Department of Biochemistry and Molecular Biology

Chang Chung University Academic Capacity Ensemble

Research Directions and Laboratory Features

(1) Development of Biomarkers for Early Diagnosis and Precision Therapeutic Targets for Oral Cancer Using an Integrative Omics Research Approach

Oral cancer is one of the most common cancers in Taiwan, with the incidence rate among men ranking the highest in the world. It has become a major public health issue and medical burden in Taiwan. However, over the past two decades, progress in early detection and precision targeted therapy for oral cancer has been very limited. Currently, there are still no effective biomarkers that can be applied to improve the detection rate of early-stage oral cancer or assist in postoperative follow-up. In addition, targeted therapy strategies specifically developed for oral cancer remain lacking, limiting the improvement of personalized treatment outcomes.

Our laboratory leads the research team at the Center for Molecular Medicine and participates in the U.S.-led International Cancer Proteogenome Consortium, an important part of the Cancer Moonshot initiative. By utilizing the well-established multi-omics analysis technology platform at the Center for Molecular Medicine, we systematically and comprehensively investigate the genomic, proteomic, and metabolomic landscapes of oral cancer in Taiwanese patients, including cancer tissues and adjacent non-tumor tissues.

The research includes genomic analyses, such as whole-exome sequencing and RNA sequencing; proteomic analyses, including quantitative proteomics and phosphoproteomics; and metabolomic analyses, including quantitative metabolomics. Through integrative omics big data analysis, we aim to understand how genomic alterations lead to changes in the proteome and metabolome. Our goal is to construct the first “multi-omics blueprint” of oral cancer, linking the genome, proteome, and metabolome, and to provide insights into the biological significance of these systematic alterations in the development and progression of oral cancer.

At the same time, by combining targeted gene, protein, and metabolite quantification technologies with humanized tumor animal models, we aim to develop biomarkers for early detection as well as drug targets or treatment guidance tools for precision medicine.

(2) Development of Clinically Applicable Cancer Biomarkers Using Advanced Proteomics Technologies

Cancer is one of the leading causes of death in humans. Most cancers are already at an advanced stage when diagnosed, which is a major reason for the persistently high cancer mortality rate. In addition to maintaining a healthy lifestyle, early diagnosis and effective treatment are currently the only effective approaches to combating cancer.

Although effective cancer biomarkers remain limited, testing body fluids such as blood, urine, and saliva for potential cancer biomarkers is still the most convenient preliminary screening method. Therefore, identifying novel and more effective body-fluid biomarkers is a highly important issue for the early diagnosis of cancer.

Mass spectrometry-based proteomics has emerged as a rapidly developing field in recent years. Because of its high sensitivity, high accuracy, and high-throughput capabilities, it is expected to be a powerful approach for systematically analyzing proteins in cancer-related samples, including both qualitative and quantitative analyses, in order to discover and validate cancer biomarkers with high application value.

In collaboration with several colleagues at Chang Gung University, our laboratory has jointly established the Proteomics Core Laboratory of Chang Gung University. We have developed multiple qualitative and quantitative proteomics technology platforms. Using three types of biological materials, including cancer patient tissues, body fluids, and cancer cell lines, we aim to identify cancer biomarkers and analyze abnormal molecular regulatory mechanisms in cancer.

Our laboratory is currently conducting research on several cancers commonly found in Taiwan, including oral cancer, colorectal cancer, liver cancer, and pancreatic cancer. Our long-term goal is to develop body-fluid biomarkers that can be practically applied in clinical settings for the detection of early-stage cancer and cancer recurrence, while also developing rapid and convenient methods for testing these biomarkers.

The major research findings on salivary biomarkers for oral cancer were published in October 2016, ahead of other international research teams. These findings have been granted patents in multiple countries and have been transferred to a local biotechnology start-up company for subsequent development of immunoassay reagents, including ELISA and paper-based rapid tests, as well as clinical trials.

This academia-industry collaboration has also received recognition through several biotechnology-related awards, including the Excellence Award in the Technology Transfer Cooperation category of the 2019 Taipei Biotech Awards in July 2019, first place in the 2019 Ministry of Science and Technology Institutional Linkage Academia-Industry Collaboration Achievement Award in November 2019, the Highlight Achievement Award of the National Applied Research Laboratories R&D Service Platform in August 2021, and the 16th National Innovation Award for Start-up Enterprises awarded to the collaborating biotechnology start-up company in December 2019.

