1. Chen, Y. C.; Hsu, P. Y.; Su, M. C.; Chen, T. W.; Hsiao, C. C.; Chin, C. H.; Liou, C. W.; Wang, P. W.; Wang, T. Y.; Lin, Y. Y.; Lee, C. P.; Lin, M. C., MicroRNA Sequencing Analysis in Obstructive Sleep Apnea and Depression: Anti-Oxidant and MAOA-Inhibiting Effects of miR-15b-5p and miR-92b-3p through Targeting PTGS1-NF-kappaB-SP1 Signaling. Antioxidants (Basel) 2021, 10 (11).
  2. Chen, T. W.; Chang, K. P.; Cheng, C. C.; Chen, C. Y.; Hong, S. W.; Sie, Z. L.; Cheng, H. W.; Yen, W. C.; Huang, Y.; Liu, S. C.; Wang, C. I., Characterization of Recurrent Relevant Genes Reveals a Novel Role of RPL36A in Radioresistant Oral Squamous Cell Carcinoma. Cancers 2021, 13, 5623.
  3. Lin, M. Y.; Hsieh, H. H.; Chen, J. C.; Chen, C. L.; Sheu, N. C.; Huang, W. S.; Ho, S. Y.; Chen, T. W.; Lee, Y. J.; Wu, C. Y. Brachytherapy Approach Using 177Lu Conjugated Gold Nanostars and Evaluation of Biodistribution, Tumor Retention, Dosimetry and Therapeutic Efficacy in Head and Neck Tumor Model. Pharmaceutics 2021, 13, 1903.
  4. Huang, P. Y.; Yang, Y. C.; Wang, C. I.; Hsiao, P. W.; Chiang, H. I.; Chen, T. W.Increase in Akkermansiaceae in Gut Microbiota of Prostate Cancer-Bearing Mice. Int J Mol Sci 2021, 22 (17).
  5. Chiu, H. S.; Somvanshi, S.; Chen, T. W.; Sumazin, P., Illuminating lncRNA Function Through Target Prediction. Methods Mol Biol 2021, 2372, 263-295.
  6. Chao, C. H.; Wang, C. Y.; Wang, C. H.; Chen, T. W.; Hsu, H. Y.; Huang, H. W.; Li, C. W.; Mai, R. T., Mutant p53 Attenuates Oxidative Phosphorylation and Facilitates Cancer Stemness through Downregulating miR-200c-PCK2 Axis in Basal-Like Breast Cancer. Mol Cancer Res 2021.
  7. Yang, C. Y.; Chen, T. W.; Lu, W. L.; Liang, S. S.; Huang, H. D.; Tseng, C. P.; Tarng, D. C., Synbiotics Alleviate the Gut Indole Load and Dysbiosis in Chronic Kidney Disease. Cells 2021, 10, (1).
  8. Lorenzi, L.; Chiu, H. S.; Avila Cobos, F.; Gross, S.; Volders, P. J.; Cannoodt, R.; Nuytens, J.; Vanderheyden, K.; Anckaert, J.; Lefever, S.; Tay, A. P.; de Bony, E. J.; Trypsteen, W.; Gysens, F.; Vromman, M.; Goovaerts, T.; Hansen, T. B.; Kuersten, S.; Nijs, N.; Taghon, T.; Vermaelen, K.; Bracke, K. R.; Saeys, Y.; De Meyer, T.; Deshpande, N. P.; Anande, G.; Chen, T. W.; Wilkins, M. R.; Unnikrishnan, A.; De Preter, K.; Kjems, J.; Koster, J.; Schroth, G. P.; Vandesompele, J.; Sumazin, P.; Mestdagh, P., The RNA Atlas expands the catalog of human non-coding RNAs. Nat Biotechnol 2021.
  9. Lai, H. C.; Lin, T. L.; Chen, T. W.; Kuo, Y. L.; Chang, C. J.; Wu, T. R.; Shu, C. C.; Tsai, Y. H.; Swift, S.; Lu, C. C., Gut microbiota modulates COPD pathogenesis: role of anti-inflammatory Parabacteroides goldsteinii lipopolysaccharide. Gut 2021.
