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Research and Development
Collaborative Research
 

Research and Development - 2019

  1. pWGBSSimla: A profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions. Chung, RH; Kang, CY, Bioinformatics., 36(3): 660-665 (2019)
  2. A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification. Chung, RH; Kang, CY, Gigascience, 8(5): giz045 (2019)
  3. The Impact of Emergency Interventions and Patient Characteristics on the Risk of Heart Failure in Patients with Nontraumatic OHCA. Cheng Hsu Chen, Chih-Yu Chang,Mei-Chueh Yang, Jr-Hau Wu, Ching-Hui Liao, Chih-Pei Su, Yu-Chih Chen, Shinn-Ying Ho, Cheng-Chieh Huang, Tsung-Han Lee, Wen-Liang Chen, Chu-Chung Chou and Yan-Ren Lin , Emergency Medicine International , 2019:6218389 (2019)
  4. Enterotype-based Analysis of Gut Microbiota along the Conventional Adenoma-Carcinoma Colorectal Cancer Pathway. Tzu-Wei Yang, Wei-Hsiang Lee, Siang-Jyun Tu, …., Shinn-Ying Ho, Wen-Liang Chen, Shun-Fa Yang, Kwo-Chang Ueng, Hsien-Da Huang, Chien-Ning Huang, Yuh-Jyh Jong & Chun-Che Lin , Scientific Reports , 9(1): 10923 (2019)
  5. CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts. Huang, P. J., Lin, H. H., Lee, C. C., Chiu, L. Y., Wu, S. M., Yeh, Y. M., Tang, P., Chiu, C. H., Lyu, P. C.*, Tsai, P. C., BMC medical genomics, 12(5): 99 (2019)
  6. The ligand-mediated affinity of brain-type fatty acid-binding protein for membranes determines the directionality of lipophilic cargo transport. Cheng, Y. Y., Huang, Y. F., Lin, H. H., Chang, W. W., Lyu, P. C.*, Biochim Biophys Acta Mol Cell Biol Lipids, 1864(12): 158506 (2019)
  7. Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer. Ko KT, Hu IC, Huang KF, Lyu PC, Hsu SD, Structure, 27(8): 1224-1233 (2019)
  8. TNF-α-induced miR-450a mediates TMEM182 expression to promote oral squamous cell carcinoma motility. Hsing EW, Shiah SG, Peng HY, Chen YW, Chuu CP, Hsiao JR, Lyu PC, Chang JY., PLoS One, 14(3): e0213463 (2019)
  9. Untying a Protein Knot by Circular Permutation. Chuang YC, Hu IC, Lyu PC, Hsu SD, J Mol Biol., 431(4): 857-863 (2019)
  10. Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature. Hong-Jie Dai, Chen-Kai Wang, Nai-Wen Chang, Ming-Siang Huang, Jitendra Jonnagaddala, Feng-Duo Wang, Wen-Lian Hsu, Database, 2019: baz030 (2019)
  11. Medical knowledge infused convolutional neural networks for cohort selection in clinical trials. Chi-Jen Chen, Neha Warikoo, Yung-Chun Chang, Jin-Hua Chen, Wen-Lian Hsu, Journal of the American Medical Informatics Association, 26(11): 1227-1236 (2019)
 

Research and Development - 2020

  1. Mortality of pregnancy following breast cancer diagnoses in Taiwanese women. Chuang, SC;Lin, CH;Lu, YS;Hsiung, CA, Oncologist, 25(2): e252-e258. (2020)
  2. Predicting lung cancer occurrence in never-smoking females in Asia: TNSF-SQ, a prediction model. Chien, LH;Chen, CH;Chen, TY;Chang, GC;Tsai, YH;Hsiao, CF;Chen, KY;Su, WC;Wang, WC;Huang, MS;Chen, YM;Chen, CY;Liang, SK;Chen, CY;Wang, CL;Lee, MH;Chung, RH; Tsai, FY;Hu, JW;Katki, HA;Chatterjee, N;Chanock, SJ;Rothman, N;Lan, Q;Yang, PC;Chen, CJ;Chang, IS; Hsiung, CA, Cancer Epidemiology, Biomarkers and Prevention, 29(2): 452-459 (2020)
  3. The paradox of aging and health-related quality of life in Asian Chinese: Results from the Healthy Aging Longitudinal Study in Taiwan. Tseng, HY;Lockenhoff, C;Lee, CY;Yu, SH;Wu, IC;Chang, HY;Chiu, YF;Hsiung, CA, BMC Geriatrics, 20(1): 91 (2020)
  4. The role of the bacterial protease Prc in the uropathogenesis of extraintestinal pathogenic Escherichia coli. Wen-Chun Huang, Chung-Yen Lin, Masayuki Hashimoto, Jiunn-Jong Wu, Ming-Cheng Wang, Wei-Hung Lin, Chang-Shi Chen & Ching-Hao Teng, Journal of Biomedical Science, 27(1): 14 (2020)
  5. Landscape of mitochondria genome and clinical outcomes in stage 1 lung adenocarcinoma. Lovely Raghav, Ya-Hsuan Chang, Shinn-Ying Ho, Hsuan-Yu Chen, Cancers, 12(3): 755 (2020)
  6. GREMA: Modelling of emulated gene regulato-ry networks with confidence levels based on evolutionary intelligence to cope with the un-derdetermined problem. Ming-Ju Tsai, Jyun-Rong Wang, Shinn-Jang Ho, Li-Sun Shu, Wen-Lin Huang, Shinn-Ying Ho, BIOINFORMATICS, 36(12): 3833-3840 (2020)
  7. Heterophilic antibodies influence immunometric assay: a case report and reviews. Yao-Feng Hu, Shinn-Ying Ho, IMMUNOLOGIC RESEARCH, 68(2)104-106 (2020)
  8. TIAM2S as a novel regulator for serotonin level enhances brain plasticity and locomotion behavior. Chun-Hsien Chu, Jia-Shing Chen, Pei-Chin Chuang, Chia-Hao Su, Ya-Ling Chan, Ying-Ju Yang, Yu-Ting Chiang, Yu-Ya Su, Po-Wu Gean, H. Sunny Sun, The FASEB Journal, 34(2): 3267-3288 (2020)
  9. Joining Illumina paired-end reads for classifying phylogenetic marker genes. Liu T*, Chen CY, Chen-Deng A, Chen YL, Wang JY, Hou YI, Lin MC, BMC Bioinformatics, 21(1): 105 (2020)
  10. sRIS: a small RNA illustration system for plant next-generation sequencing data analysis. K.C. Tseng§, Y.F. Chiang-Hsieh, H. Pai, N.Y. Wu, H.Q. Zheng, C.N. Chow, Y. Lee, S.B. Chang, N.S. Lin, and W.C. Chang, Plant and Cell Physiology, 61(6): 1204-1212 (2020)
  11. GSAlign: an efficient sequence alignment tool for intra-species genomes. Hsin-Nan Lin, Wen-Lian Hsu, BMC genomics, 21(1): 1-10 (2020)
  12. mySORT: A Web Framework by using Deconvolution Approach to Estimating Immune Cell Composition from Complex Tissues. Shu-Hwa Chen , Bo-Yi Yu , Wen-Yu Kuo , Ya-Bo Lin , Sheng-Yao Su , I-Hsuan Lu , Chung-Yen Lin, Preprints, : 2020110385 (2020)
  13. Characterization of phthalate exposure in relation to serum thyroid and growth hormones, and estimated daily intake levels in children exposed to phthalate-tainted products: A longitudinal cohort study. Po-Chin Huang , Wei-Hsiang Chang, Ming-Tsang Wu, Mei-Lien Chen, I-Jen Wang, Shu-Fang Shih, Chao A Hsiung, Kai-Wei Liao, Environmental Pollution , 264: 114648 (2020)
  14. The sex-specific association of phthalate exposure with DNA methylation and characteristics of body fat in children. Chia-Huang Chang, Chian-Feng Chen, Yen-An Tsai, Shu-Li Wang, Po-Chin Huang, Bai-Hsiun Chen, Ming-Tsang Wu, Chu-Chih Chen, Chao Agnes Hsiung, Mei-Lien Chen, The Science of The Total Environment, 737(32):139833 (2020)
  15. Novel eye genes systematically discovered through an integrated analysis of mouse transcriptomes and phenome. Chiang, CY; Ching, YH; Chang, TY; Hu, LS; Yong, YS; Keak, PY; Mustika, I; Lin, MD; Liao, BY, Comput Struct Biotechnol J, 18: 73-82 (2020)
  16. Impact of cooking oil fume exposure and fume extractor use on lung cancer risk in non-smoking Han Chinese women. Chen TY, Fang YH, Chen HL, Chang CH, Huang H, Chen YS, Liao KM, Wu HY, Chang GC, Tsai YH, Wang CL, Chen YM, Huang MS, Su WC, Yang PC, Chen CJ, Hsiao CF, Hsiung CA., Sci Rep, 10(1): 6774 (2020)
  17. Clinical characteristics and risk factors for children with norovirus gastroenteritis in Taiwan. Wu CY, Chi H, Liu CC, Huang YC, Huang YC, Lin HC, Ho YH, Huang LM, Huang CY, Shih SM, Wu FT, Mu JJ, Hsiung CA; Taiwan Pediatric Infectious Disease Alliance., J Microbiol Immunol Infect, 54(5): 909-917 (2020)
  18. Policy-driven revolution of prescription record in outpatient use of fluoroquinolones. Kuo SC, Shih SM, Lauderdale TY, Chang IS, Chen YC, Hsiung CA, Chang SC, J Microbiol Immunol Infect., 53(1): 133-140 (2020)
  19. Long-term effectiveness of pentavalent and monovalent rotavirus vaccines against hospitalization in Taiwan children. Huang YC, Wu FT, Huang YC, Liu CC, Chun-Yi-Lee, Lin HC, Chi H, Huang LM, Ho YH, Lee JT, Shih SM, Ching-Yi-Huang, Hsiung CA; Taiwan Pediatric Infectious Disease Alliance., Vaccine, 38(41): 6435-6441 (2020)
  20. HOme-based Longitudinal Investigation of the multidiSciplinary Team Integrated Care (HOLISTIC): Protocol of a prospective nationwide cohort study. Liao JY, Chen PJ, Wu YL, Cheng CH, Yu SJ, Huang CH, Li CM, Wang YW, Zhang KP, Liu IT, Umegaki H, Hamano J, Mori M, Petersen I, Sampson EL, Hsiung CA., BMC Geriatr, 20(1): 511 (2020)
  21. Reading activity prevents long-term decline in cognitive function in older people: Evidence from a 14-year longitudinal study. Yu-Hung Chang, I-Chien Wu, Chao A Hsiung, International psychogeriatrics, 33(1): 63-74 (2020)
  22. Novel miRNA signature for predicting the stage of hepatocellular carcinoma. Srinivasulu Yerukala Sathipati, Shinn‑Ying Ho, Scientific Reports, 10(1): 14452 (2020)
  23. Clinical treatment and medication in decreasing the development of major depression caused by spinal fracture. Chih-Yu Chang, Wen-Liang Chen, Pei-You Hsieh, Shinn-Ying Ho, Cheng-Chieh Huang, Tsung-Han Lee, Chu-Chung Chou, Chin-Fu Chang, Yat-Yin Law, Yan-Ren Lin, Journal of International Medical Research, 48(11): 1-13 (2020)
  24. TIAM2S Mediates Serotonin Homeostasis and Provokes a Pro-Inflammatory Immune Microenvironment Permissive for Colorectal Tumorigenesis. Ya-Ling Chan, Wei-Chung Lai, Jia-Shing Chen, Joseph Ta-Chien Tseng, Pei-Chin Chuang, Jonathan Jou, Chung-Ta Lee and H. Sunny Sun., Cancers, 12(7): 1-18 (2020)
  25. EXPath 2.0: An Updated Database for Integrating High-Throughput Gene Expression Data with Biological Pathways. K.C. Tseng, G.Z. Li, Y.C. Hung, C.N. Chow, N.Y. Wu, Y.Y. Chien, H. Q. Zheng, Y. Lee, P.L. Kuo, S.B. Chang, and W.C. Chang, Plant and Cell Physiology, 61(10): 1818-1827 (2020)
  26. Novel compound heterozygous mutations in CRTAP cause rare autosomal recessive osteogenesis imperfecta. Yen-An Tang, Lin-Yen Wang, Chiao-May Chang, I-Wen Lee, Wen-Hui Tsai*, H. Sunny Sun*, Frontiers in Genetics, 11: 897 (2020)
  27. FGF9 is a downstream target of SRY and sufficient to determine male sex fate in ex vivo XX gonad culture. Yi-Han Li, Tsung-Ming Chen, Shang-Hsun Yang, Bu-Miin Huang, Chia-Ching Wu, Jih-Ing Chuang, Shaw-Jenq Tsai and H. Sunny Sun, Biology of reproduction, 103(6): 1300-1313 (2020)
  28. Dissecting efficiency of a 5’ rapid amplification of cDNA ends (5’ RACE) approach for profiling T-cell receptor beta repertoire. Lin YH, Hung SJ, Chen YL, Lin CH, Kung TF, Yeh YC, Tseng TJ, Liu T, PLoS ONE, 15(7): e0236366 (2020)
  29. Long-term effects of fertilizers with regional climate variability on yield trends of sweet corn. P.F. Hou, Y.T. Chang, J.M. Lai, K.L. Chou, S.F. Tai, K.C. Tseng, C.N. Chow, S.L. Jeng, H.J. Huang, and C. Chang, Sustainability, 12(9): 3528 (2020)
  30. Genomic amplification of chromosome 20q13.33 is the early biomarker for the development of sporadic colorectal carcinoma. Vo-Minh-Hoang Bui, Clément Mettling, Jonathan Jou, H. Sunny Sun, BMC Medical Genomics, 13(suppl 10): 149 (2020)
  31. Structural Insights into the Active Site Formation of DUSP22 in N-loop-containing Protein Tyrosine Phosphatases. Lai CH, Chang CC, Chuang HC, Tan TH, Lyu PC, Int J Mol Sci., 21(20): 7515 (2020)
  32. An essential role of acetyl coenzyme A in the catalytic cycle of insect arylalkylamine N-acetyltransferase. Wu CY, Hu IC, Yang YC, Ding WC, Lai CH, Lee YZ, Liu YC, Cheng HC, Lyu PC, Commun Biol., 3(1): 441 (2020)
  33. Introduction to the Taiwan Biophysical Society. Lyu PC, Biophys Rev., 11(3): 263 (2020)
  34. Biomedical named entity recognition and linking datasets: survey and our recent development. Ming-Siang Huang, Po-Ting Lai, Pei-Yen Lin, Yu-Ting You, Richard Tzong-Han Tsai and Wen-Lian Hsu, Briefings in Bioinformatics, 21(6): 2219-2238 (2020)
  35. A flexible template generation and matching method with applications for publication reference metadata extraction. Ting‐Hao Yang, Yu‐Lun Hsieh, Shih‐Hung Liu, Yung‐Chun Chang, Wen‐Lian Hsu, Journal of the Association for Information Science and Technology, 72(1): 32-45 (2020)
 

