研究成果 | CSB 國立台灣大學計算與系統生物學研究中心

Lou YC, Tu CF, Chou CC, Yeh HH, Chien CY, Sadotra S, Chen C, Yang RB, Hsu CH. Structural insights into the role of N-terminal integrity in PhoSL for core-fucosylated N-glycan recognition. Int J Biol Macromol. 2023 Nov 21;255:128309. doi: 10.1016/j.ijbiomac.2023.128309. Epub ahead of print. PMID: 37995778.
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 Nov 1;11(11):1553-1567. doi: 10.1158/2326-6066.CIR-23-0133. PMID: 37669022; PMCID: PMC10618654.
Hsieh CH, Huang CT, Cheng YS, Hsu CH, Hsu WM, Chung YH, Liu YL, Yang TS, Chien CY, Lee YH, Huang HC, Juan HF. Homoharringtonine as a PHGDH inhibitor: Unraveling metabolic dependencies and developing a potent therapeutic strategy for high-risk neuroblastoma. Biomed Pharmacother. 2023 Oct;166:115429. doi: 10.1016/j.biopha.2023.115429. Epub 2023 Sep 4. PMID: 37673018.
Chen SC, Jiang BC, Lu YJ, Chang CH, Wu TH, Lin SW, Yin HW, Lee TH, Hsu CH. Characterization and Crystal Structures of a Cubebol-Producing Sesquiterpene Synthase from Antrodia cinnamomea. J Agric Food Chem. 2023 Sep 6;71(35):13014-13023. doi: 10.1021/acs.jafc.3c00570. Epub 2023 Aug 11. PMID: 37566786.
Kao YC, Chang YW, Lai CP, Chang NW, Huang CH, Chen CS, Huang HC, Juan HF. Ectopic ATP synthase stimulates the secretion of extracellular vesicles in cancer cells. Commun Biol. 2023 Jun 15;6(1):642. doi: 10.1038/s42003-023-05008-5. PMID: 37322056; PMCID: PMC10272197.
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 Apr 18;6(1):427. doi: 10.1038/s42003-023-04785-3.
Huang HC, Juan HF. Quantitative analysis of high-throughput biological data. WIREs Computational Molecular Science. doi: 10.1002/wcms.1658.
Tu YH, Juan HF, Huang HC. Context-dependent gene regulatory network reveals regulation dynamics and cell trajectories using unspliced transcripts. Brief Bioinform. 2023 Jan 18:bbac633. doi: 10.1093/bib/bbac633. Epub ahead of print.
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 Jan 27;25(1):11. doi: 10.1186/s13058-023-01608-5. PMID: 36707876; PMCID: PMC9883935.
Tung CC, Kuo SC, Yang CL, Yu JH, Huang CE, Liou PC, Sun YH, Shuai P, Su JC, Ku C, Lin YJ. Single-cell transcriptomics unveils xylem cell development and evolution. Genome Biol. 2023 Jan 9;24(1):3. doi: 10.1186/s13059-022-02845-1. PMID: 36624504; PMCID: PMC9830878.
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 Jan 6;51(D1):D1205-D1211. doi: 10.1093/nar/gkac891.
Hsieh CY, Wen JH, Lin SM, Tseng TY, Huang JH, Huang HC, Juan HF. scDrug: From single-cell RNA-seq to drug response prediction. Comput Struct Biotechnol J. 2022 Dec 1;21:150-157. doi: 10.1016/j.csbj.2022.11.055.
Chen TW, 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 Dec 1;28(23):5058-5065. doi: 10.1158/1078-0432.CCR-22-2092.
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 Dec;258(4):353-365. doi: 10.1002/path.6007. Epub 2022 Oct 21.
Tsai RX, Fang KC, Yang PC, Hsieh YH, Chiang IT, Chen Y, Lee HG, Lee JT, Chu HC. TERRA regulates DNA G-quadruplex formation and ATRX recruitment to chromatin. Nucleic Acids Res. 2022 Nov 28;50(21):12217-12234. doi: 10.1093/nar/gkac1114.
Shanks CM, Huang J, Cheng CY, Shih HS, Brooks MD, Alvarez JM, Araus V, Swift J, Henry A, Coruzzi GM. Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice. Front Plant Sci. 2022 Nov 25;13:1006044. doi: 10.3389/fpls.2022.1006044.
Chiu ST, Tseng WW, Wei AC. Mathematical modeling and analysis of mitochondrial retrograde signaling dynamics. iScience. 2022 Nov 11;25(12):105502. doi: 10.1016/j.isci.2022.105502. PMID: 36444303; PMCID: PMC9700271.
Chen CH, Chu YT, Chen YF, Ko TY, Cheng YW, Lee MJ, Chen PL, Tang SC, Jeng JS. Comparison of clinical and neuroimaging features between NOTCH3 mutations and nongenetic spontaneous intracerebral haemorrhage. Eur J Neurol. 2022 Nov;29(11):3243-3254. doi: 10.1111/ene.15485. Epub 2022 Jul 18.
Hsieh PF, Liu SY, Chen CH, Chen PL, Tang SC, Jeng JS. Genetic analysis of a family presenting with coexisting cerebral cavernous malformations and polycystic kidney disease. J Formos Med Assoc. 2022 Nov;121(11):2331-2337. doi: 10.1016/j.jfma.2022.03.010. Epub 2022 Mar 31.
Mai TL, Chen CY, Chen YC, Chiang TW, Chuang TJ. Trans-genetic effects of circular RNA expression quantitative trait loci and potential causal mechanisms in autism. Mol Psychiatry. 2022 Nov;27(11):4695-4706. doi: 10.1038/s41380-022-01714-4. Epub 2022 Aug 12.
Guh CY, Shen HJ, Chen LW, Chiu PC, Liao IH, Lo CC, Chen Y, Hsieh YH, Chang TC, Yen CP, Chen YY, Chen TW, Chen LY, Wu CS, Egly JM, Chu HC. XPF activates break-induced telomere synthesis. Nat Commun. 2022 Oct 2;13(1):5781. doi: 10.1038/s41467-022-33428-0.
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 Oct;19(4):693-701. doi: 10.1007/s10388-022-00940-7. Epub 2022 Jul 11.
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 Sep 21;13(9):809. doi: 10.1038/s41419-022-05256-z.
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. 2022 Sep 15:1-19. doi: 10.1080/15548627.2022.2123098. Epub ahead of print.
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 Sep 8;13:922513. doi: 10.3389/fimmu.2022.922513.
Chen JY, Chou HH, Lim SC, Huang YJ, Lai KC, Guo CL, Tung CY, Su CT, Wang J, Liu E, Han HF, Yeh PY, Hu CM, Dunn AR, Frank CW, Wu YC, Yang MH, Chang YC. Multiomic characterization and drug testing establish circulating tumor cells as an ex vivo tool for personalized medicine. iScience. 2022 Sep 6;25(10):105081. doi: 10.1016/j.isci.2022.105081.
Wijaya ST, Tan TZ, Ngoi NYL, Yabuno A, Takehara K, Nakazawa H, Hirasawa T, Fujiwara H, Yasuda M, Jan YH, Chen SJ, Huang RYJ, Fujiwara K, Hasegawa K, Tan DS. 577P Impact of homologous recombination deficiency (HRD) on outcomes with intraperitoneal (IP) and intravenous (IV) chemotherapy in ovarian cancer: Analyses from the translational iPocc study (TriPocc). Annals of Oncology. 2022 Sep;33(7):S811. doi: 10.1016/j.annonc.2022.07.705.
