CURRICULUM VITAE
Tongjun Gu PhD
Tongjun Gu PhD
Associate Investigator
Department of Hematopoiesis & Stem Cell Biology
Department of Hematopoiesis & Stem Cell Biology
OFFICE ADDRESS: |
EDUCATION: |
09/2000 - 06/2004 BS, Huazhong University of Science and Technology (HUST), Wuhan, China |
09/2004 - 06/2009 PhD, Institute of Biophysics, Chinese Academy of Sciences, Beijing |
POSTGRADUATE TRAINING AND FELLOWSHIP APPOINTMENTS: |
01/2010 - 09/2013 Postdoctoral Fellow, The Jackson Laboratory, Bar Harbor, ME |
09/2013 - 01/2016 Postdoc and Research Professional, The University of Chicago, Chicago, IL |
FACULTY APPOINTMENTS: |
01/2016 - 06/2023 Assistant Scientist, Interdisciplinary Center for Biotechnology Research (ICBR), Bioinformatics Group, University of Florida, Gainesville, FL |
01/2019 - 09/2023 Member, Biostatistics and Computational Biology, Division of Quantitative Sciences, University of Florida Health Cancer Center (UFHCC), Gainesville, FL |
01/2022 - 09/2023 Member, Center For Genetic Epidemiology and Bioinformatics (GeneBio), University of Florida, Gainesville, FL |
02/2022 - Present Courtesy Faculty, Department of Biostatistics, University of Florida, Gainesville, FL |
06/2023 - 09/2023 Associate Scientist, Interdisciplinary Center for Biotechnology Research (ICBR), Bioinformatics Group, University of Florida, Gainesville, FL |
09/2023 - Present Associate Investigator / Director, Bioinformatics Core, Versiti Blood Research Institute, Milwaukee, WI |
09/2024 - Present Adjunct Assistant Professor, Data Science Institute, Medical College of Wisconsin, Milwaukee, WI |
AWARDS AND HONORS: |
2000 - 2003 Outstanding student of School of Life Science and Technology, HUST, Wuhan, China |
2007 - 2008 Outstanding student of Chinese Academy of Sciences, Beijing, China |
2012 - 2014 The Jackson Lab Postdoc Fellowship (top 2; including one travel fellowship per year), Bar Harbor, ME, USA |
2012 Travel fellowship from RIKEN CDB, Japan |
2017 Reviewers' Choice Abstracts from American Society of Human Genetics (ASHG) meeting |
MEMBERSHIPS IN HONORARY AND PROFESSIONAL SOCIETIES: |
2010 - 2011 International Society for Computational Biology (Member) |
2016 - Present International Society for Computational Biology (Member) |
2017 - 2022 American Society of Human Genetics (Member) |
12/2023 - Present American Society of Hematology (ASH) (Member) |
EDITORSHIPS/EDITORIAL BOARDS/JOURNAL REVIEWS: |
Editorial Board |
2018 - Present Bioinformatics and Computational Biology, part of the journal(s) Frontiers in Genetics, Plant Science and Bioengineering and Biotechnology |
Journal Review |
2018 - Present Frontiers |
2018 - Present Cellular and Molecular Life Sciences |
2018 - Present Cell Reports Methods |
2018 - Present Briefings In Bioinformatics |
2018 - Present PLOS Genetics |
2018 - Present Bioinformatics |
2018 - Present International Journal of Molecular Sciences |
2018 - Present IEEE |
2018 - Present JCO Clinical Cancer Informatics |
2018 - Present Scientific Reports |
2018 - Present Current Bioinformatics |
2025 - Present Haematologica |
2025 - Present Blood Vessels, Thrombosis & Hemostasis |
LOCAL/REGIONAL APPOINTED LEADERSHIP AND COMMITTEE POSITIONS: |
