeting the T-type calcium channel Cav3. 2 in GABAergic arcuate nucleus neurons to treat obesity. Molecular metabolism. 2021. 54. 101391. 

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20. Liyan Mao, Sylvia M LaCourse, Soyeon Kim, Chang Liu, Bo Ning, Duran Bao, Jia Fan, Christopher J Lyon, Ziyong Sun, Sharon Nachman, Charles D Mitchell, Tony Y Hu. Evaluation of a serum-based antigen test for tuberculosis in HIV-exposed infants: a diagnostic accuracy study. BMC medicine. 2021. 19. 1-12. 

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21. Qingbo Shu, Tara Kenny, Jia Fan, Christopher J Lyon, Lisa H Cazares, Tony Y Hu. Species-specific quantification of circulating ebolavirus burden using VP40-derived peptide variants. PLoS Pathogens. 2021. 17, 11. e1010039

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22. Bo Ning, Zhen Huang, Brady M Youngquist, John W Scott, Alex Niu, Christine M Bojanowski, Kevin J Zwezdaryk, Nakhle S Saba, Jia Fan, Xiao-Ming Yin, Jing Cao, Christopher J Lyon, Chen-zhong Li, Chad J Roy, Tony Y Hu. Liposome-mediated detection of SARS-CoV-2 RNA-positive extracellular vesicles in plasma. Nature nanotechnology. 2021. 16, 9. 1039-1044.

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23. Dali Sun, Zhen Zhao, Sarah Spiegel, Yang Liu, Jia Fan, Pouya Amrollahi, Jing Hu, Christopher J Lyon, Meihua Wan, Tony Y Hu. Dye-free spectrophotometric measurement of nucleic acid-to-protein ratio for cell-selective extracellular vesicle discrimination. Biosensors and Bioelectronics. 2021. 179. 113058.

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24. Tejasav S Sehrawat, Juan P Arab, Mengfei Liu, Pouya Amrollahi, Meihua Wan, Jia Fan, Yasuhiko Nakao, Elisa Pose, Amaia Navarro‐Corcuera, Debanjali Dasgupta, Chieh‐Yu Liao, Li He, Amy S Mauer, Emma Avitabile, Meritxell Ventura‐Cots, Ramon A Bataller, Arun J Sanyal, Naga P Chalasani, Julie K Heimbach, Kymberly D Watt, Gregory J Gores, Pere Gines, Patrick S Kamath, Douglas A Simonetto, Tony Y Hu, Vijay H Shah, Harmeet Malhi. Circulating extracellular vesicles carrying sphingolipid cargo for the diagnosis and dynamic risk profiling of alcoholic hepatitis. 2021. 73, 2. 571-585.

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25. Yang Liu, Yajun Gu, Serina Ng, Zaian Deng, Christopher J Lyon, Eugene J Koay, Bo Ning, Matthew H Katz, Paul J Chiao, Jia Fan, Haiyong Han, Daniel Von Hoff, Tony Y Hu. Circulating levels of hydroxylated bradykinin function as an indicator of tissue HIF-1α expression. Science Bulletin. 2020. 65, 18. 1570-1579. 

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26. Qingbo Shu, Meena Rajagopal, Jia Fan, Lingpeng Zhan, Xiangxing Kong, Yifan He, Suwatchareeporn Rotcheewaphan, Christopher J Lyon, Wei Sha, Adrian M Zelazny, Tony Hu. IP-MS Analysis of ESX-5 and ESX-1 Substrates Enables Mycobacterial Species Identification. bioRxiv. 2020. 2020.06. 07.138784. 

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27. Ye Hu, Jia Fan, Kai Liang, Fei Liu, SUN Dali. Nanoplasmonic quantification of tumor-derived extracellular vesicles in plasma microsamples for detection and treatment monitoring. Patent. 2020. 

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28. Yang Liu, Jia Fan, Ting Xu, Navid Ahmadinejad, Kenneth Hess, Steven H Lin, Jianjun Zhang, Xi Liu, Li Liu, Bo Ning, Zhongxing Liao, Tony Y Hu. Extracellular vesicle tetraspanin-8 level predicts distant metastasis in non–small cell lung cancer after concurrent chemoradiation. Science advances. 2020. 6, 11. eaaz6162.

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29. MeiHua Wan, Yichao Wang, Lingpeng Zhan, Jia Fan, Tony Y Hu. MALDI-TOF mass spectrometry-based quantification of C-peptide in diabetes patients. European Journal of Mass Spectrometry. 2020. 26, 1. 55-62.

