Publications
2025
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38. Yoon Mee Yang, Jieun Kim, Zhijun Wang, Jina Kim, So Yeon Kim, Gyu Jeong Cho, Jee Hyung Lee, Sun Myoung Kim, Takashi Tsuchiya, Michitaka Matsuda, Vijay Pandyarajan, Stephen J Pandol, Michael S Lewis, Alexandra Gangi, Paul W Noble, Dianhua Jiang, Akil Merchant, Edwin M Posadas, Neil A Bhowmick, Shelly C Lu, Sungyong You†, Alexander M Xu†, Ekihiro Seki†
Metastatic Tumor Growth in Steatotic Liver is Promoted by HAS2-Mediated Fibrotic Tumor Microenvironment. The Journal of Clinical Investigation, 135, e180802. (2025) doi.org/10.1172/JCI180802 |
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37. Zitong Wang, Abdullah Farooq, Yu-Jen Chen, Aman Barghava, Alexander M. Xu, Matthew Thomson.
Identifying perturbations that boost T-cell infiltration into tumours via counterfactual learning of their spatial proteomic profiles. Nature Biomedical Engineering, 9, 390-404. (2025) doi.org/10.1038/s41551-025-01357-0 |
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2024
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36. Waseem Lone, Alyssa Bouska, Tyler A Herek, Catalina Amador, Joo Song, Alexander M Xu, Dylan Jochum, Issa Ismail Issa, Dennis D Weisenburger, Xuan Zhang, Sharath Kumar Bhagavathi, Tayla B Heavican‐Foral, Sunandini Sharma, Ab Rauf Shah, Abdul Rouf Mir, Aisha Ahmad Alkhinji, Dalia El‐Gamal, Bhavana J Dave, Keenan Hartert, Jiayu Yu, Mallick Saumyaranjan, Timothy C Greiner, Julie Vose, Timothy W McKeithan, Kai Fu, Michael Green, Chengfeng Bi, Akil Merchant, Wing C Chan, Javeed Iqbal.
High‐grade B‐cell lymphoma not otherwise specified, with diffuse large B‐cell lymphoma gene expression signatures: Genomic analysis and potential therapeutics. American Journal of Hematology, 100, 10-22. (2024) doi.org/10.1002/ajh.27513 |
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35. Jane C Figueiredo, Julia Levy, So Yung Choi, Alexander M Xu, Noah M Merin, Omid Hamid, Tucker Lemos, Nathalie Nguyen, Maimoona Nadri, Alma Gonzalez, Simeon Mahov, Justin M Darrah, Jun Gong, Ronald L Paquette, Alain C Mita, Robert A Vescio, Sarah J Salvy, Inderjit Mehmi, Andrew E Hendifar, Ronald Natale, Warren G Tourtellotte, V Krishnan Ramanujan, Carissa A Huynh, Kimia Sobhani, Karen L Reckamp, Akil A Merchant.
Low booster uptake in cancer patients despite health benefits. iScience, In Press. (2024) doi.org/10.1016/j.isci.2024.110596 |
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34. Sophia M Roush, Jenny Coelho, Alexander M Xu, Kaushik Puranam, Marriam Mponda, Edwards Kasonkanji, Maurice Mulenga, Tamiwe Tomoka, Jonathan Galeotti, Amy Brownlee, Hormas Ghadially, Maganizo Chagomerana, Blossom Damania, Matthew Painschab, Akil Merchant, Satish Gopal, Yuri Fedoriw.
HIV infection and ART exposure impact tumor T-cell receptor repertoire of diffuse large B-cell lymphoma. JCI Insight, 9, e180771. (2024) doi.org/10.1172/jci.insight.180771 |
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33. Jenny Coelho, Sophia M Roush, Alexander M Xu, Kaushik Puranam, Marriam Mponda, Edwards Kasonkanji, Maurice Mulenga, Tamiwe Tomoka, Jonathan Galeotti, Amy Brownlee, Hormas Ghadially, Blossom Damania, Matthew Painschab, Akil Merchant, Satish Gopal, Yuri Fedoriw.
