Publications – peer reviewed journal articles

Primary author publications
  1. Ching, T. H., Yoza, B. A., Wang, R., Masutani, S., Donachie, S., Hihara, L., & Li, Q. X. (2016). Biodegradation of biodiesel and microbiologically induced corrosion of 1018 steel by Moniliella wahieum Y12. International Biodeterioration & Biodegradation, 108, 122–126.
  2. Ching, T., Masaki, J., Weirather, J., & Garmire, L. X. (2015). Non-coding yet non-trivial: a review on the computational genomics of lincRNAs. BioData Mining, 8(1), 1.
  3. Ching, T., Peplowska, K., Huang, S., Zhu, X., Shen, Y., Molnar, J., … & Garmire, L. X. (2016). Pan-cancer analyses reveal long intergenic non-coding RNAs relevant to tumor diagnosis, subtyping and prognosis. EBioMedicine, 7, 62-72.
  4. Ching, T.*, Ha, J.*, Song, M.-A., Tiirikainen, M., Molnar, J., Berry, M. J., … Garmire, L. X. (2015). Genome-scale hypomethylation in the cord blood DNAs associated with early onset preeclampsia. Clinical Epigenetics, 7(1), 1. *Contributed equally.
  5. Li, J.*, Ching, T.*, Huang, S., & Garmire, L. X. (2015). Using epigenomics data to predict gene expression in lung cancer. BMC Bioinformatics, 16(Suppl 5), S10. *Contributed equally.
  6. Menor, M.*, Ching, T.*, Zhu, X., Garmire, D., & Garmire, L. X. (2014). mirMark: a site-level and UTR-level classifier for miRNA target prediction. Genome Biology, 15(10), 1–16. *Contributed equally.
  7. Ching, T., Song, M.-A., Tiirikainen, M., Molnar, J., Berry, M., Towner, D., & Garmire, L. X. (2014). Genome-wide hypermethylation coupled with promoter hypomethylation in the chorioamniotic membranes of early onset pre-eclampsia. Molecular Human Reproduction, 20(9), 885–904.
  8. Ching, T., Huang, S., & Garmire, L. X. (2014). Power analysis and sample size estimation for RNA-Seq differential expression. Rna, 20(11), 1684–1696.
  9. Ching, T. H., Yoza, B. A., & Li, Q. X. (2014). Quartet Analysis of Putative Horizontal Gene Transfer in Crenarchaeota. Journal of Molecular Evolution, 78(2), 163–170.
Co-author publications
  1. Wang B.D., Ceniccola K., Hwang S., Andrawis R., Horvath A., Freeman J.A., Knapp S., Ching T., Garmire L.X., Pate l.V., Garcia-Blanco M.A., Patierno S.R., Lee N.H., Aberrant Alternative Splicing in African American Prostate Cancer: novel driver of tumor aggressiveness and drug resistance. Nature Communications (accepted/pre-print).
  2. Han B., Park H.K., Ching T., Panneerselvam J., Wang H., Shen Y., Zhang J., Li L., Che R., Garmire L., & Fei P. (2017). Human DBR1 Modulates the Recycling of snRNPs to Affect RNA Alternative Splicing and Contributes to the Suppression of Cancer Development. Oncogene (accepted/preprint).
  3. Zhu X., Ching T., Pan X., Weissman S., Garmire L.X. (2016). Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization, PeerJ 5:e2888
  4. Poirion, O. B., Zhu, X., Ching, T., & Garmire, L. (2016). Single-Cell Transcriptomics Bioinformatics and Computational Challenges. Frontiers in Genetics, 7.
  5. Feng N.*, Ching T.*, Wang Y, Liu B, Lin H., Shi O., Zhang X., Yao Y, Hua L., Zheng X., Gao M., Yu H., Garmire L.X., Qian B. Analysis of Microarray Data on Gene Expression and Methylation to Identify Long Non-coding RNAs in Non-small Cell Lung Cancer. Scientific Reports 6. *Contributed equally.
  6. Baker, M. R., Tabb, D. L., Ching, T., Zimmerman, L. J., Sakharov, I. Y., & Li, Q. X. (2016). Site-specific N-glycosylation characterization of windmill palm tree peroxidase using novel tools for analysis of plant glycopeptide mass spectrometry data. Journal of Proteome Research.
  7. Gagliani, N., Vesely, M. C. A., Iseppon, A., Brockmann, L., Xu, H., Palm, N. W., … Ching, T., …. (2015). Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation. Nature, 523(7559), 221–225.
  8. Huang, S., Yee, C., Ching, T., Yu, H., & Garmire, L. X. (2014). A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer. PLoS Comput Biol, 10(9), e1003851.