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30. Fangfang Zhang, Christopher J Lyon, Robert J Walls, Bo Ning, Jia Fan, Tony Y Hu. Cathepsin B dependent cleavage product of serum amyloid A1 identifies patients with chemotherapy-related cardiotoxicity. ACS Pharmacology & Translational Science. 2019. 2, 5. 333-341. 

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31. Zaian Deng, Zhen Zhao, Bo Ning, Jeffery Basilio, Karen Mann, Jie Fu, Yajun Gu, Yuanqing Ye, Xifeng Wu, Jia Fan, Paul Chiao, Tony Hu. Nanotrap-enabled quantification of KRAS-induced peptide hydroxylation in blood for cancer early detection. Nano Research. 2019. 12. 1445-1452.

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32. Zhen Zhao, Jia Fan, Yen-Michael S Hsu, Christopher J Lyon, Bo Ning, Tony Y Hu. Extracellular vesicles as cancer liquid biopsies: From discovery, validation, to clinical application. Lab on a Chip. 2019. 19, 7. 1114-1140.

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33. Wei Zhang, Qingbo Shu, Zhen Zhao, Jia Fan, Christopher J Lyon, Adrian M Zelazny, Ye Hu. Antigen 85B peptidomic analysis allows species-specific mycobacterial identification. Clinical Proteomics. 2019. 15. 1-10. 

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34. Jia Fan, Qian Wei, Eugene J Koay, Yang Liu, Zhen Zhao, Ye Hu. Exosomal EphA2 transmits chemoresistance and predicts pancreatic cancer patient responses to therapy. Cancer Research. 2018. 78. 85-585. 

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35. Jia Fan, Qian Wei, Eugene J Koay, Yang Liu, Bo Ning, Paul W Bernard, Ning Zhang, Haiyong Han, Matthew H Katz, Zhen Zhao, Ye Hu. Chemoresistance transmission via exosome-mediated EphA2 transfer in pancreatic cancer. Theranostics. 2018. 8, 21. 5986.

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36. Meryl Rodrigues, Jia Fan, Christopher Lyon, Meihua Wan, Ye Hu. Role of extracellular vesicles in viral and bacterial infections: pathogenesis, diagnostics, and therapeutics. Theranostics. 2018. 8, 10. 2709.

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37. Jia Fan, Hedong Zhang, Duc T Nguyen, Christopher J Lyon, Charles D Mitchell, Zhen Zhao, Edward A Graviss, Ye Hu. Rapid diagnosis of new and relapse tuberculosis by quantification of a circulating antigen in HIV-infected adults in the Greater Houston metropolitan area. BMC medicine. 2017. 15. 1-10.

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38. Chang Liu, Zhen Zhao, Jia Fan, Christopher J Lyon, Hung-Jen Wu, Dobrin Nedelkov, Adrian M Zelazny, Kenneth N Olivier, Lisa H Cazares, Steven M Holland, Edward A Graviss, Ye Hu. Quantification of circulating Mycobacterium tuberculosis antigen peptides allows rapid diagnosis of active disease and treatment monitoring.Proceedings of the National Academy of Sciences. 2017. 114, 15. 3969-3974. 

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39. Kai Liang, Fei Liu, Jia Fan, Dali Sun, Chang Liu, Christopher J Lyon, David W Bernard, Yan Li, Kenji Yokoi, Matthew H Katz, Eugene J Koay, Zhen Zhao, Ye Hu. Nanoplasmonic quantification of tumour-derived extracellular vesicles in plasma microsamples for diagnosis and treatment monitoring. Nature biomedical engineering. 2017. 1, 4. 0021. 

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40. Jia Fan, Bo Ning, Christopher J Lyon, Tony Y Hu. Circulating peptidome and tumor-resident proteolysis. The Enzymes. 2017. 42. 1-25.

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41. Huan Li, Shuanghui Yang, Ge Yu, Liangfang Shen, Jia Fan, Ling Xu, Hedong Zhang, Nianxi Zhao, Zihua Zeng, Tony Hu, Jianguo Wen, Youli Zu. Aptamer internalization via endocytosis inducing s-phase arrest and priming maver-1 lymphoma cells for cytarabine chemotherapy. Theranostics. 2017. 7, 5. 1204.