Research and Development - 2021

  1. Endoscopic Images by a Single-Shot Multibox Detector for the Identification of Early Cancerous Lesions in the Esophagus: A Pilot Study. Yao-Kuang Wang, Hao-Yi Syu,Yi-Hsun Chen, Chen-Shuan Chung, Yu Sheng Tseng, Shinn-Ying Ho, Chien-Wei Huang, I-Chen Wu andHsiang-Chen Wang , Cancers, 13(2): 321 (2021)
  2. Identification of the miRNA signature associated with survival in patients with ovarian cancer. Srinivasulu Yerukala Sathipati, Shinn-Ying Ho*  , Aging, 13(9): 12660-12690 (2021)
  3. Identification and Characterization of Species-Specific Severe Acute Respiratory Syndrome Coronavirus 2 Physicochemical Properties. Srinivasulu Yerukala Sathipati Srinivasulu Yerukala Sathipati, Shinn-Ying Ho* , Journal of Proteome Research, 20(5): 2942-2952 (2021)
  4. Predicting the risk genes of autism spectrum disorders. Yenching Lin, Srinivasulu Yerukala Sathipati, Shinn-Ying Ho* Srinivasulu Yerukala Sathipati Shinn-Ying Ho , Frontiers in Genetics, section Computational Genomics, 14: 665469 (2021)
  5. Multi-omics analysis identifies CpGs near G6PC2 mediating the effects of genetic variants on fasting glucose. Chung RH, Chiu YF, Wang WC, Hwu CM, Hung YJ, Lee IT, Chuang LM, Quertermous T, Rotter JI, Chen YI, Chang IS, Hsiung CA., Diabetologia, 64(7): 1613-1625 (2021)
  6. AI4AMP: an Antimicrobial Peptide Predictor Using Physicochemical Property-Based Encoding Method and Deep Learning. Lin, T. T., Yang, L. Y., Lu, I. H., Cheng, W. C., Hsu, Z. R., Chen, S. H., & Lin, C. Y., mSystems, 6(6): e00299-21 (2021)
  7. Brachytherapy Approach Using 177Lu Conjugated Gold Nanostars and Evaluation of Biodistribution, Tumor Retention, Dosimetry and Therapeutic Efficacy in Head and Neck Tumor Model. M-Y Lin, H-H Hsieh, J-C Chen, C-L Chen, N-C Sheu, W-S Huang, S-Y Ho, T-W Chen, Y-J Lee, C-Y Wu, pharmaceutics, 13: 1903 (2021)
  8. Evolutionary Learning-Derived Clinical-Radiomic Models for Predicting Early Recurrence of Hepatocellular Carcinoma after Resection., I-C Lee, J-Y Huang, T-C Chen, C-H Yen, N-C Chiu, H-E Hwang, J-G Huang, C-A Liu, G-Y Chaug R-C Lee, Y-P Hungh, Y Chao, S-Y Ho, Y-H Huang , Liver Cancer, 10(6): 572-582 (2021)
  9. Gene expression analysis of combined RNA-seq experiments using a receiver operating characteristic calibrated procedure, Shuen-LinJeng, Yung-ChanChi, Mi-ChiaMa, Shi-HuangChan, H. SunnySun, Computational Biology and Chemistry, 93: 107515 (2021)
  10. Development and validation of an expanded targeted sequencing panel for non-invasive prenatal diagnosis of sporadic skeletal dysplasia, Ching-Yuan Wang, Yen-An Tang, I-Wen Lee, Fong-Ming Chang, Chun-Wei Chien, Hsien-An Pan, H Sunny Sun, BMC Med Genomics, 14(3): 212 (2021)
  11. A tool for analyzing and visualizing ribo-seq data at the isoform level. Wu WS, Tsao YH, Shiue SC, Chen TY, Tseng YY, Tseng JT., BMC Bioinformatics, 22(10): 271 (2021)
  12. Cancer DEIso: An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers. Yang TH, Chiang YH, Shiue SC, Lin PH, Yang YC, Tu KC, Tseng YY, Tseng JT*, Wu WS., Comput Struct Biotechnol J, 19: 5149-5159 (2021)
  13. Structure-Based Functional Analysis of a Hormone Belonging to an Ecdysozoan Peptide Superfamily: Revelation of a Common Molecular Architecture and Residues Possibly for Receptor Interaction. Chen YR, Hsiao NW, Lee YZ, Huang SS, Chang CC, Tsai JR, Lin HC, Toullec JY, Lee CY, Lyu PC, Int J Mol Sci, 22(20): 11142 (2021)
  14. MapCaller – An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data. Hsin-Nan Lin, Wen-Lian Hsu*, Journal of Bioinformatics and Comparative Genomics, 4: 1-11 (2021)
 

Research and Development - 2022

  1. MetaSquare: An integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification. Chun-Chieh Liao, Po-Ying Fu, Chih-Wei Huang, Chia-Hsien Chuang, Yun Yen, Chung-Yen Lin*, Shu-Hwa Chen*, Bioinformatics, 38(10): 2930-2931 (2022)
  2. A metagenomics study of hexabromocyclododecane degradation with a soil microbial community. Yi-Jie Li, Chia-Hsien Chuang, Wen-Chih Cheng, Shu-Hwa Chen, Wen-Ling Chen, Yu-Jie Lin, Chung-Yen Lin*, Yang-hsin Shih*, Journal of Hazardous Materials, 430: 128465 (2022)
  3. Young duplicate genic DNA. Liao, BY, Nature Ecology and Evolution, 6(3): 249-250 (2022)
  4. Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals. Lan, KY; Liao, BY, Computational and Structural Biotechnology Journal, 20: 353-367 (2022)
  5. Assessment of incident frailty hazard associated with depressive symptoms in a Taiwanese longitudinal study. Chang, CC;Wu, CS;Tseng, HY;Lee, CY;Wu, IC;Hsu, CC;Chang, HY;Chiu, YF;Hsiung, CA, International Psychogeriatrics, 34(1): 61-70 (2022)
  6. Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer. Yu-Chieh Liao*, Han-Chieh Wu2, Ci-Hong Liou, Tsai-Ling Yang Lauderdale, I-Wen Huang, Jui-Fen Lai and Feng-Jui Chen*, Frontiers in Microbiology, 13: 875347 (2022)
  7. High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination. Yu-Chieh Liao*, Feng-Jui Chen, Min-Chieh Chuang, Han-Chieh Wu, Wan-Chen Ji, Guann-Yi Yu and Tsi-Shu Huang, International Journal of Molecular Sciences, 23(6): 3257 (2022)
  8. Peptide-Based Drug Predictions for Cancer Therapy Using Deep Learning. Yih-Yun Sun†, Tzu-Tang Lin†, Wen-Chih Cheng, I-Hsuan Lu, Chung-Yen Lin,* and Shu-Hwa Chen *, Pharmaceuticals, 15(4): 422 (2022)
  9. Tracking the amino acid changes of spike proteins across diverse host species of severe acute respiratory syndrome coronavirus. S Y Sathipati,S K. Shukla and S-Y Ho , ISCIENCE, 25(1): 103560 (2022)
  10. SPIKES: Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2. S Y Sathipati, T Carter, S K. Shukla, S-Y Ho, iScience, 3(3): 101460 (2022)
  11. Nasal microbiome change during and after exacerbation in asthmatic children. Liu T, Lin CH, Chen YL, Jeng SL, Tsai HJ, Ho CL, Kuo WS, Hsieh MH, Chen PC, Wu SH, Wang JY, Frontiers in Microbiology, 12: 833726 (2022)
  12. Principle-based approach for the de-identification of code-mixed electronic health records. Chen-Kai Wang, Feng-Duo Wang, You-Qian Lee, Pei-Tsz Chen, Bo-Hong Wang, Chu-Hsien Su, Joseph Chin-Chi Kuo, Chi-Shin Wu, Yi-Ling Chien, Hong-Jie Dai, Vincent S Tseng, Wen-Lian Hsu, IEEE Access, 10: 22875-22885 (2022)
  13. A BERT-based ensemble learning approach for the BioCreative VII challenges: full-text chemical identification and multi-label classification in PubMed articles. Sheng-Jie Lin, Wen-Chao Yeh, Yu-Wen Chiu, Yung-Chun Chang, Min-Huei Hsu, Yi-Shin Chen, Wen-Lian Hsu , Database, 2022: baac056 (2022)
  14. Editorial, Sunny Sun* and Yi-Ping Phoebe Chen*, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(1): 1-2 (2022)
  15. Elegancy: Digitizing the Wisdom from Laboratories to the Cloud with Free No-Code Platform. Chih-Wei Huang, Wei-Hsuan Chuang, Chung-Yen Lin, Shu-Hwa Chen,  iScience, 25(8): 104710 (2022)
  16. Gut Microbiota Composition in Chemotherapy and Targeted Therapy of Patients with Metastatic Colorectal Cancer. Yen-Cheng Chen, Chia-Hsien Chuang, Zhi-Feng Miao, Kwan-Ling Yip, Chung-Jung Liu, Ling-Hui Li, Deng-Chyang Wu, Tian-Lu Cheng, Chung-Yen Lin* and Jaw-Yuan Wang*, Frontiers in Oncology, 12: 955313 (2022)
  17. Recalibrating risk prediction models by synthesizing data sources: Adapting the lung cancer PLCO model for Taiwan. Chien, LH;Chen, TY;Chen, CH;Chen, KY;Hsiao, CF;Chang, GC;Tsai, YH;Su, WC;Huang, MS;Chen, YM;Chen, CY;Liang, SK;Chen, CY;Wang, CL;Hung, HH;Jiang, HF;Hu, JW;Rothman, N;Lan, Q;Liu, TW;Chen, CJ;Yang, PC;Chang, IS;Hsiung, CA, Cancer Epidemiology, Biomarkers and Prevention, 31(12): 2208-2218 (2022)
  18. Mysteries of gene regulation: Promoters are not the sole triggers of gene expression. C. N. Chow, K. C. Tseng, P. F. Hou, N. Y. Wu, Y. Lee, and W.C. Chang, Computational and Structural Biotechnology Journal, 20: 4910-4920 (2022)
 