Hung CT, Su TH, Chen YT, Wu YF, Chen YT, Lin SJ, Lin SL, Yang KC. Targeting ER protein TXNDC5 in hepatic stellate cell mitigates liver fibrosis by repressing non-canonical TGFβ signalling. Gut. 2022 Sep;71(9):1876-1891. doi: 10.1136/gutjnl-2021-325065. Epub 2021 Dec 21.
Yadav A, Ramasamy TS, Lin SC, Chen SH, Lu J, Liu YH, Lu FI, Hsueh YY, Lin SP, Wu CC. Autologous Platelet-Rich Growth Factor Reduces M1 Macrophages and Modulates Inflammatory Microenvironments to Promote Sciatic Nerve Regeneration. Biomedicines. 2022 Aug 17;10(8):1991. doi: 10.3390/biomedicines10081991.
Chiu HY, Wang WH, Kuan CH, Wu YF, Tseng CJ, Huang WY, Wang SH, Lin SJ. Depilatory laser miniaturizes hair by inducing bystander dermal papilla cell necrosis through thermal diffusion. Lasers Surg Med. 2022 Aug;54(6):916-927. doi: 10.1002/lsm.23533. Epub 2022 Mar 15.
Chen PY, Tsai CY, Wu JL, Li YL, Wu CM, Chen KC, Hwang CF, Wu HP, Lin HC, Cheng YF, Lo MY, Liu TC, Yang TH, Chen PL, Hsu CJ, Wu CC. Hearing Features and Cochlear Implantation Outcomes in Patients With Pathogenic MYO15A Variants: a Multicenter Observational Study. Ear Hear. 2022 Jul-Aug 01;43(4):1198-1207. doi: 10.1097/AUD.0000000000001171. Epub 2021 Dec 29.
Liu Y, Guerrero-Juarez CF, Xiao F, Shettigar NU, Ramos R, Kuan CH, Lin YC, de Jesus Martinez Lomeli L, Park JM, Oh JW, Liu R, Lin SJ, Tartaglia M, Yang RB, Yu Z, Nie Q, Li J, Plikus MV. Hedgehog signaling reprograms hair follicle niche fibroblasts to a hyper-activated state. Dev Cell. 2022 Jul 25;57(14):1758-1775.e7. doi: 10.1016/j.devcel.2022.06.005. Epub 2022 Jun 30.
Lo JE, Cheng CY, Yang CH, Yang CM, Chen YC, Huang YS, Chen PL, Chen TC. Genotypes Influence Clinical Progression in EYS-Associated Retinitis Pigmentosa. Transl Vis Sci Technol. 2022 Jul 8;11(7):6. doi: 10.1167/tvst.11.7.6.
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 Jul 1;209(1):69-76. doi: 10.4049/jimmunol.2100567. Epub 2022 Jun 13.
Samuel TJ, Lai S, Schär M, Wu KC, Steinberg AM, Wei AC, Anderson ME, Tomaselli GF, Gerstenblith G, Bottomley PA, Weiss RG. Myocardial ATP depletion detected noninvasively predicts sudden cardiac death risk in patients with heart failure. JCI Insight. 2022 Jun 22;7(12):e157557. doi: 10.1172/jci.insight.157557.
Yang X, Zhang M, Xie B, Peng Z, Manning JR, Zimmerman R, Wang Q, Wei AC, Khalifa M, Reynolds M, Jin J, Om M, Zhu G, Bedja D, Jiang H, Jurczak M, Shiva S, Scott I, O'Rourke B, Kass DA, Paolocci N, Feng N. Myocardial brain-derived neurotrophic factor regulates cardiac bioenergetics through the transcription factor Yin Yang 1. Cardiovasc Res. 2022 Jun 15:cvac096. doi: 10.1093/cvr/cvac096. Epub ahead of print.
Pan ZJ, Hung YL, Chen TY, Shih YA, Lin YJ, Wang CN. Development of a petal protoplast transfection system for Sinningia speciosa. Appl Plant Sci. 2022 Jun 15;10(3):e11476. doi: 10.1002/aps3.11476.
Chen CN, Wang JC, Chen YT, Yang TL. Exploration of the niche effect on tumor satellite budding of head and neck cancer with biomimicking modeling. Biomaterials. 2022 Jun;285:121471. doi: 10.1016/j.biomaterials.2022.121471. Epub 2022 Mar 19.
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 Jun;16(3):562-576. doi: 10.1007/s12072-022-10315-w. Epub 2022 May 7.
Chang YW, Wang CC, Yin CF, Wu CH, Huang HC, Juan HF. Quantitative phosphoproteomics reveals ectopic ATP synthase on mesenchymal stem cells to promote tumor progression via ERK/c-Fos pathway activation. Mol Cell Proteomics. 2022 Jun;21(6):100237. doi: 10.1016/j.mcpro.2022.100237. Epub 2022 Apr 18.
Tseng HI, Zeng YS, Lin YJ, Huang JW, Lin CL, Lee MH, Yang FW, Fang TP, Mar AC, Su JC. A novel AMPK activator shows therapeutic potential in hepatocellular carcinoma by suppressing HIF1α-mediated aerobic glycolysis. Mol Oncol. 2022 Jun;16(11):2274-2294. doi: 10.1002/1878-0261.13211. Epub 2022 Apr 12.
Wu YZ, Jiang HS, Han HF, Li PH, Lu MR, Tsai IJ, Wu YC. C. elegans BLMP-1 controls apical epidermal cell morphology by repressing expression of mannosyltransferase bus-8 and molting signal mlt-8. Dev Biol. 2022 Jun;486:96-108. doi: 10.1016/j.ydbio.2022.03.011. Epub 2022 Apr 1.
Duan DM, Chiu HH, Chen PL, Yeh PT, Yu CW, Yang KC, Yu CC. Clinical manifestations and genetic characteristics in the Taiwan thoracic aortic aneurysm and dissection cohort - a prospective cohort study. J Formos Med Assoc. 2022 Jun;121(6):1093-1101. doi: 10.1016/j.jfma.2021.08.016. Epub 2021 Aug 26.
Pang QY, Tan TZ, Sundararajan V, Chiu YC, Chee EYW, Chung VY, Choolani MA, Huang RY. 3D genome organization in the epithelial-mesenchymal transition spectrum. Genome Biol. 2022 May 30;23(1):121. doi: 10.1186/s13059-022-02687-x.
Lin RT, Chen PL, Yang CY, Yeh CC, Lin CC, Huang WH, Chung AK, Lin JT. Risk factors related to age at diagnosis of pancreatic cancer: a retrospective cohort pilot study. BMC Gastroenterol. 2022 May 14;22(1):243. doi: 10.1186/s12876-022-02325-7.
Li PH, Chen TF, Yu JY, Shih SH, Su CH, Lin YH, Tsai HK, Juan HF, Chen CY, Huang JH. pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature. Nucleic Acids Res. 2022 May 10;50(W1):W616–22. doi: 10.1093/nar/gkac310. Epub ahead of print.
Chiang TW, Mai TL, Chuang TJ. CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species. BMC Bioinformatics. 2022 May 6;23(1):164. doi: 10.1186/s12859-022-04692-0.
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 Apr 30;14(5):971. doi: 10.3390/pharmaceutics14050971.
