2024

Huang PJ, Weng YC, Huang KY, Lee CC, Yeh YM, Chen YT, Chiu CH, Tang P* (2024) ProFun: A web server for functional enrichment analysis of parasitic protozoan genes J Microbiol Immunol Infect. [DOI: 10.1016/j.jmii.2024.01.007].

2023

Cheng WH, Huang PJ, Lee CC, Yeh YM, Ong SC, Lin R, Ku FM, Chiu CH, Tang P*. (2023) Metabolomics analysis reveals changes related to pseudocyst formation induced by iron depletion in Trichomonas vaginalis. Parasites & Vectors 16:226

Lee CC, Lin YC, Pan TY, Yang CH, Li PH, Chen SY, Gao JJ, Yang C, Chu LJ, Huang PJ, Yeh YM, Tang P, Chang YS, Yu JS, Hsiao YC. (2023) HeapMS: An Automatic Peak-Picking Pipeline for Targeted Proteomic Data Powered by 2D Heatmap Transformation and Convolutional Neural Networks. Anal Chem. 95(42):15486-15496

2022

Lee CC, Huang PJ, Yeh YM, Li PH, Chiu CH, Cheng WH, Tang P*. (2022) 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. (55)395-404.

Ong SC, Cheng WH, Ku FM, Tsai CY, Huang PJ, Lee CC, Yeh YM, Rada P, Hrdý I, Narayanasamy RK, Smutna T, Lin R. Luo HW, Chiu CH. Tachezy J*. Tang P* (2022) Identification of Endosymbiotic Virus in Small Extracellular Vesicles Derived from Trichomonas vaginalis. Genes (13)531

Rada P, Hrdý I, Zdrhal A, Narayanasamy RK, Smutna T, Horáčková J, Harant K, Benes V, Ong SC, Tsai CY, Luo HW, Chiu CH, Tang P*, Tachezy J*. (2022) Double-stranded RNA viruses are released from Trichomonas vaginalis inside small extracellular vesicles and modulate the exosomal cargo. Front. Microbiol. 13:893692
　

2021
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. (2021) 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. 9(12):1817
　

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. (2021) Vaginal Microbiota of the Sexually Transmitted Infections Caused by Chlamydia trachomatis and Trichomonas vaginalis in Women with Vaginitis in Taiwan. Microorganisms. 9(9):1864.

Lee CC, Feng Y, Chen CL, Yeh YM, Hsu MH, Liao WT, Zhou YL, Tang P, Chiu CH. (2021) Genomic analysis of maternal carriage of group B Streptococcus and transmission routes of neonatal sepsis. J Infect. 83(6):709-737.
　

2020

Cheng WH, Huang KY, Ong SC, Ku FM, Huang PJ, Lee CC, Yeh YM, Lin R, Chiu CH. Tang P.* (2020) Protein cysteine S-nitrosylation provides reducing power by enhancing lactate dehydrogenase activity in Trichomonas vaginalis under iron deficiency. Parasit Vectors 13(1):477

Huang PJ, Chang JH, Lin HH, Li YX, Lee CC, Su CT, Li YL, Chang MT, Weng S, Cheng WH, Chiu CH, Tang P.* (2020) DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework. Comput Math Methods Med.2020:7231205

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* (2020) Proteomic Signatures of Metronidazole-resistant Trichomonas Vaginalis reveal novel proteins associated with drug resistance. Parasit Vectors 13(1):274
　

2019

Lee CC, Huang PJ, Yeh YM, Chen SY, Chiu CH, Cheng WH, Tang P* (2019) Pathogenic Protist Transmembranome database (PPTdb): A web-based platform for searching and analysis of protist transmembrane proteins. BMC Bioinformatics 20(S13):382. [doi:10.1186/s12859-019-2857-7.]

Huang KY, Chen RM. Lin HC, Cheng WH, Lin HA, Lin WN, Huang PJ, Chiu CH, Tang P* (2019) Potential role of autophagy in proteolysis in Trichomonas vaginalis. J Microbiol Immunol Infect (52)336-344 [https://doi.org/10.1016/j.jmii.2018.11.002]

Huang PJ, Lin HH, Lee CC, Chiu LY, Wu SM, Yeh YM, Tang P, Chiu CH, Lyu PC, Tsai PC (2019) CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts.BMC Med Genomics 12(S5):99 [doi:10.1186/s12920-019-0510-y.]

