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Lee CC, Huang PJ, Yeh YM, Li PH, Chiu CH, Cheng WH, Tang P. Helminth egg analysis platform (HEAP): An opened platform for microscopic helminth egg identification and quantification based on the integration of deep learning architectures. J Microbiol Immunol Infect. 2022 Jun;55(3):395-404. doi: 10.1016/j.jmii.2021.07.014. Epub 2021 Sep 2. PubMed PMID: 34511389.
Ong SC, Cheng WH, Ku FM, Tsai CY, Huang PJ, Lee CC, Yeh YM, Rada P, Hrdý I, Narayanasamy RK, Smutná T, Lin R, Luo HW, Chiu CH, Tachezy J, Tang P. Identification of Endosymbiotic Virus in Small Extracellular Vesicles Derived from Trichomonas vaginalis. Genes (Basel). 2022 Mar 17;13(3). doi: 10.3390/genes13030531. PubMed PMID: 35328084; PubMed Central PMCID: PMC8951798.
Huang PJ, Huang CY, Li YX, Liu YC, Chu LJ, Yeh YM, Cheng WH, Chen RM, Lee CC, Chen LC, Lin HC, Chiu SF, Lin WN, Lyu PC, Tang P, Huang KY. Dissecting the Transcriptomes of Multiple Metronidazole-Resistant and Sensitive Trichomonas vaginalis Strains Identified Distinct Genes and Pathways Associated with Drug Resistance and Cell Death. Biomedicines. 2021 Dec 2;9(12). doi: 10.3390/biomedicines9121817. PubMed PMID: 34944632; PubMed Central PMCID: PMC8698965.
Lee CC, Feng Y, Chen CL, Yeh YM, Hsu MH, Liao WT, Zhou YL, Tang P, Chiu CH. Genomic analysis of maternal carriage of group B Streptococcus and transmission routes of neonatal sepsis. J Infect. 2021 Dec;83(6):709-737. doi: 10.1016/j.jinf.2021.10.003. Epub 2021 Oct 8. PubMed PMID: 34627842.
Chiu SF, Huang PJ, Cheng WH, Huang CY, Chu LJ, Lee CC, Lin HC, Chen LC, Lin WN, Tsao CH, Tang P, Yeh YM, Huang KY. Vaginal Microbiota of the Sexually Transmitted Infections Caused by Chlamydia trachomatis and Trichomonas vaginalis in Women with Vaginitis in Taiwan. Microorganisms. 2021 Sep 2;9(9). doi: 10.3390/microorganisms9091864. PubMed PMID: 34576759; PubMed Central PMCID: PMC8470505.
Chaou CH, Chiu TF, Pan SL, Yen AM, Chang SH, Tang P, Lai CC, Wang RF, Chen HH. Quantifying Dynamic Flow of Emergency Department (ED) Patient Managements: A Multistate Model Approach. Emerg Med Int. 2020;2020:2059379. doi: 10.1155/2020/2059379. eCollection 2020. PubMed PMID: 33354372; PubMed Central PMCID: PMC7737449.
Cheng WH, Huang KY, Ong SC, Ku FM, Huang PJ, Lee CC, Yeh YM, Lin R, Chiu CH, Tang P. Protein cysteine S-nitrosylation provides reducing power by enhancing lactate dehydrogenase activity in Trichomonas vaginalis under iron deficiency. Parasit Vectors. 2020 Sep 18;13(1):477. doi: 10.1186/s13071-020-04355-0. PubMed PMID: 32948226; PubMed Central PMCID: PMC7501694.
Huang PJ, Chang JH, Lin HH, Li YX, Lee CC, Su CT, Li YL, Chang MT, Weng S, Cheng WH, Chiu CH, Tang P. DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework. Comput Math Methods Med. 2020;2020:7231205. doi: 10.1155/2020/7231205. eCollection 2020. PubMed PMID: 32952600; PubMed Central PMCID: PMC7481958.
