My research

I have worked on various topics from human pigmentation to leukemia. During my undergraduate studies, I worked as a research assistant in two computational biology groups for two years (2010-2011) simultaneously. I have worked on various topics in biomedical research including microRNAs, genetic variation, protein disorder, gene expression regulation, and multiple specificity of peptide recognition domains. Through these projects, I gained extensive experience on various scientific analysis including NGS data analyses and algorithm development.

As of October 2014, I started my PhD studies at the Computational Biology group within the Department of Computer Science in the University of Toronto. My supervisor is Dr. Zhaolei Zhang and I am majorly interested in:

  • Mining genetic patterns from serial samples to predict disease recurrence and understand their clinical relevance
  • Development of NGS-based assays/models for detecting measurable residual disease in hematologic malignancies/liquid biopsy
  • Development of time-dependent risk-classification systems based on genomic and clinical features
  • Variant and fusion detection algorithms

    • Publications (first/co-first)


    Journals
  • Kim T, Tyndel MS, Huang H, Sidhu S, Bader G, Gfeller D*, and Kim PM*. MUSI: an integrated system for Multiple Specificity Identification in large peptide or nucleic acid datasets. Nucleic Acids Research. 2012, doi:10.1093/nar/gkr1294

  • Colak R*, Kim T*, Michaut M, Sun MFG, Irimia M, Bellay J, Myers CL, Blencowe BJ*, Kim PM*. Distinct types of disorder in the human proteome: functional implications for alternative splicing. PLoS Comp Biol. (2013)

  • Li J*, Kim T*, Nutiu R, Ray D, Hughes TR and Zhang Z. Identifying mRNA Sequence Elements for Target Recognition by Human Argonaute Proteins Genome Research (2014)

  • Kim T, Yoshida K, Kim YK, Tyndel MS, Park HJ, Choi SH, Ahn J, Jung S, Yang D, Lee J, Kim HJ,Kong G,Ogawa S,Zhang Z, Kim HJ, and Kim DDD. Clonal dyamics in a single AML case tracked for 9 years reveals the complexity of leukemia progression Leukemia (2015)

  • Kim T, Tyndel MS, Kim HJ, Ahn J, Choi SH, Park HJ, Kim Y, Kim SY, Lipton JH, Zhang Z, DDH Kim. Spectrum of somatic mutation dynamics in chronic myeloid leukemia following tyrosine kinase inhibitor therapy Blood (2016)

  • Kim T, Tyndel MS, Kim HJ, Ahn J, Choi SH, Park HJ, Kim Y, Yang D, Lee J, Jung SH, Kim SY, Min YH, Cheong J, Sohn SK, Moon JK, Choi M, Lee M, Zhang Z and, Kim DDH. The Clonal origins of leukemic progression of myelodysplasia Leukemia (2017)

  • Kim T, Tyndel MS, Zhang Z, Ahn J, Choi S, Szardengs M, Lipton JH, Kim HJ, Kim DDH. Exome sequencing reveals DNMT3A and ASXL1 variants associate with progression of chronic myeloid leukemia after tyrosine kinase inhibitor therapy Leukemia Research (2017)

  • Kim T*, Moon J*, Ahn JS*, Kim YK, Lee SS, Ahn SY, Jung SH, Yang DH, Lee JJ, Choi SH, Lee JY, Tyndel MS, Shin MG, Lee YJ, Sohn SK, Park SK, Zhang Z, Kim HJ, Kim DDH. Next generation sequencing-based post-transplant monitoring of acute myeloid leukemia identifies patients at high risk of relapse. Blood (2018)

  • Ahn JS*, Kim T*, Kim YK, Cho YC, Cho S, Jung SH, Ahn SY, Jung SY, Yang DH, Lee JJ, Choi SH, Lee JY, Yoshida K, Ogawa S, Kim IC, Zhang Z, Kim HJ, and Kim DDH. Remission clone in AML shows growth advantage after chemotherapy but is distinct from leukemic clone. Experimental Hematology (2019)

  • Ahn JS*, Kim T*, Jung SH, Ahn SY, Jung SY, Song GY, Yang DH, Lee JJ, Choi S, Lee JY, Park SK, Moon JH, Lee HY, Kim K, Cai Y, Zhang Z, Kim HJ, Kim DDH. Allogeneic transplant can abrogate the risk of relapse in the patients of first remission acute myeloid leukemia with detectable measurable residual disease by next-generation sequencing. Bone Marrow Transplantation (2020)

  • Kim T, Moon J, Ahn JS, Ahn SY, Jung SH, Yang DH, Lee JJ, Choi SH, Lee JY, Tyndel MS, Shin MG, Lee HY, Kim KH, Cai Y, Lee YJ, Sohn SK, Min YH, Cheong JW, Kim HJ, Zhang Z, Kim DDH. RNA sequencing as an alternative tool for detecting measurable residual disease in core-binding factor AML. Scientific Reports (2020)

  • Daher-Reyes G*, Kim T*, Novitzky-Basso I, Kim KH, Smith A, Stockley T, Capochichi JM, Al-Shaibani Z, Pasic I, Law A, Lam W, Michelis FV, Gerbitz A, Viswabandya A, Lipton J, Kumar R, Mattsson J, Schimmer A, McNamara C, Murphy T, Maze D, Gupta V, Sibai H, Chan S, Yee K, Minden M, Zhang Z, Schuh A, Kim DDH. Prognostic impact of the adverse molecular-genetic profile on long-term outcomes following allogeneic hematopoietic stem cell transplantation in acute myeloid leukemia. Bone Marrow Transplant. (2021)

  • Kim T, Lee H, Capo-Chichi JM, Chang MH, Yoo YS, Basi G, Ketela T, Smith AC, Tierens A, Zhang Z, Minden MD, Kim DDH. Single cell proteogenomic sequencing identifies a relapse-fated AML subclone carrying FLT3-ITD with CN-LOH at chr13q. eJHaem. (2022)

  • Kim T, Ahn J, Son MH, Novitzky-Basso I, Yi SY, Ahn S, Jung S, Yang D, Lee J, Choi SH, Lee J, Moon JH, Sohn SK, Kim H, Zhang Z, Kim DDH. Genetic changes during leukemic transformation to secondary acute myeloid leukemia from myeloproliferative neoplasms. Leukemia Research. (2022)

  • Ahn J*, Kim T*, Jung S, Ahn S, Song G, Kim M, Yang D, Lee J, Kim MY, Moon JH, Zhang Z, H Kim, Kim DDH. Next-generation sequencing-based analysis to assess the pattern of relapse in patients with Philadelphia-positive acute lymphoblastic leukemia. Next-generation sequencing-based analysis to assess the pattern of relapse in patients with Philadelphia-positive acute lymphoblastic leukemia. eJHaem. (2022)

  • Song GY*, Kim T*, Ahn SY, Jung SH, Kim M, Yang DH, Lee JJ, Choi SH, Kim MY, Jung CW, Jang JH, Kim HJ, Moon JH, Sohn SK, Won JH, Park SK, Kim SH, Zhang Z, Ahn JS, Kim DDH. Allogeneic hematopoietic cell transplantation can overcome the adverse prognosis of secondary-type mutation positive acute myeloid leukemia. Bone Marrow Transplantation. (2022)


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