2020 Member, AI Collaborative, University of Florida |
2020 Member, AI Initiative Committee, University of Florida Health Cancer Center |
2020 Member, AI Working Group, University of Florida Health Cancer Center |
2022 Member, Search Committee for the Director of NextGen DNA Sequencing Core, University of Florida |
2022 Reviewer, AI Supplement Grant Applications, University of Florida |
2022 Reviewer, Special Pilot Grant on utilizing Oxford Nanopore Technology, University of Florida |
2023 Member, Faculty Search Committee, Stem Cell and Hematopoiesis Program, Versiti Blood Research Institute |
2023 Reviewer, AI Supplement Grant Applications, University of Florida |
2024 Member, Endowed Chair Search Committee, Stem Cell and Hematopoiesis Program, Versiti Blood Research Institute |
2025 Member, Endowed Chair Search Committee, Hematopoiesis and Immunology Program, Versiti Blood Research Institute |
2025 - Present Co-chair, Director of Shared Resources Search Committee, Versiti Blood Research Institute |
2025 - Present Co-chair, Hematopoiesis Program Annual Symposium, Versiti Blood Research Institute |
RESEARCH GRANTS/AWARDS/CONTRACTS/PROJECTS: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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INVITED LECTURES/WORKSHOPS/PRESENTATIONS: |
International |
RNA Sciences in Cell and Developmental Biology II, The 22nd CDB Meeting, RIKEN CDB, Japan, 06/2012 |
National |
Invited Talk, 2011 CSHL meeting on Genome Informatics, 11/2011 |
Invited Talk, 2nd Generation Sequencing, GTC, 05/2012 |
Invited Talk, Institute for Genomics & Systems Biology, University of Chicago, 03/2013 |
Genetic Architectures of Quantitative Variation in RNA Editing Pathways., Intelligent Systems for Molecular Biology (ISMB) 2016, 07/2016 |
Clinical relevance of non-coding A-to-I RNA editing in multiple human cancers., American Society of Human Genetics (ASHG) meeting 2017, 10/2017 |
Integrating multi-platform genomic datasets for cancer subtype discovery using denoising autoencoders., 2018 Cold Spring Harbor Lab (CSHL) meeting on Biological Data Science, 11/2018 |
Brain 5-hydroxymethylcytosine (5hmC) and Alzhermer’s Disease., 13th Annual Rush Alzheimer’s Disease Center ROSMAP Investigator’s Meeting, 07/2022 |
Deep Learning advances omics data analysis for precision medicine., University of Texas at San Antonio, San Antonio, TX, 02/2023 |
Deep Learning---an advanced machine learning algorithm in Artificial Intelligence--- advances biological research, VBRI Annual Retreat, Milwaukee, WI, 05/2023 |
Local |
Invited Talk, The Jackson Laboratory, 06/2011 |
Deep Learning-an emerging Machine Learning algorithm in Artificial Intelligence-advances cancer study., University of Florida Health Cancer Center, 04/2021 |
miTAR: an interpretable deep learning-based approach for predicting miRNA targets., AI Day for Cancer Research, University of Florida Health Cancer Center, 09/2021 |
An interpretable deep learning-based approach for miRNA target prediction., Scientific Retreat for PREDICTION MODEL DEVELOPMENTS with Statistical, AI, and Mathematical Approaches, Division of Quantitative Sciences, University of Florida Health Cancer Center, 12/2021 |