Lin HC, Chu LJ, Huang PJ, Cheng WH, Zheng YH, Huang CY, Hong SW, Chen LC, Lin HA, Wang JY, Chen RM, Lin WN, Tang P, Huang KY. Proteomic signatures of metronidazole-resistant Trichomonas vaginalis reveal novel proteins associated with drug resistance. Parasit Vectors. 2020 Jun 1;13(1):274. doi: 10.1186/s13071-020-04148-5. PubMed PMID: 32487244; PubMed Central PMCID: PMC7268490.
Lee CC, Huang PJ, Yeh YM, Chen SY, Chiu CH, Cheng WH, Tang P. Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins. BMC Bioinformatics. 2019 Jul 24;20(Suppl 13):382. doi: 10.1186/s12859-019-2857-7. PubMed PMID: 31337335; PubMed Central PMCID: PMC6651900.
Huang PJ, Lin HH, Lee CC, Chiu LY, Wu SM, Yeh YM, Tang P, Chiu CH, Lyu PC, Tsai PC. CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts. BMC Med Genomics. 2019 Jul 11;12(Suppl 5):99. doi: 10.1186/s12920-019-0510-y. PubMed PMID: 31296206; PubMed Central PMCID: PMC6624176.
Huang KY, Chen RM, Lin HC, Cheng WH, Lin HA, Lin WN, Huang PJ, Chiu CH, Tang P. Potential role of autophagy in proteolysis in Trichomonas vaginalis. J Microbiol Immunol Infect. 2019 Apr;52(2):336-344. doi: 10.1016/j.jmii.2018.11.002. Epub 2018 Nov 22. PubMed PMID: 30503389.
Tang WF, Huang RT, Chien KY, Tang P, Horng JT. Large-Scale Proteomic Identification of Targets of Cellular miR-197 Downregulated by Enterovirus A71. J Proteome Res. 2019 Jan 4;18(1):449-460. doi: 10.1021/acs.jproteome.8b00762. Epub 2018 Oct 29. PubMed PMID: 30336044.
Chaou CH, Chen HH, Tang P, Yen AM, Wu KH, Hsiao CT, Chiu TF. Traffic Intensity of Patients and Physicians in the Emergency Department: A Queueing Approach for Physician Utilization. J Emerg Med. 2018 Nov;55(5):718-725. doi: 10.1016/j.jemermed.2018.07.024. Epub 2018 Sep 22. PubMed PMID: 30253956.
Li HP, Peng CC, Wu CC, Chen CH, Shih MJ, Huang MY, Lai YR, Chen YL, Chen TW, Tang P, Chang YS, Chang KP, Hsu CL. 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 May 10;37(1):102. doi: 10.1186/s13046-018-0754-y. PubMed PMID: 29747653; PubMed Central PMCID: PMC5946489.
Huang PJ, Lee CC, Chiu LY, Huang KY, Yeh YM, Yang CY, Chiu CH, Tang P. VAReporter: variant reporter for cancer research of massive parallel sequencing. BMC Genomics. 2018 May 9;19(Suppl 2):86. doi: 10.1186/s12864-018-4468-5. PubMed PMID: 29764369; PubMed Central PMCID: PMC5954270.
Liao HY, Chien CC, Tang P, Chen CC, Chen CY, Chen SC. The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp. J Hazard Mater. 2018 May 5;349:79-90. doi: 10.1016/j.jhazmat.2018.01.039. Epub 2018 Feb 6. PubMed PMID: 29414755.
Huang PJ, Chiu LY, Lee CC, Yeh YM, Huang KY, Chiu CH, Tang P. mSignatureDB: a database for deciphering mutational signatures in human cancers. Nucleic Acids Res. 2018 Jan 4;46(D1):D964-D970. doi: 10.1093/nar/gkx1133. PubMed PMID: 29145625; PubMed Central PMCID: PMC5753213.
Lin CC, Lee CC, Lin SH, Huang PJ, Li HP, Chang YS, Tang P, Chao M. RNA recombination in Hepatitis delta virus: Identification of a novel naturally occurring recombinant. J Microbiol Immunol Infect. 2017 Dec;50(6):771-780. doi: 10.1016/j.jmii.2015.10.013. Epub 2015 Nov 27. PubMed PMID: 26757847.