Loke P, Lin JD. Redefining inflammatory macrophage phenotypes across stages and tissues by single-cell transcriptomics. Sci Immunol. 2022 Apr 15;7(70):eabo4652. doi: 10.1126/sciimmunol.abo4652. Epub 2022 Apr 15.
Chu CH, Tseng WW, Hsu CM, Wei AC. Image Analysis of the Mitochondrial Network Morphology With Applications in Cancer Research. Front Phys. 2022 Apr 13;10. doi: 10.3389/fphy.2022.855775.
Lee RK, Li TN, Chang SY, Chao TL, Kuo CH, Pan MY, Chiou YT, Liao KJ, Yang Y, Wu YH, Huang CH, Juan HF, Hsieh HP, Wang LH. Identification of Entry Inhibitors against Delta and Omicron Variants of SARS-CoV-2. Int J Mol Sci. 2022 Apr 6;23(7):4050. doi: 10.3390/ijms23074050.
Chan LW, Sung YC, Wu DC, Chen CY, Yang CH, Yang CM, Chen PL, Chen TC. PREDICTED PROTEIN STRUCTURE VARIATIONS INDICATE THE CLINICAL PRESENTATION OF CYP4V2-RELATED BIETTI CRYSTALLINE DYSTROPHY. Retina. 2022 Apr 1;42(4):797-806. doi: 10.1097/IAE.0000000000003381.
Yin CF, Chang YW, Huang HC, Juan HF. Targeting protein interaction networks in mitochondrial dynamics for cancer therapy. Drug Discov Today. 2022 Apr;27(4):1077-1087. doi: 10.1016/j.drudis.2021.11.006. Epub 2021 Nov 10.
Wu PC, Tsai CY, Lin PH, Chou PH, Huang FL, Chen PL, Shiao JY, Liu TC, Hsu CJ, Huang CW, Wu CC. Cochlear implantation in LEOPARD syndrome: Our experience with three patients. Clin Otolaryngol. 2022 Mar;47(2):341-346. doi: 10.1111/coa.13895. Epub 2021 Nov 28.
Wu MC, Chang YY, Lan MY, Chen YF, Tai CH, Lin YF, Tsai SF, Chen PL, Lin CH. A Clinical and Integrated Genetic Study of Isolated and Combined Dystonia in Taiwan. J Mol Diagn. 2022 Mar;24(3):262-273. doi: 10.1016/j.jmoldx.2021.12.003. Epub 2022 Jan 15.
Wu YC, Lin C, Quek TQS. A Robust Distributed Hierarchical Online Learning Approach for Dynamic MEC Networks. IEEE Journal on Selected Areas in Communications. 2022 Feb;40(2):641-656. doi: 10.1109/JSAC.2021.3118342.
Ko KY, Chen CY, Juan HF, Huang HC. Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis. Bioinformatics. 2022 Jan 12;38(3):763-769. doi: 10.1093/bioinformatics/btab735.
Yu PC, Huang CH, Kuo CJ, Liang PH, Wang LH, Pan MY, Chang SY, Chao TL, Ieong SM, Fang JT, Huang HC, Juan HF. Drug Repurposing for the Identification of Compounds with Anti-SARS-CoV-2 Capability via Multiple Targets. Pharmaceutics. 2022 Jan 12;14(1):176. doi: 10.3390/pharmaceutics14010176.
Wu YC, Chen CI, Chen PY, Kuo CH, Hung YH, Peng KY, Wu VC, Tsai-Wu JJ, Hsu CL; TAIPAI group. GRAde: a long-read sequencing approach to efficiently identifying the CYP11B1/CYP11B2 chimeric form in patients with glucocorticoid-remediable aldosteronism. BMC Bioinformatics. 2022 Jan 10;22(Suppl 10):613. doi: 10.1186/s12859-022-04561-w.
Chang CS, Yu WH, Su CC, Ruan JW, Lin CM, Huang CT, Tsai YT, Lin IJ, Lai CY, Chuang TH, Lin WJ, Tan TH, Huang HC, Juan HF, Kao CY. Single-cell RNA sequencing uncovers the individual alteration of intestinal mucosal immunocytes in Dusp6 knockout mice. iScience. 2022 Jan 7;25(2):103738. doi: 10.1016/j.isci.2022.103738.
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 Jan;196(1):156-168. doi: 10.1111/bjh.17837. Epub 2021 Sep 18.
Wu MC, Chang YY, Chen YF, Lan MY, Chen PL, Tai CH, Lin CH. Investigating DYT1 in a Taiwanese dystonia cohort. J Formos Med Assoc. 2022 Jan;121(1 Pt 2):375-380. doi: 10.1016/j.jfma.2021.05.017. Epub 2021 Jun 4.
Hsieh CH, Yeh HN, Huang CT, Wang WH, Hsu WM, Huang HC, Juan HF. BI-2536 Promotes Neuroblastoma Cell Death via Minichromosome Maintenance Complex Components 2 and 10. Pharmaceuticals (Basel). 2021 Dec 28;15(1):37. doi: 10.3390/ph15010037.
Lin JL, Hsieh TT, Tung YA, Chen XJ, Hsiao YC, Yang CL, Liu TL, Chen CY. ezGeno: an automatic model selection package for genomic data analysis. Bioinformatics. 2021 Dec 22;38(1):30-37. doi: 10.1093/bioinformatics/btab588.
Chang CS, Liao YC, Huang CT, Lin CM, Cheung CHY, Ruan JW, Yu WH, Tsai YT, Lin IJ, Huang CH, Liou JS, Chou YH, Chien HJ, Chuang HL, Juan HF, Huang HC, Chan HL, Liao YC, Tang SC, Su YW, Tan TH, Bäumler AJ, Kao CY. Identification of a gut microbiota member that ameliorates DSS-induced colitis in intestinal barrier enhanced Dusp6-deficient mice. Cell Rep. 2021 Nov 23;37(8):110016. doi: 10.1016/j.celrep.2021.110016.
Lee KH, Chang YC, Chen TF, Juan HF, Tsai HK, Chen CY*. (2021) Connecting MHC-I-binding motifs with HLA alleles via deep learning. Commun Biol. 4(1):1194.
Chiu YC, Hsu TS, Huang CY, Hsu CH*. (2021) Structural and biochemical insights into a hyperthermostable urate oxidase from Thermobispora bispora for hyperuricemia and gout therapy. Int J Biol Macromol. 188:914-23.
Chiu YC, Tseng MC, Hsu CH*. (2021) Expanding the substrate specificity of macro domains toward 3″-isomer of O-acetyl-ADP-ribose. ACS Catal. 11(17):11075–90.
Li A, Huang HT, Huang HC*, Juan HF*. (2021) LncTx: A network-based method to repurpose drugs acting on the survival-related lncRNAs in lung cancer. Comput Struct Biotechnol J. 19:3990-4002.
Lee TT, Chen PL, Su MP, Li JC, Chang YW, Liu RW, Juan HF, Yang JM, Chan SP, Tsai YC, von Stockum S, Ziviani E, Kamikouchi A, Wang HD, Chen CH*. (2021) Loss of Fis1 impairs proteostasis during skeletal muscle aging in Drosophila. Aging Cell 20(6):e13379.
Wang WH, Chen SK, Huang HC*, Juan HF*. (2021) Proteomic analysis reveals metformin suppresses PSMD2, STIP1 and CAP1 for anti-gastric cancer AGS cell proliferation and migration. ACS Omega 6(22):14208-19.
