Journal Articles (* Equal contribution; @ Correspondence)

Preprint and article in press

55.     Wu X, Zeng Y, Das A, Jo S, Zhang T, Patel P, Zhang J, Gao SJ, Pratt D, Chiu YC@, Huang Y@. reguloGPT: harnessing GPT for knowledge graph construction of molecular regulatory pathways. bioRxiv 2024.01.27.577521; doi: 10.1101/2024.01.27.577521. Preprint Link


54.     Wang LJ, Ning M, Nayak T, Kasper MJ, Monga SP, Huang Y, Chen Y@, Chiu YC@. shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning. Patterns. 2024;5(2):100894. Epub 20240112. doi: 10.1016/j.patter.2023.100894. PubMed PMID: 38370127. Article Link Tool Link

53.     Zou J, Shah O, Chiu YC, Ma T, Atkinson JM, Oesterreich S, Lee AV, Tseng GC. Systems approach for congruence and selection of cancer models towards precision medicine. PLoS Computational Biology. 2024;20(1):e1011754. Epub 20240110. doi: 10.1371/journal.pcbi.1011754. PubMed PMID: 38198519. Article Link

52.     Saeed A, Park R, Pathak H, Al-Bzour AN, Dai J, Phadnis M, Al-Rajabi R, Kasi A, Baranda J, Sun W, Williamson S, Chiu YC, Osmanbeyoglu HU, Madan R, Abushukair H, Mulvaney K, Godwin AK, Saeed A. Clinical and biomarker results from a phase II trial of combined cabozantinib and durvalumab in patients with chemotherapy-refractory colorectal cancer (CRC): CAMILLA CRC cohort. Nature Communications. 2024;15(1):1533. Epub 20240220. doi: 10.1038/s41467-024-45960-2. PubMed PMID: 38378868. Article Link

51.     Hsu YC, Chiu YC, Lu TP, Hsiao TH, Chen Y. Predicting drug response through tumor deconvolution by cancer cell lines. Patterns. 2024;5(4):100949. Epub 20240305. doi: 10.1016/j.patter.2024.100949. PubMed PMID: 38645769. Article Link


50.     Das A, Meng W, Liu Z, Hasib MM, Galloway H, Ramos da Silva S, Chen L, Sica GL, Paniz-Mondolfi A, Bryce C, Grimes Z, Sordillo EM, Cordon-Cardo C, Rivera KP, Flores M, Chiu YC, Huang Y, Gao SJ. Molecular and immune signatures, and pathological trajectories of fatal COVID-19 lungs defined by in situ spatial single-cell transcriptome analysis. Journal of Medical Virology. 2023;95(8):e29009. doi: 10.1002/jmv.29009. PubMed PMID: 37563850. Article Link

49.     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. Bioinformatics Advances. 2023;3(1):vbad076. Epub 20230612. doi: 10.1093/bioadv/vbad076. PubMed PMID: 37359725; PMCID: PMC10290235. Article Link Tool Link


48.     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. Cancers (Basel). 2022;14(19). Epub 20220929. doi: 10.3390/cancers14194763. PubMed PMID: 36230685; PMCID: PMC9562172. Article Link 

47.     Iskra BS, Davis LR, Miller HE, Chiu YC, Bishop AJR, Chen Y, Aune GJ. Development and characterization of a mass cytometry panel for detecting the effect of acute doxorubicin exposure on murine cardiac non-myocytes. American Journal of Heart and Circulatory Physiology. 2022. Epub 20220603. doi: 10.1152/ajpheart.00514.2021. PubMed PMID: 35657614; ; PMCID: PMC9236860. Article Link 


46.     Chiu YC, Zheng S, Wang LJ, Iskra BS, Rao MK, Houghton PJ, Huang Y, Chen Y. Predicting and characterizing a cancer dependency map of tumors with deep learning. Science Advances. 2021;7(34). Epub 2021/08/22. doi: 10.1126/sciadv.abh1275. PubMed PMID: 34417181; PMCID: PMC8378822. Article Link Tool Link (Python) Tool Link (R) 

45.     Ramirez R, Chiu YC, Zhang S, Ramirez J, Chen Y, Huang Y, Jin YF. Prediction and Interpretation of Cancer Survival Using Graph Convolution Neural Networks. Methods. 2021. Epub 2021/01/24. doi: 10.1016/j.ymeth.2021.01.004. PubMed PMID: 33484826. Link

