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Tongjun Gu

Bioinformatics Assistant Scientist

(352) 273-8058
tgu@ufl.edu
191 CGRC

Bio

I received my B.S. on Biomedicine Engineering from Huazhong University of Science and Technology and Ph.D. on Bioinformatics from Institute of Biophysics Chinese Academy of Sciences in China. I did my Postdoc training in The Jackson Laboratory, where I developed pipelines and GWAS methods for studying the function and regulation of RNA editing in mouse populations. In addition, I made contribution to the field for the single point variants discovery from deep sequencing data and was invited to give talks at multiple professional conferences, such as Genome Informatics meeting at CSHL, 2nd generation sequencing meeting from GTC, and RNA Sciences in Cell and Developmental Biology II meeting from RIKEN CDB in Japan.

After my postdoc training, I worked at The University of Chicago on identifying key players in cancer development. Particularly, I played a leading role in the data analysis for two large projects (Chicago pancreatic cancer initiative and The Cancer Genome Atlas) and gained valuable experiences of handling samples of >2000 from getting the tumor tissue from patients to validating the data analysis results using PDX models and other experimental approaches.

In 2016, I moved to UF ICBR, where I perform consultation, experimental design and data analysis for researchers within UF and outside UF. I extended the scope of biological field beyond mouse and human, such as plants and bacteria. I also extended my data analysis skills beyond traditional machine learning and statistics, such as deep learning.

Skills and Specialization

  • Machine Learning and statistical modeling
  • Deep sequencing data analysis
  • Integrative data analysis, genome wide association analysis
  • Cancer, RNA editing, miRNA, mouse and human genetics, plants and bacteria

Selected Publications

  • T Gu, AQ Fu, MJ Bolt, X Zhao. (2020) Systematic identification of A-to-I editing associated regulators from multiple human cancers. Computers in Biology and Medicine, 103690.
  • T Gu, X Zhao, WB Barbazuk, JH Lee. (2020) miTAR: a hybrid deep learning-based approach for predicting miRNA targets. bioRxiv.
  • T Gu, X Zhao. (2019) Integrating multi-platform genomic datasets for kidney renal clear cell carcinoma subtyping using stacked denoising autoencoders. Scientific reports 9 (1), 1-11.
  • T Gu, AQ Fu, MJ Bolt, KP White. (2019) Clinical Relevance of non-coding A-to-I RNA Editing in Multiple Human Cancers. JCO clinical cancer informatics 3, 1-8.
  • Sheng, C. Fields, K. Aadland, T. Wei, O. Kolaczkowski, T. Gu, B. Kolaczkowski and M. Xie. (2018) Dicer cleaves 5′-extended microRNA precursors originating from RNA Polymerase II transcription start sites. Nucleic acids research 46 (11), 5737-5752.
  • Leah R Reznikov, Yan-Shin J Liao, Tongjun Gu, Katelyn M Davis, Shin-Ping Kuan, Kalina R Atanasova, Joshua S Dadural, Emily N Collins, Maria V Guevara, Kevin Vogt. (2018) Sex-specific airway hyperreactivity and sex-specific transcriptome remodeling in neonatal piglets challenged with intra-airway acid. Am J Physiol Lung Cell Mol Physiol 316: L131–L143.
  • SJ Ahn, T Gu, J Koh, KC Rice. (2017) Remodeling of the Streptococcus mutans proteome in response to LrgAB and external stresses. Scientific Reports 7, Article number: 14063.
  • KC Rice, ME Turner, VC O’neshia, T Gu, SJ Ahn. (2017) Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressor. MicroBial Genomics 2017 3.
  • Isabel Romcro Calvo, Ashwin Akki, Andrey Ugolkov, Mary M. Buschmann, Samantha M. Sparrow, Teresa Barry, Margaret Eber, Tongjun Gu, Shuang Qin Zhang, Hedy Kindler, William Dale, Kevin Roggin, Andrew P. Mazar, Kevin P. White, Christopher R. Weber. (2016) Organoids and patient-derived tumor xenograft of pancreatic adenocarcinoma share morphological and genetic feature with the primary tumor. AACR 2016: Abstracts 2697-5293: #4272.
  • 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. (2016) Genetic Architectures of Quantitative Variation in RNA Editing Pathways. Genetics 202, 787-798.
  • Gu T, Buaas FW, Simons AK, Ackert-Bicknell CL, Braun RE, et al. (2012) 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 7(3).
  • Tong J Gu, Xiang Yi, Xiwu Zhao, Yi Zhao, James Q. Yin. (2009) Alu-directed transcriptional regulation of some novel miRNAs. BMC Genomics, 10: 563.

Selected Presentations

  • 05/2020          2020 CSHL meeting on The Biology of Genomes
  • 10/2019           American Society Human Genetics meeting 2019
  • 11/2018            2018 Cold Spring Harbor Lab meeting on Biological Data Science
  • 10/2017           American Society Human Genetics meeting 2017
  • 07/2016           International Society for Computational Biology 2016
  • 01/2013            2013 Gordon Research Conferences on RNA editing
  • 06/2012           RNA Sciences in Cell and Developmental Biology II, The 22ndCDB Meeting, RIKEN CDB, Japan
  • 05/2012           2ndgeneration sequencing, GTC
  • 11/2011            2011 Cold Spring Harbor Laboratory meeting on Genome Informatics