Presentation, Immunology Research Roundtable: VBRI Bioinformatics Core, 10/2024 |
Bioinformatics and Resources, MCW Advanced Immunology class, 12/2024 |
Introduction to Artificial Intelligence and Its Applications in Biological Research., VBRI Seminar, 02/2025 |
Single Cell RNA Editing in Leukemia, VBRI Seminar, 04/2025 |
COMMITTEE SERVICE: |
Medical College of Wisconsin |
2023 Member, Faculty Search Committee of the Stem Cell and Hematopoiesis Program, Versiti Blood Research Institute |
2024 Member, Endowed Chair Search Committee of the Stem Cell and Hematopoiesis Program, Versiti Blood Research Institute |
2025 Member, Endowed Chair Search Committee, Hematopoiesis and Immunology Program, Versiti Blood Research Institute |
2025 Co-Chair, Director of Shared Resources Search Committee, Versiti Blood Research Institute |
2025 Co-Chair, Hematopoiesis Program Annual Symposium, Versiti Blood Research Institute |
Hospital |
2020 Member, AI Working Group, University of Florida Health Cancer Center |
2020 Member, AI Collaborative, University of Florida |
2020 Member, AI Initiative Committee, University of Florida Health Cancer Center |
2022 Reviewer, Special Pilot Grant on Utilizing Oxford Nanopore Technology, University of Florida |
2022 Member, Search Committee for the Director of NextGen DNA Sequencing, University of Florida |
2022 Reviewer, AI Supplement Grant Applications, University of Florida |
2023 Reviewer, AI Supplement Grant Applications, University of Florida |
MCW TEACHING ACTIVITIES: |
Graduate Student Education |
12/2024 Lecturer, Advanced Immunology Class |
MCW STUDENTS, FACULTY, RESIDENTS AND CLINICAL/RESEARCH FELLOWS MENTORED: |
Graduate Students |
PhD Committees |
Chris Hansen's Dissertation committee member, Medical College of Wisconsin |
MPh Committees |
Kimani Njoya's Thesis Committee Member, Medical College of Wisconsin |
EXTRAMURAL STUDENTS, FACULTY, RESIDENTS, AND CLINICAL/RESEARCH FELLOWS MENTORED: |
Graduate Students |
MA Committees |
2016 - 2021 Performed numerous trainings to a small group of researchers from undergraduate students, graduate students, Postdocs to junior faculties for NGS data analysis or developing pipelines or statistical analysis, University of Florida |
Postdoctoral Researchers |
06/2024 - Present Nisansala Wickramasinghe, Versiti Blood Research Institute |
06/2025 Hasini Gammune, Versiti Blood Research Institute |
PROGRAMMATIC DEVELOPMENTS: |
Educational Programs |
Faculty |
2025 Lunch & Learn Series on AI Awareness |
Research Programs |
2025 Co-chair, Hematopoiesis Program Annual Symposium |
BIBLIOGRAPHY |
Refereed Journal Publications/Original Papers |
1. Xu D, Li H, Gu T. Protein structure superposition by curve moment invariants and iterative closest point 2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE. 2007:25-28. |
2. Xu D, Li H, Gu T. Common substructure extraction of proteins by geometric invariants Proceedings of 2007 10th IEEE International Conference on Computer Aided Design and Computer Graphics, CAD/Graphics 2007. 2007:86-91. |
3. Xu D, Li H, Gu T. Shape representation and invariant description of protein tertiary structure in applications to shape retrieval and classification Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2008;4975 LNCS:556-562. |
