Publications

Peer-reviewed Journals

* equal contribution; # corresponding author

2025

• Shen YC, Chang NW, Yeh CP, Lin WY, Wei MF, Ou DL, Hsu CL, Cheng AL. Corticosteroid premedication on anti-tumor effect of immune checkpoint blockade in murine hepatocellular carcinoma models. J Immunother Cancer. 2025;13(2):e009704. doi: 10.1136/jitc-2024-009704.

• Yao CY, Ko TY, Yang LT, Takeuchi M, Yeh CF, Lin MS, Chen YH, Kuo CY, Hsu CL, Chou WC, Kao HL. Clonal hematopoiesis is associated with adverse clinical outcomes and left ventricular remodeling in aortic stenosis.  JACC Adv. 2025; 4(2):101532.doi: 10.1016/j.jacadv.2024.101532.

• Li CL, Hsu CL, Lin YY, Ho MC, Hu RH, Tzeng ST, Wang YC, Tanaka Y, Chen PJ, Yeh SH. HBV DNA integration and somatic mutations in HCC patients with HBV-HCV dual infection reveals profiles intermediate between HBV- and HCV-related HCC. J Biomed Sci. 2025; 32(1):2. doi: 10.1186/s12929-024-01094-7.

• Wu WK, Lo YL, Chiu JY, Hsu CL, Lo IH, Panyod S, Liao YC, Chiu THT, Yang YT, Kuo HC, Zou HB, Chen YH, Chuang HL, Yen JJY, Wang JT, Chiu HM, Hsu CC, Kuo CH, Sheen LY, Kao HL, Wu MS. Gut microbes with the gbu genes determine TMAO production from L-carnitine intake and serve as a biomarker for precision nutrition. Gut Microbes. 2025;17(1):2446374. doi: 10.1080/19490976.2024.2446374.

• Lin CC, Hsu CL, Yao CY, Wang YH, Yuan CT, Kuo YY, Lee JY, Shih PT, Kao CJ, Chuang PH, Hsu YC, Hou HA, Chou WC, Tien HF. HOPX as a tumour-suppressive protein in T-cell acute lymphoblastic leukaemia. Br J Haematol. 2025; 206(2):505-516. doi: 10.1111/bjh.19965.

• Chen IC, Lin CH, Chang DY, Wei-Wu Chen T, Wang MY, Ma WL, Lin YT, Huang SM, Hsu CL, Lu YS. Hormone therapy enhances anti-PD1 efficacy in premenopausal estrogen receptor-positive and HER2-negative advanced breast cancer. Cell Rep Med. 2025; 6(1):101879. doi: 10.1016/j.xcrm.2024.101879.

• Chen YC*, Hsu CL*, Wang HM*, Wu SG*, Chang YL, Chen JS, Wu YC, Lin YT, Yang CY, Lin MW, Lee JM, Kuo SW, Chen KC, Hsu HH, Huang PM, Huang YL, Yu CJ, Pirooznia M, Huang BE, Yang R, Shih JY, Yang PC. Multi-omics Analysis Reveals Molecular Changes During Early Progression of Precancerous Lesions to Lung Adenocarcinoma in Never-Smokers. Cancer Res. 2025; 85(3):602-617. doi: 10.1158/0008-5472.CAN-24-0821.

• Liu SY, Hsu CL, Yang SF, Lee HS, Sheu JC, Weng MT. Intratumoral administration of poly-ICLC enhances the antitumor effects of anti-PD-1. J Hepatobiliary Pancreat Sci. 2025; 32(2):139-150. doi: 10.1002/jhbp.12088.

2024

• Chen YH, Lee YM, Ou DL, Hsu CL, Hsu C, Chen CN, Ko JY, Tan CT. Regorafenib enhances M1/M2 macrophage polarization by inhibiting the secretion of plasminogen activator inhibitor-1 in head and neck squamous cell carcinoma. Life Sci. 2024; 358:123147. doi: 10.1016/j.lfs.2024.123147. 

• Huang HC, Huang YL, Chen YJ, Wu HY, Hsu CL, Kao HF, Liao BC, Hsieh MS, Lin NY, Liao YH, Chen HL, Chen CN, Chen TC, Wang CP, Yang TL, Huang MC, Lin MC, Lou PJ. The branched N-glycan of PD-L1 predicts immunotherapy responses in patients with recurrent/metastatic HNSCC. Oncogenesis. 2024;13(1):36. doi: 10.1038/s41389-024-00532-3. 

• Hung TK, Liu WC, Lai SK, Chuang HW, Lee YC, Lin HY, Hsu CL, Chen CY, Yang YC, Hsu JS, Chen PL. Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies. Genome Res. 2024; doi: 10.1101/gr.278358.123. 

