Ti-Cheng Chang

Focused on the integrative analysis of large-scale, multi-dimensional genomic data to better understand the relationship between genomic variations and diseases.

• Chang T.C. et al. Genomic determinants of outcome in acute lymphoblastic leukemia: A Children’s Oncology Group study. Submitted.
• Gao Q, [and 32 others, including Chang, T.-C]. The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Blood Journal. 2023 May 22:blood-2022019094.
• Li Z*, Chang TC*, Junco JJ*, Devidas M, Li Y, Yang W, Huang X, Hedges DJ, Cheng Z, Shago M, Carroll AJ. Genomic landscape of Down syndrome-associated acute lymphoblastic leukemia. Blood Journal. 2023 Mar 31:blood-2023019765. (* equal contribution)
• Flerlage JE, Myers JR, Maciaszek JL, Oak N, Rashkin SR, Hui Y, Wang YD, Chen W, Wu G, Chang TC, Hamilton K. Discovery of novel predisposing coding and noncoding variants in familial Hodgkin lymphoma. Blood, The Journal of the American Society of Hematology. 2023 Mar 16;141(11):1293-307.
• Davenport CM, Teubner BJ, Han SB, Patton MH, Eom TY, Garic D, Lansdell BJ, Shirinifard A, Chang TC, Klein J, Pruett-Miller SM. Innate frequency-discrimination hyperacuity in Williams-Beuren syndrome mice. Cell. 2022 Oct 13;185(21):3877-95.
• Lee S*, Chang TC*, Schreiner P, Fan Y, Agarwal N, Owens C, Dummer R, Kirkwood JM, Barnhill RL, Theodorescu D, Wu G. Targeted long-read bisulfite sequencing identifies differences in the TERT promoter methylation profiles between TERT wild-type and TERT mutant cancer cells. Cancers. 2022 Aug 19;14(16):4018. (* equal contribution)
• Sharma, Richa, [and 33 others, including Chang, T.-C]. "Gain-of-function mutations in RPA1 cause a syndrome with short telomeres and somatic genetic rescue." Blood 139.7 (2022): 1039-1051.
• Newman, Scott, [and 56 others, including Chang, T.-C]. "Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA SequencingComprehensive Clinical Sequencing in Pediatric Cancer." Cancer discovery 11.12 (2021): 3008-3027.
• Clay MR, Patel A, Tran Q, Hedges DJ, Chang TC, Stewart E, Charville G, Cline C, Dyer MA, Orr BA. Methylation profiling reveals novel molecular classes of rhabdomyosarcoma. Scientific Reports. 2021 Nov 15;11(1):22213.
• Montefiori, Lindsey E., [and 51 others, including Chang, T.-C]. "Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell LeukemiaBCL11B Hijacking in Lineage-Ambiguous Leukemia." Cancer discovery 11.11 (2021): 2846-2867.
• McLeod, Clay, [and 71 others, including Chang, T.-C.]. "St. Jude Cloud: a pediatric cancer genomic data-sharing ecosystem." Cancer discovery 11.5 (2021): 1082-1099.
• Margolis EB, Hakim H, Dallas RH, Allison KJ, Ferrolino J, Sun Y, Pui CH, Yao J, Chang TC, Hayden RT, Jeha S. Antibiotic prophylaxis and the gastrointestinal resistome in paediatric patients with acute lymphoblastic leukaemia: a cohort study with metagenomic sequencing analysis. The Lancet Microbe. 2021 Apr 1;2(4):e159-67.
• Chang, T. C., Haupfear, K. M., Yu, J., Rampersaud, E., Sheehan, V. A., Flanagan, J. M., ... & Zheng, Y. (2020). A novel algorithm comprehensively characterizes human RH genes using whole-genome sequencing data. Blood Advances, 4(18), 4347-4357.
• LeMessurier, K.S., Iverson, A.R., Chang, T.-C., Palipane, M., Vogel, P., Rosch, J.W. and Samarasinghe, A.E., 2019. Allergic inflammation alters the lung microbiome and hinders synergistic co-infection with H1N1 influenza virus and Streptococcus pneumoniae in C57BL/6 mice. Scientific Reports, 9(1), pp.1-15.
• Wang, Z., Rice, S.V., Chang, T.-C., et al. 2019. Molecular Mechanism of Telomere Length Dynamics and Its Prognostic Value in Pediatric Cancers. JNCI: Journal of the National Cancer Institute.
• Zamora A.E., et al. [and 19 others, including Chang, T.-C.]. 2019. Pediatric patients with acute lymphoblastic leukemia generate abundant and functional neoantigen-specific CD8+ T cell responses. Science Translational Medicine Vol. 11, Issue 498, eaat8549.
• Rowe HM, Karlsson E, Echlin H, Chang T.-C., Wang L, van Opijnen T, Pounds S.B., Schultz-Cherry S, Rosch J.W. 2019. Bacterial Factors Required for Transmission of Streptococcus pneumoniae in Mammalian Hosts. Cell Host Microbe. 2019 Jun 12;25(6):884-891.e6.
• Mosquera, S., Chen, L. H., Aegerter, B., Miyao, E., Salvucci, A., Chang, T. -C., & Stergiopoulos, I. 2019. Cloning of the cytochrome b gene from the tomato powdery mildew fungus Leveillula taurica reveals high levels of allelic variation and heteroplasmy for the G143A mutation. Frontiers in microbiology 10, 663
• Wang, Z., et al. [and 17 others, including Chang, T.-C.]. 2018. Polygenic Determinants for Subsequent Breast Cancer Risk in Survivors of Childhood Cancer: The St Jude Lifetime Cohort Study (SJLIFE). Clinical Cancer Research.
• Xu, K., Ding, L., Chang, T.-C., et al. 2018. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta neuropathologica, pp.1-15.
• Malik, A., et al. [and 8 others, including Chang, T.-C.]. 2018. SYK-CARD9 signaling axis promotes gut fungi- mediated inflammasome activation to restrict colitis and colon cancer. Immunity, 49(3), pp.515-530.
• Chang, T.-C., J.W. Rosch, Z. Gu, H. Hakim, C. Hewitt, A. Gaur, G. Wu, and R.T. Hayden. 2018. Whole-Genome Characterization of Bacillus cereus Associated with Specific Disease Manifestations. Infection and Immunity 86 (2), e00574-17.
• Hakim, H., et al. [and 15 others, including Chang, T.-C.]. 2018. Gut Microbiome Composition Predicts Infection Risk during Chemotherapy in Children with Acute Lymphoblastic Leukemia. Clinical Infectious Diseases.
• Chang, T.-C., Carter, R.A., Li, Y., Li, Y., Wang, H., Edmonson, M.N., Chen, X., Arnold, P., Geiger, T.L., Wu, G. and Peng, J., et al. 2017. The neoepitope landscape in pediatric cancers. Genome Medicine, 9(1), p.78.
• Haley, E., Frank, M.W., Iverson, A., Chang, T.-C. et al. 2016. Pyruvate oxidase as a critical link between metabolism and capsule biosynthesis in Streptococcus pneumoniae. PLoS Pathogen 12.10: e1005951.
• Chang, T.-C., Salvucci, A. Crous P. W. and Stergiopoulos, I. 2016. Comparative genomics of the Sigatoka disease complex on banana suggests a link between parallel evolutionary changes in Pseudocercospora fijiensis and Pseudocercospora eumusae and increased virulence on the banana host. PLoS Genetics 12 (8), e1005904.
• Zhu, X., Chang, T. C., Webby, R., & Wu, G. (2020). idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates. bioRxiv, 2020-10.
• Chang, T.-C., and Stergiopoulos, I. 2015. Evolutionary analysis of the global landscape of protein domain types and domain architectures associated with family 14 carbohydrate-binding modules. FEBS letters 589 (15), 1813- 1818.
• Chang, T.-C., and Stergiopoulos, I. 2015. Inter‐and intra‐domain horizontal gene transfer, gain‐loss asymmetry, and positive selection mark the evolutionary history of the CBM14 family. FEBS Journal 282 (10), 2014-2028.
• Chang, T.-C., Yang, Y., Retzel, E. F. & Liu, W. S. 2013. The male-specific region of the bovine Y chromosome is gene-rich with a high transcriptomic activity in testis development. PNAS 30: 12373-8.
• Chang, T.-C., Yang, Y., Yasue, H., Bharti, A. K., Retzel, E. F. & Liu, W. -S. 2011b. The expansion of the PRAME gene family in Eutheria. PLoS ONE 6: e16867.
• Natale, D. A., Arighi, C. N., Barker, W. C., Blake, J., Chang, T.-C., Hu, Z., et al. 2007. Framework for a protein ontology. BMC Bioinformatics 8 Suppl 9: S1.