4. . A novel class of endogenous shRNAs in human cells. . Gu, T., Yin, J., Xu, Y. et al. Nat Prec (2008). . |
5. Gu TJ, Yi X, Zhao XW, Zhao Y, Yin JQ. Alu-directed transcriptional regulation of some novel miRNAs. BMC Genomics. 2009 Nov 30;10:563. PMCID: PMC3087558 |
6. Gu T, Buaas FW, Simons AK, Ackert-Bicknell CL, Braun RE, Hibbs MA. Canonical A-to-I and C-to-U RNA editing is enriched at 3'UTRs and microRNA target sites in multiple mouse tissues. PLoS One. 2012;7(3):e33720. PMCID: PMC3308996 |
7. Aljakna A, Choi S, Savage H, Hageman Blair R, Gu T, Svenson KL, Churchill GA, Hibbs M, Korstanje R. Pla2g12b and Hpn are genes identified by mouse ENU mutagenesis that affect HDL cholesterol. PLoS One. 2012;7(8):e43139. PMCID: PMC3422231 |
8. Greenlee AR, Shiao MS, Snyder E, Buaas FW, Gu T, Stearns TM, Sharma M, Murchison EP, Puente GC, Braun RE. Deregulated sex chromosome gene expression with male germ cell-specific loss of Dicer1. PLoS One. 2012;7(10):e46359. PMCID: PMC3464243 |
9. Gu T, Gatti DM, Srivastava A, Snyder EM, Raghupathy N, Simecek P, Svenson KL, Dotu I, Chuang JH, Keller MP, Attie AD, Braun RE, Churchill GA. Genetic Architectures of Quantitative Variation in RNA Editing Pathways. Genetics. 2016 Feb;202(2):787-98. PMCID: PMC4788250 |
10. . Abstract 4272: Organoids and patient-derived tumor xenograft of pancreatic adenocarcinoma share morphological and genetic features with the primary tumor. . IR Calvo, A Akki, A Ugolkov, MM Buschmann, SM Sparrow, T Barry, M Eber, T Gu, SQ Zhang, H Kindler, W Dale, K Roggin, AP Mazar, KP White, CR Weber. Cancer Res 15 July 2016; 76 (14_S. |
11. Rice KC, Turner ME, Carney OV, Gu T, Ahn SJ. Modification of the <i>Streptococcus mutans</i> transcriptome by LrgAB and environmental stressors. Microb Genom. 2017 Feb;3(2):e000104. PMCID: PMC5361627 |
12. Han C, Kim MJ, Ding D, Park HJ, White K, Walker L, Gu T, Tanokura M, Yamasoba T, Linser P, Salvi R, Someya S. GSR is not essential for the maintenance of antioxidant defenses in mouse cochlea: Possible role of the thioredoxin system as a functional backup for GSR. PLoS One. 2017;12(7):e0180817. PMCID: PMC5501606 |
13. Ahn SJ, Gu T, Koh J, Rice KC. Remodeling of the Streptococcus mutans proteome in response to LrgAB and external stresses. Sci Rep. 2017 Oct 25;7(1):14063. PMCID: PMC5656683 |
14. Sheng P, Fields C, Aadland K, Wei T, Kolaczkowski O, Gu T, Kolaczkowski B, Xie M. Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites. Nucleic Acids Res. 2018 Jun 20;46(11):5737-5752. PMCID: PMC6009592 |
15. . Spiny mouse is protected from ischemia induced cardiac injury: leading role of microRNAs. . Qi, Y., Goel, R., Mandloi, A.S., Vohra, R., Walter, G., Joshua, Y., Gu, T., Katovich, M.J., Aranda, J.M., Maden, M., Raizada, M.K., & Pepine, C.J. (2017). The FASEB Journal, 31.. |
16. Reznikov LR, Liao YSJ, Gu T, Davis KM, Kuan SP, Atanasova KR, Dadural JS, Collins EN, Guevara MV, Vogt K. Sex-specific airway hyperreactivity and sex-specific transcriptome remodeling in neonatal piglets challenged with intra-airway acid. Am J Physiol Lung Cell Mol Physiol. 2019 Jan 01;316(1):L131-L143. PMCID: PMC6383496 |