The ELISA kit was registered in the European Union on December 4, 2020, with registration number 00159706, and the product is now eligible for sale in the EU market. This is the first commercially available immunoassay reagent kit for oral cancer biomarkers successfully developed independently in Taiwan. It serves as an important reference for a series of subsequent derivative or related diagnostic products and carries significant landmark importance. It is expected to have a major impact on improving Taiwan’s capability in oral cancer detection and prevention.

In addition, the major research findings on blood biomarkers for pancreatic cancer were published in May 2011. These findings have also been granted patents in multiple countries and transferred to a local biotechnology start-up company for subsequent development of immunoassay reagents and clinical trials.

(3) Development of Aptamers for Important Medical or Research Proteins

Aptamers are single-stranded RNA or DNA molecules with unique three-dimensional structures, typically 20 to 80 nucleotides in length. They can bind to specific molecular targets through structural complementarity. This binding mechanism is similar to antibody-antigen interactions. Therefore, aptamers have great potential to be developed into antibody-like antagonists or molecular targeting tools.

Our laboratory has established a PCR-based high-efficiency aptamer screening technology known as SELEX, or systematic evolution of ligands by exponential enrichment. We aim to develop high-affinity aptamers targeting important medical or research proteins, providing novel molecular tools for disease detection and targeted therapy development.

(4) Investigation of the Molecular Mechanisms of Cellular Signal Transduction Using Proteomics Technologies

Based on many years of accumulated experience in the separation, purification, and identification of protein enzymes, our laboratory has devoted itself over the past decade to successfully developing various mass spectrometry-based qualitative and quantitative proteomics technologies.

By using these powerful proteomic analysis tools, we are able to expand the scope of research on key intracellular signaling pathways, discover novel protein-protein interactions, and analyze various post-translational modifications of proteins. These possibilities greatly enhance the breadth and depth of research in the field of cell biology.

Publication

1. Wu CC#, Li HP#*, Hsieh CH#, Lin YT#, Chang IYF#, et al, Robles A, Rodriguez H, Lin HH, Yang HY, Hsueh C, Chang KP*, Yu JS* and Chang YS. (2025) Integrated multi-omics analyses of oral squamous cell carcinoma reveal precision patient stratification and personalized treatment strategies. Cancer Letters 2025 Apr 1;614:217482. doi: 10.1016/j.canlet.2025.217482.
2. 
   2. Liu CC#, Hsiao YC#, Lai WJ, Chiou CC, Chu LJ, Lin YT, Liu JC, Yu JS*. (2024) Development and optimization of a DNA aptamer to delay β bungarotoxin-induced lethality in a rodent model. Int J Biol Marcomol. 2024 May 13;270(Pt 2):132240. (IF 8.5)
   
   3. Chu LJ, Chang YT, Chien CY, Chung HC, Wu SF, Chen CJ, Liu YC, Liao WC, Chen CH, Chiang WF, Chang KP, Wang JS, Yu JS*. (2024) Clinical Validation of Saliva-Based Matrix Metalloproteinase-1 Rapid Strip Tests for Detecting Oral Cavity Cancer. Biomedical Journal 2024 Feb;47(1):100594. doi: 10.1016/j.bj.2023.04.002. Epub 2023 Apr 10.
   
   4. Chang YT, Chu LJ, Liu YC, Chen CJ, Wu SF, Chen CH, Chang IYF, Wang JS, Wu TY, Dash S, Chiang WF, Chiu SF, Gou SB, Chien CY, Chang KP, Yu JS*. (2020) Verification of saliva matrix metalloproteinase-1 as a strong diagnostic marker of oral cavity cancer. Cancers (Basel). 2020 Aug 13;12(8):2273. doi: 10.3390/cancers12082273.
   
   5. Yu JS#, Chen YT#, Chiang WF#, Hsiao YC#, Chu LJ#, See LC, et al., Chang YS*, Hartwell LH* (2016) Saliva protein biomarkers to detect oral squamous cell carcinoma in a high-risk population in Taiwan. PNAS USA 2016 Oct 11;113(41):11549-11554. doi: 10.1073/pnas.1612368113.
   