• Chung KP, Cheng CN, Chen YJ, Hsu CL, Huang YL, Hsieh MS, Kuo HC, Lin YT, Juan YH, Nakahira K, Chen YF, Liu WL, Ruan SY, Chien JY, Plataki M, Cloonan SM, Carmeliet P, Choi AMK, Kuo CH, Yu CJ. Alveolar epithelial cells mitigate neutrophilic inflammation in lung injury through regulating mitochondrial fatty acid oxidation. Nat Commun. 2024;15(1):7241. doi: 10.1038/s41467-024-51683-1.

• Lin CC, Yao CY, Wang YH, Hsu YC, Yuan CT, Chen TC, Hsu CL, Lee SH, Lee JY, Shih PT, Kao CJ, Chuang PH, Kuo YY, Hou HA, Chou WC, Tien HF. IDH2 mutation accelerates TPO-induced myelofibrosis with enhanced S100a8/a9 and NFκB signaling in vivo. eJHaem. 2024;5(4):738-748. doi.org/10.1002/jha2.983

• Huang MC, Chen PL#, Hsu CL#. Transcriptome analysis of mesenchymal progenitor cells revealed molecular insights into metabolic dysfunction and inflammation in polycystic ovary syndrome. Int J Mol Sci. 2024;25(14):7948. doi: 10.3390/ijms25147948. 

• Cheng CL, Lin YY, Hsu CL, Li CL, Yuan CT, Lai YY, Fang WQ, Chen PJ, Yeh SH, Tien HF. Unraveling the role of hepatitis B virus DNA integration in B-cell lymphomagenesis. Br J Cancer. 2024; 131(6):996-1004. doi: 10.1038/s41416-024-02763-y 

• Chen YC, Chuang EY, Tu YK, Hsu CL, Cheng NC. Human platelet lysate-cultured adipose-derived stem cell sheets promote angiogenesis and accelerate wound healing via CCL5 modulation. Stem Cell Res Ther. 2024; 15(1):163. doi: 10.1186/s13287-024-03762-9. 

• Yao CY, Lin CC, Wang YH, Kao CJ, Tsai XC, Hou HA, Tien HF, Hsu CL#, Chou WC. Kinome expression profiling improves risk stratification and therapeutic targeting in myelodysplastic syndromes. Blood Adv. 2024; 8(10):2442-2454. doi: 10.1182/bloodadvances.2023011512.

• Li CL, Hsu CL, Lin YY, Ho MC, Hu RH, Chen CL, Ho TC, Lin YF, Tsai SF, Tzeng ST, Huang CF, Wang YC, Yeh SH, Chen PJ. HBV DNA integration into telomerase or MLL4 genes and TERT promoter point mutation as three independent signatures in subgrouping HBV-related HCC with distinct features. Liver Cancer. 2024; 13(1):41-55. doi: 10.1159/000530699

• Lin MC, Chuang YT, Wu HY, Hsu CL, Lin NY, Huang MC, Lou PJ. Targeting tumor O-glycosylation modulates cancer-immune-cell crosstalk and enhances anti-PD-1 immunotherapy in head and neck cancer. Mol Oncol. 2024; 18(2):350-368. doi: 10.1002/1878-0261.13489.

• Wu YH, Chang WT, Hsu CL, Lu YF, Wang JT, Tzeng SJ. FcγRIIB modulates splenic germinal center response against immune subversion during acute influenza A virus infection. J Microbiol Immunol Infect. 2024; 57(1):64-75. doi: 10.1016/j.jmii.2023.11.007.

• Wu SG, Chang TH, Tsai MF, Liu YN, Huang YL, Hsu CL, Jheng HN, Shih JY. miR-204 suppresses cancer stemness and enhances osimertinib sensitivity in non-small cell lung cancer by targeting CD44. Mol Ther Nucleic Acids. 2024; 35(1):102091. doi: 10.1016/j.omtn.2023.102091. 

• Jian CZ, Lin L, Hsu CL, Chen YH, Hsu C, Tan CT, Ou DL. A potential novel cancer immunotherapy: Agonistic anti-CD40 antibodies. Drug Discov Today. 2024; 29(3):103893. doi: 10.1016/j.drudis.2024.103893. 