44.     Mostavi M, Chiu YC, Chen Y, Huang Y. CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training. BMC Bioinformatics. 2021;22(1):244. Epub 2021/05/14. doi: 10.1186/s12859-021-04157-w. PubMed PMID: 33980137; PMCID: PMC8117642. Link Tool Link

43.     Flores M, Liu Z, Zhang T, Hasib MM, Chiu YC, Ye Z, Paniagua K, Jo S, Zhang J, Gao SJ, Jin YF, Chen Y, Huang Y. Deep learning tackles single-cell analysis-a survey of deep learning for scRNA-seq analysis. Briefings in Bioinformatics. 2021. Epub 2021/12/21. doi: 10.1093/bib/bbab531. PubMed PMID: 34929734. Link 

42.     Huang SB, Thapa D, Munoz AR, Hussain SS, Yang X, Bedolla RG, Osmulski P, Gaczynska ME, Lai Z, Chiu YC, Wang LJ, Chen Y, Rivas P, Shudde C, Reddick RL, Miyamoto H, Ghosh R, Kumar AP. Androgen deprivation-induced elevated nuclear SIRT1 promotes prostate tumor cell survival by reactivation of AR signaling. Cancer Letters. 2021;505:24-36. Epub 2021/02/23. doi: 10.1016/j.canlet.2021.02.008. PubMed PMID: 33617947. Link


41.     Chiu YC, Chen HH, Gorthi A, Mostavi M, Zheng S, Huang Y, Chen Y. Deep learning of pharmacogenomics resources: moving towards precision oncology. Briefings in Bioinformatics. 2020;21(6):2066-83. Epub 2019/12/10. doi: 10.1093/bib/bbz144. PubMed PMID: 31813953. Link

40.     Mostavi M, Chiu YC, Huang Y, Chen Y. Convolutional neural network models for cancer type prediction based on gene expression. BMC Medical Genomics. 2020;13(Suppl 5):44. Epub 2020/04/04. doi: 10.1186/s12920-020-0677-2. PubMed PMID: 32241303. Article Link Tool Link

39.     Ramirez R, Chiu YC, Hererra A, Mostavi M, Ramirez J, Chen Y, Huang Y, Jin YF. Classification of cancer types using graph convolutional neural networks. Frontiers in Physics. 2020;8(203). doi: 10.3389/fphy.2020.00203. Article Link Tool Link

38.     Salekin S, Mostavi M, Chiu YC, Chen Y, Zhang J, Huang Y. Predicting sites of epitranscriptome modifications using unsupervised representation learning based on generative adversarial networks. Frontiers in Physics. 2020;8(196). doi: 10.3389/fphy.2020.00196. Article Link Tool Link

37.     Zhou F, Elzi DJ, Jayabal P, Ma X, Chiu YC, Chen Y, Blackman B, Weintraub ST, Houghton PJ, Shiio Y. GDF6-CD99 signaling regulates Src and Ewing sarcoma growth. Cell Reports. 2020;33(5):108332. Epub 2020/11/05. doi: 10.1016/j.celrep.2020.108332. PubMed PMID: 33147457. Link

36.     Lin CC, Yao CY, Hsu YC, Hou HA, Yuan CT, Li YH, Kao CJ, Chuang PH, Chiu YC, Chen Y, Chou WC, Tien HF. Knock-out of Hopx disrupts stemness and quiescence of hematopoietic stem cells in mice. Oncogene. 2020 Jun 12. doi: 10.1038/s41388-020-1340-2. Epub ahead of print. PMID: 32533098. Link


35.     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. BMC Medical Genomics. 2019;12(Suppl 1):18. Epub 2019/02/02. doi: 10.1186/s12920-018-0460-9. PubMed PMID: 30704458. Link Tool Link

34.     Chiu YC, Hsiao TH, Tsai JR, Wang LJ, Ho TC, Hsu SL, Teng CJ. Integrating resistance functions to predict response to induction chemotherapy in de novo acute myeloid leukemia. European Journal of Haematology. 2019. Epub 2019/07/30. doi: 10.1111/ejh.13301. PubMed PMID: 31356696. Link