   6. Wu CC#, Lu YT#, Yeh TS#, Chan YH, Dash S, Yu JS* (2021) Fucosylated SERPINA1 is a novel serum marker for pancreatic cancer revealed by lectin affinity capture coupled with iTRAQ-based quantitative glycoproteomics approach. Int J Mol Sci 2021 Jun 4;22(11):6079. doi: 10.3390/ijms22116079.
   
   7. Liu JC, Chen YT, Hsieh YJ, Wu CC, Huang MC, Hsu YC, Wu CT, Chen CK, Dash S, Yu JS* (2021) Association of urinary ketamine and APOA1 levels with bladder dysfunction in ketamine abusers revealed via proteomics and targeted metabolite analyses. Scientific Reports 2021 May 5;11(1):9583. doi: 10.1038/s41598-021-89089-4.
   
   8. Chiang SF+, Huang HH+, Tsai WS+, Tan BCM, Yang CY, Huang PJ, Chang IYF, Lin J, Lu PS, Chin E, Liu YH, Yu JS, Chiang JM, Hung HY, You JF, Liu H*. (2021) Comprehensive functional genomic analyses link APC somatic mutation and mRNA-miRNA networks to the clinical outcome of stage-III colorectal cancer patients. Biomedical Journal. Available online 16 March 2021. doi: 10.1016/j.bj.2021.03.001.
   
   9. Wu CP*, Hung CY, Lusvarghi S, Chang YF, Hsiao SH, Huang YH, Hung TH, Yu JS, Ambudkar SV. (2021) Overexpression of human ABCB1 and ABCG2 reduces the susceptibility of cancer cells to the histone deacetylase 6-specific inhibitor citarinostat. Int J Mol Sci 2021 Mar 5;22(5):2592. doi: 10.3390/ijms22052592.
   
   10. Liu CC#, Yang YH#, Hsiao YC, Wang PJ, Liu JC, Liu CH, Hsieh WC, Lin CC, Yu JS* (2021) Rapid and efficient enrichment of snake venoms from human plasma by a strong cation exchange tip column to improve snakebite diagnosis. Toxins 2021 Feb 13;13(2):140. doi: 10.3390/toxins13020140.
   
   11. Chang YT, Chu LJ, Liu YC, Chen CJ, Wu SF, Chen CH, Chang IYF, Wang JS, Wu TY, Dash S, Chiang WF, Chiu SF, Gou SB, Chien CY, Chang KP, Yu JS*. (2020) Verification of saliva matrix metalloproteinase-1 as a strong diagnostic marker of oral cavity cancer. Cancers (Basel). 2020 Aug 13;12(8):E2273. doi: 10.3390/cancers12082273.
   
   12. Chen YT#, Chang IYF#, Kan CH, Liu YH, Kuo YP, Tseng HH, Chen HC, Liu H, Chang YS, Yu JS, Chang KP, Tan BCM*. (2020) circRNAome profiling unveils a novel oncogenic circFLNB circuit in oral cancer. Cells. 2020 Aug 10;9(8):E1868. doi: 10.3390/cells9081868.
   
   13. Lin YH*, Wu CC, Su WT, Tseng PC, Hsueh YY, Hsiao YC, Chang KP, Yu JS*, Chuang YR. (2020) Target peptide enrichment microfluidic chip for rapid detection of oral squamous cell carcinoma using stable isotope standards and capture by anti-peptide antibodies. Sensors and Actuators B: Chemical 2020 Nov 1;322:128607.
   
   14. Wu CP*, Hung CY, Lusvarghi S, Huang YH, Tseng PJ, Hung TH, Yu JS, Ambudkar SV. (2020) Overexpression of ABCB1 and ABCG2 contributes to reduced efficacy of the PI3K/mTOR inhibitor samotolisib (LY3023414) in cancer cell lines. Biochemical Pharmacology 2020 Jul 4:114137. doi: 10.1016/j.bcp.2020.114137.
   
   15. Hsueh PC, Wu KA, Yang CY, Hsu CW, Wang CL, Hung CM, Chen YT, Yu JS, Wu CC* (2020) Metabolomic profiling of parapneumonic effusion reveals a regulatory role of dipeptides in interleukin-8 production in neutrophil-like cells. Analytica Chimica Acta 2020 Sep 1;1128:238-250. doi: 10.1016/j.aca.2020.06.022.
   