Hsu CL†, Ou DL†, Bai LY, Chen CW, Lin L, Huang SF, Cheng AL, Cheng YM*, Hsu C*. (2021) Exploring markers of exhausted CD8 T cells to predict response to immune checkpoint inhibitor therapy for hepatocellular carcinoma. Liver Cancer 10(4):346-59.
Wang MH†, Hsu CL†, Wu CH, Chiou LL, Tsai YT, Lee HS*, Lin SP*. (2021) Timing does matter: Nerve-mediated HDAC1 paces the temporal expression of morphogenic genes during axolotl limb regeneration. Front Cell Dev Biol. 9:641987.
Ou DL, Tseng SJ, Kempson IM, Hsu CL, Yang PC, Liao ZX*. (2021) Enhanced targeting and immune activation of tumor microenvironment by nanomodified anti-PD1 in liver cancer. Adv Therapeutics. 4(6):2100048.
Ou DL†, Chen CW†, Hsu CL†, Chung CH, Feng ZR, Lee BS, Cheng AL, Yang MH*, Hsu C*. (2021) Regorafenib enhances antitumor immunity via inhibition of p38 kinase/Creb1/Klf4 axis in tumor-associated macrophages. J Immunother Cancer. 9(3):e001657.
Peng C, Li YH. Yu CW, Cheng ZH, Liu JR, Hsu JL, Hsin LW, Huang CT, Juan HF, Chern JW, Cheng YS*. (2021) Inhibitor development of MTH1 via high-throughput screening with fragment based library and MTH1 substrate binding cavity. Bioorg Chem. 110:104813.
Lin MH, Cho CC, Chiu YC, Chien CY, Huang YP, Chang CF, Hsu CH*. (2021) Elucidating the tunability of binding behavior for the MERS-CoV macro domain with NAD metabolites. Commun Biol. 4(1):123.
He MY, Lin YJ, Kao YL, Kuo P, Grauffel C, Lim C, Cheng YS, Chou HHD*. (2021) Sensitive and specific cadmium biosensor developed by reconfiguring metal transport and leveraging natural gene repositories. ACS Sens. 6(3): 995-1002.
Chen TF, Chang YC, Hsiao Y, Lee KH, Hsiao YC, Lin YH, Tu YCE, Huang HC, Chen CY*, Juan HF*. (2021) DockCoV2: a drug database against SARS-CoV-2. Nucleic Acids Res. 49(D1):D1152-59.
Chiang CS, Fu SJ, Hsu CL, Jeng CJ, Tang CY, Huang YS, Tang SC*. (2021) Neuronal exosomes secreted under oxygen-glucose deprivation/reperfusion presenting differentially expressed miRNAs and affecting neuronal survival and neurite outgrowth. Neuromolecular Med. 23(3):404-15.
Wen JD, Kuo ST, Chou HHD*. (2020) The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation. RNA Biol. DOI: 10.1080/15476286.2020.1861406.
Huang CT, Chao TL, Kao HC, Pang YH, Lee WH, Hsieh CH, Chang SY*, Huang HC*, Juan HF*. (2020) Enhancement of the IFN-β-induced host signature informs repurposed drugs for COVID-19. Heliyon 6(12):e05646 (Cell Press).
Hung SY, Lin CC, Hsu CL, Yao CY, Wang YH, Tsai CH, Hou HA, Chou WC*, Tien HF*. (2021) The expression levels of long non‐coding RNA KIAA0125 are associated with distinct clinical and biological features in myelodysplastic syndromes. Br J Haematol. 192(3):589-98.
Wang YH, Lin CC, Hsu CL, Hung SY, Yao CY, Lee SH, Tsai CH, Hou HA, Chou WC*, Tien HF*. (2021) Distinct clinical and biological characteristics of acute myeloid leukemia with higher expression of long noncoding RNA KIAA0125. Ann Hematol. 100(2):487-98.
Chung KP, Huang YL, Chen YJ, Juan YH, Hsu CL, Nakahira K, Huang YT, Lin MW, Wu SG, Shih JY, Chang YL, Yu CJ*. (2021) Multi-kinase framework regulates activation of dynamin-related protein 1 to promote proliferation and invasion of lung adenocarcinoma. Mol Oncol. 15(2):560-78.
Lin MH, Chang SC, Chiu YC, Jiang Bc, Wu TH, Hsu CH*. (2020) Structural, biophysical, and biochemical elucidation of the SARS-CoV-2 nonstructural protein 3 macro domain. ACS Infect Dis. 6(11):2970-78.
Wu AYT, Sung YC, Chen YJ, Chou STY, Guo V, Chien JCY, Ko JJS, Yang AL, Huang HC, Chuang JC, Wu S, Ho MR, Ericsson M, Lin WW, Cheung CHY, Juan HF, Ueda K, Chen Y, Lai C PK*. (2020) Multi-resolution imaging using bioluminescence resonance energy transfer identifies distinct biodistribution profiles of extracellular vesicles and exomeres with redirected tropism. Adv Sci. 7(19):2001467.
Chang YW, Hsu CL, Tang CW, Chen XJ, Huang HC*, Juan HF*. (2020) Multiomics reveals ectopic ATP synthase blockade induces cancer cell death via a lncRNA-mediated phospho-signaling network. Mol Cell Proteomics 19(11):1805-25.
Chang YY, Hagawa S, Hsu CH*. (2020) Adaptation of thermophilic acetyltransferase to a water-mediated catalytic mechanism. Chem Commun. 56(72):10537-40.
Wang HY, Liu YN, Wu SG, Hsu CL, Chang TH, Tsai MF, Lin YT, Shih JY*. (2020) 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. 28(3):351-63.
Cheung HYC, Hsu CL, Lin TY, Chen WT, Wang YC, Huang HC*, Juan HF*. (2020) ZNF322A-mediated protein phosphorylation induces autophagosome formation through modulation of IRS1-AKT glucose uptake and HSP-elicited UPR in lung cancer. J Biomed Sci. 27(1):75.
Wang WH, Hsu CL, Huang HC*, Juan HF*. (2020) Quantitative phosphoproteomics reveals cell alignment and mitochondrial length change under cyclic stretching in lung cells. Int J Mol Sci. 21(11):4074.
Kuo ST, Jahn RL, Cheng YJ, Chen YL, Lee YJ, Hollfelder F, Wen JD, Chou HHD*. (2020) Global fitness landscapes of the Shine-Dalgarno sequence. Genome Res. 30(5): 711-23.
Chen SC, Wu SP, Chang YY, Hwang TS, Lee* TH, Hsu CH*. (2020) Crystal structure of α-galactosidase from Thermus thermophilus: Insight into hexamer assembly and substrate specificity. J Agric Food Chem. 68(22):6161-69.
Yin CF, Kao SC, Hsu CL, Cheung CHY, Chang YW, Huang HC*, Juan HF*. (2020) Phosphoproteome analysis reveals dynamic heat shock protein 27 phosphorylation in tanshinone IIA-induced cell death. J Proteome Res. 19(4):1620-34.
Ho TC, Wang EY, Yeh KH, Jeng YM, Horng JH, Wu LL, Chen YT, Huang HC, Hsu CL, Chen PJ, Yeh SH*, Chen DS*. (2020) Complement C1q mediates the expansion of periportal hepatic progenitor cells in senescence-associated inflammatory liver. PNAS. (2020) 117(12):6717-25.