33.     Hsiao TH*, Chiu YC*, Shao YHJ. Multi-omics analysis reveals the BRCA1 mutation and mismatch repair gene signatures associated with survival, protein expression, and copy number alterations in prostate cancer. Translational Cancer Research. 2019. Epub 2019/07/30. doi: 10.21037/tcr.2019.07.05. Link

32.     Tsai CH, Yao CY, Tien FM, Tang JL, Kuo YY, Chiu YC, Lin CC, Tseng MH, Peng YL, Liu MC, Liu CW, Yao M, Lin LI, Chou WC, Chen CY, Hou HA, Tien HF. Incorporation of long non-coding RNA expression profile in the 2017 ELN risk classification can improve prognostic prediction of acute myeloid leukemia patients. EBioMedicine. 2019. Epub 2019/01/22. doi: 10.1016/j.ebiom.2019.01.022. PubMed PMID: 30662003. Link

31.     Mohammad TA, Tsai YS, Ameer S, Chen HIH, Chiu YC, Chen Y. CeL-ID: Cell Line Identification using RNA-seq data. BMC Genomics. 2019;20(Suppl 1):81. Epub 2019/02/05. doi: 10.1186/s12864-018-5371-9. PubMed PMID: 30712511. Article Link Tool Link

30.    Wang LJ, Zhang CW, Su SC, Chen HH, Chiu YC, Lai Z, Bouamar H, Ramirez AG, Cigarroa FG, Sun LZ, Chen Y. An ancestry informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data. BMC Genomics. 2019;20(Suppl 12):1007. Epub 2020/01/01. doi: 10.1186/s12864-019-6333-6. PubMed PMID: 31888480. Article Link Tool Link


29.     Chiu YC, Hsiao TH, Wang LJ, Chen Y, Shao YJ. scdNet: a computational tool for single-cell differential network analysis. BMC Systems Biology. 2018;12(Suppl 8):124. Epub 2018/12/24. doi: 10.1186/s12918-018-0652-0. PubMed PMID: 30577836.31. Article Link Tool Link

28.     Chiu YC, Hsiao TH, Wang LJ, Chen Y, Chuang EY. Analyzing differential regulatory networks modulated by continuous-state genomic features in glioblastoma multiforme. IEEE/ACM transactions on computational biology and bioinformatics. 2018;15(6):1754-64. Epub 2017/01/24. doi: 10.1109/TCBB.2016.2635646. PubMed PMID: 28114032. Link

27.     Chen HH, Chiu YC, Zhang T, Zhang S, Huang Y, Chen Y. GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization. BMC Systems Biology. 2018;12(Suppl 8):142. Epub 2018/12/24. doi: 10.1186/s12918-018-0642-2. PubMed PMID: 30577835. Link

26.     Tien FM, Hou HA, Tsai CH, Tang JL, Chiu YC, Chen CY, Kuo YY, Tseng MH, Peng YL, Liu MC, Liu CW, Liao XW, Lin LI, Lin CT, Wu SJ, Ko BS, Hsu SC, Huang SY, Yao M, Chou WC, Tien HF. GATA2 zinc finger 1 mutations are associated with distinct clinico-biological features and outcomes different from GATA2 zinc finger 2 mutations in adult acute myeloid leukemia. Blood Cancer Journal. 2018;8(9):87. Epub 2018/09/08. doi: 10.1038/s41408-018-0123-2. PubMed PMID: 30190467. Link

25.     Yang YT, Chiu YC, Kao CJ, Hou HA, Lin CC, Tsai CH, Tseng MH, Chou WC, Tien HF. The prognostic significance of global aberrant alternative splicing in patients with myelodysplastic syndrome. Blood Cancer Journal. 2018;8(8):78. Epub 2018/08/15. doi: 10.1038/s41408-018-0115-2. PubMed PMID: 30104611. Link 

24.     Hsiao TH, Chiu YC, Chen YH, Hsu YC, Chen HH, Chuang EY, Chen Y. Utilizing cancer - functional gene set - compound networks to identify putative drugs for breast cancer. Combinatorial Chemistry & High Throughput Screen. 2018. Epub 2018/01/06. doi: 10.2174/1574888X13666180105125347. PubMed PMID: 29303076. Link