• Yuan CT, Huang WT, Hsu CL, Wang H, Pan YH, Wu UI, Wang JT, Sheng WH, Chen YC, Chang SC. CXCL9 as a reliable biomarker for discriminating anti-IFN-γ-autoantibody-associated lymphadenopathy that mimics lymphoma. J Clin Immunol. 2024; 44(1):35. doi: 10.1007/s10875-023-01643-z

2023

• Lin TY, Jiang D, Chen WR, Lin JS, Zhang XY, Chen CH, Hsu CL, Lai LC, Chen PH, Yang KC, Sansing LH, Chang CF. Trained immunity induced by high-salt diet impedes stroke recovery. EMBO Rep. 2023; 24(12):e57164. doi: 10.15252/embr.202357164. [IF: 7.7]

• Chen YL, Liu YN, Lin YT, Tsai MF, Wu SG, Chang TH, Hsu CL, Wu HD, Shih JY. LncRNA SLCO4A1-AS1 suppresses lung cancer progression by sequestering the TOX4-NTSR1 signaling axis. J Biomed Sci. 2023; 30(1):80. doi: 10.1186/s12929-023-00973-9. [IF: 11.0]

• Lee YM*, Hsu CL*, Chen YH, Ou DL, Hsu C, Tan CT. Genomic and transcriptomic landscape of an oral squamous cell carcinoma mouse model for immunotherapy. Cancer Immunol Res. 2023; 11(11):1553-1567. doi: 10.1158/2326-6066.CIR-23-0133. [IF: 10.1]

• Li CW, Young TH, Wang MH, Pei MY, Hsieh TY, Hsu CL, Cheng NC. Low-glucose culture environment can enhance the wound healing capability of diabetic adipose-derived stem cells. Stem Cell Res Ther. 2023; 14(1):236. doi: 10.1186/s13287-023-03478-2. [IF: 7.5]

• Chang EM, Chao CC, Wang MT, Hsu CL, Chen PC. PM2.5 promotes pulmonary fibrosis by mitochondrial dysfunction. Environ Toxicol. 2023; 38(8):1905-1913. doi: 10.1002/tox.23817 [IF: 4.5]

• Guo JC, Hsu CL, Hsieh MS, Lin CC, Huang TC, Kuo HY, Shao YY, Hsu CH. Different immune contextures underlie tumor site-specific responses to immune checkpoint blockade in esophageal cancer. Thorac Cancer. 2023; 14(22):2216-2221. doi: 10.1111/1759-7714.14997. [IF: 2.9]

• Yao CY, Lin CC, Wang YH, Hsu CL, Kao CJ, Hou HA, Chou WC, Tien HF. The clinical and biological characterization of acute myeloid leukemia patients with S100A4 overexpression. J Formos Med Assoc. 2023; 122(7):636-647. doi: 10.1016/j.jfma.2022.11.003 [IF: 3.2]

• Chang YW, Tony Yang T, Chen MC, Liaw YG, Yin CF, Lin-Yan XQ, Huang TY, Hou JT, Hung YH, Hsu CL, Huang HC, Juan HF. Spatial and temporal dynamics of ATP synthase from mitochondria toward the cell surface. Commun Biol. 2023; 6(1):427. doi: 10.1038/s42003-023-04785-3. [IF: 5.9]

• Wu SY, Wu HT, Wang YC, Chang CJ, Shan YS, Wu SR, Chiu YC, Hsu CL, Juan HF, Lan KY, Chu CW, Lee YR, Lan SH, Liu HS. Secretory autophagy promotes RAB37-mediated insulin secretion under glucose stimulation both in vitro and in vivo. Autophagy. 2023; 19(4):1239-1257. doi: 10.1080/15548627.2022.2123098 [IF: 13.3]

• Chen HY, Lin HI, Hsu CL, Chen PL, Huang CY, Teng SC, Lin CH. A novel C19orf12 frameshift mutation in a MPAN pedigree impairs mitochondrial function and connectivity leading to neurodegeneration. Parkinsonism Relat Disord. 2023; 109:105353. doi: 10.1016/j.parkreldis.2023.105353 [IF: 4.1]

• Tsai YC, Wang TY, Hsu CL, Lin WC, Chen JY, Li JH, Pu YS, Cheng AL, Cheng JC, Su SF. Selective inhibition of HDAC6 promotes bladder cancer radiosensitization and mitigates the radiation-induced CXCL1 signalling. Br J Cancer. 2023; 128(9):1753-1764. doi: 10.1038/s41416-023-02195-0 [IF: 8.8]

• Liao YH, Hsu CL, Leu CY, Lai SF, Huang YL, Hsieh MS, Chen TC, Chen CN, Wang CP, Yang TL, Tsai MH, Lin MC, Lou PJ. Radiation-induced sarcoma of head and neck: clinical characteristics and molecular signatures. Head Neck. 2023; 45(3):638-646. doi:10.1002/hed.27279 [IF: 2.9]

• Lien HC*, Hsu CL*, Lu YS, Chen TW, Chen IC, Li YC, Huang CS, Cheng AL, Lin CH. Transcriptomic alterations underlying metaplasia into specific metaplastic components in metaplastic breast carcinoma. Breast Cancer Res. 2023; 25(1):11. doi: 10.1186/s13058-023-01608-5. [IF: 7.4]

• Lee YM. Chen YH, Ou DL, Hsu CL, Liu JH, Ko JY, Hu MC, Tan CT. SN-38, an active metabolite of irinotecan, enhances anti-PD1 treatment efficacy in head and neck squamous cell carcinoma. J Pathol. 2023; 259(4):428-440. doi: 10.1002/path.6055. [IF: 7.3]