HIV and prior exposure to antiretroviral therapy alter tumour composition and tumour: T‐cell associations in diffuse large B‐cell lymphoma. British Journal of Haematology, 205, 192-206. (2024) doi.org/10.1111/bjh.19531 |
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32. Alexander M. Xu†, Marcela Haro, Ann E. Walts, Ye Hu, Joshi John, Beth Y. Karlan, Akil Merchant, Sandra Orsulic†.
Spatiotemporal Architecture of Immune Cells and Cancer-Associated Fibroblasts in High-Grade Serous Ovarian Carcinoma. Science Advances, 10, eadk8805. (2024) doi.org/10.1126/sciadv.adk8805 |
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2023
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31. Tomohiro Aoki*, Aixiang Jiang*, Alexander M. Xu*, Yifan Yin, Alicia Gamboa, Katy Milne, Katsuyoshi Takata, Tomoko Miyata-Takata, Shaocheng Wu, Mary Warren, Celia Strong, Talia Goodyear, Kayleigh Morris, Lauren C. Chong, Monirath Hav, Anthony R. Colombo, Adele Telenius, Susana Ben-Neriah, Andrew P. Weng, Aly Karsan, Andrew Roth, Pedro Farinha, David W. Scott, Kerry J. Savage, Brad H. Nelson, Akil Merchant†, Christian Steidl†.
The spatially resolved tumor microenvironment predicts treatment outcome in relapsed/refractory Hodgkin lymphoma. Journal of Clinical Oncology, 42, 1077-1087. (2023) doi.org/10.1200/jco.23.01115 |
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30. Dalin Li, Ana Jimena Pavlovitch-Bedzyk, Joseph E. Ebinger, Abdul Khan, Mohamed Hamideh, Akil Merchant, Jane C. Figueiredo, Susan Cheng, Mark M. Davis, Dermot P. B. McGovern, Gil Y. Melmed, Alexander M. Xu, Jonathan Braun.
A Paratope-Enhanced Method to Determine Breadth and Depth TCR Clonal Metrics of the Private Human T-Cell Vaccine Response after SARS-CoV-2 Vaccination. International Journal of Molecular Sciences, 24, 14223. (2023) doi.org/10.3390/ijms241814223 |
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29. William Chour, Jongchan Choi, Jingyi Xie, Mary Chaffee, Thomas Schmitt, Kathryn Finton, Diana Delucia, Alexander M. Xu, Yapeng Su, Daniel Chen, Rongyu Zhang, dan Yuan, Sunga Hong, Alphonsus Ng, Jonah Butler, Rick Edmark, Lesley Jones, Kim Murray, Songming Peng, Guideng Li, Roland Strong, John Lee, Jason Goldman, Philip Greenberg, James R. Heath.
Large libraries of single-chain trimer peptide-MHCs enable rapid antigen-specific CD8+ T cell discovery and analysis. Communications Biology, 6, 528. (2023) doi.org/10.1038/s42003-023-04899-8 |
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28. Zhijun Wang*, Wei Tu*, Yoon Mee Yang*, So Yeon Kim*, Jieun Kim*, Alexander Xu*, Alexandra Gangi, Ben A Falk, Mazen Noureddin, Michael Lewis, Sungyong You, Wei Fan, Dolores Di Vizio, Sungjin Kim, Mourad Tighiouart, Stephen Pandol, Akil Merchant, Edwin Posadas, Neil Bhowmick, Shelly C. Lu, Ekihiro Seki.
Fatty Liver Regulation of Production of Extracellular Vesicles Promotes Liver Metastasis via YAP activation. Cell Metabolism, 35, 1209-1226. (2023) doi.org/10.1016/j.cmet.2023.04.013 |
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27. Alexander M Xu†, William Chour, Diana C DeLucia, Yapeng Su, Ana Jimena Pavlovitch-Bedzyk, Rachel Ng, Yusuf Rasheed, Mark Davis, John K Lee, James R Heath†.