Research and Development - 2023

  1. Prevalence of comorbidities and their impact on survival among older adults with the five most common cancers in Taiwan: a population study. Chien, LH; Tseng, TJ; Chen, TY; Chen, CH;Chen, CY; Jiang, HF; Tsai, FY; Ku, HY; Jiang, SS; Hsiung, CA; Liu, TW; Chang, IS, Scientific Reports, 13 :6727. (2023)
  2. Prevalence and predictive modeling of undiagnosed diabetes and impaired fasting glucose in Taiwan: A Taiwan Biobank study. Chung, RH; Chuang, SY; Chen, YE; Li, GH; Hsieh, CH; Chiou, HY; Hsiung, CA, BMJ Open Diabetes Research and Care, 11(3) :e003423. (2023)
  3. Polygenic Risk Score, Environmental Tobacco Smoke, and Risk of Lung Adenocarcinoma in Never-Smoking Women in Taiwan. Blechter B, Chien LH, Chen TY, Chang IS, Choudhury PP, Hsiao CF, Shu XO, Wong JYY, Chen KY, Chang GC, Tsai YH, Su WC, Huang MS, Chen YM, Chen CY, Hung HH, Hu JW, Shi J, Zheng W, Rositch AF, Chen CJ, Chatterjee N, Yang PC, Rothman N, Hsiung CA, Lan Q., JAMA Network Open, 6(11) :e2339254. (2023)
  4. Incidence of Lung Adenocarcinoma by Age, Sex, and Smoking Status in Taiwan. Chien LH, Jiang HF, Tsai FY, Chang HY, Freedman ND, Rothman N, Lan Q, Hsiung CA, Chang IS., JAMA Network Open, 6(11) :e2340704. (2023)
  5. Cost-Effective Complete Genome Sequencing Using the MinION Platform for Identification of Recombinant Enteroviruses. Yeh-Sheng Chien, Feng-Jui Chen, Han-Chieh Wu, Chieh-Hua Lin, Wen-Chiung Chang, David Perera, Jyh-Yuan Yang, Min-Shi Lee, Yu-Chieh Liao, Microbiology Spectrum, e0250723. (2023)
  6. Prediction of extranodal extension in head and neck squamous cell carcinoma by CT images using an evolutionary learning model. Tzu-Ting Huang, Yi-Chen Lin, Chia-Heng Yen, Jui Lan, Chiun-Chieh Yu, Wei-Che Lin, Yueh-Shng Chen, Cheng-Kang Wang, Eng-Yen Huang*, Shinn-Ying Ho*,Cancer Imaging, 23(1) :1-11. (2023)
  7. Prognostic microRNA signature for estimating survival in patients with hepatocellular carcinoma. Srinivasulu Yerukala Sathipati, Nikhila Aimalla, Ming-Ju Tsai, Tonia Carter, Sohyun Jeong, Zhi Wen, Sanjay K Shukla, Rohit Sharma, Shinn-Ying Ho*,Carcinogenesis, :bgad062. (2023)
  8. Survival associated miRNA signature in patients with head and neck carcinomas. Srinivasulu Yerukala Sathipati, Shinn-Ying Ho*,Heliyon, 9(6):e17218. (2023)
  9. Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning. Jiahui Guan, Lantian Yao, Chia-Ru Chung, Peilin Xie, Yilun Zhang, Junyang Deng, Ying-Chih Chiang, Tzong-Yi Lee*,Journal of Chemical Information and Modeling, 63(24) :7886-7898. (2023)
  10. A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology. Zhuo Wang, Yuxuan Pang, Chia-Ru Chung, Hsin-Yao Wang, Haiyan Cui, Ying-Chih Chiang, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee*,Briefings in Bioinformatics, 24(6) :bbad330. (2023)
  11. Short-term effects of Chlorhexidine mouthwash and Listerine on oral microbiome in hospitalized patients. Liu T, Chen YC, Jeng SL, Chang JJ, Wang JY, Lin CH, Tsai PF, Ko NY, Ko WC, Wang JL*,Frontiers in Cellular and Infection Microbiology, 13:1056534. (2023)
  12. Relationships between rectal swab and tissue samples in mucosa-associated microbiota in patients with inflammatory bowel disease. Liu T, Lin CH, Chen YL, Yeh CC, Chiou YY, Wang JY, Lee CT, Lee KT, Shiau AL, Wu CL, Chen CC, Kang JW, Chen PJ, Kuo HY, Yang EH, Chuang CH*,Inflammatory Bowel Diseases, 30(3):447-458. (2023)
  13. Databases and prospects of dynamic gene regulation in eukaryotes: A mini review. C. N. Chow, C. W. Yang, and C. Chang*,Computational and Structural Biotechnology Journal, 21 :2147-2159. (2023)
  14. JustRNA: a database of plant long noncoding RNA expression profiles and functional network. K. C. Tseng, N. Y. Wu, C. N. Chow, H. Q. Zheng, C. Y. Chou, C. W. Yang, M. J. Wang, S. B. Chang and C. Chang*,Journal of Experimental Botany, 74(17):4949-4958 . (2023)
  15. TIAM2S-positive microglia enhance inflammation and neurotoxicity through soluble ICAM-1-mediated immune priming. Chun-Hsien Chu, Jia-Shing Chen, Ya-Ling Chan, Wei-Jen Lu, Yi-Te Huang, Pin-Cheng Mao, Chun-I Sze, Sunny Sun,The FASEB Journal, 37(11):e23242 . (2023)
  16. Elucidation of the folding pathway of a circular permutant of topologically knotted YbeA by tryptophan substitutions. Puri S, Liu CY, Hu IC, Lai CH, Hsu SD, Lyu PC.,Biochem Biophys Res Commun., 672 :81-88. (2023)
  17. Semantic Template-based Convolutional Neural Network for Text Classification. Yung-Chun Chang, Siu Hin Ng, Jung-Peng Chen, Yu-Chi Liang, Wen-Lian Hsu*,ACM Transactions on Asian and Low-Resource Language Information Processing, 11(22) :1-21. (2023)
 

Research and Development - 2024

  1. Evaluating polygenic risk scores for predicting cardiometabolic traits and disease risks in the Taiwan Biobank. Chung, RH;Chuang, SY;Zhuang, YS;Jhang, YS;Huang, TH;Li, GH;Chang, IS; Hsiung, CA;Chiou, HY, HGG Advances, 5(1) :100260. (2024)
  2. Develop and validate a prognostic index with laboratory tests to predict mortality in middle-aged and older adults using machine learning models: a prospective cohort study. Chi-Hsien Huang, MD, Yao-Hwei Fang, PhD, Shu Zhang, PhD,….,Chao Agnes Hsiung, PhD, The Journals of Gerontology: Series A, 79(5) :glae041. (2024)
  3. Age at lung cancer diagnosis in females versus males who never smoke by race and ethnicity. Blechter, B;Wong, JYY; Chien, LH;Shiraishi, K;Shu, XO;…;Chang, IS;Hsiung, CA;Rothman, N;Lan, Q, British Journal of Cancer, 130 :1286-1294. (2024)
  4. Low-dose CT screening among never-smokers with or without a family history of lung cancer in Taiwan: a prospective cohort study. Gee-Chen Chang , Chao-Hua Chiu , Chong-Jen Yu , Yeun-Chung Chang , …… , Chao Agnes Hsiung, Pan-Chyr Yang ; TALENT Investigators, Lancet Respiratory Medicine, 12(2) :141-152. (2024)
  5. Sputum bacterial microbiota signature as a surrogate for predicting disease progression of nontuberculous mycobacterial lung disease. Huang, HL;Lin, CH;Lee, MR;Huang, WC;Sheu, CC;Cheng, MH;Lu, PL;Huang, CH;Yeh, YT;Yang, JM;Chong, IW;Liao, YC;Wang, JY, International Journal of Infectious Diseases, 149:107085. (2024)
  6. Tracing the footprints of MPXV in Asia: Phylogenetic insights and lineage dynamics,Chen, YC;Liao, YC;Mao, YC;Yeh, TK;Liu, PY, Sexually Transmitted Infections, 100(6):384-387 . (2024)
  7. Degeneration of the olfactory system in a murid rodent that evolved diurnalism. Liao, BY;Weng, MP;Chang, TY;Chang, AY;Ching, YH;Wu, CH, Molecular Biology and Evolution, 41(3) :Article number msae037. (2024)
  8. Convergent evolution of kidney sizes and supraorbital salt glands for birds living in saline habitats. Chiu, CC;Yao, CT; Liao, BY;Li, SH, iScience, 27(3) :Article number 109169. (2024)
  9. UHRF1P contributes to IL-17A-mediated systemic lupus erythematosus via UHRF1-MAP4K3 axis. Chuang, HC;Lan, KY;Hsu, PM;Chen, MH;Chen, YM;Yen, JH;Liao, BY;Tan, TH, Journal of Autoimmunity, 146 :Article number 103221. (2024)
  10. Interaction of the Gut Microbiota and Brain Functional Connectivity in Late Life Depression. Chia-Fen Tsai, Chia-Hsien Chuang, Pei-Chi Tu, Wan-Chen Chang,Yen-Po Wang, Pei-Yi Liu, Po-Shan Wu, Chung-Yen Lin, Ching-Liang Lu, Journal of Psychiatry and Neuroscience, 49(5) :E289-E300. (2024)
  11. Transcriptomics and gut microbiome analysis of the edible herb Bidens pilosa as a functional feed additive to promote growth and metabolism in tilapia (Oreochromis spp.) . Che-Chun Chen, Chung-Yen Lin, Hsin-Yun Lu, Chyng-Hwa Liou, Ying-Ning Ho, Chang-Wen Huang, Zhong-Fu Zhang, Chih-Hsin Kao, Wen-Chin Yang, Hong-Yi Gong, BMC Genomics, 25 :785. (2024)
  12. Decoding the genome of bloodsucking midge Forcipomyia taiwana (diptera: Ceratopogonidae): Insights into odorant receptor expansion. Ming-Der Lin, Chia-Hsien Chuang, Chih-Hsin Kao, Shu-Hwa Chen, Szu-Chieh Wang, Ping-Heng Hsieh, Guan-Yu Chen, Chun-Chia Mao, Jeng-Yi Li, Mei-Yeh Jade Lu, Chung-Yen Lin, Insect Biochemistry and Molecular Biology, 168() :104115. (2024)
  13. A hierarchical fusion strategy of deep learning networks for detection and segmentation of hepatocellular carcinoma from computed tomography images. I-Cheng Lee, Yung-Ping Tsai, Yen-Cheng Lin, Ting-Chun Chen, Chia-Heng Yen, Nai-Chi Chiu, Hsuen-En Hwang, Chien-An Liu, Jia-Guan Huang, Rheun-Chuan Lee, Yee Chao, Shinn-Ying Ho, Yi-Hsiang Huang, Cancer Imaging, 24(1) :43-53. (2024)
  14. Developing a practical neurodevelopmental prediction model for targeting high-risk very preterm infants during visit after NICU: a retrospective national longitudinal cohort study. Hao Wei Chung, Ju-Chieh Chen, Hsiu-Lin Chen, Fang-Yu Ko, Shinn-Ying Ho, Taiwan Premature Infant Follow-up Network Chang Jui-Hsing Tsou Kuo-Inn Tsao Po-Nien Mu Shu-Chi Hsu Chyong-Hsin Lien Reyin Lin Hung-Chih Hsiao Chien-Chou Huang Chao-Ching Chen Chih-Cheng, BMC medicine, 22(1) :68. (2024)
  15. Machine Learning-Based Characterization and Identification of Tertiary Lymphoid Structures Using Spatial Transcriptomics Data. Songyun Li, Zhuo Wang, Hsien-Da Huang, Tzong-Yi Lee, International Journal of Molecular Sciences, 25(7) :3887. (2024)
  16. Interpretable Multi-Scale Deep Learning for RNA Methylation Analysis across Multiple Species. Rulan Wang, Chia-Ru Chung, Tzong-Yi Lee, International Journal of Molecular Sciences, 25(5) :2869-. (2024)
  17. KinPred-RNA-Kinase Activity Inference and Cancer Type Classification using Machine Learning on RNA-seq Data. Yuntian Zhang, Lantian Yao, Chia-Ru Chung, Yixian Huang, Shangfu Li, Wenyang Zhang, Yuxuan Pang, Tzong-Yi Lee, iScience, 27(4) :109333. (2024)
  18. Identifying Antitubercular Peptides via Deep Forest Architecture with Effective Feature Representation. Lantian Yao, Jiahui Guan, Wenshuo Li, Chia-Ru Chung, Junyang Deng, Ying-Chih Chiang*, Tzong-Yi Lee*, Analytical Chemistry, 96(4) :1538-1546. (2024)
  19. Multi-epitope vaccine design of African swine fever virus considering T cell and B cell immunogenicity. Ting-Yu Chen, Yann-Jen Ho, Fang-Yu Ko, Pei-Yin Wu, Chia-Jung Chang, Shinn-Ying Ho, AMB Express, 14(1) :95. (2024)
  20. PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters. C.N. Chow, C. W. Yang, N. Y. Wu, H. T. Wang, K. C. Tseng, Y. H. Chiu, Y. Lee and W.C. Chang, Nucleic Acids Research, 52(D1) :1569-1578. (2024)
  21. Blastocyst telomere length shapes successful implantation after frozen-thawed embryo transfer. Chun-Wei Chien, Yen-An Tang, Shuen-Lin Jeng, Hsien-An Pan, H. Sunny Sun, Human Reproduction Open, 2024(2):hoae012. (2024)
  22. Overexpression of TIAM2S, a critical regulator for the hippocampal-medial prefrontal cortex network, progresses age-related spatial memory impairment. Chun-Hsien Chu, Chia-Hao Su, Ya-Hsin Hsiao, Chun-Chieh Yu, Yi-Chun Liao, Pin-Cheng Mao, Jia-Shing Chen, H. Sunny Sun, The Journals of Gerontology, 79(11):glae191. (2024)
  23. pH-Responsive β-Glucans-Complexed mRNA in LNPs as an Oral Vaccine for Enhancing Cancer Immunotherapy. Luo PK, Ho HM, Chiang MC, Chu LA, Chuang YH, Lyu PC, Hu IC, Chang WA, Peng SY, Jayakumar J, Chen HL, Huang MH, Sung HW, Adv Mater., 36(33) :e2404830. (2024)
  24. Integrating molecular dynamics simulation with small- and wide-angle X-ray scattering to unravel the flexibility, antigen-blocking, and protease-restoring functions in a hindrance-based pro-antibody. Liao JM, Hong ST, Wang YT, Cheng YA, Ho KW, Toh SI, Shih O, Jeng US, Lyu PC, Hu IC, Huang MY, Chang CY, Cheng TL, Protein Sci., 33(9) :e5124. (2024)
  25. Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource. Ming-Siang Huang, Jen-Chieh Han, Pei-Yen Lin, Yu-Ting You, Richard Tzong-Han Tsai, Wen-Lian Hsu, Briefings in Bioinformatics, 25(3) :bbae132. (2024)
  26. Polygenic risk score and lung adenocarcinoma risk among never-smokers by EGFR mutation status-a brief report. Blechter, B., Hsiung, C. A., Wang, X., Zhang, H., ..., Rothman, N., Shiraishi, K., Shen, H., Chanock, S. J., Kohno, T., & Lan, Q., Journal of Thoracic Oncology, 24 :02482-1. (2024)
 