• Chen KP, Hsu CL, Oyang YJ, Huang HC, Juan HF. BIC: a database for the transcriptional landscape of bacteria in cancer. Nucleic Acids Res. 2023; 51(D1):D1205-D1211. doi: 10.1093/nar/gkac891 [IF: 14.9]

• Chen KH, Hsu CL, Su YL, Yuan CT, Lin LI, Tsai JH, Liang YH, Cheng AL, Yeh KH. Novel prognostic implications of complement activation in the tumour microenvironment for de novo metastatic BRAF V600E mutant colorectal cancer. Br J Cancer. 2023; 128(1):102-111. doi: 10.1038/s41416-022-02010-2  [IF: 8.8]

• Lee WH, Lin CC, Wang YH, Yao CY, Kuo YY, Tseng MH, Peng YL, Hsu CA, Sun HI, Chuang YK, Hsu CL, Tien FM, Tsai CH, Chou WC, Hou HA, Tien HF. Distinct genetic landscapes and their clinical implications in younger and older patients with myelodysplastic syndromes. Hematol Oncol. 2023; 41(3):463-473. doi: 10.1002/hon.3109 [IF: 3.3]

• Lin MC, Hsu CL, Lai SF, Huang YL, Hsieh MS, Chen TC, Chen CN, Wang CP, Yang TL, Ko JY, Tsai MH, Lou PJ. Spindle cell carcinoma of the head and neck: clinical characteristics and molecular signatures. Laryngoscope. 2023; 133(9):2183-219. doi: 10.1002/lary.30467 [IF: 2.6]

2022

• Chen TWW, Hsu CL, Hong RL, Lee JC, Chang K, Yu CW, Chen SC, Guo JC, Chen ML, Hsu MC, Kung TF, Cheng AL, Yen CC. A single-arm phase Ib/II study of lenvatinib plus eribulin in advanced liposarcoma and leiomyosarcoma. Clin Cancer Res. 2022; 28(23):5058-5065. doi: 10.1158/1078-0432.CCR-22-2092 [IF: 11.5]

• Hsu CL, Yin CF, Chang YW, Fan YC, Lin SH, Wu YC, Huang HC, Juan HF. LncRNA SNHG1 regulates neuroblastoma cell fate via interactions with HDAC1/2. Cell Death Dis. 2022; 13(9):809. doi: 10.1038/s41419-022-05256-z [IF: 9.0]

• Jhuang YL, Yang CW, Tseng YF, Hsu CL, Li HY, Yuan RH, Jeng YM. SIN3-HDAC complex-associated factor, a chromatin remodelling gene located in the 12p amplicon, is a potential germ cell tumour-specific oncogene. J Pathol. 2022; 258(4):353-365. doi: 10.1002/path.6007  [IF: 7.3]

• Wang YH, Yao CY, Lin CC, Chen CL, Hsu CL, Tsai CH, Hou HA, Chou WC, Tien HF. Higher RUNX1 expression levels are associated with worse overall and leukaemia-free survival in myelodysplastic syndrome patients. eJHaem. 2022; 3:1209–1219. doi: 10.1002/jha2.547 

• Lin MJ, Lin YC, Chen NC, Luo AC, Lai SK, Hsu CL, Hsu JS, Chen CY, Yang WS, Chen PL. Profiling genes encoding the adaptive immune receptor repertoire with gAIRR suite. Front Immunol. 2022; 13:922513. doi: 10.3389/fimmu.2022.922513 [IF: 7.3]

• Guo JC, Lin CC, Hsu CL, Huang TC, Kuo HY, Lin CY, Lien MY, Cheng AL, Hsu CH. Deleterious alterations of DNA damage response and repair genes and clinical benefit to Anti-PD-1 therapy in esophageal squamous cell carcinoma. Esophagus. 2022; 19(4):693-701. doi: 10.1007/s10388-022-00940-7 [IF: 2.4]

• Guo JC*, Hsu CL*, Huang YL, Lin CC, Huang TC, Wu IC, Lin CY, Lien MY, Kuo HY, Cheng AL, Hsu CH. B cells in tumor microenvironment associated with the clinical benefit to programmed cell death protein-1 blockade therapy in patients with advanced esophageal squamous cell carcinoma. Front Oncology. 2022; 12:879398. doi: 10.3389/fonc.2022.879398 [IF: 4.7]

• Chen IC, Awasthi D, Hsu CL, Song M, Chae CS, Dannenberg AJ, Cubillos-Ruiz JR. High fat diet-induced obesity alters dendritic cell homeostasis by enhancing mitochondrial fatty acid oxidation. J Immunol 2022; 209(1):69-76. doi: 10.4049/jimmunol.2100567. [IF: 4.4]