   16. Chakraborty A, Lin WC, Lin YT, Huang KJ, Wang PY, Chang YF, Wang HI, Ma KT, Wang CY, Huang XR, Lee YH, Chen BC, Hsieh YJ, Chien KY, Lin TY, Liu JL, Sung LY, Yu JS, Chang YS, Pai LM*. (2020) SNAP29 mediates the assembly of histidine-induced CTP synthase filaments in proximity to the cytokeratin network. J Cell Sci 2020 May 11;133(9):jcs240200. doi: 10.1242/jcs.240200.
   
   17. Hsiao TF#, Wang CL#, Wu YC, Feng HP, Chiu YC, Lin HY, Liu KJ, Chang GC, Chien KY, Yu JS, Yu CJ*. (2020) Integrative omics analysis reveals soluble cadherin-3 as a survival predictor and an early monitoring marker of EGFR tyrosine kinase inhibitor therapy in lung cancer. Clin Cancer Res. 2020 Jul 1;26(13):3220-3229. doi: 10.1158/1078-0432.CCR-19-3972.
   
   18. Liu CC#, Chou YS#, Chen CY, Liu KL, Huang GJ, Yu JS, Wu CJ, Liaw GW, Hsieh CH*, Chen CK*. (2020) Pathogenesis of local necrosis induced by Naja atra venom: Assessment of the neutralization ability of Taiwanese freeze-dried neurotoxic antivenom in animal models. PLOS Neglected Tropical Diseases. 2020 Feb 7;14(2):e0008054. doi: 10.1371/journal.pntd.0008054.
   
   19. Hsiao YC, Lin SY, Chien KY, Chen SF, Wu CC, Chang YT, Chi LM, Chu LJ, Chiang WF, Chien CY, Chang KP, Chang YS, Yu JS* (2020) An immuno-MALDI mass spectrometry assay for the oral cancer biomarker, matrix metalloproteinase-1, in dried saliva spot samples. Anal Chim Acta 1100:118-130. doi: 10.1016/j.aca.2019.12.006.
   
   20. Chi LM#, Hsiao YC#, Chien KY#, Chen SF, Chuang YN, Lin SY, Wang WS, Chang IYF, Yang C, Chu LJ, Chiang WF, Chien CY, Chang YS, Chang KP*, Yu JS*. (2020) Assessment of candidate biomarkers in paired saliva and plasma samples from oral cancer patients by targeted mass spectrometry. J Proteomics. 2020 Jan 16;211:103571. doi: 10.1016/j.jprot.2019.103571.
   
   21. Lin WR*, Chiang JM, Lim SN, Su MY, Chen TH, Huang SW, Chen CW, Wu RC, Tsai CL, Lin YH, Alison MR, Hsieh SY, Yu JS, Chiu CT, Yeh CT. (2019) Dynamic bioenergetic alterations in colorectal adenomatous polyps and adenocarcinomas. EBioMedicine. 2019 Jun;44:334-345. doi: 10.1016/j.ebiom.2019.05.031.
   
   22. Yu J-S. (2019) From discovery of tyrosine phosphorylation to targeted cancer therapies: The 2018 Tang Prize in Biopharmaceutical Science. Biomedical Journal 2019 Apr;42(2):80-83. doi: 10.1016/j.bj.2019.03.004. (Invited article)
   
   23. Chen Y-T*, Tsai C-H, Chen C-L, Yu J-S, Chang Y-H*. (2019) Development of biomarkers of genitourinary cancer using mass spectrometry-based clinical proteomics. J Food Drug Anal. 2019 Apr;27(2):387-403. doi: 10.1016/j.jfda.2018.09.005.
   
   24. Chen Y-T*, Huang H-C, Hsieh Y-J, Fu S-H, Li L, Chen C-L, Chu L-J, Yu J-S. (2019) Targeting amine- and phenol-containing metabolites in urine by dansylation isotope labeling and liquid chromatography mass spectrometry for evaluation of bladder cancer biomarkers. J Food Drug Anal. 2019 Apr;27(2):460-474. doi: 10.1016/j.jfda.2018.11.008.
   
   25. Chou PH, Liao WC, Tsai KW, Chen KC, Yu JS, Chen TW*. (2019) TACCO, a database connecting transcriptome alterations, pathway alterations and clinical outcomes in cancers. Scientific Reports 2019 Mar 7;9(1):3877. doi: 10.1038/s41598-019-40629-z.
   