Collaborative Research - 2019

  1. Genomic analysis of serologically untypable human enteroviruses in Taiwan. Chien, YS;Luo, ST;Tsao, KC;Huang, YC;Chung, WY;Liao, YC;Tan, Y;Das, SR;Lee, MS, Journal of Biomedical Science, 26(1): 49 (2019)
  2. Completing circular bacterial genomes with assembly complexity by using a sampling strategy from a single MinION run with barcoding. Liao, YC;Cheng, HW;Wu, HC;Kuo, SC;Lauderdale, TLY;Chen, FJ, Frontiers in Microbiology, 10: 2068 (2019)
  3. Using high-throughput transcriptome sequencing to investigate the biotransformation mechanism of hexabromocyclododecane with Rhodopseudomonas palustris in water. Reuben Wang, Chung-Yen Lin, Shu-Hwa Chen, Kai-Jiun Lo, Chi-Te Liu, Tzu-Ho Chou, Yang-hsin Shih, Science of The Total Environment, 692: 249-258 (2019)
  4. An Intuitive Web-based Framework for Genome-wide DNA Methylation Analysis. Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Pao-Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung-Yen Lin, BMC Genomics, 21(suppl 3): 163 (2019)
  5. A benchmark dose study of prenatal exposure to di(2-ethylhexyl) phthalate and behavioral problems in children. Chen, CC;Wang, YH;Chen, WJ;Hsiung, CA;Leon Guo, YL;Julie Wang, SL, International Journal of Hygiene and Environmental Health, 222(6): 971-980 (2019)
  6. Fungal diseases in Taiwan-National insurance data and estimation. Huang, YS;Denning, DW;Shih, SM;Hsiung, CA;Wu, UI;Sun, HY;Chen, PY;Chen, YC;Chang, SC, J Fungi (Basel)., 5(3): 78 (2019)
  7. Phthalate exposure and prostate cancer in a population-based nested case-control study. Chuang SC, Chen HC, Sun CW, Chen YA, Wang YH, Chiang CJ, Chen CC, Wang SL, Chen CJ, Hsiung CA, Environmental Research, 181: 108902 (2019)
  8. Expanding the mesodermal transcriptional network by genome-wide identification of Zinc finger homeodomain 1 (Zfh1) targets. Wu WH, Kuo TH, Kao CW, Girardot C, Hung SJ, Liu T, Furlong EEM, Liu YH, FEBS Letters, 593(14): 1698-1710 (2019)
  9. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. W.J. Zhuang, H. Chen, M. Yang, J.P. Wang, M.K. Pandey, C. Zhang, W.C. Chang, L.S. Zhang, X.T. Zhang, R.H. Tang, V. Garg, X.J. Wang, H.B. Tang, C.N. Chow, J.P. Wang, Y. Deng, D.P. Wang, A.W. Khan, Q. Yang, T.C. Cai, P. Bajaj, K.C. Wu, B.Z. Guo, X.Y. Zhang, J.J. Li, F. Liang, J. Hu, B.S. Liao, S.Y. Liu, A. Chitikineni, H.S. Yan, Y.X. Zheng, S.H. Shan, Q.Z. Liu, D.Y. Xie, Z.Y. Wang, S.A. Khan, N. Ali, C.Z. Zhao, X.G. Li, Z.L. Luo, S.B. Zhang, R.R. Zhuang, Z. Peng, S.Y. Wang, G. Mamadou, Y.H. Zhuang, Z.F. Zhao, W.C. Yu, F.G. Xiong, W.P. Quan, M. Yuan, Y. Li, H.S. Zou, H. Xia, L. Zha, J.P. Fan, J.G. Yu, W.P. Xie, J.Q. Yuan, K. Chen, S.S. Zhao, W.T. Chu, Y.T. Chen, P.C. Sun, F.B. Meng, T. Zhuo, Y.H. Zhao, C.J. Li, G.H. He, Y.L. Zhao, C.C. Wang, P.B. Kavikishor, R.L. Pan, A.H. Paterson, X.Y. Wang, R. Ming and R.K. Varshney, Nature Genetics, 51: 865-876 (2019)
  10. FGF9/FGFR2 increase cell proliferation by activating ERK1/2, Rb/E2F1, and cell cycle pathways in mouse Leydig tumor cells. Chang MM, Lai MS, Hong SY, Pan BS, Huang H, Yang SH, Wu CC, Sun HS, Chuang JI, Wang CY, Huang BM, Cancer Sci, 109(11): 3503-3518 (2019)
  11. Nuclear KIT induces a NFKBIB-RELA-KIT autoregulatory loop in imatinib-resistant gastrointestinal stromal tumors. Yuan-Shuo Hsueh, Hui Hua Chang, Yan-Shen Shan, H. Sunny Sun, Jonathan Alfred Fletcher, Chien-Feng Li, Li-Tzong Chen, Oncogene, 38(38): 6550-6565 (2019)
  12. MAP4K3/GLK Promotes Lung Cancer Metastasis by Phosphorylating and Activating IQGAP1. Chuang, H. C., Chang, C. C., Teng, C. F., Hsueh, C. H., Chiu, L. L., Hsu, P. M., Lee, M. C., Hsu, C. P., Chen, Y. R., Liu, Y. C., Lyu, P. C., Tan, T. H., Cancer Res., 79(19): 4978-4993 (2019)
  13. Programmable One-Pot Synthesis of Oligosaccharides. Cheng-Wei Cheng, Chung-Yi Wu, Wen-Lian Hsu, Chi-Huey Wong, Biochemistry, 59(34): 3078-3088 (2019)
 