Entropic Analysis of Antigen-Specific CDR3 Domains Identifies Essential Binding Motifs Shared by CDR3s with Different Antigen Specificities. Cell Systems, 14, 273-284. (2023) doi.org/10.1016/j.cels.2023.03.001 |
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2022
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26. Yapei Huang*, Juliana E Shin*, Alexander M Xu*, Changfu Yao*, Sandy Joung, Min Wu, Ruan Zhang, Bongha Shin, Joslyn Foley, Simeon B Mahov, Joseph E Ebinger, Jonathan G Braun, Caroline A Jefferies, Tanyalak Parimon, Chelsea Hayes, Kimia Sobhani, Akil Merchant, Sina Gharib, Stanley C Jordan, Susan Cheng, Helen S Goodridge, Peter Chen.
Evidence of premature lymphocyte aging in people with low anti-spike antibody levels after BNT162b2 vaccination. iScience, 105209. (2022) doi.org/10.1016/j.isci.2022.105209 |
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25. Anthony Colombo, Monirath Hav, Mohan Singh, Alexander Xu, Alicia Gamboa, Tucker Lemos, Erik Gerdtsson, Denaly Chen, Jane Houldsworth, Rita Shaknovich, Tomohiro Aoki, Lauren Chong, Katsuyoshi Takata, Elizabeth A Chavez, Christian Steidl, James Hicks, Peter Kuhn, Imran Siddiqi, Akil Merchant.
Single-cell spatial analysis of tumor immune architecture in diffuse large B-cell lymphoma. Blood Advances, 6, 4675-4690. (2022) doi.org/10.1182/bloodadvances.2022007493 |
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24. Dalin Li*, Alexander Xu*, Emebet Mengesha, Rebecca Elyanow, Rachel M. Gittelman, Heidi Chapman, John C. Prostko, Edwin C. Frias, James L. Stewart, Valeriya Pozdnyakova, Philip Debbas, Angela Mujukian, Arash A Horizon, Noah Merin, Sandy Joung, Gregory J. Botwin, Kimia Sobhani, Jane C. Figueiredo, Susan Cheng, Ian M. Kaplan, Dermot P.B. McGovern, Akil Merchant, Gil Y. Melmed, Jonathan Braun.
Effects of age and immunotherapy on the clonal T cell response to SARS-CoV-2 vaccination in patients with inflammatory bowel disease. Inflammatory Bowel Diseases, izac071. (2022) doi.org/10.1093/ibd/izac071 |
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23. Alexander M. Xu*, Dalin Li*, Emebet Mengesha, Rebecca Elyanow, Rachel M Gittelman, Heidi Chapman, John C Prostko, Edwin C Frias, James L Stewart, Valeriya Pozdnyakova, Philip Debbas, Angela Mujukian, Arash A Horizon, Noah Merin, Sandy Joung, Gregory J Botwin, Kimia Sobhani, Jane C Figueiredo, Susan Cheng, Ian M Kaplan, Dermot PB McGovern, Akil Merchant, Gil Y Melmed, Jonathan Braun.
Differences in SARS-CoV-2 Vaccine Response Dynamics Between Class-I- and Class-II-Specific T-Cell Receptors in Inflammatory Bowel Disease. Frontiers in Immunology, 13, 880190. (2022) doi.org/10.3389/fimmu.2022.880190 |
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2015-2020
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22. Yapeng Su, …, Alexander M Xu, … Wei Wei, Nathan D. Price, Sui Huang, Naeha Subramanian, Kai Wang, Andrew T Magis, Jennifer Hadlock, Leroy Hood, Alan Aderem, Jeffrey A Bluestone, Lewis L Lanier, Phil Greenberg, Raphael Gottardo, Mark M Davis, Jason D Goldman, James R Heath.