  10. Chou, L. F.; Chen, T. W.; Yang, H. Y.; Tian, Y. C.; Chang, M. Y.; Hung, C. C.; Hsu, S. H.; Tsai, C. Y.; Ko, Y. C.; Yang, C. W., Transcriptomic signatures of exacerbated progression in leptospirosis subclinical chronic kidney disease with secondary nephrotoxic injury. Am J Physiol Renal Physiol 2021, 320, (5), F1001-F1018.
  11. Chen, Y. C.; Tsai, Y. H.; Wang, C. C.; Liu, S. F.; Chen, T. W.; Fang, W. F.; Lee, C. P.; Hsu, P. Y.; Chao, T. Y.; Wu, C. C.; Wei, Y. F.; Chang, H. C.; Tsen, C. C.; Chang, Y. P.; Lin, M. C.; Epigenome-wide association study on asthma and chronic obstructive pulmonary disease overlap reveals aberrant DNA methylations related to clinical phenotypes. Sci Rep 2021, 11, (1), 5022.
  12. Lin BZ, Wan SY, Lin MY, Chang CH, Chen TW, Yang MH, Lee YJ: Involvement of Differentially Expressed microRNAs in the PEGylated Liposome Encapsulated 188Rhenium-Mediated Suppression of Orthotopic Hypopharyngeal Tumor. Molecules 2020, 25(16):3609.
  13. Yang WF, Qin N, Song X, Jiang C, Li T, Ji P, Li Y, Ding D, Wang C, Dai J, Jin G, Chen TW, Chang YS, Quyang DQ, Liao, GQ, Hu Z, Chang KP, Su YX, Ma H: Genomic Signature of Mismatch Repair Deficiency in Areca Nut–Related Oral Cancer. Journal of Dental Research 2020, 99(11):1252-1261.
  14. Chen YC, Hsiao CC, Chen TW, Wu CC, Chao TY, Leung SY, Eng HL, Lee CP, Wang TY, Lin MC: Whole Genome DNA Methylation Analysis of Active Pulmonary Tuberculosis Disease Identifies Novel Epigenotypes: PARP9/miR-505/RASGRP4/GNG12 Gene Methylation and Clinical Phenotypes. International journal of molecular sciences 2020, 21(9):3180.
  15. Chen TW, Chen CW: Melanin production as a visual indicator of conjugal transfer in Streptomyces. J Appl Genet 2020.
  16. Cheng YH, Huang TW, Juan CH, Chou SH, Tseng YY, Chen TW, Yang TC, Lin YT: Tigecycline-non-susceptible hypervirulent Klebsiella pneumoniae strains in Taiwan. J Antimicrob Chemother 2019.
  17. Wang CI, Kao HK, Chen TW, Huang Y, Cheng HW, Yi JS, Hung SY, Wu CS, Lee YS, Chang KP: Characterization of Copy Number Variations in Oral Cavity Squamous Cell Carcinoma Reveals a Novel Role for MLLT3 in Cell InvasivenessOncologist 2019.
  18. Huang SY, Huang CH, Chen CJ, Chen TW, Lin CY, Lin YT, Kuo SM, Huang CG, Lee LA, Chen YH et al: Novel Role for miR-1290 in Host Species Specificity of Influenza A Virus. Molecular therapy Nucleic acids 2019, 17:10-23.
  19. Chou PH, Liao WC, Tsai KW, Chen KC, Yu JS, Chen TW*: TACCO, a Database Connecting Transcriptome Alterations, Pathway Alterations and Clinical Outcomes in CancersSci Rep 2019, 9(1):3877.
  20. Hsu CW, Chen YT, Hsieh YJ, Chang KP, Hsueh PC, Chen TW, Yu JS, Chang YS, Li L, Wu CC: Integrated analyses utilizing metabolomics and transcriptomics reveal perturbation of the polyamine pathway in oral cavity squamous cell carcinoma. Analytica chimica acta 2019, 1050:113-122.