Shen YC, Hsu CL, Jeng YM, Ho MC, Ho CM, Yeh CP, Yeh CY, Hsu MC, Hu RH, Cheng AL*. (2020) Reliability of a single-region tumor sample for evaluating the immune tumor microenvironment of hepatocellular carcinoma tumors. J Hepatol. 72(3):489-97.
Wang YH, Lin CC, Yao CY, Hsu CL, Hou HA, Tsai HC, Chou WC*, Tien HF*. (2020) A four-gene leukemic stem cell score can independently predict the prognosis of myelodysplastic syndrome patients. Blood Adv. 4(4):644-54.
Lee PC, Chen ST, Kuo TC, Lin TC, Lin MC, Huang J, Hung JS, Hsu CL, Juan HF, Lee PH, Huang MC*. (2020) C1GALT1 is associated with poor survival and promotes soluble Ephrin A1-mediated cell migration through activation of EPHA2 in gastric cancer. Oncogene 39(13):2724-40.
Chang HC, Huang HC, Juan HF*, Hsu CL*. (2019) Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation. BMC Genomics 20(Suppl 10):896.
Lee WH, Chen KP, Wang K, Huang HC*, Juan HF*. (2020) Characterizing the cancer-associated microbiome with small RNA sequencing data. Biochem Biophys Res Commun. 522(3):776-82.
Wu PY, Yu IS, Lin YC, Chang YT, Chen CC, Lin KH, Tseng TH, Kargren M, Tai YL, Shen TL, Liu YL, Wang BJ, Chang CH, Chen WM, Juan HF, Huang SF, Chan YY, Liao YF, Hsu WM*, Lee H*. (2019) Activation of aryl hydrocarbon receptor by kynurenine impairs progression and metastasis of neuroblastoma. Cancer Res. 79(21):5550-62.
Cheung HYC, Hsu CL, Tsuei CY, Kuo TT, Huang CT, Hsu WM, Chung YH, Wu HY, Hsu CC, Huang HC*, Juan HF*. (2019) Combinatorial targeting of MTHFD2 and PAICS in purine synthesis as a novel therapeutic strategy. Cell Death Dis. 10(11):786.
Hsieh CH, Cheung CHY, Liu YL, Hou CL, Hsu CL, Huang CT, Yang TS, Chen SF, Chen CN, Hsu WM*, Huang HC*, Juan HF*. (2019) Quantitative proteomics of Th-MYCN transgenic mice reveals aurora kinase inhibitor altered metabolic pathways and enhanced ACADM to suppress neuroblastoma progression. J Proteome Res. 18(11):3850-66.
Huang CT, Hsieh CH, Lee WC, Liu YL, Yang TS, Hsu WM, Oyang YJ, Huang HC*, Juan HF*. (2019) Therapeutic targeting of non-oncogene dependencies in high-risk neuroblastoma. Clin Cancer Res. 25(13):4063-78.
Cho CC, Chien CY, Chiu YC, Lin MH, Hsu CH*. (2019) Structural and biochemical evidence supporting poly ADP-ribosylation in the bacterium Deinococcus radiodurans. Nat Commun. 10(1):1491.
Huang CT, Hsieh CH, Chung YH, Oyang YJ, Huang HC*, Juan HF*. (2019) Perturbational gene-expression signatures for combinatorial drug discovery. iScience 15:291-306 (Cell Press).
Yang TW, Sahu D, Chang YW, Hsu CL, Hsieh CH, Huang HC*, Juan HF*. (2019) RNA-binding proteomics reveals MATR3 interacting with lncRNA SNHG1 to enhance neuroblastoma progression. J Proteome Res. 18(1):406-16.
Chang JY, Yu WH, Juan HF*, Huang HC*. (2018) Dynamics of alternative polyadenylation in human preimplantation embryos. Biochem Biophys Res Commun. 504(4):727-33.
Huang CT, Hsieh CH, Oyang YJ, Huang HC*, Juan HF*. (2018) A large-scale gene expression intensity-based similarity metric for drug repositioning. iScience 7: 40-52. (Cell Press)
Lin MC, Chien PH, Wu HY, Chen ST, Juan HF, Lou PJ*, Huang MC*. (2018) C1GALT1 predicts poor prognosis and is a potential therapeutic target in head and neck cancer. Oncogene 37(43):5780-93.
Sahu D, Ho SY, Juan HF*, Huang HC*. (2018) High-risk, expression-based prognostic long noncoding RNA signature in neuroblastoma. JNCI Cancer Spectr. 2(2):pky015.
Cheng AN, Fan CC, Lo YK, Kuo CL, Wang HC, Lien IH, Lin SY, Chen CH, Jiang SS, Chang IS, Juan HF, Lyu PC, Lee AYL* (2017) Cdc7-Dbf4-mediated phosphorylation of HSP90-S164 stabilizes HSP90-HCLK2-MRN complex to enhance ATR/ATM signaling that overcomes replication stress in cancer. Sci Rep. 7(1):17024.
Cheung HYC, Hsu CL, Chen KP, Chong ST, Huang HC*, Juan HF*. (2017) MCM2-regulated functional networks in lung cancer by multi-dimensional proteomic approach. Sci Rep. 7(1):13302.
Hsu CL, Wang JK, Lu PC, Huang HC*, Juan HF*. (2017) DynaPho: a web platform for inferring the dynamics of time-series phosphoproteomics. Bioinformatics 33(22):3664-66.
Hua KT, Liu YF, Hsu CL, Cheng TY, Yang CY, Chang JS, Lee WJ, Hsiao M, Juan HF, Chien MH*, Yang SF*. (2017) 3'UTR polymorphisms of carbonic anhydrase IX determine the miR-34a targeting efficiency and prognosis of hepatocellular carcinoma. Sci Rep. 7(1):4466.
Cheung CHY, Juan HF*. (2017) Quantitative Proteomics in Lung Cancer. J Biomed Sci. 224(1):37
Liao SY, Chiang CW, Hsu CH, Jen J, Juan HF, Lai WW, Wang YC*. (2017) CK1δ/GSK3β/FBXW7α axis promotes degradation of the ZNF322A oncoprotein to suppress lung cancer progression. Oncogene 36(41):5722-33.
Lin TC, Chen ST, Huang MC, Huang J, Hsu CL, Juan HF, Lin HH, Chen CH*. (2017) GALNT6 expression enhances aggressive phenotypes of ovarian cancer cells by regulating EGFR activity. Oncotarget 8(26):42588-601.
Lin MC, Lin JJ, Hsu CL, Juan HF, Lou PJ*, Huang MC*. (2017) GATA3 interacts with and stabilizes HIF-1α to enhance cancer cell invasiveness. Oncogene 36(30):4243-52.
Chang HH, Liu YL, Lu MY, Jou ST, Yang YL, Lin DT, Lin KH, Tzen KY, Yen RF, Lu CC, Liu CJ, Peng S SF, Jeng YM, Huang SF, Lee H, Juan HF, Huang MC, Liao YF, Lee YL*, Hsu WM*. (2017) A multidisciplinary team care approach to improving outcomes in pediatric patients with high-risk neuroblastoma. Oncotarget 8(3):4360-72.
Chepyala SR, Chen YC, Yan CC, Lu CY, Wu YC* and Hsu CP*. (2016) Noise propagation with interlinked feed-forward pathways. Sci. Rep. 6:23607. doi: 10.1038/srep23607
Hang YL, Hsieh MH, Chang WW, Wang HY, Lin MC, Wang CP, Lou PJ, Teng SC. Instability of succinate dehydrogenase in SDHD polymorphism connects reactive oxygen species production to nuclear and mitochondrial genomic mutations in yeast. (2015) Antioxidants& Redox Signaling, 22, 587-602.