Multiomics Resolves Coordinated Immune Responses to Mild, Moderate, and Severe COVID-19. Cell, 183, 1479-1495. (2020) doi.org/10.1016/j.cell.2020.10.037 |
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21. *Gen He, *Ning Hu, *Alexander M Xu, Xiangling Li, Yunlong Zhao, Xi Xie.
Nanoneedle Platforms: The Many Ways to Pierce the Cell Membrane. Advanced Functional Materials, 30, 1909890. (2020) doi.org/10.1002/adfm.201909890 |
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20. Yapeng Su, Melissa Ko, Hanjun Cheng, Ronghui Zhu, Min Xue, Jessica Wang, Jihoon Lee, Luke Frankiw, Alexander M Xu, …, Sui Huang, Antoni Ribas, Raphael Levine, Garry Nolan, Wei Wei, Sylvia Plevritis, Guideng Li, David Baltimore, James R Heath.
Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line. Nature Communications, 11, 1-12. (2020) doi.org/10.1038/s41467-020-15956-9 |
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19. *Alphonsus Ng, *Songming Peng, *Alexander M Xu, Won Jun Noh, Katherine Guo, Michael T. Bethune, William Chour, Jongchan Choi, Sung Yang, David Baltimore, James R Heath.
MATE-Seq: Microfluidic Antigen-TCR Engagement Sequencing. Lab on a Chip, 19, 3011-3021. (2019) doi.org/10.1039/C9LC00538B |
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18. *Songming Peng, *Jesse M Zaretsky, *Alphonsus Ng, *William Chour, Michael T Bethune, Jongchan Choi, Alice Hsu, Elizabeth Holman, Xiaozhe Ding, Katherine Guo, Jungwoo Kim, Alexander M Xu, John E. Heath, Won Jun Noh, Jing Zhou, Yapeng Su, Yue Lu, Jami McLaughlin, Donghui Cheng, Owen N Witte, David Baltimore, Antoni Ribas, James R Heath.
Sensitive detection and analysis of neoantigen-specific T-cell populations from tumors and blood. Cell Reports, 28, 2728-2738. (2019) doi.org/10.1016/j.celrep.2019.07.106 |
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17. Alexander M Xu, Qianhe Liu, Kaitlyn Takata, Sarah Jeoung, Yapeng Su, Igor Antoshechkin, Sisi Chen, Matthew Thomson, James R Heath.
Integrated Measurement of Cytosolic Proteins and Transcripts in Single Cells. Lab on a Chip, 18, 3251-3262. (2018) doi.org/10.1039/C8LC00639C |
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16. *J Sander, *SV Schmidt, B Cirovic, N Mcgovern, O Papontanopoulou, A-L Hardt, AC Aschenbrenner, C Kreer, T Quast., Alexander M Xu, LM Schmidleithner,… NA Melosh, EW Nowell, F Ginhoux, A Schlitzer, JL Schultze.
Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2. Immunity, 47, 1051-1066. (2017) doi.org/10.1016/j.immuni.2017.11.024 |
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15. Alexander M Xu, Derek S Wang, Peyton Shieh, Yuhong Cao, Nicholas A Melosh.
Direct Intracellular Delivery of Cell-Impermeable Probes of Protein Glycosylation by Using Nanostraws. ChemBioChem, 18, 623-628. (2017) doi.org/10.1002/cbic.201600689 |
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14. Cade B Fox, Yuhong Cao, Cameron L Nemeth, Hariharasudhan D Chirra, Rachel W Chevalier, Alexander M Xu, Nicholas A Melosh, Tejal A Desai.
Fabrication of Sealed Nanostraw Microdevices for Oral Drug Delivery. ACS Nano, 10, 5873–5881. (2016) doi.org/10.1021/acsnano.6b00809 |
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13. Alexander M Xu, Sally A Kim, Derek S Wang, Amin Aalipour, Nicholas A Melosh.
Temporally Resolved Direct Delivery of Second Messengers into Cells Using Nanostraws. Lab on a Chip, 16, 2434-2439. (2016) doi.org/10.1039/c6lc00463f |
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2010-2015
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12. Amin Aalipour, Alexander M Xu, Sergio Leal-Ortiz, Craig C Garner, Nicholas A Melosh.