  21. Wei-Cheng Lin, Archan Chakraborty, Shih-Chia Huang, Pei-Yu Wang, Ya-Ju Hsieh, Kun-Yi Chien, Yen-Hsien Lee, Chia-Chun Chang, Hsiang-Yu Tang, Yu-Tsun Lin, Chang-Shung Tung, Ji-Dung Luo, Ting-Wen Chen, Tzu-Yang Lin, Mei-Ling Cheng, Yi-Ting Chen, Chau-Ting Yeh, Ji-Long Liu, Li-Ying Sung, Ming-Shi Shiao, Jau-Song Yu, Yu-Sun Chang, Li-Mei Pai: Histidine-Dependent Protein Methylation Is Required for Compartmentalization of CTP Synthase. Cell reports 2018, 24(10):2733-2745 e2737.
  22. Chou LF, Chen TW, Yang HY, Chang MY, Shu SH, Tsai CY, Ko YC, Huang CT, Tian YC, Hung CC et al: Murine Renal Transcriptome Profiles upon Leptospiral Infection: Implications for Chronic Kidney Diseases The Journal of Infectious Diseases 2018, 218(9):1411-1423.
  23. Li HP, Peng CC, Wu CC, Chen CH, Shih MJ, Huang MY, Lai YR, Chen YL, Chen TW, Tang P et al: Inactivation of the tight junction gene CLDN11 by aberrant hypermethylation modulates tubulins polymerization and promotes cell migration in nasopharyngeal carcinoma. J Exp Clin Cancer Res 2018, 37(1):102.
  24. Joshua D Campbell 1, Christina Yau 2, Reanne Bowlby 3, Yuexin Liu 4, Kevin Brennan 5, Huihui Fan, Alison M Taylor, Chen Wang, Vonn Walter, Rehan Akbani, Lauren Averett Byers, Chad J Creighton, Cristian Coarfa, Juliann Shih, Andrew D Cherniack, Olivier Gevaert, Marcos Prunello, Hui Shen, Pavana Anur, Jianhong Chen, Hui Cheng, D Neil Hayes, Susan Bullman, Chandra Sekhar Pedamallu, Akinyemi I Ojesina, Sara Sadeghi, Karen L Mungall, A Gordon Robertson, Christopher Benz, Andre Schultz, Rupa S Kanchi, Carl M Gay, Apurva Hegde, Lixia Diao, Jing Wang, Wencai Ma, Pavel Sumazin, Hua-Sheng Chiu, Ting-Wen Chen, Preethi Gunaratne, Larry Donehower, Janet S Rader, Rosemary Zuna, Hikmat Al-Ahmadie, Alexander J Lazar, Elsa R Flores, Kenneth Y Tsai, Jane H Zhou, Anil K Rustgi, Esther Drill, Ronglei Shen, Christopher K Wong, Cancer Genome Atlas Research Network; Joshua M Stuart, Peter W Laird, Katherine A Hoadley, John N Weinstein, Myron Peto, Curtis R Pickering, Zhong Chen, Carter Van Waes: Genomic, pathway network, and immunologic features distinguishing squamous carcinomas.Cell Rep 2018, 23(1):194-212 e196.
  25. Ashton C Berger, Anil Korkut, Rupa S Kanchi, Apurva M Hegde, Walter Lenoir, Wenbin Liu, Yuexin Liu, Huihui Fan, Hui Shen, Visweswaran Ravikumar, Arvind Rao, Andre Schultz, Xubin Li, Pavel Sumazin, Cecilia Williams, Pieter Mestdagh, Preethi H Gunaratne, Christina Yau, Reanne Bowlby, A Gordon Robertson, Daniel G Tiezzi, Chen Wang, Andrew D Cherniack, Andrew K Godwin, Nicole M Kuderer, Janet S Rader, Rosemary E Zuna, Anil K Sood, Alexander J Lazar, Akinyemi I Ojesina, Clement Adebamowo, Sally N Adebamowo, Keith A Baggerly, Ting-Wen Chen, Hua-Sheng Chiu, Steve Lefever, Liang Liu, Karen MacKenzie, Sandra Orsulic, Jason Roszik, Carl Simon Shelley, Qianqian Song, Christopher P Vellano, Nicolas Wentzensen, Cancer Genome Atlas Research Network; John N Weinstein, Gordon B Mills, Douglas A Levine, Rehan Akbani: A comprehensive Pan-Cancer molecular study of gynecologic and breast cancers.Cancer Cell 2018, 33(4):690-705 e699.