23.     Lin CC, Hsu YC, Li YH, Kuo YY, Hou HA, Lan KH, Chen TC, Tzeng YS, Kuo YY, Kao CJ, Chuang PH, Tseng MH, Chiu YC@, Chou WC@, Tien HF@. Higher HOPX expression is associated with distinct clinical and biological features and predicts poor prognosis in de novo acute myeloid leukemia. Haematologica. 2017;102(6):1044-53. doi: 10.3324/haematol.2016.161257. PubMed PMID: 28341738. Link

22.     Hsu YC, Chiu YC, Lin CC, Kuo YY, Hou HA, Tzeng YS, Kao CJ, Chuang PH, Tseng MH, Hsiao TH, Chou WC, Tien HF. The distinct biological implications of Asxl1 mutation and its roles in leukemogenesis revealed by a knock-in mouse model. Journal of Hematology and Oncology. 2017;10(1):139. doi: 10.1186/s13045-017-0508-x. PubMed PMID: 28697759. Link

21.     Tsai CH, Hou HA, Tang JL, Kuo YY, Chiu YC, Lin CC, Liu CY, Tseng MH, Lin TY, Liu MC, Liu CW, Lin LI, Yao M, Li CC, Huang SY, Ko BS, Hsu SC, Lin CT, Wu SJ, Chen CY, Tsay W, Chuang EY, Chou WC, Tien HF. Prognostic impacts and dynamic changes of cohesin complex gene mutations in de novo acute myeloid leukemia. Blood Cancer Journal. 2017;7(12):663. Epub 2017/12/31. doi: 10.1038/s41408-017-0022-y. PubMed PMID: 29288251. Link

20.     Lee SH*, Chiu YC*, Li YH, Lin CC, Hou HA, Chou WC, Tien HF. High expression of dedicator of cytokinesis 1 (DOCK1) confers poor prognosis in acute myeloid leukemia. Oncotarget. 2017;8(42):72250-9. Epub 2017/10/27. doi: 10.18632/oncotarget.19706. PubMed PMID: 29069784. Link

19.     Chiu YC*, Wang LJ*, Hsiao TH, Chuang EY, Chen Y. Genome-wide identification of modulators of gene-gene interaction networks in breast cancer. BMC Genomics. 2017;18(Suppl 6):679. doi: 10.1186/s12864-017-4028-4. PubMed PMID: 28984209. Link

18.     Chiu YC*, Wang LJ*, Hsiao TH, Lu TP, Chuang EY, Chen Y. Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival. BMC Bioinformatics. 2017;18(1):132. doi: 10.1186/s12859-017-1557-4. PubMed PMID: 28241741. Link


17.     Chiu YC*, Tsai MH*, Chou WC*, Liu YC, Kuo YY, Hou HA, Lu TP, Lai LC, Chen Y, Tien HF, Chuang EY. Prognostic significance of NPM1 mutation-modulated microRNA-mRNA regulation in acute myeloid leukemia. Leukemia. 2016;30(2):274-84. doi: 10.1038/leu.2015.253. PubMed PMID: 26376228. Link

16.     Hsiao TH*, Chiu YC*, Hsu PY, Lu TP, Lai LC, Tsai MH, Huang TH, Chuang EY, Chen Y. Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers. Scientific Reports. 2016;6:23035. doi: 10.1038/srep23035. PubMed PMID: 26972162. Article Link Tool Link

15.     Hsu YC*, Chiu YC*, Chen Y, Hsiao TH, Chuang EY. A simple gene set-based method accurately predicts the synergy of drug pairs. BMC Systems Biology. 2016;10 Suppl 3:66. doi: 10.1186/s12918-016-0310-3. PubMed PMID: 27585722. Link

14.     Chang YH*, Chiu YC*, Hsu YC, Tsai HM, Chuang EY, Hsiao TH. Applying gene set analysis to characterize the activities of immune cells in estrogen receptor positive breast cancer. Translational Cancer Research. 2016;5(2):176-185. doi: 10.21037/tcr.2016.04.09. Link


13.     Chuang MK*, Chiu YC*, Chou WC, Hou HA, Chuang EY, Tien HF. A 3-microRNA scoring system for prognostication in de novo acute myeloid leukemia patients. Leukemia. 2015;29(5):1051-9. doi: 10.1038/leu.2014.333. PubMed PMID: 25428263. Link