Collaborative Research - 2020

  1. Cost-effectiveness of preventing hepatitis B virus reactivation in patients with lymphoma and resolved HBV infection. Tsou, HH;Yang, HC;Hsiao, CF;Hsiung, CA;Liu, TW;Chuang, MH;Wu, HY;Hsu, YT;Tsui, CW;Chen, PJ;Cheng, AL;Hsu, C;the Taiwan Cooperative Oncology Group, Journal of the Formosan Medical Association, 119(1 Pt 2): 335-344 (2020)
  2. Genetic polymorphisms in the opioid receptor delta 1 (OPRD1) gene are associated with methadone dose in methadone maintenance treatment for heroin dependence. Fang, CP;Wang, SC;Tsou, HH;Chung, RH;Hsu, YT;Liu, SC;Kuo, HW;Liu, TH;Chen, ACH;Liu, YL, Journal of Human Genetics - Nature, 65(4): 381-386 (2020)
  3. nanoMLST: Accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples. Liou, CH;Wu, HC;Liao, YC;Yang Lauderdale, TL;Huang, IW;Chen, FJ, Microbial Genomics., 6(3): e000336 (2020)
  4. Establishment of tetracyclineregulated bimolecular fluorescence complementation assay to detect protein-protein interactions in Candida albican. Wei-Chung Lai, H. Sunny Sun, Jia-Ching Shieh, Scientific Reports, 10(1): 2936 (2020)
  5. The role of physical fitness in cognitive-related biomarkers in persons at genetic risk of familial Alzheimer's disease. Chia-Liang Tsai, H. Sunny Sun, Yu-Min Kuo, Ming-Chyi Pai, Journal of Clinical Medicine, 8(10): 1639 (2020)
  6. FGF9 induces functional differentiation to Schwann cells from human adipose derived stem cells. Chia-Wei Huang, Shih-Yu Lu, Tzu-Chieh Huang, Bu-Miim Huang, H. Sunny Sun, Shang-Hsun Yang, Jih-Ing Chuang, Yuan-Yu Hsueh, Yi-Ting Wu, Chia-Ching Wu, Theranostics, 10(6): 2817-2831 (2020)
  7. mRNAsi Index: Machine Learning in Mining Lung Adenocarcinoma Stem Cell Biomarkers. Zhang Y, Tseng JT, Lien IC, Li F, Wu W, Li H, Genes (Basel), 11(3): 257 (2020)
  8. The novel roles of dusp6 in gut barrier modulation and microbiome shaping. Kao, CY;Chang, CS;Liao, YC;Huang, CT;Lin, CM;Ruan, JW;Liao, YC, FASEB, 34(S1): 1 (2020)
  9. Comparative transcriptomics across nematode life cycles reveal gene expression conservation and correlated evolution in adjacent developmental stages. Lu, MR;Lai, CK;Liao, BY;Tsai, IJ, Genome Biol Evol, 12(7): 1019-1030 (2020)
  10. ATACgraph: profiling genome wide chromatin accessibility from ATAC-seq. Rita Jui-Hsein Lu, Yen-Ting Liu, Chih Wei Huang, Ming-Ren Yen, Chung-Yen Lin and Pao-Yang Chen, Frontiers in Genetics, 11: 618478 (2020)
  11. Genetic variants in NECTIN4 encoding an adhesion molecule are associated with continued opioid use. Chiu-Ping Fang,Tung-Hsia Liu,Ren-Hua Chung,Hsiao-Hui Tsou,Hsiang-Wei Kuo,Sheng-Chang Wang,Chia-Chen Liu,Shu Chih Liu,Andrew C. H. Chen,Yu-Li Liu, PLoS ONE, 15(6): e0234549 (2020)
  12. The 10-year prognosis and prevalence of brugada-type electrocardiograms in elderly women: A longitudinal nationwide community-based prospective study. Sherri Shih-Fan Yeh 1, Ching-Yu Julius Chen, I-Chien Wu, Chih-Cheng Hsu, Tzu-Yu Chen, Wei-Ting Tseng, Feng-Cheng Tang, Chi-Chung Wang, Chung-Chou Juan, Hou-Chang Chiu, Huey-Ming Lo, Dun-Hui Yang, Jyh-Ming Jimmy Juang, Chao Agnes Hsiung, Journal of Cardiovascular Nursing, 35(6): E25-E32 (2020)
  13. AI4AMP: Sequence-based antimicrobial peptides predictor using physicochemical properties-based encoding method and deep learning. Tzu-Tang Lin, Li-Yen Yang, I-Hsuan Lu, Wen-Chih Cheng, Zhe-Ren Hsu, Shu-Hwa Chen, Chung-Yen Lin, BioRxiv, 6(6): e0029921 (2020)
  14. Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Li, XH;Li, ZL;Zhou, HF;Gaynor, SM;Liu, YW;Chen,…..; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Benjamin M Neale , Shamil R Sunyaev , Gonçalo R Abecasis , Jerome I Rotter , Cristen J Willer , Gina M Peloso , Pradeep Natarajan , Xihong Lin, et al., Nature Genetics, 52: 969-983 (2020)
  15. Piwi Reduction in the Aged Niche Eliminates Germline Stem Cells via Toll-GSK3 Signaling. Kun-Yang Lin , Wen-Der Wang , Chi-Hung Lin , Elham Rastegari , Yu-Han Su , Yu-Tzu Chang , Yung-Feng Liao , Yi-Chieh Chang , Haiwei Pi , Bo-Yi Yu , Shu-Hwa Chen , Chung-Yen Lin , Mei-Yeh Lu , Tsu-Yi Su , Fei-Yang Tzou , Chih-Chiang Chan , Hwei-Jan Hsu, Nat Commun., 11(1): 3147 (2020)
  16. Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease. Nielsen JB, Rom O, Surakka I, Graham SE, Zhou W, ….., Chung RH, Schwander K, Nouraie SM, Gordeuk VR, Zhang Y, Kooperberg C, Reiner AP, Jackson RD, Bleecker ER, Meyers DA, Li X, Das S, Yu K, LeFaive J, Smith A, Blackwell T, Taliun D, Zollner S, Forer L, Schoenherr S, Fuchsberger C, Pandit A, Zawistowski M, Kheterpal S, Brummett CM, Natarajan P, Schlessinger D, Lee S, Kang HM, Cucca F, Holmen OL, Åsvold BO, Boehnke M, Kathiresan S, Abecasis GR, Chen YE, Willer CJ, Hveem K., Nat Commun, 11(1): 6417 (2020)
  17. Cocarriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single sequence type 11 carbapenem-resistant klebsiella pneumoniae isolate. Wang, YC;Tang, HL;Liao, YC;Chiou, CS;Chen, YT;Chiang, MK;Lu, MC;Lai, YC, J Antimicrob Chemother, 63(6): e02282-18 (2020)
  18. Susceptibility of Elizabethkingia spp. to commonly tested and novel antibiotics and concordance between broth microdilution and automated testing methods. Kuo, SC;Tan, MC;Huang, WC;Wu, HC;Chen, FJ;Liao, YC;Wang, HY;Shiau, YR;Lauderdale, TL, J Antimicrob Chemother, 76(3): 653-658 (2020)
  19. Index of Cancer-Associated Fibroblasts Is Superior to the Epithelial-Mesenchymal Transition Score in Prognosis Prediction. Ko, Ying-Chieh; Lai, Ting-Yu; Hsu, Shu-Ching, CANCERS, 12(7): 1718 (2020)
  20. Gut Fecal Microbiota Transplant in a Mouse Model of Orthotopic Rectal Cancer. Chen Yen-Cheng, Miao Zhi-Feng, Yip Kwan-Ling, Cheng Yi-An, Liu Chung-Jung, Li Ling-Hui, Lin Chung-Yen, Wang Jiunn-Wei, Wu Deng-Chyang, Cheng Tian-Lu, Wang Jaw-Yuan, Front Oncol, 10: 568012 (2020)
  21. Plasmid- and chromosome-located mcr-3 in mcr-1-positive Escherichia coli in Taiwan. Hsu, CY;Chen, FJ;Huang, WC;Liao, YC;Lauderdale, TL;Kuo, SC, Int J Antimicrob Agents, 56(1): 105996 (2020)
  22. CUX2, BRAP and ALDH2 are associated with metabolic traits in people with excessive alcohol consumption. Chen, IC;Kuo, PH;Yang, AC;Tsai, SJ;Liu, TH;Liu, HJ;Lan, TH;Chen, HM;Huang, HN;Chung, RH;Liu, YL, Sci Rep, 10(1): 18118 (2020)
  23. Real-time dengue forecast for outbreak alerts in southern Taiwan. Yu-Chieh Cheng , Fang-Jing Lee , Ya-Ting Hsu , Eric V Slud , Chao A Hsiung, Chun-Hong Chen , Ching-Len Liao , Tzai-Hung Wen, Chiu-Wen Chang , Jui-Hun Chang , Hsiao-Yu Wu , Te-Pin Chang , Pei-Sheng Lin , Hui-Pin Ho , Wen-Feng Hung, Jing-Dong Chou , Hsiao-Hui Tsou, PLoS Negl Trop Dis. 14(7):e0008434 (2020)
  24. Single-cell analysis reveals immune modulation and metabolic switch in tumor-draining lymph nodes. Li, YL;Chen, CH;Chen, JY;Lai, YS;Wang, SC;Jiang, SS;Hung, WC, OncoImmunology, 9(1): Article number 1830513. (2020)
  25. Single-cell analysis of different stages of oral cancer carcinogenesis in a mouse model. Huang, LY;Hsieh, YP;Wang, YY;Hwang, DY;Jiang, SS;Huang, WT;Chiang, WF;Liu, KJ;Huang, TT, International Journal of Molecular Sciences., 21(21): Article number 8171. (2020)
  26. DNA-induced 2'3'-cGAMP enhances haplotype-specific human STING cleavage by dengue protease. Chan-I Su, Yu-Ting Kao, Chao-Chen Chang, Yao Chang, Tzong-Shiann Ho, H. Sunny Sun, Yi-Ling Lin, Michael M. C. Lai, Yu-Huei Liu, and Chia-Yi Yu, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(27): 15947-15954 (2020)
  27. SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites. H.J. Kao, V.N. Nguyen, K.Y. Huang, C. Chang, T.Y. Lee, Genomics, Proteomics & Bioinformatics, 18(2): 208-219 (2020)
  28. Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens. Trieu-Duc Vu, Yuki Iwasaki, Shuji Shigenobu, Akiko Maruko, Kenshiro Oshima, Erica Iioka, Chao-Li Huang, Takashi Abe, Satoshi Tamaki, Yi-Wen Lin, Chih-Kuan Chen, Mei- Yeh Lu, Masaru Hojo, Hao-Ven Wang, Shun-Fen Tzeng, Hao-Jen Huang, Akio Kanai, Takashi Gojobori, Tzen-Yuh Chiang, H. Sunny Sun, Wen-Hsiung Li, and Norihiro Okada, PLOS Genetics, 16(6): 1-29 (2020)
  29. Relationships between Follicle-Stimulating Hormone and Adiponectin in Postmenopausal Women. Huang WY, Chen DR, Kor CT, Chen TY, Lin PT, Tseng JTC, Wu HM, Metabolites, 10(10): 420 (2020)
  30. Antimicrobial Peptide TP4 Targets Mitochondrial Adenine Nucleotide Translocator 2. Su BC, Liu YC, Ting CH, Lyu PC, Chen JY, Mar Drugs, 18(8): E417 (2020)
  31. Cafestol Inhibits High-Glucose-Induced Cardiac Fibrosis in Cardiac Fibroblasts and Type 1-Like Diabetic Rats. Liu JC, Chen PY, Hao WR, Liu YC, Lyu PC, Hong HJ, Evidence-Based Complementary and Alternative Medicine, 2020: 4503747 (2020)
  32. Kider: Knowledge-infused document embedding representation for text categorization. Yu-Ting Chen, Zheng-Wen Lin, Yung-Chun Chang, Wen-Lian Hsu, International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, : 18-29 (2020)
  33. A New Approach for Natural Language Understanding, Wen-Lian Hsu, Sven Riemenschneider. Chun-Hung Chen, Ching-Ching Lu, 2020 International Conference on Pervasive Artificial Intelligence (ICPAI), 148-151 (2020)
 