17. Gu T, Fu AQ, Bolt MJ, White KP. Clinical Relevance of Noncoding Adenosine-to-Inosine RNA Editing in Multiple Human Cancers. JCO Clin Cancer Inform. 2019 Jun;3:1-8. PMCID: PMC6874002 |
18. Gu T, Zhao X. Integrating multi-platform genomic datasets for kidney renal clear cell carcinoma subtyping using stacked denoising autoencoders. Sci Rep. 2019 Nov 13;9(1):16668. PMCID: PMC6853929 |
19. . Streamlining DNA Sequencing and Bioinformatics Analysis Using Software Containers . (Riva A, Boatwright JL, Gu T, Yu F, Barbazuk WB.) J Biomol Tech. 2019 Dec;30(Suppl):S38–9. PMCID: PMC6938045.. |
20. Gu T, Zhao X. Author Correction: Integrating multi-platform genomic datasets for kidney renal clear cell carcinoma subtyping using stacked denoising autoencoders. Sci Rep. 2019 Dec 19;9(1):19821. PMCID: PMC6920134 |
21. Gu T, Fu AQ, Bolt MJ, Zhao X. Systematic identification of A-to-I editing associated regulators from multiple human cancers. Comput Biol Med. 2020 Apr;119:103690. |
22. Yu K, Rodriguez M, Paul Z, Gordon E, Gu T, Rice K, Triplett EW, Keller-Wood M, Wood CE. Transfer of oral bacteria to the fetus during late gestation. Sci Rep. 2021 Jan 12;11(1):708. PMCID: PMC7804304 |
23. Elsadek LA, Matthews JH, Nishimura S, Nakatani T, Ito A, Gu T, Luo D, Salvador-Reyes LA, Paul VJ, Kakeya H, Luesch H. Genomic and Targeted Approaches Unveil the Cell Membrane as a Major Target of the Antifungal Cytotoxin Amantelide A. Chembiochem. 2021 May 14;22(10):1790-1799. PMCID: PMC8220859 |
24. Gu T, Zhao X, Barbazuk WB, Lee JH. miTAR: a hybrid deep learning-based approach for predicting miRNA targets. BMC Bioinformatics. 2021 Feb 27;22(1):96. PMCID: PMC7912887 |
25. Gu T, Xie M, Barbazuk WB, Lee JH. Biological features between miRNAs and their targets are unveiled from deep learning models. Sci Rep. 2021 Dec 10;11(1):23825. PMCID: PMC8664955 |
26. Fields CJ, Li L, Hiers NM, Li T, Sheng P, Huda T, Shan J, Gay L, Gu T, Bian J, Kilberg MS, Renne R, Xie M. Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a. PLoS Genet. 2021 Dec;17(12):e1009934. PMCID: PMC8675727 |
27. Palma-Gudiel H, Yu L, Huo Z, Yang J, Wang Y, Gu T, Gao C, De Jager PL, Jin P, Bennett DA, Zhao J. Fine-mapping and replication of EWAS loci harboring putative epigenetic alterations associated with AD neuropathology in a large collection of human brain tissue samples. Alzheimers Dement. 2023 Apr;19(4):1216-1226. PMCID: PMC9922334 |
28. Chang Y, Ahlawat YK, Gu T, Sarkhosh A, Liu T. Transcriptional profiling of two muscadine grape cultivars "Carlos" and "Noble" to reveal new genes, gene regulatory networks, and pathways that involved in grape berry ripening. Front Plant Sci. 2022;13:949383. PMCID: PMC9435441 |
29. Ghayee HK, Xu Y, Hatch H, Brockway R, Multani AS, Gu T, Bollag WB, Turcu A, Rainey WE, Rege J, Nanba K, Bhagwandin VJ, Nwariaku F, Stastny V, Gazdar AF, Shay JW, Auchus RJ, Tevosian SG. Development of Human Adrenocortical Adenoma (HAA1) Cell Line from Zona Reticularis. Int J Mol Sci. 2022 Dec 29;24(1). PMCID: PMC9820690 |
30. Gobin C, Inkabi S, Lattimore CC, Gu T, Menefee JN, Rodriguez M, Kates H, Fields C, Bian T, Silver N, Xing C, Yates C, Renne R, Xie M, Fredenburg KM. Investigating miR-9 as a mediator in laryngeal cancer health disparities. Front Oncol. 2023;13:1096882. PMCID: PMC10112398 |