• Yuan RH*, Hsu CL*, Jhuang YL, Liu YR, Hsieh TH, Jeng YM. Tumor-matrix interaction induces phenotypic switching in liver cancer cells. Hepatol Int. 2022; 16(3):562-576. doi: 10.1007/s12072-022-10315-w. [IF: 6.6]

• Li A, Chen JY, Hsu CL, Oyang YJ, Huang HC, Juan HF. A single-cell network-based drug repositioning strategy for post-COVID-19 pulmonary fibrosis. Pharmaceutics. 2022; 14:971. doi: 10.3390/pharmaceutics14050971 [IF: 5.4]

• Chyuan IT, Chu CL, Hsu CL, Pan MH, Liao HJ, Wu CS, Hsu PN. T Cell-specific deletion of TRAIL receptor reveals its critical role for regulating Ppathologic T cell activation and disease induction in experimental autoimmune encephalomyelitis. J Immunol. 2022; 208(7):1534-1544. doi: 10.4049/jimmunol.2100788 [IF: 4.4]

• Wang YH, Lin CC, Yao CY, Hsu CL, Tsai CH, Hou HA, Chou WC, Tien HF. Immune signatures of bone marrow cells can independently predict prognosis in patients with myelodysplastic syndrome. Br J Haematol. 2022; 196(1):156-168. doi: 10.1111/bjh.17837. [IF: 6.5]

2021

• Yu WH, Hsu CL, Lin CC, Oyang YJ, Juan HF, Huang HC. Stratification of lncRNA modulation networks in breast cancer. BMC Med Genomics. 2021; 14(Suppl 3):300. doi: 10.1186/s12920-022-01236-6. 

• Wu YC, Chen CI, Chen PY, Kuo CH, Hung YH, Peng KY, Wu VC, Tasi-Wu JJ#, Hus CL#. GRAde: a long-read sequencing approach to efficiently identifying the CYP11B1/CYP11B2 chimeric form in patients with glucocorticoid-remediable aldosteronism. BMC Bioinformatics. 2021; 22:613. doi: 10.1186/s12859-022-04561-w 

• Li A, Yu WH, Hsu CL, Huang HC, Juan HF. Modular signature of long non-coding RNA association networks as a prognostic biomarker in lung cancer. BMC Med Genomics. 2021; 14(Suppl 3):290. doi: 10.1186/s12920-021-01137-0. 

• Wang HY, Hou HA, Lin CC, Kuo YY, Yao CY, Hsu CL, Tseng MH, Tsai CH, Peng YL, Kao CJ, Chou WC, Tien HF. A CIBERSORTx-based immune-cell scoring system could independently predict prognosis of myelodysplastic syndrome patients. Blood Adv. 2021; 5(22):4535-4548. doi: 10.1182/bloodadvances.2021005141.

• Chen HY, Hsu CL, Lin HY, Lin YF, Tsai SF, Ho YJ, Li YR, Tsai JW, Teng SC, Lin CH. Clinical and functional characterization of a novel STUB1 frameshift mutation in autosomal dominant spinocerebellar ataxia type 48 (SCA48). J Biomed Sci. 2021; 28(1):65. doi: 10.1186/s12929-021-00763-1. 

• Chang KH, Huang CY, Ou-Yang CH, Ho CH, Lin HY, Hsu CL, Chen YT, Chou YC, Chen YJ, Chen Y, Lin JL, Wang JK, Lin PW, Lin YR, Lin MH, Tseng CK, Lin CH. In vitro genome editing rescues parkinsonism phenotypes in induced pluripotent stem cells-derived dopaminergic neurons carrying LRRK2 p.G2019S mutation. Stem Cell Res Ther. 2021; 12(1):508. doi: 10.1186/s13287-021-02585-2. 

• Ou DL, Tseng SJ, Kempson IM, Hsu CL, Yang PC, Liao ZX. Enhanced targeting and immune activation of tumor microenvironment by nanomodified anti-PD1 in liver cancer. Adv Therapeutics. 2021; 2021:2100048. doi: 10.1002/adtp.202100048

• Wang MH*, Hsu CL*, Wu CH, Chiou LL, Tsai YT, Lee HS, Lin SP. Timing does matter: Nerve-mediated HDAC1 paces the temporal expression of morphogenic genes during axolotl limb regeneration. Front Cell Dev Biol. 2021; 9:641987. doi: 10.3389/fcell.2021.641987 

• Hsu CL*, Ou DL*, Bai LY, Chen CW, Lin L, Huang SF, Cheng AL, Cheng YM, Hsu C. Exploring markers of exhausted CD8 T cells to predict response to immune checkpoint inhibitor therapy for hepatocellular carcinoma. Liver Cancer. 2021; 10(4):346-359. doi: 10.1159/000515305 