• Chang, T. C., Xu, K., Cheng, Z., & Wu, G. (2022). Somatic and Germline Variant Calling from Next-Generation Sequencing Data. In Computational Methods for Precision Oncology (pp. 37-54). Cham: Springer International Publishing.
• Liu, W.-S., Chang, T.-C. (2014) Y chromosome-linked genes implicated in spermatogenesis in cattle. Reproduction in Domestic Ruminants VIII. Context Products Ltd., England. P239-255. DOI: 10.13140/2.1.1392.9922
  

• Chang, T.-C. et al (2023). Genomic determinants of outcome in acute lymphoblastic leukemia: A Children’s Oncology Group study. ASCO Annual Meeting. June 2-6. Chicago.
• Chang, T.-C. et al (2021) Accelerating Primary Genomics Analyses for Big Data Challenges
• Chang, T.-C. et al (2019). Mobile element activity in TARGET ALS patients. Clinical Research in ALS and related disorders for Therapeutic Development’ (CReATe) Consortium (RDCRC) 5th Annual Meeting. Mar 11-12. Miami, Florida.
  

Karlstrom A., Chang, T.-C., Gentry, D., et al (2020). An innovative integrated cloud-based data portal for orthotopic patient-derived xenografts (O-PDX) available through the Childhood Solid Tumor Network (CSTN) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6149.

Chang, T.-C. et al (2018). Accurate Prediction of RH Genotypes Using Whole Genome Sequencing Data. American Society of Hematology annual meeting. San Diego, CA.
Chang, T.-C. et al (2017) Characterizing the viromes in pediatric cancers through whole genome sequencing. April 1, 2017. American Association for Cancer Research, DC.
Chang, T.-C. et al (2016) Differential microbial composition associated with asthma. Cold Spring Harbor, Biology of Genomes, May 10, 2016. Cold Spring Harbor, NY.
Chang, T.-C. and Stergiopoulos, I. (2015) Comparative genomics of the Sigatoka disease complex on banana. 28th Fungal Genetics Conference. March 17-22, 2015. Pacific Grove, CA.
Chang, T.-C. (2014) Evolution of carbohydrate-binding module 14 (CBM14), plant-microbe interactions meeting, February 13, 2014. Davis, CA.
Chang, T.-C., Yang, Y., Retzel, E., & Liu, W.-S. (2011) The genomic organization and gene content of the male- specific region in the bovine Y chromosome. Conference Abstract, PAG-XX, January 14-18, 2012. San Diego, CA.