  26. Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS, Cancer Genome Atlas Research N et al: Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context.Cell Rep 2018, 23(1):297-312 e212.
  27. Lai YH, Liu H, Chiang WF, Chen TW, Chu LJ, Yu JS, Chen SJ, Chen HC, Tan BC: MiR-31-5p-ACOX1 Axis Enhances Tumorigenic Fitness in Oral Squamous Cell Carcinoma Via the Promigratory Prostaglandin E2Theranostics 2018, 8(2):486-504.
  28. Chen PC*, Chen TW*, Han YA, Ng WV, Yang CS: Complete Genome Sequence of a New Halophilic Archaeon, Haloarcula taiwanensis, Isolated from a Solar Saltern in Southern TaiwanGenome Announc 2018, 6(5).*
  29. Sablok G*, Chen TW*, Lee CC, Yang C, Gan RC, Wegrzyn JL, Porta NL, Nayak KC, Huang PJ, Varotto C et alChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applicationsDNA Res 2017.*
  30. Chen YC, Chen KD, Su MC, Chin CH, Chen CJ, Liou CW, Chen TW, Chang YC, Huang KT, Wang CC et alGenome-wide gene expression array identifies novel genes related to disease severity and excessive daytime sleepiness in patients with obstructive sleep apneaPLoS One 2017, 12(5):e0176575.
  31. Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IYF, Yeh YM, Chen CD et alAPOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphismNat Commun 2017, 8.*
  32. Chen TW, Gan RC, Fang YK, Chien KY, Liao WC, Chen CC, Wu TH, Chang IY, Yang C, Huang PJ et alFunctionAnnotator, a versatile and efficient web tool for non-model organism annotationSci Rep 2017, 7(1):10430.*本人為第一作者
  33. Bradic M, Warring SD, Tooley GE, Scheid P, Secor WE, Land KM, Huang PJ, Chen TW, Lee CC, Tang P et alGenetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalisGenome Biol Evol 2017, 9(6):1658-1672.
  34. Tsai KW, Leung CM, Lo YH, Chen TW, Chan WC, Yu SY, Tu YT, Lam HC, Li SC, Ger LP et alArm Selection Preference of MicroRNA-193a Varies in Breast CancerSci Rep 2016, 6:28176.
  35. Gan RC*, Chen TW*, Wu TH, Huang PJ, Lee CC, Yeh YM, Chiu CH, Huang HD, Tang P: PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organismsBMC bioinformatics 2016, 17(Suppl 19):513.*
  36. Fang YK, Chien KY, Huang KY, Cheng WH, Ku FM, Lin R, Chen TW, Huang PJ, Chiu CH, Tang P: Responding to a Zoonotic Emergency with Multi-omics Research: Pentatrichomonas hominis Hydrogenosomal Protein Characterization with Use of RNA Sequencing and ProteomicsOmics : a journal of integrative biology 2016, 20(11):662-669.
  37. Chen YC, Chen TW, Su MC, Chen CJ, Chen KD, Liou CW, Tang P, Wang TY, Chang JC, Wang CC et alWhole Genome DNA Methylation Analysis of Obstructive Sleep Apnea: IL1R2, NPR2, AR, SP140 Methylation and Clinical PhenotypeSleep 2016, 39(4):743-755.
  38. Chang PY, Chen CC, Chang YS, Tsai WS, You JF, Lin GP, Chen TW, Chen JS, Chan EC: MicroRNA-223 and microRNA-92a in stool and plasma samples act as complementary biomarkers to increase colorectal cancer detectionOncotarget 2016.