Publications – in submission

  • Ching, T., Himmelstein, D. S., Beaulieu-Jones, B. K., Kalinin, A. A., Do, B. T., Way, G. P., Ferrero, E., Agapow, P.-M., Xie, W., Rosen, G. L., Lengerich, B. J., Israeli, J., Lanchantin, J., Woloszynek, S., Carpenter, A. E., Shrikumar, A., Xu, J., Cofer, E. M., Harris, D. J., DeCaprio, D., Qi, Y., Kundaje, A., Peng, Y., Wiley, L. K., Segler, M. H. S., Gitter, A. & Greene, C. S. (2017). Opportunities and Obstacles for Deep Learning in Biology and Medicine. Doi: 10.1101/142760. (under review).
  • Ching T., Garmire L.X. Pan-cancer analysis of expressed single nucleotide variants in long intergenic non-coding RNA (in preparation).
  • Ching T., Zhu X., Garmire L.X. Cox-nnet: an artificial neural network Cox regression for prognosis prediction. Submitted to PLoS Comp Biol (in revision).
  • Yamasato K., Ching T., Garmire L.X., Berry M., Towner D., Evaluation of a maternal cardiovascular gene array in early on-set preeclampia in a dominantly Asian cohort. Submitted to Pregnancy and hypertension (under review).

Conference abstracts/posters

  • Pan-cancer analyses reveal lincRNAs relevant to tumour diagnosis, subtyping and prognosis. Stanford Big Data in Biomedicine 2016.
  • Neural network survival applied to pancancer lincRNA data. Pacific Symposium on Biocomputing 2016.
  • Pan-cancer analysis of lincRNAs reveals robust diagnostic biomarkers. Pacific Symposium on Biocomputing 2015.
  • Differential methylation in cord blood in early-onset preeclampsia in a predominantly Asian cohort. ISPD 18th International Conference on Prenatal Diagnosis and Therapy.
  • Differential methylation in the chorioamnion membranes in early-onset preeclampsia in a predominantly Asian cohort. ISPD 18th International Conference on Prenatal Diagnosis and Therapy.

Master’s thesis

  • Ching, T. H. “Characterization of Biocontaminants in Biodiesel Fuels and Potential Roles in the Formation of Microbially Induced Corrosion.” University of Hawaii at Manoa (2012). (PDF)

Ph.D. dissertation

  • Ching, T. H. “Integrative transcriptomic analysis of long intergenic non-coding RNAs in cancer.” University of Hawaii at Manoa (2017). (PDF)


Roche/ARCS PhD student scholarship 2015 (link)

“The Roche/ARCS Scholar Award provides support for the next generation of outstanding graduate life sciences scholars in the US. All awardees are Ph.D. candidates in the life sciences at universities that are ARCS Foundation academic partners, which includes the study of medically relevant fields including the scientific study of living organisms, such as microorganisms, animals and human beings, as well as related work in chemistry, computer sciences, engineering and materials sciences that could eventually be applied towards the study of living organisms.”

Cancer Center: Paper of the month award Dec. 2014 (link)

“HONOLULU, HI – Dr. Lana Garmire won University of Hawai’i Cancer Center’s November Publication of the Month award for her collaborative paper, “mirMark: a site-level and UTR-level classifier for miRNA target prediction,” printed on October 25th 2014 in Genome Biology. Dr. Lana Garmire is a tenure-track assistant professor in the Cancer and Epidemiology Program at University of Hawai’i Cancer Center.”

Weinman Symposium 2014 Award (link)

“The 2014 Weinman Symposium was a conference held on May 5th to welcome Nobel Laureates Dr. Jules Hoffmann and Dr. Bruce Beutler as well as Dr. Ann Chao Director of the National Cancer Institute to the University of Hawaii Cancer Center. There were many inspirational presentations on Toll-like receptors, genetic recombination and a variety of other topics. During lunch, students and faculty were given the opportunity to give a poster presentation of their work to these Nobel Laureates. The presenters of the best poster in the categories of wet lab work and epidemiology were given a personal award of $1000.”