   26. Wang P#, Geng J#, Gao J, Zhao H, Li J, Shi Y, Yang B, Xiao C, Linghu Y, Sun X, Chen X, Hong L, Qin F, Li X, Yu JS, You H, Yuan Z, Zhou D, Johnson RL, Chen L*. (2019) Macrophage achieves self-protection against oxidative stress-induced ageing through Mst-Nrf2 axis. Nature Communications 2019 Feb 14;10(1):755. doi: 10.1038/s41467-019-08680-6.
   
   27. Hsu C-W#, Chen Y-T#, Hsieh Y-J, Chang K-P, Hsueh P-C, Yu J-S, Chang Y-S, Li L*, Wu C-C*. (2019) Integrated analyses utilizing metabolomics and transcriptomics reveal perturbation of the polyamine pathway in oral cavity squamous cell carcinoma. Anal Chim Acta 2019 Mar 7;1050:113-122. doi: 10.1016/j.aca.2018.10.070.
   
   28. Lin Y-H*, Chang H-Y, Wu C-C, Wu C-W, Chang K-P, Yu J-S*. (2019) BRAF protein immunoprecipitation, elution, and digestion from cell extract using a microfluidic mixer for mutant BRAF protein quantification by mass spectrometry. Anal Bioanal Chem. 2019 Feb;411(5):1085-1094. doi: 10.1007/s00216-018-1536-2.
   
   29. Lee C-C#, Hsieh Y-J#, Chen S-W, Fu S-H, Hsu C-W, Wu C-C, Han W, Li Y, Tao H, Chang Y-S, Yu J-S, Li L*, Chang C-H*, Chen Y-T*. (2018) Bretschneider solution-induced alterations in the urine metabolome in cardiac surgery patients. Scientific Reports 2018 Dec 11;8(1):17774.
   
   30. Liu C-C#, Yu J-S#, Wang P-J, Hsiao Y-C, Liu C-H, Chen Y-C, Lai P-F, Hsu C-P, Fann W-C, Lin C-C*. (2018) Development of sandwich ELISA and lateral flow strip assays for diagnosing clinically significant snakebite in Taiwan. PLOS Neglected Tropical Diseases. 2018 Dec 3;12(12):e0007014.
   
   31. Lin W-C, Chakraborty A, Huang S-C, Wang P-Y, Hsieh Y-J, Chien K-Y, Lee Y-H, Chang C-C, Tang H-Y, Lin Y-T, Tung C-S, Luo J-D, Chen T-W, Lin T-Y, Cheng M-L, Chen Y-T, Yeh C-T, Liu J-L, Sung L-Y, Shiao M-S, Yu J-S, Chang Y-S, Pai L-M*. (2018) Histidine-dependent protein methylation is required for compartmentalization of CTP synthase. Cell Reports 2018 Sep 4;24(10):2733-2745.e7.
   
   32. Wu CP*, Hsieh YJ, Murakami M, Vahedi S, Hsiao SH, Yeh N, Chou AW, Li YQ, Wu YS, Yu JS, Ambudkar SV. (2018) Human ATP-binding cassette transporters ABCB1 and ABCG2 confer resistance to histone deacetylase 6 inhibitor ricolinostat (ACY-1215) in cancer cell lines. Biochem Pharmacol. 2018 Jul 17;155:316-325.
   
   33. Liu C-C#, Lin C-C#, Hsiao Y-C, Wang P-J, Yu J-S*. (2018) Proteomic characterization of six Taiwanese snake venoms: Identification of species-specific proteins and development of a SISCAPA-MRM assay for cobra venom factors. J Proteomics 2018 Sep 15;187:59-68.
   
   34. Huang Y-H, Lin K-H, Yu J-S, Wu T-J, Lee W-C, Chao C-K, Pan T-L, Yeh C-T*. (2018) Targeting HSP60 by subcutaneous injections of jetPEI/HSP60-shRNA destabilizes cytoplasmic survivin and inhibits hepatocellular carcinoma growth. Mol Carcinog. 2018;57:1087-1101.
   
   35. Chen C-T, Liu C-C, Yu J-S, Li H-H, Lai M-C*. (2018) Integrated omics profiling identifies hypoxia-regulated genes in HCT116 colon cancer cells. J Proteomics 2018;188:139-151.
   
