Conference articles

Conference Articles for Oral Presentations

20.    Liu Z, Chiu YC, Chen Y, Huang Y. Metastatic cancer expression generator (MetGen): A generative contrastive learning framework for metastatic cancer generation. International Conference on Intelligent Biology and Medicine (ICIBM) 2023 (Tampa, FL).

19.    Hsu YC, Chiu YC, Lu TP, Hsiao TH, Chen Y. Pan-cancer drug response prediction through tumor decomposition by cancer cell lines. International Conference on Intelligent Biology and Medicine (ICIBM) 2023 (Tampa, FL).

18.    Nayak T*, Wang LJ*, Ning M, Rubannelsonkumar G, Jin E, Zheng S, Houghton PJ, Huang Y, Chiu YC@, Chen Y@. DepLink: an R Shiny app to systematically link genetic and pharmacologic dependencies of cancer.  Great Lakes Bioinformatics (GLBIO) Conference 2023 (Montreal, Canada).

17.     Tsai HM, Hsiao TH, Chiu YC, Huang Y, Chen Y, Chuang EY. DeepG2P: predicting protein abundance from mRNA expression. International Conference on Intelligent Biology and Medicine (ICIBM) 2022 (Philadelphia, PA).

16.     Zhang TH, Hasib MM, Chiu YC, Han ZF, Jin YF, Flores M, Chen Y, Huang Y. Transformer for Gene Expression Modeling (T-GEM): An interpretable deep learning model for gene expression-based phenotype predictions. International Conference on Intelligent Biology and Medicine (ICIBM) 2022 (Philadelphia, PA).

15.     Mostavi M, Chiu YC, Huang Y, Chen Y. Convolutional neural network models for cancer type prediction based on gene expression. International Conference on Intelligent Biology and Medicine (ICIBM) 2019 (Columbus, OH).

14.     Wang LJ, Zhang C, Su S, Chen HIH, Chiu YC, Lai Z, Bouamar H, Cigarroa FG, Sun LZ, Chen Y. An ancestral informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data. International Conference on Intelligent Biology and Medicine (ICIBM) 2019 (Columbus, OH).

13.     Chiu YC, Chen HIH, Zhang T, Zhang S, Wang LJ, Huang Y, Chen Y. Predicting drug response of tumors from integrated genomic profiles by deep neural networks. International Conference on Intelligent Biology and Medicine (ICIBM) 2018 (Los Angeles, CA).

12.     Chiu YC, Hsiao TH, Wang LJ, Chen Y, Shao Shao YHJ. scDNA: a fast and comprehensive tool for single-cell differential network analysis. International Conference on Intelligent Biology and Medicine (ICIBM) 2018 (Los Angeles, CA).

11.     Chen HIH, Chiu YC, Zhang T, Zhang S, Wang LJ, Huang Y, Chen Y. GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization. International Conference on Intelligent Biology and Medicine (ICIBM) 2018 (Los Angeles, CA).

10.     Mohammad TA, Tsai YS, Ameer S, Chen HIH, Chiu YC, Chen Y. CeL-ID: Cell Line Identification using RNA-seq data. International Conference on Intelligent Biology and Medicine (ICIBM) 2018 (Los Angeles, CA).

9.     Chiu YC, Wang LJ, Hsiao TH, Chuang EY, Chen Y. Genome-wide identification of modulators of gene-gene interaction networks in breast cancer. International Conference on Intelligent Biology and Medicine (ICIBM) 2016 (Houston, TX). ICIBM Student Travel Award.

8.     Huang CY, Lu TP, Chiu YC, Chuang EY, Hsiao TH. A hybrid analysis method for construction of heterogeneous networks from multi-omics data. International Conference on Intelligent Biology and Medicine (ICIBM) 2016 (Houston, TX).

7.     Chiu YC, Liang KW, Hsiao TH, Chen Y, Chuang EY. Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2015 (Washington D.C.). BIBM Student Travel Award and FAOS Outstanding Students Conference Travel Grant.

6.     Wu CT, Hsiao TH, Chiu YC, Chuang EY, Chen Y. Patho-finder – a fast and accurate program for pathogen identification through RNA-seq. Workshop of Computational Regulatory Genomics and Metagenomics, IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2015 (Washington D.C.).

5.     Hsu YC, Chiu YC, Chen Y., Hsiao TH, Chuang EY. A simple gene set-based method accurately predicts the synergy of drug pairs. International Conference on Intelligent Biology and Medicine (ICIBM) 2015 (Indianapolis, IN).

4.     Chiu YC, Wu CT, Hsiao TH, Lai YP, Hsiao CK, Chen Y, Chuang EY. Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes. International Conference on Intelligent Biology and Medicine (ICIBM) 2014 (San Antonio, TX).

3.     Hsu YC, Chiu YC, Chen Y., Hsiao TH, Chuang EY. A gene set approach to analyze copy number alterations profiles of breast cancer. International Conference on Intelligent Biology and Medicine (ICIBM) 2014 (San Antonio, TX).

2.     Chiu YC, Chuang EY, Hsiao TH, Chen Y. Modeling competing endogenous RNA regulatory networks in glioblastoma multiforme. IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2013 (Shanghai, China). BIBM Student Travel Award.

1.     Chiu YC, Chuang EY, Hsiao TH, Chen Y. Characterization of conditions for competing endogenous RNA regulation in GBM. IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2013 (Houston, TX).