Convolutional neural network models for cancer type prediction based on gene expression
Mostavi, Milad, Chiu, Yu-Chiao, Huang, Yufei, Chen, Yidong
Published in BMC medical genomics (03.04.2020)
Published in BMC medical genomics (03.04.2020)
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Journal Article
Predicting drug response of tumors from integrated genomic profiles by deep neural networks
Chiu, Yu-Chiao, Chen, Hung-I Harry, Zhang, Tinghe, Zhang, Songyao, Gorthi, Aparna, Wang, Li-Ju, Huang, Yufei, Chen, Yidong
Published in BMC medical genomics (31.01.2019)
Published in BMC medical genomics (31.01.2019)
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Journal Article
CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training
Mostavi, Milad, Chiu, Yu-Chiao, Chen, Yidong, Huang, Yufei
Published in BMC bioinformatics (12.05.2021)
Published in BMC bioinformatics (12.05.2021)
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Journal Article
Deep learning of pharmacogenomics resources: moving towards precision oncology
Chiu, Yu-Chiao, Chen, Hung-I Harry, Gorthi, Aparna, Mostavi, Milad, Zheng, Siyuan, Huang, Yufei, Chen, Yidong
Published in Briefings in bioinformatics (01.12.2020)
Published in Briefings in bioinformatics (01.12.2020)
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Journal Article
Systems approach for congruence and selection of cancer models towards precision medicine
Zou, Jian, Shah, Osama, Chiu, Yu-Chiao, Ma, Tianzhou, Atkinson, Jennifer M, Oesterreich, Steffi, Lee, Adrian V, Tseng, George C
Published in PLoS computational biology (10.01.2024)
Published in PLoS computational biology (10.01.2024)
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Journal Article
GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization
Chen, Hung-I Harry, Chiu, Yu-Chiao, Zhang, Tinghe, Zhang, Songyao, Huang, Yufei, Chen, Yidong
Published in BMC systems biology (21.12.2018)
Published in BMC systems biology (21.12.2018)
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Journal Article
Deep learning tackles single-cell analysis—a survey of deep learning for scRNA-seq analysis
Flores, Mario, Liu, Zhentao, Zhang, Tinghe, Hasib, Md Musaddaqui, Chiu, Yu-Chiao, Ye, Zhenqing, Paniagua, Karla, Jo, Sumin, Zhang, Jianqiu, Gao, Shou-Jiang, Jin, Yu-Fang, Chen, Yidong, Huang, Yufei
Published in Briefings in bioinformatics (17.01.2022)
Published in Briefings in bioinformatics (17.01.2022)
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Journal Article
Molecular and immune signatures, and pathological trajectories of fatal COVID‐19 lungs defined by in situ spatial single‐cell transcriptome analysis
Das, Arun, Meng, Wen, Liu, Zhentao, Hasib, Md Musaddaqul, Galloway, Hugh, Ramos da Silva, Suzane, Chen, Luping, Sica, Gabriel L., Paniz‐Mondolfi, Alberto, Bryce, Clare, Grimes, Zachary, Sordillo, Emilia M., Cordon‐Cardo, Carlos, Rivera, Karla Paniagua, Flores, Mario, Chiu, Yu‐Chiao, Huang, Yufei, Gao, Shou‐Jiang
Published in Journal of medical virology (01.08.2023)
Published in Journal of medical virology (01.08.2023)
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Journal Article
Transformer for Gene Expression Modeling (T-GEM): An Interpretable Deep Learning Model for Gene Expression-Based Phenotype Predictions
Zhang, Ting-He, Hasib, Md Musaddaqul, Chiu, Yu-Chiao, Han, Zhi-Feng, Jin, Yu-Fang, Flores, Mario, Chen, Yidong, Huang, Yufei
Published in Cancers (29.09.2022)
Published in Cancers (29.09.2022)
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Journal Article
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
Saeed, Anwaar, Park, Robin, Pathak, Harsh, Al-Bzour, Ayah Nedal, Dai, Junqiang, Phadnis, Milind, Al-Rajabi, Raed, Kasi, Anup, Baranda, Joaquina, Sun, Weijing, Williamson, Stephen, Chiu, Yu-Chiao, Osmanbeyoglu, Hatice Ulku, Madan, Rashna, Abushukair, Hassan, Mulvaney, Kelly, Godwin, Andrew K, Saeed, Azhar
Published in Nature communications (20.02.2024)
Published in Nature communications (20.02.2024)
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Journal Article
Classification of Cancer Types Using Graph Convolutional Neural Networks
Ramirez, Ricardo, Chiu, Yu-Chiao, Hererra, Allen, Mostavi, Milad, Ramirez, Joshua, Chen, Yidong, Huang, Yufei, Jin, Yu-Fang
Published in Frontiers in physics (01.06.2020)
Published in Frontiers in physics (01.06.2020)
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Journal Article
CeL-ID: cell line identification using RNA-seq data
Mohammad, Tabrez A, Tsai, Yun S, Ameer, Safwa, Chen, Hung-I Harry, Chiu, Yu-Chiao, Chen, Yidong
Published in BMC genomics (04.02.2019)
Published in BMC genomics (04.02.2019)
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Journal Article
An ancestry informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data
Wang, Li-Ju, Zhang, Catherine W, Su, Sophia C, Chen, Hung-I H, Chiu, Yu-Chiao, Lai, Zhao, Bouamar, Hakim, Ramirez, Amelie G, Cigarroa, Francisco G, Sun, Lu-Zhe, Chen, Yidong
Published in BMC genomics (30.12.2019)
Published in BMC genomics (30.12.2019)
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Journal Article
GDF6-CD99 Signaling Regulates Src and Ewing Sarcoma Growth
Zhou, Fuchun, Elzi, David J., Jayabal, Panneerselvam, Ma, Xiuye, Chiu, Yu-Chiao, Chen, Yidong, Blackman, Barron, Weintraub, Susan T., Houghton, Peter J., Shiio, Yuzuru
Published in Cell reports (Cambridge) (03.11.2020)
Published in Cell reports (Cambridge) (03.11.2020)
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Journal Article
Knock-out of Hopx disrupts stemness and quiescence of hematopoietic stem cells in mice
Lin, Chien-Chin, Yao, Chi-Yuan, Hsu, Yueh-Chwen, Hou, Hsin-An, Yuan, Chang-Tsu, Li, Yi-Hung, Kao, Chein-Jun
Published in Oncogene (09.07.2020)
Published in Oncogene (09.07.2020)
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Journal Article
Integrating resistance functions to predict response to induction chemotherapy in de novo acute myeloid leukemia
Chiu, Yu‐Chiao, Hsiao, Tzu‐Hung, Tsai, Jia‐Rong, Wang, Li‐Ju, Ho, Tzu‐Chieh, Hsu, Shih‐Lan, Teng, Chieh‐Lin Jerry
Published in European journal of haematology (01.10.2019)
Published in European journal of haematology (01.10.2019)
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Journal Article
scdNet: a computational tool for single-cell differential network analysis
Chiu, Yu-Chiao, Hsiao, Tzu-Hung, Wang, Li-Ju, Chen, Yidong, Shao, Yu-Hsuan Joni
Published in BMC systems biology (21.12.2018)
Published in BMC systems biology (21.12.2018)
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Journal Article
Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer
Chiu, Yu-Chiao, Wang, Li-Ju, Hsiao, Tzu-Hung, Chuang, Eric Y, Chen, Yidong
Published in BMC genomics (03.10.2017)
Published in BMC genomics (03.10.2017)
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