   36. Chu LJ#, Hsiao YC#, Chiang WF#, Tsai CJ, Lin SY, Chang KP, Chien CY, Yu JS*. (2018) Use of saliva protein biomarkers for diagnosis of oral cavity cancer. International Journal of Head and Neck Science 2018 Jun;2(2):56-68. (Invited review article)
   
   37. Tsai C-H,#, Chen Y-T*,#, Chang Y-H#, Hsueh C, Liu C-Y, Chang Y-S, Chen C-L*, Yu J-S*. (2018) Systematic verification of bladder cancer-associated tissue protein biomarker candidates in urine specimens. Oncotarget 2018 Jul 20;9(56):30731-30747.
   
   38. Lai YH, Liu H, Chiang WF, Chen TW, Chu LJ, Yu JS, Chen SJ, Chen HC, Tan BC*. (2018) MiR-31-5p-ACOX1 axis enhances tumorigenic fitness in oral squamous cell carcinoma via the promigratory prostaglandin E2. Theranostics 2018 Jan 1;8(2):486-504.
   
   39. Hsiao YC#, Chu LJ#, Chen YT, Chi LM, Chien KY, Chiang WF, Chang YT, Chen SF, Wang WS, Chuang YN, Lin SY, Chien CY, Chang KP, Chang YS, Yu JS*. (2018) Variability assessment of 90 salivary proteins in intra-day and inter-day samples from healthy donors by multiple reaction monitoring-mass spectrometry. Proteomics Clin Appl. 2018 Mar;12(2). doi: 10.1002/prca.201700039.
   
   40. Wu CC#, Lin JD#, Chen JT, Chang CM, Weng HF, Hsueh C, Chien HP, Yu JS*. (2018) Integrated analysis of fine-needle-aspiration cystic fluid proteome, cancer cell secretome, and public transcriptome datasets for papillary thyroid cancer biomarker discovery. Oncotarget 2018;9:12079-12100.
   
   41. Liu CC, You CH, Yu JS*, Huang GJ, Liu CH, Wang PJ, Lin CC*. (2017) Analysis of the efficacy of Taiwanese freeze neurotoxic antivenom against Southeast Asian cobra venoms through proteomics and animal model approaches. PLOS Neglected Tropical Disease. 2017 Dec 15;11(12):e0006138.
   
   42. Hsiao Y-C, Chi L-M, Chien K-Y, Chiang W-F, Chen S-F, Chuang Y-N, Lin S-Y, Wu C-C, Chu LJ, Chen Y-T, Chia S-L, Chien C-Y, Chang K-P, Chang Y-S, Yu J-S*. (2017) Development of a multiplexed assay for oral cancer candidate biomarkers using peptide immunoaffinity enrichment and targeted mass spectrometry. Mol Cell Proteomics 2017 Oct;16(10):1829-1849.
   
   43. Chen TW#, Lee CC#, Liu H#, Wu CS#, Pickering CR#, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP*, Chang YS*. (2017) APOBEC3A is an oral cancer prognostic biomarker in carriers of an APOBEC deletion polymorphism. Nature Communications. 2017 Sep 6;8(1):465.
   
   44. Hsiao YC#, Chu LJ#, Chen JT, Yeh TS, Yu JS*. (2017) Proteomic profiling of the cancer cell secretome: informing clinical research. Expert Review of Proteomics 2017 Sep;14(9):737-756. (Invited review article)
   
   45. Peng Y#, Zhang M#, Zheng L#, Liang Q#, Li H#, Chen J-T, Guo H, Yoshina S, Chen Y-Z, Zhao X, Wu X, Liu B, Mitani S, Yu J-S, Ding Xue*. (2017) Cysteine protease cathepsin B mediates radiation-induced bystander effects. Nature 2017 Jul 27;547(7664):458-462.
   
   46. Cheng JC*, Tseng CP, Liao MH, Peng CY, Yu JS, Chuang PH, Huang JT, Chen JJW. (2017) Activation of hepatic stellate cells by the ubiquitin C-terminal hydrolase 1 protein secreted from hepatitis C virus-infected hepatocytes. Scientific Reports. 2017 Jun 30;7:4448. doi: 10.1038/s41598-017-04259-7.
   