Hsieh MS, Tsai CH, Lin CC, Li TK, Hung TW, Chang LT, Hsin LW, Teng SC. (2015) Topoisomerase II inhibition suppresses the proliferation of telomerase-negative cancers. Cellular and Molecular Life Sciences, 72: 1825-1837.
Kuo YC, Wu HT, Hung JJ, Chou TY, Teng SC, Wu KJ. (2015) Nijmegen breakage syndrome protein 1 (NBS1) modulates hypoxia inducible factor-1α (HIF-1α) stability and promotes in vitro migration and invasion under ionizing radiation. Int. J. Biochem. Cell Biol. 64: 229-238.
Hung SY, Huang WP, Liou HC, Fu WM. (2015) LC3 overexpression reduces Aβ neurotoxicity through increasing α7nAchR expression and autophagic activity in neurons and mice. Neuropharmacol., 93: 243-251. (SCI)
Hung TM, Yuan RH, HuangWP, Chen YH, Lin YC, Lin CW, Lai HS, Lee PH. (2015) Increased Autophagy Markers Are Associated with Ductular Reaction during the Development of Cirrhosis. Am. J. Pathol., 185: 2454-2467.
Lee SJ, Tsao KC, Cherng BW and Liao YH. Lysophospholipid receptor signaling in zebrafish development. Transl Cancer Res, 2015, 4: 544-556.
Wu BT, Wen SH, Hwang SP, Huang CJ and Kuan YS.*. Control of Wnt5b secretion by Wntless modulates chondrogenic cell proliferation through fine-tuning fgf3 expression. (2015). J. Cell Sci. 128:2328-2339.
Kuan YS, Roberson S, Akitake CM, Fortuno L, Gamse JT, Moens CB, and Halpern ME. (2015). Distinct requirement for Wntless in habenular development. Dev. Biol. 406(2):117-128.
Li MY, Lai PL, Chou YT, Chi AP, Mi YZ, Khoo KH, Chang GD, Wu CW, Meng TC, Chen GC. (2015) Protein tyrosine phosphatase PTPN3 inhibits lung cancer cell proliferation and migration by promoting EGFR endocytic degradation. Oncogene 34: 3791-803.
Lee DY and Chang GD.* (2015), Quantitative LC-ESI-MS analysis of amine-containing metabolites derivatized with cyanuric chloride and methylamine isotopologues, J. Chromatography A 1338: 60-68.
Yu CH, Chou CC, Lee YJ, Khoo KY, and Chang GD.* (2015) Uncovering Protein Polyamination by the Spermine-specific Antiserum and Mass Spectrometric Analysis, Amino Acids, 47, 469–481
Lee, DY and Chang GD*. (2015) Simultaneous Immunoblotting Analysis with Activity Gel Electrophoresis and 2-D Gel Electrophoresis, Methods Mol. Biol. 1312:61-72.
Lee, DY and Chang GD*. (2015) Post-staining electroblotting for reliable peptide blotting, Methods Mol. Biol. 1312:185-195.
Lin SJ, Lee DY, Wang HC, Kang ST, Hwang PP, Kou GH, Huang MF, Chang GD*, Lo CF*. (2015) White Spot Syndrome Virus Protein Kinase 1 (PK1) Defeats the Host Cell's Iron Withholding Defense Mechanism by Interacting with Host Ferritin. J. Virol. 89, 1083-1093.
Klionsky DJ, et al. "Guidelines for the use and interpretation of assays for monitoring autophagy" Autophagy (in press).
Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC* and Juan HF.* (2015) "Temporal phosphoproteome dynamics induced by an ATP synthase inhibitor citreoviridin" Molecular & Cellular Proteomics 14(12):3284-98.
Hsu CL, Juan HF.*, and Huang HC.* (2015) "Characterization and functional analysis of differential coexpression networks" Scientific Reports 5:13295.
Jen J, Lin LL, Chen HT, Liao SY, Lo FY, Tang YA, Hsu HS, Salgia R, Hsu CL, Huang HC, Juan HF*, Wang YC.* (2015) "Oncoprotein ZNF322A transcriptionally deregulates alpha-adducin, cyclin D1 and p53 to promote tumor growth and metastasis in lung cancer" Oncogene (doi: 10.1038/onc.2015.296).
Lin LL, Hsu CL, Hu CW, Ko SY, Hsieh HL, Huang HC*, Juan HF.* (2015) "Integrating phosphoproteomics and bioinformatics to study brassinosteroid-regulated phosphorylation dynamics in Arabidopsis" BMC Genomics 16:533. (Highly accessed)
Lin LL, Huang HC*, Juan HF.* (2015) "Circadian systems biology in metazoa" Briefings in Bioinformatics 16(6):1008-24
Huang MJ, Hu RH, Chou CH, Hsu CL, Liu YW, Huang J, Hung JS, Lai IR, Juan HF, Yu SL, Wu YM.* and Huang MC.* (2015) "Knockdown of GALNT1 suppresses malignant phenotype of hepatocellular carcinoma by suppressing EGFR signaling" Oncotarget 6(8):5650-65.
Lee AYL*, Chiu YC, Fang WC, Cheng CW, Kuo CY, Juan HF, Wu SH* and Kao TY.* (2015) "Mitochondrial Lon regulates apoptosis through the association with Hsp60-mtHsp70 complex" Cell Death & Disease 6:e1642.
Lin LL, Hsia CR, Hsu CL, Huang HC* and Juan HF.* (2015) "Integrating transcriptomics and proteomics to show that tanshinone IIA suppresses cell growth by blocking glucose metabolism in gastric cancer cells" BMC Genomics 16(1):41.
Chang HY, Li MH, Huang TC, Hsu CL, Tsai SR, Lee SC*, Huang HC* and Juan HF.* (2015) "Quantitative proteomics reveals middle infrared radiation-interfered networks in breast cancer cells" Journal of Proteome Research 14(2):1250-62.
Chan CC, Fan MY, Wan WH, Lin SJ*. (2015) A two-stepped culture method for efficient production of trichogenic keratinocytes. Tissue Engineering Part C Methods 21:1070-9.
Lin YC, Lin MW, Yen MH, Fan SMY, Wu JT, Young TH, Cheng JY, Lin SJ*. (2015) Programmable laser-assisted surface microfabrication on a polyvinyl alcohol-coated glass chip with self-changing cell adhesivity for heterotypic cell patterning. ACS Applied Materials& Interfaces 7:22322-32.
Chen KL, Chiu HY, Chan CC, Chan JY, Lin SJ*. Extensive cicatricial alopecia in a patient with long-term trichotillomania. Journal of Dermatology (accepted).
Wu YF, Wang SH, Wu PS, Sabrina Fan MY, Chiu HY, Tsai TH, Lin SJ*. (2015) Enhancing hair follicle regeneration by nonablative fractional laser: assessment of irradiation parameters and tissue response. Lasers in Surgery and Medicine 47:331-41.
Chiu HY, Wang TS, Chan CC, Lin SJ, Tsai TF. Risk factor analysis for the immunogenicity of adalimumab associated with decreased clinical response in Chinese patients with psoriasis. Acta Dermato-Venereologica 95:71-6, 2015.