Cheng WH, Huang KY, Huang PJ, Lee CC, Yeh YM, Ku FM, Lin R, Cheng ML, Chiu CH, Tang P. γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis. Parasit Vectors. 2017 Sep 26;10(1):443. doi: 10.1186/s13071-017-2381-4. PubMed PMID: 28950916; PubMed Central PMCID: PMC5615479.
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. APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Nat Commun. 2017 Sep 6;8(1):465. doi: 10.1038/s41467-017-00493-9. PubMed PMID: 28878238; PubMed Central PMCID: PMC5587710.
Chen TW, Gan RC, Fang YK, Chien KY, Liao WC, Chen CC, Wu TH, Chang IY, Yang C, Huang PJ, Yeh YM, Chiu CH, Huang TW, Tang P. FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. Sci Rep. 2017 Sep 5;7(1):10430. doi: 10.1038/s41598-017-10952-4. PubMed PMID: 28874813; PubMed Central PMCID: PMC5585236.
Bradic M, Warring SD, Tooley GE, Scheid P, Secor WE, Land KM, Huang PJ, Chen TW, Lee CC, Tang P, Sullivan SA, Carlton JM. Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis. Genome Biol Evol. 2017 Jun 1;9(6):1658-1672. doi: 10.1093/gbe/evx110. PubMed PMID: 28633446; PubMed Central PMCID: PMC5522705.
Sablok G, Chen TW, Lee CC, Yang C, Gan RC, Wegrzyn JL, Porta NL, Nayak KC, Huang PJ, Varotto C, Tang P. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications. DNA Res. 2017 Jun 1;24(3):327-332. doi: 10.1093/dnares/dsw044. PubMed PMID: 28419256; PubMed Central PMCID: PMC5499650.
Xie YT, Gao JM, Wu YP, Tang P, Hide G, Lai DH, Lun ZR. Recombinant α-actinin subunit antigens of Trichomonas vaginalis as potential vaccine candidates in protecting against trichomoniasis. Parasit Vectors. 2017 Feb 16;10(1):83. doi: 10.1186/s13071-017-2009-8. PubMed PMID: 28209207; PubMed Central PMCID: PMC5312525.
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 organisms. BMC Bioinformatics. 2016 Dec 22;17(Suppl 19):513. doi: 10.1186/s12859-016-1366-1. PubMed PMID: 28155708; PubMed Central PMCID: PMC5260104.
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 Proteomics. OMICS. 2016 Nov;20(11):662-669. doi: 10.1089/omi.2016.0111. PubMed PMID: 27828770.
Zhang J, Sze DM, Yung BY, Tang P, Chen WJ, Chan KH, Leung PH. Distinct expression of interferon-induced protein with tetratricopeptide repeats (IFIT) 1/2/3 and other antiviral genes between subsets of dendritic cells induced by dengue virus 2 infection. Immunology. 2016 Aug;148(4):363-76. doi: 10.1111/imm.12615. PubMed PMID: 27135915; PubMed Central PMCID: PMC4948034.
Chen YC, Chen TW, Su MC, Chen CJ, Chen KD, Liou CW, Tang P, Wang TY, Chang JC, Wang CC, Lin HC, Chin CH, Huang KT, Lin MC, Hsiao CC. Whole Genome DNA Methylation Analysis of Obstructive Sleep Apnea: IL1R2, NPR2, AR, SP140 Methylation and Clinical Phenotype. Sleep. 2016 Apr 1;39(4):743-55. doi: 10.5665/sleep.5620. PubMed PMID: 26888452; PubMed Central PMCID: PMC4791608.
Kao CM, Liao HY, Chien CC, Tseng YK, Tang P, Lin CE, Chen SC. The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis. J Hazard Mater. 2016 Jan 25;302:144-150. doi: 10.1016/j.jhazmat.2015.09.047. Epub 2015 Sep 26. PubMed PMID: 26474376.