   47. Hsieh Y-J#, Chien K-Y#, Yang I-F, Lee I-N, Wu C-C, Huang T-Y, Yu J-S*. (2017) Oxidation of protein-bound methionine in Photofrin-photodynamic therapy-treated human tumor cells explored by methionine-containing peptide enrichment and quantitative proteomics approach. Scientific Reports 2017 May 2;7(1):1370. doi: 10.1038/s41598-017-01409-9.
   
   48. Shao CH, Chen CL, Lin JY, Chen CJ, Fu SH, Chen YT, Chang YS, Yu JS, Tsui KH, Juo CG*, Wu KP*. (2017) Metabolite marker discovery for the detection of bladder cancer by comparative metabolomics. Oncotarget 2017 Mar 21;8:38802-38810. doi: 10.18632/oncotarget.16393.
   
   49. Chen Y-T*, Chen H-W, Wu C-F, Chu L-J, Chiang W-F, Wu C-C, Yu J-S, Tsai C-H, Liang K-H, Chang Y-S, Wu M, Ou Yang W-T. (2017) Development of a multiplexed LC-MRM/MS method for evaluation of salivary proteins as oral cancer biomarkers. Mol Cell Proteomics 2017 May;16(5):799-811.
   
   50. Lin YT, Chien KY, Wu CC, Chang WY, Chu LJ, Yeh CT*, Yu JS*. (2017) Super-SILAC mix coupled with SIM/AIMS assays for targeted verification of phosphopeptides discovered in a large-scale phosphoproteome analysis of hepatocellular carcinoma. J Proteomics. 2017 Mar 22;157:40-51.
   
   51. Chung I-C, OuYang C-N, Yuan S-N, Li H-P, Chen J-T, Shieh H-R, Chen Y-J, Ojcius DM, Yu J-S, Chang Y-S, Chen L-C*. (2016) Pyk2 activates the NLRP3 inflammasome by directly phosphorylating ASC and contributes to inflammasome-dependent peritonitis. Scientific Reports 2016 Oct 31;6:36214.
   
   52. Yu JS#, Chen YT#, Chiang WF#, Hsiao YC#, Chu LJ#, See LC, Wu CS, Tu HT, Chen HW, Chen CC, Liao WC, Chang YT, Wu CC, Lin CY, Liu SY, Chiou ST, Cha SL, Chang KP, Chien CY, Chang SW, Chang CJ, Young JD, Pao CC, Chang YS*, Hartwell LH*. (2016) Saliva Protein Biomarkers to Detect Oral Squamous Cell Carcinoma in a High-Risk Population in Taiwan. Proc Natl Acad Sci USA. 2016 Oct 11;113(41):11549-11554. (#Co-first authors)
   
   53. Hsu CH, Hsu CW, Hsueh C, Wang CL, Wu YC, Wu CC, Liu CC, Yu JS, Chang YS, Yu CJ.* (2016) Identification and characterization of potential biomarkers by quantitative tissue proteomics of primary lung adenocarcinoma. Mol Cell Proteomics 2016 Jul;15(7):2396-2410.
   
   54. Chen H#, Hsiao Y-C#, Chiang S-F, Wu C-C, Lin Y-T, Liu H, Zhao H, Chen J-S, Chang Y-S, Yu J-S*. (2016) Quantitative analysis of wild-type and V600E mutant BRAF proteins in colorectal carcinoma using immunoenrichment and targeted mass spectrometry. Anal Chim Acta 2016 Aug 24;933:144-155.
   
   55. Wang C-I, Chan Y-Y, Wang C-L, Yu J-S, Chang Y-S, Yu C-J*. (2016) mTOR regulates proteasomal degradation and Dp1/E2F1-mediated transcription of KPNA2 in lung cancer cells. Oncotarget 2016 May 3;7(18):25432-25442.
   
   56. Wu C-P*, Hsieh Y-J, Hsiao S-H, Su C-Y, Li Y-Q, Huang Y-H, Huang C-W, Hsieh C-H, Yu J-S, Wu Y-S*. (2016) Human ATP-Binding Cassette transporter ABCG2 confers resistance to CUDC-907, a dual inhibitor of histone deacetylase and phosphatidylinositol 3-kinase. Mol Pharm. 2016 Mar 7;13(3):784-794.