Sheen YS, Fan SMY, Chan CC, Wu YF, Jee SH, Lin SJ*. Visible red light enhances physiological anagen entry in vivo and has direct and indirect stimulative effects in vitro. Lasers in Surgery and Medicine 47: 50-9, 2015.
Chiu HY, Huang HL, Li CH, Yin YJ, Chen HA, Hsu ST, Lin SJ, Tsai TF, Ho SY. Increased risk of glomerulonephritis and chronic kidney disease in relation to the severity of psoriasis, concomitant medication, and comorbidity: a nationwide population-based cohort study. British Journal of Dermatology 173:146-54, 2015.
Oh JW, Lin SJ, Plikus MV. Regenerative metamorphosis in hairs and feathers: follicle as a programmable biological printer. Experimental Dermatology 24:262-4, 2015.
Lin KH, Liao BY, Chang HW, Huang SW, Chang TY, Yang CY, Wang YB, Kirk Lin YT, Wu YW, Tang SL and Yu HT Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. BMC Genomics 2015, 16:1029
Wada K, Lee JY, Hung HY, Shi Q, Lin L, Zhao Y, Goto M, Yang PC, Kuo SC, Chen HW*, Lee KH*. Novel curcumin analogs to overcome EGFR-TKI lung adenocarcinoma drug resistance and reduce EGFR-TKI-induced GI adverse effects. Bioorg Med Chem. 2015 Apr 1;23(7):1507-14.
Huang CH, Tsai MS, Chiang CY, Su YJ, Wang TD, Chang WT, Chen HW, Chen WJ. Activation of mitochondrial STAT-3 and reduced mitochondria damage during hypothermia treatment for post-cardiac arrest myocardial dysfunction. Basic Res Cardiol. 2015 Nov;110(6):59.
Yuan A, Hsiao YJ, Chen HY, Chen HW, Ho CC, Chen YY, Liu YC, Hong TH, Yu SL, Chen JJ, Yang PC. Opposite Effects of M1 and M2 Macrophage Subtypes on Lung Cancer Progression. Sci Rep. 2015, 5:14273.
Lai YH, Chen MH, Lin SY, Lin SY, Wong YH, Yu SL, Chen HW, Yang CH, Chang GC, Chen JJ. Rhodomycin A, a novel Src-targeted compound, can suppress lung cancer cell progression via modulating Src-related pathways. Oncotarget. 2015 Sep 22;6(28):26252-65.
Tsai MS, Huang CH, Yu PH, Tsai CY, Chen HW, Cheng HJ, Chang WT, Wang TD, Chen WJ. Prolonged cooling duration mitigates myocardial and cerebral damage in cardiac arrest. Am J Emerg Med. 2015 Oct;33(10):1374-81.
Liao HY, Chen JH, Shyue JJ, Shun CT, Chen HW, Liao SW, Hong CK, Chen PS. Rapid label-free determination of ketamine in whole blood using secondary ion mass spectrometry. Talanta. 2015 Oct 1;143:50-5.
Chen HY, Yu SL, Ho BC, Su KY, Hsu YC, Chang CS, Li YC, Yang SY, Hsu PY, Ho H, Chang YH, Chen CY, Yang HI, Hsu CP, Yang TY, Chen KC, Hsu KH, Tseng JS, Hsia JY, Chuang CY, Yuan S, Lee MH, Liu CH, Wu GI, Hsiung CA, Chen YM, Wang CL, Huang MS, Yu CJ, Chen KY, Tsai YH, Su WC, Chen HW, Chen JJ, Chen CJ, Chang GC, Yang PC, Li KC. R331W Missense Mutation of Oncogene YAP1 Is a Germline Risk Allele for Lung Adenocarcinoma With Medical Actionability. J Clin Oncol. 2015, 33(20):2303-10.
Huang CH, Chiang CY, Pen RH, Tsai MS, Chen HW, Hsu CY, Wang TD, Ma MH, Chen SC, Chen WJ. Hypothermia treatment preserves mitochondrial integrity and viability of cardiomyocytes after ischaemic reperfusion injury. Injury. 2015, 46(2):233-9.
Bowman, J.L., Araki, T., Arteaga-Vazquez, M.A., Berger, F., Dolan, L., Haseloff, J., Ishizaki, K., Kyozuka, J., Lin, S.S., Nagasaki, H., Nakagami, H., Nakajima, K., Nakamura, Y., Ohashi-Ito, K., Sawa, S., Shimamura, M., Solano, R., Tsukaya, H., Ueda, T., Watanabe, Y., Yamato, K.T., Zachgo, S., Kohchi, T. 2015. The naming of names: guidelines for gene nomenclature in Marchantia. Plant Cell Physiol. (Accepted)
Chen KI, Pan CY, Li KH, Huang YC, Lu CW, Tang CY, Su YW,Tseng LW, Tseng KC, Lin CY, Chen CD, Lin SS*, Chen YT*. 2015. Isolation and identification of post-transcriptional gene silencing-related micro-RNAs by functionalized silicon nanowire field-effect transistor. Sci. Rep. 5, 17375
Liu CT, Huang HM, Hong SF, Kuo-Huang LL, Yang CY, Lin YY, Lin CP*, Lin SS.* 2015. Peanut witches’ broom (PnWB) phytoplasma-mediated leafy flower symptoms and abnormal vascular bundles development. Plant Signal Behav. (Accepted)
Lee CT, Chen IT, Yang YT, Ko TP, Huang YT, Huang JY, Huang MF, Lin SJ, Chen CY, Lin SS, Lightener DV, Wang HC, Wang AHJ, Wang HC, Hor LI, Lo CF. 2015. The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin. PNAS 112:10798-10803.
Liao HF, Mo CF, Wu SC, Cheng DH, Yu CY, Chang KW, Kao TH, Lu CW, Pinskaya M, Morillon A, Lin SS, Cheng WT, Bourc'his D, Bestor T, Sung LY, Lin SP. 2015. Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency. Reproduction 150:245-256.
Yang CY, Huang YH, Lin CP, Lin YY, Hsu HC, Wang CN, Liu LY, Shen BN, Lin SS.* 2015. MiR396-targeted SHORT VEGETATIVE PHASE is required to repress flowering and is related to the development of abnormal flower symptoms by the Phyllody Symptoms1 effector. Plant Physiol. 168:1702-1716.