Plasma Membrane and Actin Cytoskeleton as Synergistic Barriers to Nanowire Cell Penetration. Langmuir, 30, 12362-12367. (2014) doi.org/10.1021/la502273f |
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11. Alexander M Xu, Amin Aalipour, Sergio Leal-Ortiz, Armen H Mekhdjian, Xi Xie, Alexander R Dunn, Craig C Garner, Nicholas A Melosh.
Quantification of Nanowire Penetration into Living Cells. Nature Communications, 5, 3613. (2014) doi.org/10.1038/ncomms4613 |
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10. Xi Xie, Alexander M Xu, Matthew R Angle, Noureddine Tayebi, Piyush Verma, Nicholas A Melosh.
Mechanical Model of Vertical Nanowire Cell Penetration. Nano Letters, 13, 6002-6008. (2013) doi.org/10.1021/nl403201a |
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9. Xi Xie, Alexander M Xu, Sergio Leal-Ortiz, Yuhong Cao, Craig C Garner, Nicholas A Melosh.
Nanostraw-Electroporation System for Highly Efficient Intracellular Delivery and Transfection. ACS Nano, 7, 4351-4358. (2013) doi.org/10.1021/nn400874a |
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8.Bryan Ronain Smith, Paul Kempen, Donna Bouley, Alexander Xu, Zhuang Liu, Nicholas Melosh, Hongjie Dai, Robert Sinclair, Sanjiv Sam Gambhir.
Shape Matters: Intravital Microscopy Reveals Surprising Geometrical Dependence for Nanoparticles in Tumor Models of Extravasation. Nano Letters, 12, 3369-3377. (2012) doi.org/10.1021/nl204175t |
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7. *Jules J VanDersarl, *Alexander M Xu, Nicholas A Melosh.
Nanostraws for Direct Fluidic Intracellular Access. Nano Letters, 12, 3881-3886. (2011) doi.org/10.1021/nl204051v |
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6. Jules J VanDersarl, Alexander M Xu, Nicholas A Melosh.
Rapid Spatial and Temporal Controlled Signal Delivery over Large Cell Culture Areas. Lab on a Chip, 11, 3057-3063. (2011) doi.org/10.1039/C1LC20311H |
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Before 2010
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5. Brian Neltner, Brian Peddie, Alex Xu, William Doenlen, Keith Durand, Dong Soo Yun, Scott Speakman, Andrew Peterson, Angela Belcher.
Production of Hydrogen using Nanocrystalline Protein-Templated Catalysts on M13 Phage. ACS Nano, 4, 3227-3235. (2010) doi.org/10.1021/nn100346h |
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4. Alexander M Xu, Paul H Huang.
Receptor Tyrosine Kinase Coactivation Networks in Cancer. Cancer Research, 70, 3587-3590. (2010) doi.org/10.1158/0008-5472.CAN-10-0163 |
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3. Paul H Huang, Emily R Miraldi, Alexander M Xu, Vibin A Kundukulam, Amanda M Del Rosario, Ryan A Flynn, Webster K Cavenee, Frank B Furnari, Forest M White.
Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth. Molecular Biosystems, 7, 1227-1237. (2010) doi.org/10.1039/c001196g |
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2. Paul H Huang, Alexander M Xu, Forest M White.
Oncogenic EGFR Signaling Networks in Glioma. Science Signaling, 2, 6. (2009) doi.org/10.1126/scisignal.287re6 |
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1. Melakeberhan, Haddish; Xu, Alex; Kravchenko, Alexandra; Mennan, Sevilhan; Riga, Ekaterini.
Potential use of arugula (Eruca sativa L.) as a trap crop for Meloidogyne hapla. Nematology, 8, 793-799. (2006) doi.org/10.1163/156854106778877884 |
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* - Co-First
† - Co-Corresponding
† - Co-Corresponding