Collaborative Research - 2021

  1. LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations. Neha Warikoo, Yung-Chun Chang, Wen-Lian Hsu, Bioinformatics, 37(3): 404-412 (2021)
  2. The degradation mechanisms of Rhodopseudomonas palustris toward hexabromocyclododecane by time-course transcriptome analysis. Yi-Jie Li, Reuben Wang, Chung-Yen Lin, Shu-Hwa Chen, Chia-Hsien Chuang, Tzu-Ho Chou, Chi-Fang Ko, Pei-Hsin Chou, Chi-Te Liu, Yang-hsin Shih, Chemical Engineering Journal, 425: 130489 (2021)
  3. Nonpolio enterovirus activity during the COVID-19 pandemic, Taiwan, 2020. Kuo, SC;Tsou, HH;Wu, HY;Hsu, YT;Lee, FJ;Shih, SM;Hsiung, CA;Chen, WJ, Emerging Infectious Diseases, 27(1): 306-308 (2021)
  4. A Yes-Associated Protein (YAP) and Insulin-Like Growth Factor 1 Receptor (IGF-1R) Signaling Loop Is Involved in Sorafenib Resistance in Hepatocellular Carcinoma. Ngo M-HT, Peng S-W, Kuo Y-C, Lin C-Y, Wu M-H, Chuang C-H, Kao C-X, Jeng H-Y, Lin G-W, Ling T-Y, Chang T-S, Huang Y-H., Cancers, 13(15): 3812 (2021)
  5. Association between Alzheimer's disease genes and trajectories of cognitive function decline in Han Chinese in Taiwan. Hsieh TJ, Lee WJ, Liao YC, Hsu CC, Fang YH, Chen TY, Lin YS, Chang IS, Wang SJ, Hsiung CA, Fuh JL; Alzheimer’s Disease Neuroimaging Initiative., Aging-US, 13(13): 17237-17252 (2021)
  6. Mobile resistomes of human pathogens in swine wastewater treatment plants. Kuo HC, Liao YC, Cheng HW, Shih SM, Chen FJ, Kuo SC., Journal of Microbiology Immunology and Infection, 54(4): 752-754 (2021)
  7. Cumulative risks of colorectal cancer in Han Chinese patients with Lynch syndrome in Taiwan. Kamiza, AB;Wang, WC;You, JF;Tang, R;Chien, HT;Lai, CH;Chiu, LL;Lo, TP;Hung, KY;Hsiung, CA;Yeh, CC, Scientific Reports, 11(1): 8899 (2021)
  8. Androgenic Sensitivities and Ovarian Gene Expression Profiles Prior to Treatment in Japanese Eel (Anguilla japonica). Huang YS, Cheng WC, Lin CY., Marine Biotechnology, 23: 430-444 (2021)
  9. Clinical and epidemiological features in hospitalized young children with acute gastroenteritis in Taiwan: A multicentered surveillance through 2014-2017. Lin, FJ;Huang, YC;Huang, YC;Huang, LM;Liu, CC;Chi, H;Lin, HC;Ho, YH;Wu, FT;Mu, JJ;Hsiung, CA;Huang, CY;Shih, SM;Taiwan Pediatric Infectious Disease Alliance, Journal of the Formosan Medical Association, 121(2): 519-528 (2021)
  10. Investigating the Transcriptomic and Expression Presence-Absence Variation Exist in Japanese Eel (Anguilla japonica), a Primitive Teleost. Huang YS, Lin CY, Cheng WC., Marine Biotechnology, 23: 943-954 (2021)
  11. Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis. Chu P-Y, Li J-X, Hsu T-H, Gong H-Y, Lin C-Y, Wang J-H, Huang C-W., Animals, 11(12): 3538 (2021)
  12. Identification of a gut microbiota member that ameliorates DSS-induced colitis in intestinal barrier enhanced Dusp6-deficient mice. 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, Cell reports, 37(7): 110016 (2021)
  13. Comparative pan-genome analysis of oral Veillonella species. Mashima, I;Liao, YC;Lin, CH;Nakazawa, F;Haase, EM;Kiyoura, Y;Scannapieco, FA, Microorganisms, 9(8): Article number 1775 (2021)
  14. Programmed Death Ligand 2 Gene Polymorphisms Are Associated With Lung Adenocarcinoma Risk in Female Never-Smokers. Liang, SK;Chien, LH;Chang, GC;Tsai, YH;Su, WC;Chen, YM;Huang, MS;Lin, HC;Fang, WT;Hung, HH;Jiang, SS;Chen, CY;Chen, KY;Chang, IS;Hsiung, CA;Chen, CJ;Yang, PC;the GELAC Study Group, Frontiers in Oncology, 11: 753788 (2021)
  15. Metformin and the risk of anemia of advanced chronic kidney disease in patients with type 2 diabetes mellitus. Wu, CT;Tsai, YT;Jung, HK;Fu, SL;Hsiung, CA;Liu, HY;Lai, JN, JOURNAL OF CLINICAL PHARMACOLOGY, 62(2): 276-284 (2021)
  16. Develop and apply electrocardiography-based risk score to identify community-based elderly individuals at high-risk of mortality. Lu, TP;Chattopadhyay, A;Lu, KC;Chuang, JY;Yeh, SS;Chang, IS;Chen, CJ;Wu, IC;Hsu, CC;Chen, TY;Tseng, WT;Hsiung, CA;Juang, JJ, Frontiers in Cardiovascular Medicine, 8: 1291 (2021)
  17. Reliability and validity of the traditional Chinese version of the advance care planning engagement survey: A pilot evaluation in Taiwanese outpatients. Wei, FC;Hsu, CK;Wu, YL;Liao, JY;Huang, CH;Hsiung, CA;Yu, SJ;Lin, CP;Chen, PJ, Journal of Palliative Care, : 08258597211051208 (2021)
  18. Impact of rotavirus vaccination on rotavirus hospitalizations in Taiwanese children. Burke, RM;Shih, S;Hsiung, CA;Yen, C;Jiang, B;Parashar, UD;Tate, JE;Wu, FT;Huang, YC, Vaccine, 39(49): 7135-7139 (2021)
  19. Brachytherapy Approach Using 177Lu Conjugated Gold Nanostars and Evaluation of Biodistribution, Tumor Retention, Dosimetry and Therapeutic Efficacy in Head and Neck Tumor Model. MY Lin, HH Hsieh, JC Chen, CL Chen, NC Sheu, WS Huang, SY Ho, TW Chen, YJ Lee, CY Wu , Pharmaceutics, 13(11): 1903 (2021)
  20. Fibroblast CEBPD/SDF4 axis in response to chemotherapy-induced angiogenesis through CXCR4. Wang JM, Chi JY, Hsiao YW, Liu HL, Fan XJ, Wan XB, Liu T, Hung SJ, Chen YT, Liang HY, Cell Death Discovery, 7(1): 94 (2021)
  21. Complexity of Transcriptional and Translational Interference of Laminin-332 Subunits in Junctional Epidermolysis Bullosa with LAMB3 Mutations. Ping-Chen Hou 1, Ken Natsuga, Wei-Ting Tu, Hsin-Yu Huang, Brandon Chen, Liang-Yu Chen, Wan-Rung Chen, Yi-Kai Hong, Yen-An Tang, Julia Yu-Yun Lee, Peng-Chieh Chen, H Sunny Sun, John A McGrath, Chao-Kai Hsu, Acta Derm Venereol, 101(8): adv00522 (2021)
  22. Extracellular Vesicle miR-200c Enhances Gefitinib Sensitivity in Heterogeneous EGFR-Mutant NSCLC. Lin CC, Wu CY, Tseng JT, Hung CH, Wu SY, Huang YT, Chang WY, Su PL, Su WC, Biomedicines, 9(3): 243 (2021)
  23. Exploring the Multifunctional Roles of Odontoglossum Ringspot Virus P126 in Facilitating Cymbidium Mosaic Virus Cell-to-Cell Movement during Mixed Infection. S.C. Lee, H. Pai, Y.W. Huang, M.H. He, Y.L. Song, S.Y. Kuo, C. Chang, Y.H. Hsu, and N.S. Lin, Viruses, 13(8): 1552 (2021)
  24. A cross-sectional examination of a family history of Alzheimer’s disease and ApoE epsilon 4 on physical fitness, molecular biomarkers, and neurocognitive performance. Chia-Liang Tsai*, Kirk I Erickson, H-Sunny Sun, Yu-Min Kuo, Ming-Chyi Pai*, Physiology & Behavior, 230(1): 113268 (2021)
  25. Co-AMPpred for in silico-aided predictions of antimicrobial peptides by integrating composition-based features. Onkar Singh, Wen-Lian Hsu, Emily Chia-Yu Su, BMC bioinformatics, 22(1): 1-21 (2021)
 

Collaborative Research - 2022

  1. Increase in plasma CCL11 (Eotaxin-1) in patients with alcohol dependence and changes during detoxification. Huang, M. C., Chung, R. H., Lin, P. H., Kuo, H. W., Liu, T. H., Chen, Y. Y., ... & Liu, Y. L., Brain Behavior and Immunity, 99: 83-90 (2022)
  2. Development of Disease-Resistance-Associated Microsatellite DNA Markers for Selective Breeding of Tilapia (Oreochromis spp.) Farmed in Taiwan. Chen, Che-Chun, Chang-Wen Huang, Chung-Yen Lin, Chia-Hui Ho, Hong N. Pham, Te-Hua Hsu, Tzu-Tang Lin, Rong-Hwa Chen, Shuenn-Der Yang, Chin-I. Chang, and Hong-Yi Gong., Genes, 13(1): 99 (2022)
  3. Association of the D-amino acid oxidase gene with methadone dose in heroin dependent patients under methadone maintenance treatment. Liu, TH;Tsou, HH;Chung, RH;Liu, SC;Wang, SC;Kuo, HW;Fang, CP;Chen, ACH;Liu, YL, Journal of Human Genetics, 67(5): 273-278 (2022)
  4. Longitudinal changes in oxidative stress and early renal injury in children exposed to DEHP and melamine in the 2011 Taiwan food scandal. Tsai, HJ;Wu, CF;Hsiung, CA;Lee, CH;Wang, SL;Chen, ML;Chen, CC;Huang, PC;Wang, YH;Chen, YA;Chen, BH;Chuang, YS;Hsieh, HM;Wu, MT, Environment International, 158: 107018 (2022)
  5. Tracking the amino acid changes of spike proteins across diverse host species of severe acute respiratory syndrome coronavirus 2. Y S Srinivasulu*, Sanjay K Shukla, Shinn-Ying Ho, iScience, 25(1): 103560 (2022)
  6. MicroRNA signature for estimating the survival time in patients with bladder urothelial carcinoma. Y S Srinivasulu*, MJ Tsai, SK Shukla, SY Ho, Y Liu, A Behesthi, Scientific reports, 12(1): 1-12 (2022)
  7. Novel potential functions of amoeboid cells in thraustochytrids revealed by Aurantiochytrium limacinum BL10. Chou SC, Su YM, Liu T, Li ZW, Liao HE, Renta PP, Chen YM, European Journal of Protistology, 82(8): 125860 (2022)
  8. dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. Z.Li, S. Li, M. Luo, J.H. Jhong, W. Li, L. Yao, Y. Pang, Z. Wang, R. Wang, R. Ma, J. Yu, Y. Huang, X. Zhu, Q. Cheng, H. Feng, J. Zheng, C. Wang, J. B.K. Ksu, C. Chang, F.X. Wei, H.D. Huang, T.Y. Lee, Nucleic Acids Research, 50: 471-479 (2022)
  9. ILeukin10Pred: A Computational Approach for Predicting IL-10-Inducing Immunosuppressive Peptides Using Combinations of Amino Acid Global Features. Onkar Singh, Wen-Lian Hsu, Emily Chia-Yu Su, Biology, 11(1): 5 (2022)
  10. Estradiol-mediated inhibition of Sp1 decreases miR-3194-5p expression to enhance CD44 expression during lung cancer progression. Young MJ, Chen YC, Wang SA, Chang HP, Yang WB, Lee CC, Liu CY, Tseng YL, Wang YC, Sun HS, Chang WC, Hung JJ, Journal of Biomedical Science, 29(1): 3 (2022)
  11. Discrimination of methicillin-resistant staphylococcus aureus by MALDI-TOF mass spectrometry with machine learning techniques in patients with staphylococcus aureus bacteremia. Kong, PH;Chiang, CH;Lin, TC;Kuo, SC;Li, CF;Hsiung, CA;Shiue, YL;Chiou, HY;Wu, LC;Tsou, HH, Pathogens, 11(5): 586 (2022)
  12. A comprehensive evaluation of COVID-19 policies and outcomes in 50 countries and territories. Tsou, HH;Kuo, SC;Lin, YH;Hsiung, CA;Chiou, HY;Chen, WJ;Wu, SI;Sytwu, HK;Chen, PC;Wu, MH;Hsu, YT;Wu, HY;Lee, FJ;Shih, SM;Liu, DP;Chang, SC, Scientific Reports, 12: 8802 (2022)
  13. Prevalence of exposure to benzodiazepines among pregnant women in Taiwan: A nationwide longitudinal study. Lin, YH;Chen, MH;Chang, YC;Chen, L;Hsiung, CA;Wu, SI, Journal of Sleep Research, 31(6): e13678 (2022)
  14. Sleep habits are associated with cognition decline in physically robust, but not in frail participants: A longitudinal observational study. Chuang, SC;Wu, IC;Chang, JJ;Tsai, YF;Cheng, CW;Chiu, YF;Chang, HY;Lee, MRM;Hsu, CC;Hsiung, CA, Scientific Reports, 12: Article number 11595 (2022)
  15. A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids. Ramdas, S;Judd, J;Graham, SE;……;Hsiung, CA;Warren, HR;Ramirez, J;Bork-Jensen, J;Kårhus, LL;Goel, A;Sabater-Lleal, M, .;et al., American Journal of Human Genetics, 109(8): 1366-1387 (2022)
  16. Engineered multivalent DNA capsules for multiplexed detection of genotoxicants via versatile controlled release mechanisms. Singuru, MMR;Liao, YC;Lin, GMH;Chen, WT;Lin, YH;To, CT;Liao, WC;Hsu, CH;Chuang, MC, Biosensors and Bioelectronics, 216: Article number 114608 (2022)
  17. A predominant genotype of azole-resistant Candida tropicalis clinical strains. Tseng, KY;Liao, YC;Chen, FC;Chen, FJ;Lo, HJ, Lancet Microbe, 3(9): e646 (2022)
  18. Galectin-1 orchestrates an inflammatory tumor-stroma crosstalk in hepatoma by enhancing TNFR1 protein stability and signaling in carcinoma-associated fibroblasts. Yao-Tsung Tsai, Chih-Yi Li, Yen-Hua Huang, Te-Sheng Chang, Chung-Yen Lin, Chia-Hsien Chuang, Chih-Yang Wang, Gangga Anuraga, Tzu-Hao Chang, Tsung-Chieh Shih, Zu-Yau Lin, Yuh-Ling Chen, Ivy Chung, Kuen-Haur Lee, Che-Chang Chang, Shian-Ying Sung, Kai-Huei Yang, Wan-Lin Tsui, Chee-Voon Yap, Ming-Heng Wu, Oncogene, 41: 3011-3023 (2022)
  19. Differences in gut microbiota correlate with symptoms and regional brain volumes in patients with late-life depression. Tsai, Chia-Fen, Chuang, Chia-Hsien, Wang, Yen-Po, Lin, Ya-Bo, Tu, Pei-Chi, Liu Pei-Yi, Wu, Po-Shan, Lin, Chung-Yen, Lu, Ching-Liang*, Frontiers in Aging Neuroscience, 14: 885393 (2022)
  20. The gut microbiota regulates acute foreign body reaction and tissue repair after biomaterial implantation. Chen SL, Lundy DJ, Ruan SC, Chen HC, Chao YK, Cheng YY, Prajnamitra PR, Liao CC, Lin CY, Lai JJ, Hsieh, PC, Biomaterials, 289: 121807 (2022)
  21. The transformation from hospital-based to community-based mental healthcare: The hospital–clinic disparity in the psychiatric workforce in Taiwan from 2005 to 2030. Lin, YH;Ho, YC;Chang, YH;Hsiung, CA;Chiou, HY, Psychiatry Research, 317: Article number 114816 (2022)
  22. Enrichment of Prevotella intermedia in human colorectal cancer and its additive effects with Fusobacterium nucleatum on the malignant transformation of colorectal adenomas. Chia-Hui Lo; Deng-Chyang Wu; Shu-Wen Jao; Chang-Chieh Wu; Chung-Yen Lin; Chia-Hsien Chuang; Ya-Bo Lin; Chien-Hsiun Chen; Ying-Ting Chen; Jiann-Hwa Chen; Koung-Hung Hsiao; Ying-Ju Chen; Yuan-Tsong Chen; Jaw-Yuan Wang; Ling-Hui Li, Journal of Biomedical Science, 29: 88 (2022)
  23. Microbiome dysbiosis inhibits carcinogen-induced murine oral tumorigenesis. Chen YL, Huang KC, Wu JH, Liu T, Chen JW, Xie JY, Chen MY, Wu LW, Tung CL, Journal of Cancer, 13(10): 3051-3060 (2022)
  24. Multifaceted Assessments of Traditional Chinese Word Segmentation Tool on Large Corpora. Wen-Chao Yeh, Yu-Lun Hsieh, Yung-Chun Chang, Wen-Lian Hsu*, Proceedings of the 34th Conference on Computational Linguistics and Speech Processing (ROCLING 2022), : 193-199 (2022)
 