Hu SF, Huang YH, Lin, C.P., Liu, L.Y.D., Hong, S.F., Yang, C.Y., Lo, H.F., Tseng, T.Y., Chen, W.Y., Lin, S.S.* 2015. Development of a mild viral expression system for gain-of-function study of phytoplasma effector in planta. PLOS ONE. 10:e0130139
Huang CH, Hsiao WR, Huang CW, Chen KC, Lin SS, Chen TC, Raja JAJ, Wu HW, Yeh SD. 2015. Two novel motifs of Watermelon silver mottle virus NSs protein are responsible for RNA silencing suppression and pathogenicity. PLOS ONE. 10:e0126161
Lin YL, Ma LT, Lee YR, Lin SS, Wang SY, Chang TT, Shaw JF, Li WH, Chu FF. 2015. MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea. PLOS ONE. 10:e0123245
Lin PC, Hu WC, Lee SC, Chen YL, Lee CY, Chen YR, Liu LYD, Chen PY., Lin SS.*, Chang YC.* 2015. Application of an integrated omics approach for identifying host proteins that interact with Odontoglossum ringspot virus capsid protein. Mol. Plant Microbe Interact. 28:711-726
Yang HW, He BZ, Ma HJ, Tsaur SC, Ma CY, Wu Y, Ting CT, Zhang YE* (2015) Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in Drosophila populations. Molecular Biology and Evolution. 32: 216-228. (IF= 13.649 in 2015)

Chen WY, Shih HT, Liu KY, Shih ZS, Chen LK, Tsai TH, Chen MJ, Liu H, Tan BCM, Chen CY, Lee HH, Loppin B, Ait-Ahmed O, Wu JT*(2015) Intellectual disability-associated dBRWD3 regulates gene expression through inhibition of HIRA/YEM-mediated chromatin deposition of histone H3.3. EMBO Reports 16:528-538. (IF= 7.739 in 2015)
Sheen YS, Liao YH, Lin MH, Chu CY, Ho BY, Hsieh MC, Chen PC, Cha ST, Jeng YM, Chang CC, Chiu HC, Jee SH, Kuo ML, Chu CY* (2015) IMP-3 promotes tumor invasion and predicts poor prognosis in melanoma by regulating HMGA2 expression. J. Invest. Dermatol. 135(4):1065-1073. (IF= 6.915 in 2015)
Yi YH, Ma TH, Lee LW, Chiou PT, Chen PH, Lee CM, Chu YD, Yu H, Hsiung KC, Tsai YT, Lee CC, Chang YS, Chan SP*, Tan BC*, Lo SJ.* (2015) A genetic cascade of let-7-ncl-1-fib-1 modulates nucleolar size and rRNA pool in Caenorhabditis elegans. PLoS Genet. 11(10):e1005580.

Chen YC, Chiang HH, Cho YT, Chang CY, Chen KL, Yang CW, Lee YH, Chu CY* (2015) Human herpes virus reactivations and dynamic cytokine profiles in patients with cutaneous adverse drug reactions—a prospective comparative study. Allergy 70(5):568-575. (IF= 6.335 in 2015)

Chang CF, Chu PC, Wu PY, Yu MY, Lee JY, Tsai MD, Chang MS* (2015) PHRF1 promotes genome integrity by modulating non-homologous end-joining. Cell Death Dis. 6:e1716. (IF= 5.378 in 2015)
Chang YY, Hsu CH*(2015) Structural basis for substrate-specific acetylation of Nalpha-acetyltransferase Ard1 from Sulfolobus solfataricus. Sci. Rep. 5:8673-8681. (IF= 5.228 in2015)
Chen KI, Pan CY, Li KH, Huang YC, Lu CW, Tang CY, Su YW,Tseng LW, Tseng KC, Lin CY, Chen CD, Lin SS*, Chen YT*(2015) Isolation and identification of post-transcriptional gene silencing-related microRNAs by functionalized silicon nanowire field-effect transistor. Sci. Rep. 5:17575-17584 (IF= 5.228 in 2015)
Lin IC, Yang HC, Strong C, Yang CW, Cho YT, Chen KL, Chu CY* (2015) Liver injury in drug reaction with eosinophilia and systemic symptoms (DRESS): a clinical study of 72 cases. J. Am. Acad. Dermatol. 72(6):984-991. (IF= 5.621 in 2015)
Chang KW, Huang NA, Liu IH, Wang YH, Wu P, Tseng YT, Hughes MW, Jiang TX, Tsai MH, Chen CY, Oyang YJ, Lin EC*, Chuong CM*, Lin SP*. 2015. Emergence of differentially regulated pathways associated with the development of regional specificity in chicken skin. BMC Genomics.16:22.
Chen WJ, Ho CC, Chang YL, Chen HY, Lin CA, Lin TY, Yu SL, Yuan SS, Chen YL, Lin CY, Pan SH, Chou HYE, Chen YJ, Chang GC, Chu WC, Lee YM, Lee JY, Lee PJ, Li KC, Chen HW*, Yang PC*. Cancer-Associated Fibroblasts Regulate the Plasticity of Lung Cancer Stemness via Paracrine Signalling. Nature Comm., 2014, 5:3472. *Corresponding author.

Yang DK, Chen LC*, Lee MY, Hsu CH, Chen CS. (2014) Selection of aptamers for fluorescent detection of alpha-methylacyl-CoA racemase by single-bead SELEX. Biosens. Bioelectron. 62:106-112. (IF= 7.476 in 2015)

Lu KY, Lin CW, Hsu CH, Ho YC, Chuang EY, Sung HW*, Mi FL* (2014) FRET-based dual-emission and pH-responsive nanocarriers for enhanced delivery of protein across intestinal epithelial cell barrier. ACS Appl. Mater. Interfaces 6:18275-18289. (IF= 7.145 in 2015)
Su MA, Huang YT, Chen IT, Lee DY, Hsieh YC, Li CY, Ng TH, Liang SY, Lin SY, Huang SW, Chiang YA, Yu HT, Khoo KH, Chang GD, Lo CF, Wang HC (2014). An invertebrate Warburg effect: a shrimp virus achieves successful replication by altering the host metabolome via the PI3K-Akt-mTOR pathway. PLoS Pathogens. 10:e1004196. (IF= 7.003 in 2015)
Jiang HS, Wu YC*. (2014) LIN-3/EGF promotes the programmed cell death of specific cells death in Caenorhabditis elegans by transcriptional activation of the pro-apoptotic gene egl-1. PLoS Genet. 10(8): e1004513. (IF= 6.661 in 2015)
Yoshizawa G, Ho CW, Zhu W, Hu C, Syukriani Y, Lee I, Kim H, Tsai DFC, Minari1Jand Kato K. (2014) ELSI practices in genomic research in East Asia: implications for research collaboration and public participation. Genome Medicine 6:39. (IF= 5.700 in 2015)
Cheng JCC, Yen WJ, Chang WT, Wu KCC, Ko MC, Li CY. (2014) Risk of adolescent offspring’s completed suicide increases with the history of their same-sex parent’s death by suicide. Psychol. Med. 44: 1845-1854. (IF= 5.491 in 2015)
Lu TP, Hsu YY, Lai LC, Tsai MH, Chuang EY. (2014) Identification of gene expression biomarkers for predicting radiation exposure. Sci. Rep. 4:6293-6299. (IF= 5.228 in 2015)
Liu LY, Tseng HI, Lin CP, Lin YY, Huang YH, Huang CK, Chang TH, Lin SS*. 2014. High-throughput transcriptome analysis of the leafy flower transition of Catharanthus roseus induced by peanut witches’-broom phytoplasma infection. Plant Cell Physiol. 55:942-957. (17/209 in Plant Sciences)
Kao L, Wang YT, Chen YC, Tseng SF, Jhang JC, Chen YJ, Teng SC. Global analysis of Cdc14 dephosphorylation sites reveals essential regulatory role in mitosis and cytokinesis. (2014) Mol Cell Proteomics. 13, 594-605.
Huang YL, Chang CL, Tang CH, Lin YC, Ju TK, Huang WP *, and Lee H. * Extrinsic sphingosine 1-phosphate activates S1P5 and induces autophagy through generating endoplasmic reticulum stress in human prostate cancer PC-3 cells. Cell. Signal., 26: 611-618. (2014)
Tung YT, Wang BJ, Hsu WM, Hu MK, Her GM, Huang WP, and Liao YF.* Presenilin-1 Regulates the Expression of p62 to Govern p62-dependent Tau Degradation. Mol. Neurobiol., 49: 10-27. (2014)