• Ou DL*, Chen CW*, Hsu CL*, Chung CH, Feng ZR, Lee BS, Cheng AL, Yang MH, Hsu C. Regorafenib enhances antitumor immunity via inhibition of p38 kinase/Creb1/Klf4 axis in tumor-associated macrophages. J Immunother Cancer. 2021; 9(3):e001657. doi: 10.1136/jitc-2020-001657 

• Chiang CS, Fu SJ, Hsu CL, Jeng CJ, Tang CY, Huang YS, Tang SC. Neuronal exosomes secreted under oxygen-glucose deprivation/reperfusion presenting differentially expressed miRNAs and affecting neuronal survival and neurite outgrowth. Neuromolecular Med. 2021; 23(3):404-415. doi: 10.1007/s12017-020-08641-z 

• Wang YH, Lin CC, Hsu CL, Hung SY, Yao CY, Lee SH, Tsai CH, Hou HA, Chou WC, Tien HF. Distinct clinical and biological characteristics of acute myeloid leukemia with higher expression of long noncoding RNA KIAA0125. Ann Hematol. 2021; 100(2):487-498.  doi: 10.1007/s00277-020-04358-y 

• Hung SY, Lin CC, Hsu CL, Yao CY, Wang YH, Tsai CH, Hou HA, Chou WC, Tien HF. The expression levels of long non‐coding RNA KIAA0125 are associated with distinct clinical and biological features in myelodysplastic syndromes. Br J Haematol. 2021; 192(3):589-598. doi: 10.1111/bjh.17231  

• Chung KP, Huang YL, Chen YJ, Juan YH, Hsu CL, Nakahira K, Huang YT, Lin MW, Wu SG, Shih JY, Chang YL, Yu CJ. Multi-kinase framework regulates activation of dynamin-related protein 1 to promote proliferation and invasion of lung adenocarcinoma. Mol Oncol. 2021; 15(2):560-578. doi: 10.1002/1878-0261.12843. 

2020

• Chang YW, Hsu CL, Tang CW, Chen XJ, Hang HC, Juan HF. Multiomics reveals ectopic ATP synthase blockade induces cancer cell death via a lncRNA-mediated phospho-signaling network. Mol Cell Proteomics. 2020; 19(11):1805-1825. doi: 10.1074/mcp.RA120.002219. 

• Cheung CHY, Hsu CL, Lin TY, Chen WT, Wang YC, Huang HC, Juan HF. ZNF322A-mediated protein phosphorylation induces autophagosome formation through modulation of IRS1-AKT glucose uptake and HSP-elicited UPR in lung cancer. J Biomed Sci. 2020; 27(1):75. doi: 10.1186/s12929-020-00668-5. 

• Wang WH, Hsu CL, Huang HC, Juan HF. Quantitative phosphoproteomics reveals cell alignment and mitochondrial length change under cyclic stretching in lung cells. Int J Mol Sci. 2020; 21(11):E4074. doi: 10.3390/ijms21114074 

• Wang HY, Liu YN, Wu SG, Hsu CL, Chang TH, Tsai MF, Lin YT, Shih JY. MiR-200c-3p suppression is associated with development of acquired resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in EGFR mutant non-small cell lung cancer via a mediating epithelial-to-mesenchymal transition (EMT) process. Cancer Biomark. 2020; 28(3):351-363. doi: 10.3233/CBM-191119. 

• Yin CF, Kao SC, Hsu CL, Chang YW, Cheung CHY, Huang HC, Juan HF. Phosphoproteome analysis reveals dynamic heat shock protein 27 phosphorylation in tanshinone IIA-induced cell death. J Proteome Res. 2020; 19(4):1620-1634. doi: 10.1021/acs.jproteome.9b00836 

• Ho TC, Wang EY, Yeh KH, Jeng YM, Horng JH, Wu LL, Chen YT, Huang HC, Hsu CL, Chen PJ, Yeh SH, Chen DS. Complement C1q mediates the expansion of periportal hepatic progenitor cells in senescence-associated inflammatory liver. Proc Natl Acad Sci U S A. 2020; 117(12):6717-6725. doi: 10.1073/pnas.1918028117 

• Shen YC, Hsu CL, Jeng YM, Ho MC, Ho CM, Yeh CP, Yeh CY, Hsu MC, Hu RH, Cheng AL. Reliability of a single-region tumor sample for evaluating the immune tumor microenvironment of hepatocellular carcinoma tumors. J Hepatol. 2020; 72:489-497. doi: 10.1016/j.jhep.2019.09.032. 

• Wang YH, Lin CC, Yao CY, Hsu CL, Hou HA, Tsai HC, Chou WC, Tien HF. A four-gene leukemic stem cell score can independently predict the prognosis of myelodysplastic syndrome patients. Blood Advances. 2020; 4(4):644-654. doi: 10.1182/bloodadvances.2019001185. 