Collaborative Research - 2023

  1. Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis. Weinstock, JS;Gopakumar, J;Burugula, BB;Uddin, MM;Jahn, N;Belk, JA;Bouzid, H;Daniel, B;Miao, Z;Ly, N;Mack, TM;Luna, SE;Prothro, KP;Mitchell, SR;Laurie, CA;Broome, JG;Taylor, KD;Guo, XQ;Sinner, MF;von Falkenhausen, AS;Kaab, S;Shuldiner, AR;O'Connell, JR;Lewis, JP;Boerwinkle, E;Barnes, KC;Chami, N;Kenny, EE;Loos, RJF;Fornage, M;Hou, LF;Lloyd-Jones, DM;Redline, S;Cade, BE;Psaty, BM;Bis, JC;Brody, JA;Silverman, EK;Yun, JH;Qiao, DD;Palmer, ND;Freedman, BI;Bowden, DW;Cho, MH;DeMeo, DL;Vasan, RS;Yanek, LR;Becker, LC;Kardia, SLR;Peyser, PA;He, J;Rienstra, M;Van der Harst, P;Kaplan, R;Heckbert, SR;Smith, NL;Wiggins, KL;Arnett, DK;Irvin, MR;Tiwari, H;Cutler, MJ;Knight, S;Muhlestein, JB;Correa, A;Raffield, LM;Gao, Y;de Andrade, M;Rotter, JI;Rich, SS;Tracy, RP;Konkle, BA;Johnsen, JM;Wheeler, MM;Smith, JG;Melander, O;Nilsson, PM;Custer, BS;Duggirala, R;Curran, JE;Blangero, J;McGarvey, S;Williams, LK;Xiao, SJ;Yang, M;Gu, CC;Chen, YDI;Lee, WJ;Marcus, GM;Kane, JP;Pullinger, CR;Shoemaker, MB;Darbar, D;Roden, DM;Albert, C;Kooperberg, C;Zhou, Y;Manson, JE;Desai, P;Johnson, AD;Mathias, RA, .;et al., Nature, 616 :755-763. (2023)
  2. Clonal haematopoiesis and risk of chronic liver disease. Waihay J. Wong, Connor Emdin, Alexander G. Bick, ….., Christie Ballantyne, NHLBI TOPMed Hematology Working Group, Benjamin L. Ebert & Pradeep Natarajan; et al., Nature, 616 :747-754. (2023)
  3. Genome-wide association study and functional characterization identifies candidate genes for insulin-stimulated glucose uptake. Williamson, A;Norris, DM;Yin, X;…..;Chung, RH;…..;Rauramaa, R;Rotter, JI;Schwarz, PEH, .;et al., Nature Genetics, 55 :973-983. (2023)
  4. Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. Xihao Li, Corbin Quick, Hufeng Zhou, Sheila M. Gaynor, Yaowu Liu, Han Chen, ….., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Jerome I. Rotter, Pradeep Natarajan, Gina M. Peloso, Zilin Li & Xihong Lin.;et al., Nature Genetics, 55 :154-164. (2023)
  5. Low-dose CT screening in relatives with a family history of lung cancer. Wang, CL;Hsu, KH;Chang, YH;Ho, CC;Chiang, CJ;Chen, KC;Cheung, YC;Huang, PC;Chen, YR;Chen, CY;Hsu, CP;Hsia, JY;Chen, HY;Yang, SY;Li, YJ;Yang, TY;Tseng, JS;Chuang, CY;Hsiung, CA;Chen, YM;Huang, MS;Yu, CJ;Chen, KY;Su, WC;Chen, JJW;Yu, SL;Chen, CJ;Yang, PC;Tsai, YH;Chang, GC, Journal of Thoracic Oncology, 18(11) :1492-1503. (2023)
  6. Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population. Jianxin Shi, Kouya Shiraishi, Jiyeon Choi, Keitaro Matsuo, Tzu-Yu Chen, Juncheng Dai, Rayjean J. Hung, Kexin Chen,…., I-Shou Chang, …..., Chao Agnes Hsiung, Christopher I. Amos, Hongbing Shen, Stephen J. Chanock, Nathaniel Rothman, Takashi Kohno & Qing Lan; et al., Nature Communications, 14 :3043. (2023)
  7. Clinical manifestations and risk factors of campylobacter gastroenteritis in children in Taiwan. Yen-Ting Guo , Chao A. Hsiung, Fang-Tzy Wu , Hsin Chi , Yhu-Chering Huang , Ching-Chuan Liu, Yi-Chuan Huang , Hsiao-Chuan Lin , Shu-Man Shih , Ching-Yi Huang , Luan-Yin Chang , Yu-Huai Ho , Chun-Yi Lu , Li-Min Huang on behalf of the Taiwan Pediatric Infectious Disease Alliance, Biomedical Journal, 46(6):100590. (2023)
  8. Splice-site variants in the gene encoding GABA-A receptor delta subunit are associated with amphetamine use in patients under methadone maintenance treatment. Lin, YF; Chou, WH; Liu, TH; Fang, CP; Kuo, HW; Kuo, PH; Tsai, SJ; Wang, SC; Chung, RH; Tsou, HH; Chen, ACH; Liu, YL, International Journal of Molecular Sciences, 24(1) :721. (2023)
  9. Changes of neurofilament light chain in patients with alcohol dependence following withdrawal and the genetic effect from ALDH2 Polymorphism. Huang, MC; Tu, HY; Chung, RH; Kuo, HW; Liu, TH; Chen, CH; Mochly-Rosen, D; Liu, YL, European Archives of Psychiatry and Clinical Neuroscience, 274(2):423-432. (2023)
  10. Mortality rate and its determinants among people with dementia receiving home healthcare: a nationwide cohort study. Lai, YC; Tsai, KT; Ho, CH; Liao, JY; Tseng, WZ; Petersen, I; Wang, YC; Chen, YH; Chiou, HY; Hsiung, CA; Yu, SJ; Sampson, EL; Chen, PJ, Internal and Emergency Medicine, () :-. (2023)
  11. Interregional mobility in different age groups is associated with COVID-19 transmission in the Taipei metropolitan area, Taiwan. Jiang WM, Wen TH, Huang YC, Chiou HY, Chen WJ, Hsiung CA, Sytwu HK, Tsou HH., Scientific Reports, 13 :17285. (2023)
  12. Dietary inflammatory patterns are associated with serum TGs and insulin in adults: A community-based study in Taiwan. Chuang, SC; Wu, IC; Hsiung, CA; Chan, HT; Cheng, CW; Chen, HL; Chiu, YF; Lee, MM; Chang, HY; Hsu, CC, Journal of Nutrition, 153(6) :1783-1792. (2023)
  13. Fruits are vehicles of drug-resistant pathogenic Candida tropicalis. Yin-Zhi Chen, Kuo-Yun Tseng, Si-Chong Wang, Ciao-Lin Huang, Chih-Chao Lin, Zi-Li Zhou, De-Jiun Tsai, Chiao-Mei Lin, Yu-Lian Chen, Kai-Ting Chen, Yu-Chieh Liao, Feng-Jui Chen, Huey-Kang Sytwu, Chung-Yu Lan, Hsiu-Jung Lo, Microbiology Spectrum, e0147123. (2023)
  14. Country-Level Factors Associated With Nurse Salaries: Empirical Evidence From Organisation for Economic Co-operation and Development Countries and Taiwan. Chang YH, Hsu CH, Tseng YC, Hsiung CA., Journal of Nursing Research, 31(6):e303 (2023)
  15. Identification of Sexually Dimorphic Genes in Pectoral Fin as Molecular Markers for Assessing the Sex of Japanese Silver Eels (Anguilla japonica) . Hsiang-Yi Hsu, Chia-Hsien Chuang, I-Hsuan Lu, Chung-Yen Lin, and Yu-San Han, Zoological Studies, 62(2) :1-16. (2023)
  16. Assessing Non-Specific Neck Pain through Pose Estimation from Images Based on Ensemble Learning. Jiunn-Horng Kang, En-Han Hsieh, Cheng-Yang Lee, Yi-Ming Sun, Tzong-Yi Lee, Justin Bo-Kai Hsu, Tzu-Hao Chang, Life-Basel, 13(12) :2292. (2023)
  17. Kruppel-like factor 10 modulates stem cell phenotypes of pancreatic adenocarcinoma by transcriptionally regulating notch receptors. Tsai, YC; Cheng, KH; Jiang, SS; Hawse, JR; Chuang, SE; Chen, SL; Huang, TS; Ch'ang, HJ, Journal of Biomedical Science, 30 :Article number 39-. (2023)
  18. Targeting Conserved Pathways in 3D Spheroid Formation of Diverse Cell Types for Translational Application: Enhanced Functional and Antioxidant Capacity. Chia-Chi Chang, Shih-Sheng Jiang, Fang-Yu Tsai, Pei-Ju Hsu, Chen-Chan Hsieh, Li-Tzu Wang, Men-Luh Yen, B Linju Yen., Cells, 12(16) :Article number 2050. (2023)
  19. ASO visual abstract: Distinct failure patterns in hypopharyngeal cancer patients receiving surgery-based versus radiation-based treatment. Lin, YH; Hsiao, JR; Wu, YH; Chang, JS; Ou, CY; Lee, WT;Huang, CC; Chang, CC; Lai, YH; Tsai, ST; Hsueh, WT; Yen, CJ; Lin, CL; Chen, YS; Jiang, SS; Su, YC; Wu, SY, Annals of Surgical Oncology, 30 :1182-1183. (2023)
  20. Residential greenness and air pollution’s association with nasal microbiota among asthmatic children. Asri AK, Liu T, Tsai HJ, Lee HY, Pan WC, Wu CD*, Wang JY*, Environmental Research, 219(15) :115095. (2023)
 