  39. Chen TW, Gan RC, Chang YF, Liao WC, Wu TH, Lee CC, Huang PJ, Lee CY, Chen YY, Chiu CH et alIs the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencingBMC genomics 2015, 16:648.*
  40. Tsai KW, Chang B, Pan CT, Lin WC, Chen TW, Li SC: Evaluation and application of the strand-specific protocol for next-generation sequencingBioMed research international 2015, 2015:182389.
  41. Tsai KW, Hu LY, Chen TW, Li SC, Ho MR, Yu SY, Tu YT, Chen WS, Lam HC: Emerging role of microRNAs in modulating endothelin-1 expression in gastric cancerOncology reports 2015, 33(1):485-493.
  42. Huang PJ, Lee CC, Tan BC, Yeh YM, Huang KY, Gan RC, Chen TW, Lee CY, Yang ST, Liao CS et alVanno: a visualization-aided variant annotation toolHuman mutation 2015, 36(2):167-174.
  43. Huang PJ, Lee CC, Tan BC, Yeh YM, Julie Chu L, Chen TW, Chang KP, Lee CY, Gan RC, Liu H et alCMPD: cancer mutant proteome databaseNucleic acids research 2015, 43(Database issue):D849-855.
  44. Weng RR, Shu HW, Chin SW, Kao Y, Chen TW, Liao CC, Tsay YG, Ng WV: OMICS in Ecology: Systems Level Analyses of Halobacterium salinarum Reveal Large-scale Temperature-Mediated Changes and a Requirement of CctA for ThermotoleranceOmics : a journal of integrative biology 2014, 18(1):65-80.
  45. Leung CM, Li SC, Chen TW, Ho MR, Hu LY, Liu WS, Wu TT, Hsu PC, Chang HT, Tsai KW: Comprehensive microRNA profiling of prostate cancer cells after ionizing radiation treatmentOncology reports 2014, 31(3):1067-1078.
  46. Leung CM, Chen TW, Li SC, Ho MR, Hu LY, Liu WS, Wu TT, Hsu PC, Chang HT, Tsai KW: MicroRNA expression profiles in human breast cancer cells after multifraction and single-dose radiation treatmentOncology reports 2014, 31(5):2147-2156.
  47. Chou LF, Chen TW, Ko YC, Pan MJ, Tian YC, Chiu CH, Tang P, Hung CC, Yang CW: Potential impact on kidney infection: a whole-genome analysis of Leptospira santarosai serovar ShermaniEmerging microbes & infections 2014, 3(11):e82.
  48. Chen TW, Li HP, Lee CC, Gan RC, Huang PJ, Wu TH, Lee CY, Chang YF, Tang P: ChIPseek, a web-based analysis tool for ChIP dataBMC genomics 2014, 15:539.*
  49. Huang PJ, Yeh YM, Gan RC, Lee CC, Chen TW, Lee CY, Liu H, Chen SJ, Tang P: CPAP: Cancer Panel Analysis PipelineHuman mutation 2013, 34(10):1340-1346.
  50. Chen WS*, Chen TW*, Yang TH, Hu LY, Pan HW, Leung CM, Li SC, Ho MR, Shu CW, Liu PF et alCo-modulated behavior and effects of differentially expressed miRNA in colorectal cancerBMC genomics 2013, 14.*
  51. Wu TH, Chu LJ, Wang JC, Chen TW, Tien YJ, Lin WC, Ng WV: Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidatesBMC genomics 2012, 13 Suppl 7:S12.
  52. Chen TW, Gan RR, Wu TH, Lin WC, Tang P: VIP DB–a viral protein domain usage and distribution databaseGenomics 2012, 100(3):149-156.*
  53. Chen TW, Gan RC, Wu TH, Huang PJ, Lee CY, Chen YY, Chen CC, Tang P: FastAnnotator–an efficient transcript annotation web toolBMC genomics 2012, 13 Suppl 7:S9. *
  54. Chen TW, Wu TH, Ng WV, Lin WC: Interrogation of alternative splicing events in duplicated genes during evolutionBMC genomics 2011, 12 Suppl 3:S16. *
  55. Chen TW, Wu TH, Ng WV, Lin WC: DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detectionBMC bioinformatics 2010, 11 Suppl 7:S6.