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42. T Xu, J Fan, LB Levy, Y Zhuang, C Bone, J Huo, DR Gomez, Z Liao, Y Hu. Predictive Value of Serum Hepcidin for Disease Outcome in Non-Small Cell Lung Cancer Patients Received Definitive Radio (chemo) therapy. International Journal of Radiation Oncology, Biology, Physics. 2016. 96, 2. E473.

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43. Luchang Zhu, Randall J Olsen, Nicola Horstmann, Samuel A Shelburne, Jia Fan, Ye Hu, James M Musser. Intergenic Variable-Number Tandem-Repeat Polymorphism Upstream of rocA Alters Toxin Production and Enhances Virulence in Streptococcus pyogenes. Infection and immunity. 2016. 84, 7. 2086-2093. 

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44. Jia Fan, Muy-Kheng M Tea, Chuan Yang, Li Ma, Qing H Meng, Tony Y Hu, Christian F Singer, Mauro Ferrari. Profiling of cross-functional peptidases regulated circulating peptides in BRCA1 mutant breast cancer. Journal of proteome research. 2016. 15, 5. 1534-1545. 

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45. Guangjun Nie, Tony Hu, Jia Fan, Yuliang Zhao, Mauro Ferrari. Method and kit for detecting hepcidin. Patent. 2015.

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46. Ye Hu, Xin Ma, Hung-Jen Wu, Jia Fan, Tong Sun. Rapid detection and quantitation of pathogen-specific biomarkers using nanoporous dual-or multi-layer silica films. Patent. 2015.

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47. Jia Fan, Qing H Meng, Christopher Bone, Stephen Igo, Ye Hu. Circulating peptides for predicting subsequent cardiotoxicity in cancer patients with chemotherapies. Cancer Research. 2015. 75, 15_Supplement. 598-598.

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48. Zaian Deng, Yaojun Li, Jia Fan, Guohui Wang, Yan Li, Yaou Zhang, Guoping Cai, Haifa Shen, Mauro Ferrari, Tony Y Hu. Circulating peptidome to indicate the tumor-resident proteolysis. Scientific reports. 2015. 5, 1. 9327. 

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49. Jia Fan, Shiwen Niu, Ailian Dong, Jian Shi, Hung-Jen Wu, Daniel H Fine, Yaping Tian, Chunxi Zhou, Xuewu Liu, Tong Sun, Gregory J Anderson, Mauro Ferrari, Guangjun Nie, Ye Hu, Yuliang Zhao. Nanopore film based enrichment and quantification of low abundance hepcidin from human bodily fluids. Nanomedicine: Nanotechnology, Biology and Medicine. 2014. 10, 5. e879-e888. 

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50. Hung-Jen Wu, Yaojun Li, Jia Fan, Zaian Deng, Zhao Hu, Xuewu Liu, Edward A Graviss, Mauro Ferrari, Xin Ma, Ye Hu. Antibody-Free Detection of Mycobacterium tuberculosis Antigen Using Customized Nanotraps. Analytical chemistry. 2014. 86, 4. 1988-1996.

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51. Jia Fan, Yi Huang, Inez Finoulst, Hung-jen Wu, Zaian Deng, Rong Xu, Xiaojun Xia, Mauro Ferrari, Haifa Shen, Ye Hu. Serum peptidomic biomarkers for pulmonary metastatic melanoma identified by means of a nanopore-based assay. Cancer letters. 2013. 334, 2. 202-210.

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52.Jia Fan, Xiaoyong Deng, James W Gallagher, Haiyu Huang, Yi Huang, Jianguo Wen, Mauro Ferrari, Haifa Shen, Ye Hu. Monitoring the progression of metastatic breast cancer on nanoporous silica chips. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2012. 370, 1967. 2433-2447. 

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53. Jia Fan, James W Gallagher, Hung-Jen Wu, Matthew G Landry, Jason Sakamoto, Mauro Ferrari, Ye Hu. Low molecular weight protein enrichment on mesoporous silica thin films for biomarker discovery. JoVE (Journal of Visualized Experiments). 2012. 62. e3876.

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54. Jia Fan, Jun-Jie Yin, Bo Ning, Xiaochun Wu, Ye Hu, Mauro Ferrari, Gregory J Anderson, Jingyan Wei, Yuliang Zhao, Guangjun Nie. Direct evidence for catalase and peroxidase activities of ferritin–platinum nanoparticles. Biomaterials. 2011. 32, 6. 1611-1618. 

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