31. Duarte PM, Gurgel BCV, Miranda TS, Sardenberg J, Gu T, Aukhil I. Distinctive genes and signaling pathways associated with type 2 diabetes-related periodontitis: Preliminary study. PLoS One. 2024;19(1):e0296925. PMCID: PMC10798476 |
32. Yang C, Trivedi V, Dyson K, Gu T, Candelario KM, Yegorov O, Mitchell DA. Identification of tumor rejection antigens and the immunologic landscape of medulloblastoma. Genome Med. 2024 Aug 19;16(1):102. PMCID: PMC11331754 |
33. Mohammad N, Oshins R, Gu T, Clark V, Lascano J, Assarzadegan N, Marek G, Brantly M, Khodayari N. Liver Characterization of a Cohort of Alpha-1 Antitrypsin Deficiency Patients with and without Lung Disease. J Clin Transl Hepatol. 2024 Oct 28;12(10):845-856. PMCID: PMC11491504 |
34. Zhu W, Zheng Y, Yu M, Witman N, Zhou L, Wei J, Zhang Y, Topchyan P, Nguyen C, Wang D, Janecke R, Padmanabhan A, Baumann Kreuziger L, White GC, Hari P, Gu T, Fields AT, Kornblith LZ, Aster R, Zhu J, Cui W, Jobe S, Graham MB, Wang D, Wen R. Prothrombotic antibodies targeting the spike protein's receptor-binding domain in severe COVID-19. Blood. 2025 Feb 06;145(6):635-647. PMCID: PMC11811936 |
35. Yu F, Zheng S, Yu C, Gao S, Shen Z, Nar R, Liu Z, Huang S, Wu L, Gu T, Qian Z. KRAS mutants confer platinum resistance by regulating ALKBH5 posttranslational modifications in lung cancer. J Clin Invest. 2025 Feb 04;135(6). PMCID: PMC11910214 |
36. Zhao J, Gu T, Gao C, Miao G, Palma-Gudiel H, Yu L, Yang J, Wang Y, Li Y, Lim J, Li R, Yao B, Wu H, Schneider JA, Seyfried N, Grodstein F, De Jager PL, Jin P, Bennett DA. Brain 5-hydroxymethylcytosine alterations are associated with Alzheimer's disease neuropathology. Nat Commun. 2025 Mar 22;16(1):2842. PMCID: PMC11929800 |
37. Tao H, Chen D, Yang C, Nguyen DT, Abboud G, Liu R, Liu T, Chakraborty A, Hou AY, Petit NA, Abbas M, Davis RW, Zhang J, Von Roemeling C, Gbadamosi MO, Jin L, Gu T, Lin T, Wang P, Pepe A, Pedro DI, Mendez-Gomez HR, Xie C, Karachi A, Weidert F, Jin D, Wang C, Long-James K, Molchan EK, Castillo P, Ligon JA, Ghiaseddin AP, Sayour EJ, Rahman M, Deleyrolle LP, Kim BY, Mitchell DA, Sawyer WG, Huang J. Targeting immune checkpoint LAIR1 with antibody blockade or 3-in-1 CAR T cells enhances antitumor response. J Clin Invest. 2025 Aug 15;135(16). PMCID: PMC12352909 |
38. Tao H, Chen D, Yang C, Nguyen DT, Abboud G, Liu R, Liu T, Chakraborty A, Hou AY, Petit NA, Abbas M, Davis RW, Zhang J, Von Roemeling C, Gbadamosi MO, Jin L, Gu T, Lin T, Wang P, Pepe A, Pedro DI, Mendez-Gomez HR, Xie C, Karachi A, Weidert F, Jin D, Wang C, Long-James K, Molchan EK, Castillo P, Ligon JA, Ghiaseddin AP, Sayour EJ, Rahman M, Deleyrolle LP, Kim BY, Mitchell DA, Sawyer WG, Huang J. Targeting immune checkpoint LAIR1 with antibody blockade or 3-in-1 CAR T cells enhances antitumor response. J Clin Invest. 2025 Aug 15;135(16). PMCID: PMC12352909 |
39. Rosenbalm KE, Wong TL, Hoang D, Andersen VL, Steinhardt G, Zheng S, Griffiths EA, Gu T, Hoffmeister KM, Lau JTY, Nemeth MJ. Platelet glycosylation in myelodysplastic syndromes correlates with disease severity. Blood Adv. 2025 Sep 23;9(18):4656-4660. PMCID: PMC12496252 |