Fang YK, Huang KY, Huang PJ, Lin R, Chao M, Tang P. Gene-expression analysis of cold-stress response in the sexually transmitted protist Trichomonas vaginalis. J Microbiol Immunol Infect. 2015 Dec;48(6):662-75. doi: 10.1016/j.jmii.2014.07.013. Epub 2014 Nov 1. PubMed PMID: 25440978.
Huang KY, Ku FM, Cheng WH, Lee CC, Huang PJ, Chu LJ, Cheng CC, Fang YK, Wu HH, Tang P. Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis. Antimicrob Agents Chemother. 2015 Nov;59(11):6891-903. doi: 10.1128/AAC.01779-15. Epub 2015 Aug 24. PubMed PMID: 26303799; PubMed Central PMCID: PMC4604415.
Chen TW, Gan RC, Chang YF, Liao WC, Wu TH, Lee CC, Huang PJ, Lee CY, Chen YY, Chiu CH, Tang P. Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing. BMC Genomics. 2015 Aug 28;16:648. doi: 10.1186/s12864-015-1859-8. PubMed PMID: 26315384; PubMed Central PMCID: PMC4552406.
Cheng WH, Huang KY, Huang PJ, Hsu JH, Fang YK, Chiu CH, Tang P. Nitric oxide maintains cell survival of Trichomonas vaginalis upon iron depletion. Parasit Vectors. 2015 Jul 25;8:393. doi: 10.1186/s13071-015-1000-5. PubMed PMID: 26205151; PubMed Central PMCID: PMC4513698.
Chen SJ, Liu H, Liao CT, Huang PJ, Huang Y, Hsu A, Tang P, Chang YS, Chen HC, Yen TC. Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature. Oncotarget. 2015 Jul 20;6(20):18066-80. doi: 10.18632/oncotarget.3768. PubMed PMID: 25980437; PubMed Central PMCID: PMC4621868.
Huang PJ, Lee CC, Tan BC, Yeh YM, Huang KY, Gan RC, Chen TW, Lee CY, Yang ST, Liao CS, Liu H, Tang P. Vanno: a visualization-aided variant annotation tool. Hum Mutat. 2015 Feb;36(2):167-74. doi: 10.1002/humu.22684. PubMed PMID: 25196204.
Huang PJ, Lee CC, Tan BC, Yeh YM, Julie Chu L, Chen TW, Chang KP, Lee CY, Gan RC, Liu H, Tang P. CMPD: cancer mutant proteome database. Nucleic Acids Res. 2015 Jan;43(Database issue):D849-55. doi: 10.1093/nar/gku1182. Epub 2014 Nov 14. PubMed PMID: 25398898; PubMed Central PMCID: PMC4383976.
Wang F, Chan LW, Law HK, Cho WC, Tang P, Yu J, Shyu CR, Wong SC, Yip SP, Yung BY. Exploring microRNA-mediated alteration of EGFR signaling pathway in non-small cell lung cancer using an mRNA:miRNA regression model supported by target prediction databases. Genomics. 2014 Dec;104(6 Pt B):504-11. doi: 10.1016/j.ygeno.2014.09.004. Epub 2014 Sep 22. PubMed PMID: 25257143.
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 Shermani. Emerg Microbes Infect. 2014 Nov;3(11):e82. doi: 10.1038/emi.2014.78. Epub 2014 Nov 26. PubMed PMID: 26038504; PubMed Central PMCID: PMC4274889.
Weng KF, Hung CT, Hsieh PT, Li ML, Chen GW, Kung YA, Huang PN, Kuo RL, Chen LL, Lin JY, Wang RY, Chen SJ, Tang P, Horng JT, Huang HI, Wang JR, Ojcius DM, Brewer G, Shih SR. A cytoplasmic RNA virus generates functional viral small RNAs and regulates viral IRES activity in mammalian cells. Nucleic Acids Res. 2014 Nov 10;42(20):12789-805. doi: 10.1093/nar/gku952. Epub 2014 Oct 28. PubMed PMID: 25352551; PubMed Central PMCID: PMC4227785.