Tang WF, Huang RT, Chien KY, Tang P, Horng JT*. (2018) Large-Scale Proteomic Identification of Targets of Cellular miR-197 Downregulated by Enterovirus A71. J Proteome Res. [https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00762]

2018

Huang PJ, Chiu LY, Lee CC, Yeh YM, Huang KY, Chiu CH, Tang P* (2018) mSignatureDB: a database for deciphering mutational signatures in human cancers. Nucleic Acids Research 46(D1)964-970 [doi: 10.1093/nar/gkx1133]

Huang PJ, Lee CC, Chiu LY, Huang KY, Yeh YM, Yang CY, Chiu CH, Tang P.* (2018) VAReporter: Variant reporter for cancer research of massive parallel sequencing. BMC Genomics 19(S2):86. [doi: 10.1186/s12864-018-4468-5]

Huang KY, Ong SC, Wu CC, Lin HC, Fang YK, Cheng WH, Tang P* (2018) Metabolic reprogramming of hydrogenosomal amino acids in T. vaginalis upon under glucose restriction. J Microbiol Immunol Infect. [doi: 10.1016/j.jmii.2017.10.005]

Liao HY, Chien CC, Tang P, Chen CC, Chen CT, Chen SC* (2018) The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp. J Hazard Mater. 349(5)79–90 [doi: 10.1016/j.jhazmat.2018.01.039]

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. (2018) 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. 10;37(1):102. [doi: 10.1186/s13046-018-0754-y]

Chaou CH, Chen HH, Tang P, Yen AM, Wu KH, Hsiao CT, Chiu TF* (2018) Traffic Intensity of Patients and Physicians in the Emergency Department: A Queueing Approach for Physician Utilization. J Emerg 55(5):718-725.[https://doi.org/10.1016/j.jemermed.2018.07.024]

2017

Cheng WH, Huang KY, Huang PJ, Lee CC, Yeh YH, Ku FM, Lin R, Cheng ML, Chiu CH Tang P* (2017) γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis. Parasites & Vectors 10:443.[doi 10.1186/s13071-017-2381-4]

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*.(2017) FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. Sci Rep. 7(1):10430 [doi 10.1038/s41598-017-10952-4]

Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP*, Chang YS*. (2017) APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Nat Commun. 8(1):465. [doi: 10.1038/s41467-017-00493-9]

Sablok G*, Chen TW, Lee CC, Yang C, Gan RC, Varotto C, Porta NL, Nayak KC, Huang PJ, Wegrzyn JL, Tang P*. (2017) ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications. DNA Research 24(3):327-332. [doi: 10.1093/dnares/dsw044]

Bradic M, Warring SD, Tooley GE, Scheid P, Secor WE, Land KM, Huang PJ, Chen TW, Lee CC, Tang P, Sullivan SA, Carlton JM* (2017) Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis. Genome Biol Evol. 9(6):1658-1672 [doi: 10.1093/gbe/evx110]

Xie YT, Gao JM, Wu YP, Tang P, Hide G, Lai DH, Lun ZR* (2017) Recombinant α-actinin subunit antigens of Trichomonas vaginalis as potential vaccine candidates in protecting against trichomoniasis. Parasites & Vectors 10(1):83 [doi: 10.1186/s13071-017-2009-8]

2016
Gan RC, Chen TW, Wu TH, Huang PJ, Lee CC, Yeh YM, Chiu CH, Huang HD, Tang P*. (2016) PARRoT- A homology-based strategy to quantify and compare RNA-Sequencing from non-model organisms. BMC Bioinformatics 17(S19):513.

Fang YK, Chien KY, Huang KY, Cheng WH, Ku FM, Lin R, Chen TW, Huang PJ, Chiu CH, Tang P* (2016)
Responding to a zoonotic emergency with multi-omics research: Pentatrichomonas hominis hydrogenosomal protein characterization with use of RNA sequencing and proteomics. OMICS: A Journal of Integrative Biology. 20(11): 662-669.

Lin CC, Lee CC, Lin SH, Huang PJ, Li HP, Chang YS, Tang P*, Chao M*.(2016) RNA recombination in Hepatitis delta virus: Identification of a novel naturally occurring recombinant. J Microbiol Immunol Infect. 2015 Nov 27. [doi: 10.1016/j.jmii.2015.10.013]

Chen CL, Tang P, Wu CC, Chung T, Yu JS, Chang YS, Chang PL, Chen YT* (2016) The urinary microparticle tumor-associated calcium-signal transducer 2 as a bladder cancer biomarker Urological Science 27(2):S2

Kao CM, Liao HY, Chien CC, Tseng YK, Tang P, Lin CE, Chen SC. (2016) The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis. J Hazard Mater. 302:144-50.

Zhang JS, Sze DMY, Yung BYM, Tang P, Chen WJ, Chan KH , Leung PHM* (2016) 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 148(4):363-76.

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. (2016) Whole Genome DNA Methylation Analysis of Obstructive Sleep Apnea: IL1R2/ NPR2/ AR/ SP140 Methylation and Clinical Phenotype. Sleep. 39(4):743-55.