12.     Chuang MK*, Chiu YC*, Chou WC, Hou HA, Tseng MH, Kuo YY, Chen Y, Chuang EY, Tien HF. An mRNA expression signature for prognostication in de novo acute myeloid leukemia patients with normal karyotype. Oncotarget . 2015. doi: 10.18632/oncotarget.5390. PubMed PMID: 26517675. Link

11.     Chiu YC*, Hsiao TH*, Chen Y, Chuang EY. Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers. BMC Genomics. 2015;16 Suppl 4:S1. doi: 10.1186/1471-2164-16-S4-S1. PubMed PMID: 25917195; PMCID: 4416191. Link

10.     Chiu YC*, Wu CT*, Hsiao TH, Lai YP, Hsiao C, Chen Y, Chuang EY. Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes. BMC Genomics. 2015;16 Suppl 7:S19. doi: 10.1186/1471-2164-16-S7-S19. PubMed PMID: 26100352; PMCID: 4474423. Link

9.     Hsu YC*, Chiu YC*, Chen Y, Hsiao TH, Chuang EY. A gene-set approach to analyze copy number alterations in breast cancer. Translational Cancer Research. 2015;4(3):291-302. Link


8.     Liao HF, Chen WS, Chen YH, Kao TH, Tseng YT, Lee CY, Chiu YC, Lee PL, Lin QJ, Ching YH, Hata K, Cheng WT, Tsai MH, Sasaki H, Ho HN, Wu SC, Huang YH, Yen P, Lin SP. DNMT3L promotes quiescence in postnatal spermatogonial progenitor cells. Development. 2014;141(12):2402-13. doi: 10.1242/dev.105130. PubMed PMID: 24850856. Link

7.     Luo EC, Chang YC, Sher YP, Huang WY, Chuang LL, Chiu YC, Tsai MH, Chuang EY, Lai LC. MicroRNA-769-3p down-regulates NDRG1 and enhances apoptosis in MCF-7 cells during reoxygenation. Scientific Reports. 2014;4:5908. doi: 10.1038/srep05908. PubMed PMID: 25081069; PMCID: 4118187. Link


6.     Hsu PY, Hsu HK, Lan X, Juan L, Yan PS, Labanowska J, Heerema N, Hsiao TH, Chiu YC, Chen Y, Liu Y, Li L, Li R, Thompson IM, Nephew KP, Sharp ZD, Kirma NB, Jin VX, Huang TH. Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell. 2013;24(2):197-212. doi: 10.1016/j.ccr.2013.07.007. PubMed PMID: 23948299; PMCID: 3890247. Link

5.     Yeh SH, Lee BH, Liao SC, Tsai MH, Tseng YH, Chang HC, Yang CC, Jan HC, Chiu YC, Wang AY. Identification of genes differentially expressed during the growth of Bambusa oldhamii. Plant Physiology and Biochemistry . 2013;63:217-26. doi: 10.1016/j.plaphy.2012.11.030. PubMed PMID: 23291655. Link

4.     Lee CY*, Chiu YC*, Wang LB*, Kuo YL*, Chuang EY, Lai LC, Tsai MH. Common applications of next-generation sequencing technologies in genomic research. Translational Cancer Research. 2013;2(1):33-45. Link

3.     Flores M, Hsiao TH, Chiu YC, Chuang EY, Huang Y, Chen Y. Gene regulation, modulation, and their applications in gene expression data analysis. Advances in Bioinformatics. 2013;2013:360678. doi: 10.1155/2013/360678. PubMed PMID: 23573084; PMCID: 3610383. Link


2.     Lu TP, Lee CY, Tsai MH, Chiu YC, Hsiao CK, Lai LC, Chuang EY. miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets. PLOS One. 2012;7(8):e42390. doi: 10.1371/journal.pone.0042390. PubMed PMID: 22870325; PMCID: 3411648. Article Link Tool Link

1.     Chou SH, Ko BS, Chiou JS, Hsu YC, Tsai MH, Chiu YC, Yu IS, Lin SW, Hou HA, Kuo YY, Lin HM, Wu MF, Chou WC, Tien HF. A knock-in Npm1 mutation in mice results in myeloproliferation and implies a perturbation in hematopoietic microenvironment. PLOS One. 2012;7(11):e49769. doi: 10.1371/journal.pone.0049769. PubMed PMID: 23226219; PMCID: 3511491. Link