Tongjun Gu PhD
Research Areas of Interest
BiostatisticsCarcinoma, Non-Small-Cell LungCarcinoma, Renal CellComputational BiologyEarly Detection of CancerEpigenomicsGeneticsGenetics, PopulationGenomicsHuman GeneticsLeukemiaLeukemia, Megakaryoblastic, AcuteLeukemia, Monocytic, AcuteLeukemia, MyeloidMachine LearningRNARegulatory Sequences, Nucleic AcidResearch Experience
Computational BiologyMethodologies and Techniques
Computational BiologyLeadership Positions
Leader, Bioinformatics CoreEducational Expertise
Computational BiologyPublications (40)
Platelet glycosylation in myelodysplastic syndromes correlates with disease severity 07/11/2025 Platelet glycosylation in myelodysplastic syndromes correlates with disease severity. (Rosenbalm KE, Wong TL, Hoang D, Andersen VL, Steinhardt G, Zheng S, Griffiths EA, Gu T, Hoffmeister KM, Lau JTY, Nemeth MJ) Blood Adv 2025 Sep 23;9(18):4656-4660 PMID: 40644615 PMCID: PMC12496252 SCOPUS ID: 2-s2.0-105015731888 07/11/2025 The small GTPase ARF6 regulates sphingolipid homeostasis and supports proliferation in acute myeloid leukemia 07/10/2025 Targeting immune checkpoint LAIR1 with antibody blockade or 3-in-1 CAR T cells enhances antitumor response. (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) J Clin Invest 2025 Aug 15;135(16) PMID: 40591413 PMCID: PMC12352909 SCOPUS ID: 2-s2.0-105013808661 07/01/2025 3 CitationsBrain 5-hydroxymethylcytosine alterations are associated with Alzheimer's disease neuropathology. (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) Nat Commun 2025 Mar 22;16(1):2842 PMID: 40121201 PMCID: PMC11929800 SCOPUS ID: 2-s2.0-105000708928 03/23/2025 10 CitationsKRAS mutants confer platinum resistance by regulating ALKBH5 posttranslational modifications in lung cancer. (Yu F, Zheng S, Yu C, Gao S, Shen Z, Nar R, Liu Z, Huang S, Wu L, Gu T, Qian Z) J Clin Invest 2025 Feb 04;135(6) PMID: 39960727 PMCID: PMC11910214 SCOPUS ID: 2-s2.0-105001221945 02/17/2025 18 CitationsProthrombotic antibodies targeting the spike protein's receptor-binding domain in severe COVID-19. (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) Blood 2025 Feb 06;145(6):635-647 PMID: 39576992 PMCID: PMC11811936 SCOPUS ID: 2-s2.0-85214228692 11/22/2024 4 CitationsLiver Characterization of a Cohort of Alpha-1 Antitrypsin Deficiency Patients with and without Lung Disease. (Mohammad N, Oshins R, Gu T, Clark V, Lascano J, Assarzadegan N, Marek G, Brantly M, Khodayari N) J Clin Transl Hepatol 2024 Oct 28;12(10):845-856 PMID: 39440224 PMCID: PMC11491504 SCOPUS ID: 2-s2.0-85207494093 10/23/2024 4 CitationsIdentification of tumor rejection antigens and the immunologic landscape of medulloblastoma. (Yang C, Trivedi V, Dyson K, Gu T, Candelario KM, Yegorov O, Mitchell DA) Genome Med 2024 Aug 19;16(1):102 PMID: 39160595 PMCID: PMC11331754 SCOPUS ID: 2-s2.0-85201551538 08/20/2024 4 CitationsDistinctive genes and signaling pathways associated with type 2 diabetes-related periodontitis: Preliminary study. (Duarte PM, Gurgel BCV, Miranda TS, Sardenberg J, Gu T, Aukhil I) PLoS One 2024;19(1):e0296925 PMID: 38241313 PMCID: PMC10798476 SCOPUS ID: 2-s2.0-85182863661 01/19/2024 1 CitationInvestigating miR-9 as a mediator in laryngeal cancer health disparities. (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) Front Oncol 2023;13:1096882 PMID: 37081981 PMCID: PMC10112398 SCOPUS ID: 2-s2.0-85153496865 04/21/2023 5 CitationsDevelopment of Human Adrenocortical Adenoma (HAA1) Cell Line from Zona Reticularis. (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) Int J Mol Sci 2022 Dec 29;24(1) PMID: 36614027 PMCID: PMC9820690 SCOPUS ID: 2-s2.0-85145969165 01/09/2023 2 CitationsTranscriptional profiling of two muscadine grape cultivars "Carlos" and "Noble" to reveal new genes, gene regulatory networks, and pathways that involved in grape berry ripening. (Chang Y, Ahlawat YK, Gu T, Sarkhosh A, Liu T) Front Plant Sci 2022;13:949383 PMID: 36061784 PMCID: PMC9435441 SCOPUS ID: 2-s2.0-85137763252 09/06/2022 3 CitationsFine-mapping and replication of EWAS loci harboring putative epigenetic alterations associated with AD neuropathology in a large collection of human brain tissue samples. (Palma-Gudiel H, Yu L, Huo Z, Yang J, Wang Y, Gu T, Gao C, De Jager PL, Jin P, Bennett DA, Zhao J) Alzheimers Dement 2023 Apr;19(4):1216-1226 PMID: 35959851 PMCID: PMC9922334 SCOPUS ID: 2-s2.0-85135911457 08/13/2022 8 CitationsSequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a. (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) PLoS Genet 2021 Dec;17(12):e1009934 PMID: 34914716 PMCID: PMC8675727 SCOPUS ID: 2-s2.0-85121763186 12/17/2021 15 CitationsBiological features between miRNAs and their targets are unveiled from deep learning models. (Gu T, Xie M, Barbazuk WB, Lee JH) Sci Rep 2021 Dec 10;11(1):23825 PMID: 34893648 PMCID: PMC8664955 SCOPUS ID: 2-s2.0-85120986190 12/12/2021 8 CitationsmiTAR: a hybrid deep learning-based approach for predicting miRNA targets. (Gu T, Zhao X, Barbazuk WB, Lee JH) BMC Bioinformatics 2021 Feb 27;22(1):96 PMID: 33639834 PMCID: PMC7912887 SCOPUS ID: 2-s2.0-85101814272 03/01/2021 36 CitationsGenomic and Targeted Approaches Unveil the Cell Membrane as a Major Target of the Antifungal Cytotoxin Amantelide A. (Elsadek LA, Matthews JH, Nishimura S, Nakatani T, Ito A, Gu T, Luo D, Salvador-Reyes LA, Paul VJ, Kakeya H, Luesch H) Chembiochem 2021 May 14;22(10):1790-1799 PMID: 33527693 PMCID: PMC8220859 SCOPUS ID: 2-s2.0-85103276944 02/03/2021 12 CitationsTransfer of oral bacteria to the fetus during late gestation. (Yu K, Rodriguez M, Paul Z, Gordon E, Gu T, Rice K, Triplett EW, Keller-Wood M, Wood CE) Sci Rep 2021 Jan 12;11(1):708 PMID: 33436911 PMCID: PMC7804304 SCOPUS ID: 2-s2.0-85099202903 01/14/2021 9 CitationsSystematic identification of A-to-I editing associated regulators from multiple human cancers. (Gu T, Fu AQ, Bolt MJ, Zhao X) Comput Biol Med 2020 Apr;119:103690 PMID: 32339124 SCOPUS ID: 2-s2.0-85080981006 04/28/2020 2 CitationsAuthor Correction: Integrating multi-platform genomic datasets for kidney renal clear cell carcinoma subtyping using stacked denoising autoencoders. (Gu T, Zhao X) Sci Rep 2019 Dec 19;9(1):19821 PMID: 31852923 PMCID: PMC6920134 SCOPUS ID: 2-s2.0-85076923314 12/20/2019 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. 12/01/2019 Integrating multi-platform genomic datasets for kidney renal clear cell carcinoma subtyping using stacked denoising autoencoders. (Gu T, Zhao X) Sci Rep 2019 Nov 13;9(1):16668 PMID: 31723226 PMCID: PMC6853929 SCOPUS ID: 2-s2.0-85074960051 11/15/2019 11 CitationsClinical Relevance of Noncoding Adenosine-to-Inosine RNA Editing in Multiple Human Cancers. (Gu T, Fu AQ, Bolt MJ, White KP) JCO Clin Cancer Inform 2019 Jun;3:1-8 PMID: 31162949 PMCID: PMC6874002 SCOPUS ID: 2-s2.0-85077481605 06/05/2019 10 CitationsSex-specific airway hyperreactivity and sex-specific transcriptome remodeling in neonatal piglets challenged with intra-airway acid. (Reznikov LR, Liao YSJ, Gu T, Davis KM, Kuan SP, Atanasova KR, Dadural JS, Collins EN, Guevara MV, Vogt K) Am J Physiol Lung Cell Mol Physiol 2019 Jan 01;316(1):L131-L143 PMID: 30407862 PMCID: PMC6383496 SCOPUS ID: 2-s2.0-85059227590 11/09/2018 8 CitationsSpiny 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. 