Chen KY, Cheng CJ, Yen CM, Tang P, Wang LC. Comparative studies on the proteomic expression patterns in the third- and fifth-stage larvae of Angiostrongylus cantonensis. Parasitol Res. 2014 Oct;113(10):3591-600. doi: 10.1007/s00436-014-4024-4. Epub 2014 Jul 16. PubMed PMID: 25028210.
Wang F, Chan LW, Cho WC, Tang P, Yu J, Shyu CR, Tsui NB, Wong SC, Siu PM, Yip SP, Yung BY. Novel approach for coexpression analysis of E2F1-3 and MYC target genes in chronic myelogenous leukemia. Biomed Res Int. 2014;2014:439840. doi: 10.1155/2014/439840. Epub 2014 Aug 10. PubMed PMID: 25180182; PubMed Central PMCID: PMC4142389.
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 data. BMC Genomics. 2014 Jun 30;15:539. doi: 10.1186/1471-2164-15-539. PubMed PMID: 24974934; PubMed Central PMCID: PMC4092222.
Yen HC, Li SL, Hsu WC, Tang P. Interference of Co-amplified nuclear mitochondrial DNA sequences on the determination of human mtDNA heteroplasmy by Using the SURVEYOR nuclease and the WAVE HS system. PLoS One. 2014;9(3):e92817. doi: 10.1371/journal.pone.0092817. eCollection 2014. PubMed PMID: 24664244; PubMed Central PMCID: PMC3963942.
Huang KY, Chen YY, Fang YK, Cheng WH, Cheng CC, Chen YC, Wu TE, Ku FM, Chen SC, Lin R, Tang P. Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis. Biochim Biophys Acta. 2014 Jan;1840(1):53-64. doi: 10.1016/j.bbagen.2013.08.008. Epub 2013 Aug 17. PubMed PMID: 23958562.
Huang PJ, Yeh YM, Gan RC, Lee CC, Chen TW, Lee CY, Liu H, Chen SJ, Tang P. CPAP: Cancer Panel Analysis Pipeline. Hum Mutat. 2013 Oct;34(10):1340-6. doi: 10.1002/humu.22386. Epub 2013 Aug 13. PubMed PMID: 23893859.
Yeh YM, Huang KY, Richie Gan RC, Huang HD, Wang TC, Tang P. Phosphoproteome profiling of the sexually transmitted pathogen Trichomonas vaginalis. J Microbiol Immunol Infect. 2013 Oct;46(5):366-73. doi: 10.1016/j.jmii.2012.07.010. Epub 2012 Aug 21. PubMed PMID: 22921107.
Huang KY, Shin JW, Huang PJ, Ku FM, Lin WC, Lin R, Hsu WM, Tang P. Functional profiling of the Tritrichomonas foetus transcriptome and proteome. Mol Biochem Parasitol. 2013 Jan;187(1):60-71. doi: 10.1016/j.molbiopara.2012.12.001. Epub 2012 Dec 17. PubMed PMID: 23254202.
Chen TW, Gan RC, Wu TH, Huang PJ, Lee CY, Chen YY, Chen CC, Tang P. FastAnnotator--an efficient transcript annotation web tool. BMC Genomics. 2012;13 Suppl 7:S9. doi: 10.1186/1471-2164-13-S7-S9. Epub 2012 Dec 13. PubMed PMID: 23281853; PubMed Central PMCID: PMC3521244.
Chen CL, Lai YF, Tang P, Chien KY, Yu JS, Tsai CH, Chen HW, Wu CC, Chung T, Hsu CW, Chen CD, Chang YS, Chang PL, Chen YT. Comparative and targeted proteomic analyses of urinary microparticles from bladder cancer and hernia patients. J Proteome Res. 2012 Dec 7;11(12):5611-29. doi: 10.1021/pr3008732. Epub 2012 Oct 31. PubMed PMID: 23082778.
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