• Lee PC, Chen ST, Kuo TC, Lin TC, Lin MC, Huang J, Hung JS, Hsu CL, Juan HF, Lee PH, Huang MC. C1GALT1 is associated with poor survival and promotes soluble Ephrin A1-mediated cell migration through activation of EPHA2 in gastric cancer. Oncogene. 2020; 39(13):2724-2740. doi: 10.1038/s41388-020-1178-7. 

2019

• Cheung CHY, Hsu CL, Tsuei CY, Kuo TT, Huang CT, Hsu WM, Chung YH, Wu HY, Hsu CC, Huang HC, Juan HF. Combinatorial targeting of MTHFD2 and PAICS in purine synthesis as a novel therapeutic strategy. Cell Death Dis. 2019; 10(11):786.

• Chang HC*, Huang HC*, Juan HF#, Hsu CL#. Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation. BMC Genomics. 2019; 20(Suppl 10):896.

• Hsieh CH, Cheung CHY, Liu YL, Hou CL, Hsu CL, Huang CT, Yang TS, Chen SF, Chen CN, Hsu WM, Huang HC, Juan HF. Quantitative proteomics of Th-MYCN transgenic mice reveals aurora kinase inhibitor altered metabolic pathways and enhanced ACADM to suppress neuroblastoma progression. J Proteome Res. 2019; 18(11):3850-3866. doi: 10.1021/acs.jproteome.9b00245. 

• Hsu YC, Chen TC, Lin CC, Yuan CT, Hsu CL, Hou HA, Kao CJ, Chuang PH, Chen YR, Chou WC, Tien HF. Phf6-null hematopoietic stem cells have enhanced self-renewal capacity and oncogenic potentials. Blood Advances. 2019; 3(15):2355-2367. 

• Chung KP, Hsu CL, Fan LC, Huang Z, Bhatia D, Chen YC, Hisata S, Cho SJ, Nakahira K, Imamura M, Choi ME, Yu CJ, Cloonan SM, Choi MK. Mitofusins regulate lipid metabolism to mediate the development of lung fibrosis. Nat Communication. 2019; 10:3390. 

• Wu SG, Chang TH, Tsai MF, Liu YN, Hsu CL, Chang YL, Yu CJ, Shih JY. IGFBP7 drives resistance to epidermal growth factor receptor tyrosine kinase inhibition in lung cancer. Cancers (Basel). 2019; 11(1):36. doi: 10.3390/cancers11010036. 

• Ou DL, Lin YY, Hsu CL, Lin YY, Chen CW, Yu JS, Miaw SC, Hsu PN, Cheng AL, Hsu C. Development of a PD-L1-expressing orthotopic liver cancer model: implications for immunotherapy for hepatocellular carcinoma. Liver Cancer. 2019; 8(3):155-171. doi: 10.1159/000489318.  

• Yang TW, Sahu D, Chang YW, Hsu CL, Hsieh CH, Huang HC, Juan HF. RNA-binding proteomics reveals MATR3 interacting with lncRNA SNHG1 to enhance neuroblastoma progression. J Proteome Res. 2019; 18(1):406-416. doi: 10.1021/acs.jproteome.8b00693. 

2017

• Cheung CHY, Hsu CL, Chen KP, Chong ST, Wu CH, Huang HC, Juan HF. MCM2-regulated functional networks in lung cancer by multi-dimensional proteomic approach. Sci Rep. 2017; 7:13302.

• Hsu CL, Wang JK, Lu PC, Huang HC, and Juan HF. DynaPho: a web platform for inferring the dynamics of time-series phosphoproteomics. Bioinformatics. 2017; 33:3664–3666.

• Hua KT, Liu YF, Hsu CL, Cheng TY, Yang CY, Chang JS, Lee WJ, Hsiao M, Juan HF, Chien MH, Yang SF. 3'UTR polymorphisms of carbonic anhydrase IX determine the miR-34a targeting efficiency and prognosis of hepatocellular carcinoma. Sci Rep. 2017; 7(1):4466.  

• Lin TC, Chen ST, Huang MC, Huang J, Hsu CL, Juan HF, Lin HH, Chen CH. GALNT6 expression enhances aggressive phenotypes of ovarian cancer cells by regulating EGFR activity. Oncotarget. 2017;8(26):42588-42601.

• Lin MC, Lin JJ, Hsu CL, Juan HF, Lou PJ, and Huang MC. (2017) GATA3 interacts with and stabilizes HIF-1α to enhance cancer cell invasiveness. Oncogene. 2017;36(30):4243-4252. 

2016

• Wu CH*, Hsu CL*, Lu PC, Lin WC, Juan HF, and Huang HC. Identification of lncRNA functions in lung cancer based on associated protein-protein interaction modules. Sci Rep. 2016;6:35939. 