10/03/2018 Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites. (Sheng P, Fields C, Aadland K, Wei T, Kolaczkowski O, Gu T, Kolaczkowski B, Xie M) Nucleic Acids Res 2018 Jun 20;46(11):5737-5752 PMID: 29746670 PMCID: PMC6009592 SCOPUS ID: 2-s2.0-85056904755 05/11/2018 54 CitationsRemodeling of the Streptococcus mutans proteome in response to LrgAB and external stresses. (Ahn SJ, Gu T, Koh J, Rice KC) Sci Rep 2017 Oct 25;7(1):14063 PMID: 29070798 PMCID: PMC5656683 SCOPUS ID: 2-s2.0-85032260643 10/27/2017 19 CitationsGSR is not essential for the maintenance of antioxidant defenses in mouse cochlea: Possible role of the thioredoxin system as a functional backup for GSR. (Han C, Kim MJ, Ding D, Park HJ, White K, Walker L, Gu T, Tanokura M, Yamasoba T, Linser P, Salvi R, Someya S) PLoS One 2017;12(7):e0180817 PMID: 28686716 PMCID: PMC5501606 SCOPUS ID: 2-s2.0-85022324447 07/08/2017 28 CitationsModification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors. (Rice KC, Turner ME, Carney OV, Gu T, Ahn SJ) Microb Genom 2017 Feb;3(2):e000104 PMID: 28348880 PMCID: PMC5361627 03/30/2017 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_Supplement): 4272. 07/15/2016 Genetic Architectures of Quantitative Variation in RNA Editing Pathways. (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) Genetics 2016 Feb;202(2):787-98 PMID: 26614740 PMCID: PMC4788250 SCOPUS ID: 2-s2.0-84979884843 11/29/2015 19 CitationsDeregulated sex chromosome gene expression with male germ cell-specific loss of Dicer1. (Greenlee AR, Shiao MS, Snyder E, Buaas FW, Gu T, Stearns TM, Sharma M, Murchison EP, Puente GC, Braun RE) PLoS One 2012;7(10):e46359 PMID: 23056286 PMCID: PMC3464243 SCOPUS ID: 2-s2.0-84867126724 10/12/2012 44 CitationsPla2g12b and Hpn are genes identified by mouse ENU mutagenesis that affect HDL cholesterol. (Aljakna A, Choi S, Savage H, Hageman Blair R, Gu T, Svenson KL, Churchill GA, Hibbs M, Korstanje R) PLoS One 2012;7(8):e43139 PMID: 22912808 PMCID: PMC3422231 SCOPUS ID: 2-s2.0-84865097380 08/23/2012 20 CitationsCanonical A-to-I and C-to-U RNA editing is enriched at 3'UTRs and microRNA target sites in multiple mouse tissues. (Gu T, Buaas FW, Simons AK, Ackert-Bicknell CL, Braun RE, Hibbs MA) PLoS One 2012;7(3):e33720 PMID: 22448268 PMCID: PMC3308996 SCOPUS ID: 2-s2.0-84858682499 03/27/2012 69 CitationsAlu-directed transcriptional regulation of some novel miRNAs. (Gu TJ, Yi X, Zhao XW, Zhao Y, Yin JQ) BMC Genomics 2009 Nov 30;10:563 PMID: 19943974 PMCID: PMC3087558 SCOPUS ID: 2-s2.0-73149098353 12/01/2009 44 CitationsA novel class of endogenous shRNAs in human cells. Gu, T., Yin, J., Xu, Y. et al. Nat Prec (2008). 01/23/2008 Shape representation and invariant description of protein tertiary structure in applications to shape retrieval and classification (Xu D, Li H, Gu T) Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics 2008;4975 LNCS:556-562 SCOPUS ID: 2-s2.0-70349303355 01/01/2008 3 CitationsCommon substructure extraction of proteins by geometric invariants (Xu D, Li H, Gu T) Proceedings of 2007 10th IEEE International Conference on Computer Aided Design and Computer Graphics CAD Graphics 2007 2007:86-91 SCOPUS ID: 2-s2.0-48149087561 12/01/2007 Protein structure superposition by curve moment invariants and iterative closest point (Xu D, Li H, Gu T) 2007 1st International Conference on Bioinformatics and Biomedical Engineering Icbbe 2007:25-28 SCOPUS ID: 2-s2.0-35348834247 10/23/2007 2 Citations
© 2026 Clinical & Translational Science Institute