2015

Huang KY, Ku FM, Cheng WH, Lee CC, Huang PJ, Chu LCJ, Cheng CC, Fang YK, Wu HH, Tang P* (2015) Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis. Antimicrob. Agents Chemother.59(11):6891-903

Chen WH, Huang KY, Huang PJ, Hsu JH, Fang YK, Chiu CH, Tang P* (2015) Nitric oxide maintains cell survival of Trichomonas vaginalis upon iron depletion. Parasites & Vectors 8:393

Huang PJ, Lee CC, Yeh YM, Huang KY, Gan RC, Chen TW, Lee CY, Yang ST, Liao CS, Liu H*, Tang P.* (2015) Vanno: A Visualization-aided Variant Annotation Tool. Hum Mutat 36(2):167-74

Chen TW, Gan RC, Chang YF, Liao WC, Wu TH, Lee CC, Huang PJ, Lee CY, Chen YYM, Chiu CH, Tang P* (2015) Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing. BMC Genomics 16:648

Fang YK, Huang KY, Huang PJ, Lin R, Chao M, Tang P* (2015) Gene expression analysis of cold-stress response in the sexually transmitted protist Trichomonas vaginalis.J Microbiol Immunol Infect. 48(6):662-75

Chen SJ, Liu H, Liao CT, Huang PJ, Huang Y, Hsu A, Tang P, Chang YS, Chen HC, Yen Tc (2015) Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature. Oncotarget 6(20):18066-18080.

2014

Huang PJ, Lee CC, Tan BCM, Yeh YM, Chu JLC, Chen TW, Chang KP, Gan RC, Liu H, Tang P.* (2015) CMPD: Cancer Mutant Proteome Database. Nucleic Acids Res. 43:D849-55

Huang KY, Chen YYM, Fang YK, Cheng WH, Cheng CC, Chen YC, Wu TE, Ku FM, Chen SC, Lin R, Tang P*. (2014) Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis. BBA-Gen Subjects. 1840(1):53–64.

Chen TW, Li HP, Lee CC, Gan RC, Huang PJ, Wu TH, Lee CY, Chang YF and Tang P*. (2014) ChIPseek, a web-based analysis tool for ChIP data. BMC Genomics 13:539

Weng KF, Hung CT, Hiej PT, Li ML, Chen GW, Kung YA, Huang PN, Kuo RL, Chen LL, Lin JY, Wang RYL, Chen SJ, Tang P, Horng JT, Huang I, Wang JR, Qjcius D, Brewer G, Shih SR. (2014) A Cytoplasmic RNA Virus Generates Functional Viral Small RNAs and Regulates Viral IRES Activity in Mammalian Cells. Nucleic Acids Res. 42(20):12789-805.

Chou LF, Chen TW, Ko YC, Pan MJ, Tian YC, Chiu CH, Tang P, Hung CC, Yang CW (2014) Potential Impact on Kidney Infection: Whole Genome Analysis for Leptospira santarosai serovar Shermani. Emerging Microbes & Infections. 3:e82

Wang F, Chan LW, Law HK, Cho WC, Tang P, Yu J, Shyu CR, Wong SC, Yip SP, Yung BY.(2014) 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 104(6 Pt B):504-11.

Yen HC, Li SL, Hsu C, Tang P. (2014) 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 9(3)e92817

Wang FF, Chan W, Cho WC, Tang P, Yu J, Shyu CR, Tsui NBY,Wong SCC, Siu PM, Yip SP, Yung BYM ( (2015) Novel Approach for Co-expression Analysis of E2F1–3 and MYC Target Genes in Chronic Myelogenous Leukemia. Biomed Res Int. 2014:439840

Chang SH, Tang P, Yen CM, Chow KP, Wang LC*. (2014) A transcriptomic analysis on gene expressions in the infective third and pathogenic fifth larval stages of Angiostrongylus cantonensis. Parasitol Int. 63(1):42-48.

Chen KY, Cheng CJ, Yen CM, Tang P, Wang LC*. (2014) Comparative studies on the proteomic expression patterns in the third- and fifth-stage larvae of Angiostrongylus cantonensis. Parasitol Res. 113(10):3591-600.
　

2013

Huang PJ^#, Yeh YM^#, Gan RCR, Lee CC, Chen TW, Lee CY, Liu H, Chen SJ, Tang P*. (2013) CPAP: Cancer Panel Analysis Pipeline. Hum Mutat. 34(10):1340-1346.

Huang KY, Shin JW, Huang PJ, Ku FM, Lin WC, Lin R, Hsu WM, Tang P*. (2013) Functional profiling of the Tritrichomonas foetus transcriptome and proteome. Mol. Biochem. Parasitol. 187:60– 71.

Yeh YM, Huang KY, Gan RRC, Huang HD, Wang TC, Tang P*. (2013) Phosphoproteome profiling of the sexually transmitted pathogen Trichomonas vaginalis. J. Microbiol. Infect. Immunol. 46:366-373.

Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Burglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Soon Heng Tan C, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus B*. (2013) Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biol. 14(2):R11.

Chen YC, Hsiao CC, Chen KD, Hung YC, Wu CY, Lie CH, Liu SF, Sung MT, Chen CJ, Wang TY, Chang JC, Tang P, Fang WF, Wang YH, Chung YH, Chao TY, Leung SY, Su MC, Wang CC, Lin MC*. (2013) Peripheral immune cell gene expression changes in advanced non-small cell lung cancer patients treated with first line combination chemotherapy. PLoS One 8(2):e57053.

Wang LC*, Chen KY, Chang SH, Chung LY, Gan RCR, Cheng CL, Tang P*. (2013) Transcriptome profiling of the fifth-stage larvae of Angiostrongylus cantonensis by next-generation sequencing. Parasitol Res. 112(9):3193-3202.

Chang SH, Tang P, Lai CH, Kuo ML, Wang LC* (2013) Identification and characterization of microRNAs in young adults of Angiostrongylus cantonensis by a deep-sequencing approach. Mem I Oswaldo Cruz 108(6): 699-706.

2012

Chen CL^#, Lai YF^#, Tang P^#, Chien KY, Yu JS, Tsai CN, Chen HW, Wu CC, Chung T, Hsu CW, Chen CD, Chang YS, Chang PL, Chen YT* (2012) Comparative and targeted proteomic analyses of urinary microparticles from bladder cancer and hernia patients. J. Proteome Res. 11(12):5611-29.

Horváthová L, Šafaříková L, Basler M, Hrdý I, Campo NB, Shin JW, Huang KY, Huang PJ, Lin R, Tang P*, Tachezy J*. (2012) Transcriptomic identification of iron-regulated and iron-independent gene copies within the heavily duplicated Trichomonas vaginalis genome. Genome Biol. Evol. 4: 905-917.

Huang KY, Huang PJ, Ku FM, Lin R. Alderete JF*, Tang P* (2012) New perspectives on the responses of Trichomonas vaginalis following adherence to fibronectin by comparative transcriptomic and proteomic analyses. Infect. Immun. 80(11):3900-3911.

Chen TW, Gan RCR, Wu TH, Huang PJ, Lee CY, Chen YYM, Chen CC and Tang P*. (2012) FastAnnotator: an efficient transcript annotation web tool. BMC Genomics Genomics 13:Suppl 8, S9

Chen TW, Gan RRC, Wu TH, Lin WC, Tang P*.(2012) VIP DB -a viral protein domain usage and distribution database. Genomics 100:149-156.

Geng J, Chiu CH, Tang P, ChenY, Shieh HR, Hu SN, and Chen YM*. (2012). Complete genome and transcriptomes of Streptococcus parasanguinis FW213: phylogenic relations and potential virulence mechanisms. PLoS ONE 7(4): e34769.

Yu D, Wang Y, Fang X, Hu S, Tang P, Fu Y* (2012) Acquisition of hydrogenosomal presequences: examples from Trichomonas vaginalis. FEMS Microbiology Letters 330(2):127-31.

Huang PJ, Lin WC, Chen SC, Lin YH, Sun CH, Lyu PC, Tang P* (2012) Identification of putative miRNA from the deep-branching unicellular flagellates. Genomics 99(2):201-207

Conferences (Panel/Invited Speaker)

1. “Re-sequencing and re-annotation of the Angiostrongulus cantonensis genome and transcriptome” in the 5th World Lungworm Meeting. Nov 23-25, 2017 Bangkok, Thailand.

2. “Whole Genome Sequencing of a Dwarf Trichomonas vaginalis Genome Illustrates Challenges on the Taxonomy and Evolution of Trichomonadidae” in EMBO Conference Anaerobic protists: Integrating parasitology with mucosal microbiota and immunology. 31 August – 03 September 2017, Newcastle upon Tyne, United Kingdom.

3. "The Systems Biology of Trichomonas vaginalis" in "The 14th Asian Pacific Congress for Parasitic Zoonoses", Nov 26-27, 2016. Kanagawa, Japan.

4. “Cross-Talk between Parasite Genome and Proteome” in “The Symposium on Mass Spectrometry, Molecular and Cellular Proteomics”, Nov 8-12, 2015, Puerto Vallarta, Mexico.

5. “Visualization and Analysis of Targeted Sequencing Datasets” in “2013 International Conference of Genomics”, Oct 28 -30, 2013, Qingdao, China.

6. “Automated Bioinformatics Pipelines for RNA-sequencing of Non-model Organisms” in the “High-Throughput Sequencing Data Analysis and Approached Workshop” Dec 5-7, 2012, Beijing, China.