• Wang YT, Chiang HH, Huang YS, Hsu CL, Yang PJ, Juan HF, and Yang WS. A link between adipogenesis and innate immunity: RNase-L promotes 3T3-L1 adipogenesis by destabilizing Pref-1 mRNA. Cell Death Dis. 2016;7(11):e2458. 

• Sahu D, Hsu CL, Lin CC, Yang TW, Hsu WM, Ho SY, Juan HF, and Huang HC. Co-expression analysis identifies long noncoding RNA SNHG1 as a novel predictor for event-free survival in neuroblastoma. Oncotarget. 2016;7(36):58022:58037. 

• Hsu CL, Chang HY, Chang JY, Hsu WM, Huang HC, and Juan HF. Unveiling MYCN regulatory networks in neuroblastoma via integrative analysis of heterogeneous genomics data. Oncotarget. 2016;7(24):36293-36310. 

• Liu SY, Shun CT, Hung KY, Juan HF, Hsu CL, Huang MC, and Lai IR. Mucin glycosylating enzyme GALNT2 suppresses malignancy in gastric adenocarcinoma by reducing MET phosphorylation. Oncotarget. 2016;7(10):11251-11262. 

• Jen J, Lin LL, Chen HT, Liao SY, Lo FY, Tang YA, Hsu HS, Salgia R, Hsu CL, Huang HC, Juan HF and Wang YC. Oncoprotein ZNF322A transcriptionally deregulates alpha-adducin, cyclin D1 and p53 to promote tumor growth and metastasis in lung cancer. Oncogene. 2016;35(18):2357-69. 

2015

• Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC, and Juan HF. Temporal phosphoproteome dynamics induced by an ATP synthase inhibitor citreoviridin. Mol Cell Proteomics. 2015;14:3284-98. 

• Hsu CL, Juan HF, and Huang HC. Functional analysis and characterization of differential coexpression networks. Sci Rep. 2015;5:13295 

• Lin LL*, Hsu CL*, Hu CW, Ko SY, Hsieh HL, Huang HC, and Juan HF. Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis. BMC Genomics. 2015;16:533 

• Lin LL, Hsia CR, Hsu CL, Huang HC, and Juan HF. Integrating Transcriptomics and Proteomics to show that Tanshinone IIA Suppresses Cell Growth by Blocking Glucose Metabolism in Gastric Cancer Cells. BMC Genomics. 2015;16(1):41 

• Huang MJ, Hu RH, Chou CH, Hsu CL, Liu YW, Huang J, Hung JS, Lai IR, Juan HF, Yu SL, Wu YM, Huang MC. Knockdown of GALNT1 suppresses malignant phenotype of hepatocellular carcinoma by suppressing EGFR signaling. Oncotarget. 2015;6(8):5650-65

• Chang HY, Li MH, Huang TC, Hsu CL, Tsai SR, Lee SC, Huang HC, and Juan HF. Quantitative proteomics reveals middle infrared radiation-interfered networks in breast cancer cells. J Proteome Res. 2015;14(2):1250-62 

Before 2015

• Yang KC*, Hsu CL*, Lin CC*, Juan HF, and Huang HC. Mirin: Identifying MicroRNA Regulatory Modules in Protein-Protein Interaction Networks. Bioinformatics. 2014;30:2527-28 

• Hsu CL and Yang UC. Discovering pathway cross-talks based on the functional relations between pathways. BMC Genomics. 2012;13 Suppl 8:S25 

• Yang CP, Wang HA, Tsai TH, Fan A, Hsu CL, Chen CJ, Hong CJ, and Chen YM. Characterization of the neuropsychological phenotype of glycine N-methyltransferase -/- mice and evaluation of its responses to Clozapine and Sarcosine treatments. Eur Neuropsychopharmacol. 2012;22(8):596-606 

• Hsu CL, Huang YH, Hsu CT, and Yang UC. Prioritizing disease candidate genes by a gene Interconnectedness-based approach. BMC Genomics. 2011;12 Suppl 3:S25 

• Sudhir PR, Hsu CL, Wang MJ, Wang YT, Chen YJ, Sung TY, Hsu WL, Yang UC, and Chen JY. Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas. Plos One. 2011;6(5):e20199 

• Wang YT, Huang YH, Chen YC, Hsu CL, and Yang UC. PINT: Pathways integration tool. Nucleic Acids Res. 2010;38 Suppl:W124-131

Book Chapters

• Hsu CL and Cheung CHY. Transcriptomic data analysis: RNA-seq analysis using Galaxy. A Practice Guide to Cancer Systems Biology. 2018. World Scientific Publishing.  

• Hsu CL and Wang WH. Phosphorylation data analysis. A Practice Guide to Cancer Systems Biology. 2018. World Scientific Publishing.