Collaborative Research - 2024

  1. Gender difference on the mediation effects of filial piety on the association between chronic obstructive pulmonary disease and depressive symptoms in older adults: A community-based study. Chang, CC; Hsu, K; Chen, CM; Huang, SS; Wu, IC; Hsu, CC; Hsiung, AC; Chang, HY, PLoS ONE, 19(2) :e0298360. (2024)
  2. Suppression of the alpha, delta, and omicron variants of SARS-Cov-2 in Taiwan. Hsiao-Hui Tsou, Fang-Jing Lee, Shiow-Ing Wu, Byron Fan , Hsiao-Yu Wu , Yu-Hsuan Lin, Ya-Ting Hsu , Chieh Cheng , Yu-Chieh Cheng , Wei-Ming Jiang , Hung-Yi Chiou , Wei J Chen, Chao A Hsiung, Pau-Chung Chen , Huey-Kang Sytwu , PLoS ONE, 18(3) :e0300303. (2024)
  3. Examining the role of living alone and loneliness in predicting health-related quality of life: Results from the Healthy Aging Longitudinal Study in Taiwan (HALST) . Tseng, HY; Lee, CY; Wu, CS; Wu, IC; Chang, HY; Hsu, CC; Hsiung, CA, Quality of Life Research, 33(4) :1015-1028. (2024)
  4. Impact of physical activity on disability‐free and disabled life expectancies in middle‐aged and older adults: Data from the healthy aging longitudinal study in Taiwan. Shu-Chun Chuang, Yu-Hung Chang, I-Chien Wu, Yao-Hwei Fang, Huei-Ting Chan, Ray-Chin Wu, Marion M Lee, Chi-Tsun Chiu, Hsing-Yi Chang, Chao Agnes Hsiung, Chih-Cheng Hsu, Geriatrics & Gerontology International, 24 :229-239. (2024)
  5. The mutagenic forces shaping the genomic landscape of lung cancer in never smokers. Díaz-Gay, M;Zhang, T;Hoang, PH;Khandekar, A;Zhao, W;Steele, CD;Otlu, B;Nandi, SP;Vangara, R;Bergstrom, EN;Kazachkova, M;Pich, O;Swanton, C;Hsiung, CA;Chang, IS;Wong, MP;Leung, KC;Sang, J;McElderry, J;Yang, L;Nowak, MA;Shi, J;Rothman, N;Wedge, DC;Homer, R;Yang, SR;Lan, Q;Zhu, B;Chanock, SJ;Alexandrov, LB;Landi, MT, medRxiv, (2024)
  6. Psychometric properties and measurement invariance of the awareness of age-related change short form in older adult samples from Taiwan and Germany. Tseng, HY;Wu, CS;Lee, CY;Wu, IC;Chang, HY;Hsu, CC;Hsiung, CA;Kaspar, R;Wahl, HW;Diehl, M, Gerontologist, 64(9) :gnae086. (2024)
  7. Pulse pressure is associated with decline in physical function in older adults,Chuang, SY;Liu, WL;Cheng, HM;Chung, RH;Lai, CH;Chuang, SC;Wu, IC;Chang, HY;Hsiung, CA;Chen, WJ;Hsu, CC, Maturitas, 185 :108000. (2024)
  8. Intestinal dual-specificity phosphatase 6 regulates the cold-induced gut microbiota remodeling to promote white adipose browning. Chen, PC;Tsai, TP;Liao, YC;Liao, YC;Cheng, HW;Weng, YH;Lin, CM;Kao, CY;Tai, CC;Ruan, JW, NPJ Biofilms and Microbiomes, 10(1):22 (2024)
  9. Understanding and alleviating informal caregiver burden through the development and validation of a caregiver strain index-based model in Taiwan. Chien, SC;Chang, YH;Yen, CM;Chen, YE;Liu, CC;Hsiao, YP;Yang, PY;Lin, HM;Yang, TE;Lu, XH;Wu, IC;Hsu, CC;Chiou, HY;Chung, RH, BMC Geriatrics, 24 :Article number 558. (2024)
  10. Classifying Alzheimer's disease and normal subjects using machine learning techniques and genetic-environmental features. Huang, YH;Chen, YC;Ho, WM;Lee, RG;Chung, RH;Liu, YL;Chang, PY;Chang, SC;Wang, CW;Chung, WH;Tsai, SJ;Kuo, PH;Lee, YS;Hsiao, CC, Journal of the Formosan Medical Association, 123(6) :701-709. (2024)
  11. Machine learning models for predicting blood pressure phenotypes by combining multiple polygenic risk scores. Hrytsenko, Y;Shea, B;Elgart, M;Kurniansyah, N;Lyons, G;Morrison, AC;Carson, AP;Haring, B;Mitchell, BD;Psaty, BM;Jaeger, BC;Gu, CC;Kooperberg, C;Levy, D;Lloyd-Jones, D;Choi, E;Brody, JA;Smith, JA;Rotter, JI;Moll, M;Fornage, M;Simon, N;Castaldi, P;Casanova, R;Chung, RH;Kaplan, R;Loos, RJF;Kardia, SLR;Rich, SS;Redline, S;Kelly, T;O'Connor, T;Zhao, W;Kim, W;Guo, X;Ida Chen, YD;Sofer, T, Scientific Reports, 14() :Article number 12436. (2024)
  12. Stratifying Lung Adenocarcinoma Risk with Multi-ancestry Polygenic Risk Scores in East Asian Never-Smokers. Batel Blechter, Xiaoyu Wang, Jianxin Shi, Kouya Shiraishi,......, I-Shou Chang, …., Chao Agnes Hsiung, Stephen J Chanock, Nathaniel Rothman, Takashi Kohno, Qing Lan, Haoyu Zhang, medRxiv, . (2024)
  13. Secretome from estrogen‑responding human placenta‑derived mesenchymal stem cells rescues ovarian function and circadian rhythm in mice with cyclophosphamide‑induced primary ovarian insufficiency. Duy-Cuong Le, Mai-Huong T Ngo, Yung-Che Kuo, Shu-Hwa Chen, Chung-Yen Lin, Thai-Yen Ling, Quoc Thao Trang Pham, Heng-Kien Au, Jihwan Myung, Yen-Hua Huang, Journal of Biomedical Science, 31(95) :1-29. (2024)
  14. The association between dietary inflammatory patterns and the incidence of frailty and its reversal in older adults: A community-based longitudinal follow-up study in Taiwan. Chuang, SC;Hsiung, CA;Tao, MH;Wu, IC;Cheng, CW;Tseng, WT;Lee, MM;Chang, HY;Hsu, CC, Nutrients, 16(7) :Article number 2862. (2024)
  15. Cross-sectional and longitudinal associations of magnesium intake and cognition in the Healthy Aging Longitudinal Study in Taiwan. Tao, MH;Chuang, SC;Wu, IC;Chan, HT;Cheng, CW;Chen, HL;Lee, MM;Chang, HY;Hsiung, CA;Hsu, CC, European Journal of Nutrition, 63(8) :3061-3073. (2024)
  16. Rare variant contribution to the heritability of coronary artery disease. Rocheleau, G;Clarke, SL;Auguste, G;Hasbani, NR;Morrison, AC;Heath, AS;Bielak, LF;Iyer, KR…...;Chung, RH;….;Hsiung, CA;....;Tcheandjieu, C;Peyser, PA;Vasan, RS;Rotte, JI;Miller, CL;Assimes, TL;de Vries, PS;Do, R, Nature Communications, 15 :Article number 8741. (2024)
  17. Detection in orchards of predominant azole-resistant Candida tropicalis genotype causing human candidemia, Taiwan. Tseng, KY;Chen, YZ;Zhou, ZL;Tsai, JN;Tseng, MN;Liu, HL;Wu, CJ;Liao, YC;Lin, CC;Tsai, DJ;Chen, FJ;Hsieh, LY;Huang, KC;Huang, CH;Chen, KT;Chu, WL;Lin, CM;Shih, SM;Hsiung, CA;Chen, YC;Sytwu, HK;Yang, YL;Lo, HJ, Emerging Infectious Diseases, 30(11) :2323-2332. (2024)
  18. Rapid identification of the predominant azole-resistant genotype in Candida tropicalis. Tseng, KY;Liao, YC;Chen, YZ;Chen, FC;Chen, FJ;Sytwu, HK;Hsieh, LY;Lan, CY;Lo, HJ,FEMS Yeast Research, 24:Article number foae025. (2024)
  19. An evolutionary learning-based method for identifying a circulating miRNA signature for breast cancer diagnosis prediction. Srinivasulu Yerukala Sathipati, Ming-Ju Tsai, Nikhila Aimalla, Luke Moat, Sanjay K Shukla, Patrick Allaire, Scott Hebbring, Afshin Beheshti, Rohit Sharma, Shinn-Ying Ho, NAR Genomics and Bioinformatics, 6(1) :lqae022. (2024)
  20. The clinical impacts of lung microbiome in bronchiectasis with fixed airflow obstruction: A prospective cohort study. Yen-Fu Chen, Hsin-Han Hou, Ning Chien, Kai-Zen Lu, Chieh-Hua Lin, Yu-Chieh Liao, Kuo-Lung Lor, Jung-Yien Chien, Chung-Ming Chen, Chung-Yu Chen, Shih-Lung Cheng, Hao-Chien Wang, Po-Ren Hsueh & Chong-Jen Yu, Respiratory Research, 25(1) :308. (2024)
  21. An Ensemble Deep Learning Model for Predicting Minimum Inhibitory Concentrations of Antimicrobial Peptides Against Pathogenic Bacteria. Chia-Ru Chung, Chung-Yu Chien, Yun Tang, Li-Ching Wu, Justin Bo-Kai Hsu, Jang-Jih Lu, Tzong-Yi Lee, Chen Bai, Jorng-Tzong Horng,iScience, 27(9) :110718-. (2024)
  22. Multi-Omics Characterization of E3 Regulatory Patterns in Different Cancer Types. Zhongyan Li, Jingting Wan, Shangfu Li, Yun Tang, Yang-Chi-Dung Lin, Jie Ni, Xiaoxuan Cai, Jinhan Yu, Hsien-Da Huang, Tzong-Yi Lee , International Journal of Molecular Sciences, 25(14) :7639. (2024)
  23. CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network. Lantian Yao, Peilin Xie, Jiahui Guan, Chia-Ru Chung, Yixian Huang, Yuxuan Pang, Huacong Wu, Ying-Chih Chiang, Tzong-Yi Lee,Journal of Chemical Information and Modeling, 64(14) :5725-5736. (2024)
  24. AMPActiPred: A three‐stage framework for predicting antibacterial peptides and activity levels with deep forest. Lantian Yao, Jiahui Guan, Peilin Xie, Chia‐Ru Chung, Junyang Deng, Yixian Huang, Ying‐Chih Chiang, Tzong‐Yi Lee, Protein Science, 33(6) :e5006. (2024)
  25. A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy. Jiahui Guan, Lantian Yao, Peilin Xie, Chia-Ru Chung, Yixian Huang, Ying-Chih Chiang, Tzong-Yi Lee, Briefings in Bioinformatics, 25(3) :bbae208. (2024)
  26. Guided Diffusion for molecular generation with interaction prompt. Peng Wu, Huabin Du, Yingchao Yan, Tzong-Yi Lee, Chen Bai, Song Wu, Briefings in Bioinformatics, 25(3) :bbae174. (2024)
  27. dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era. Lantian Yao, Jiahui Guan, Peilin Xie, Chia-Ru Chung, Zhihao Zhao, Danhong Dong, Yilin Guo, Wenyang Zhang, Junyang Deng, Yuxuan Pang, Yulan Liu, Yunlu Peng, Jorng-Tzong Horng, Ying-Chih Chiang, Tzong-Yi Lee, Nucleic Acids Research, :gkae1019. (2024)
  28. dbPTM 2025 update: Comprehensive Integration of PTMs and Proteomic Data for Advanced Insights into Cancer Research. Chia-Ru Chung, Yun Tang, Yen-Peng Chiu, Shangfu Li, Wen-Kai Hsieh, Lantian Yao, Ying-Chih Chiang, Yuxuan Pang, Guan-Ting Chen, Kai-Chen Chou, You Sheng Paik, Phuong Lam Tran, Cheng-Pei Lin, Yu-Min Kao, Yi-Jie Chen, Wen-Chi Chang, Justin Bo-Kai Hsu, Jorng-Tzong Horng, Tzong-Yi Lee, Nucleic Acids Research, :gkae1005. (2024)
  29. ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network. Lantian Yao, Peilin Xie, Jiahui Guan, Chia-Ru Chung, Wenyang Zhang, Junyang Deng, Yixian Huang, Ying-Chih Chiang, Tzong-Yi Lee, Briefings in Bioinformatics, 25(5) :bbae460. (2024)
  30. Enhanced hippocampal TIAM2S expression alleviates cognitive deficits in Alzheimer’s disease model mice. Kuan-Chin Sung, Li-Yun Wang, Che-Chuan Wang, Chun-Hsien Chu, H. Sunny Sun & Ya-Hsin Hsiao, Pharmacological Reports, 76 :1032-1043. (2024)
  31. Imbalance in Unc80 RNA Editing Disrupts Dynamic Neuronal Activity and Olfactory Perception. Chen HW, Ma CP, Chin E, Chen YT, Wang TC, Kuo YP, Su CH, Huang PJ, Tan BC., Int J Mol Sci., 25(11) :5985. (2024)
 

Collaborative Research - 2025

  1. Activated single nucleotide mismatch determination through toehold-embedded hairpin-mediated strand displacement reaction alongside CRISPR-Cas12a for detection of TP53 point mutation, Marpaung. DSS; Jiang, SS; Fang, WT; Liao, YC; Chuang, MC, Sensors and Actuators B-Chemical, 423 :Article number 136751. (2025)