Chiu, S. -F.; Huang, P. -J.; Cheng, W. -H.; Huang, C. -Y.; Chu, L. J.; Lee, C. -C.; Lin, H. -C.; Chen, L. -C.; Lin, W. -N.; Tsao, C. -H.; Tang, P.; Yeh, Y. -M.; Huang, K. -Y.

Vaginal microbiota of the sexually transmitted infections caused by chlamydia trachomatis and trichomonas vaginalis in women with vaginitis in Taiwan Journal Article

In: Microorganisms, 9 (9), 2021, ISSN: 20762607, (cited By 0).

Abstract | Links | BibTeX | 標籤:

Lee, C. -C.; Huang, P. -J.; Yeh, Y. -M.; Li, P. -H.; Chiu, C. -H.; Cheng, W. -H.; 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 Journal Article

In: Journal of Microbiology, Immunology and Infection, 2021, ISSN: 16841182, (cited By 0).

Abstract | Links | BibTeX | 標籤:


Cheng, W. -H.; Huang, K. -Y.; Ong, S. -C.; Ku, F. -M.; Huang, P. -J.; Lee, C. -C.; Yeh, Y. -M.; Lin, R.; Chiu, C. -H.; Tang, P.

Protein cysteine S-nitrosylation provides reducing power by enhancing lactate dehydrogenase activity in Trichomonas vaginalis under iron deficiency Journal Article

In: Parasites and Vectors, 13 (1), 2020, ISSN: 17563305, (cited By 1).

Abstract | Links | BibTeX | 標籤: Cysteine; Glycolysis; Iron; L-Lactate Dehydrogenase; NAD; Nitric Oxide; Oxidation-Reduction; Protein Modification, Translational; Protozoan Proteins; Pyruvic Acid; Trichomonas vaginalis

Lin, H. -C.; Chu, L. J.; Huang, P. -J.; Cheng, W. -H.; Zheng, Y. -H.; Huang, C. -Y.; Hong, S. -W.; Chen, L. -C.; Lin, H. -A.; Wang, J. -Y.; Chen, R. -M.; Lin, W. -N.; Tang, P.; Huang, K. -Y.

Proteomic signatures of metronidazole-resistant Trichomonas vaginalis reveal novel proteins associated with drug resistance Journal Article

In: Parasites and Vectors, 13 (1), 2020, ISSN: 17563305, (cited By 1).

Abstract | Links | BibTeX | 標籤: alanine; arginine; aspartic acid; bafilomycin A1; glutamic acid; hydrolase; metronidazole; oligomycin; proline; proteome; proton transporting adenosine triphosphate synthase; antiprotozoal agent; metronidazole; protozoal protein, Antiprotozoal Agents; Down-Regulation; Drug Resistance; Mass Spectrometry; Metronidazole; Protein Interaction Maps; Proteomics; Protozoan Proteins; Trichomonas vaginalis; Up-Regulation

Huang, P. -J.; Chang, J. -H.; Lin, H. -H.; Li, Y. -X.; Lee, C. -C.; Su, C. -T.; Li, Y. -L.; Chang, M. -T.; Weng, S.; Cheng, W. -H.; Chiu, C. -H.; Tang, P.

DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework Journal Article

In: Computational and Mathematical Methods in Medicine, 2020 , 2020, ISSN: 1748670X, (cited By 1).

Abstract | Links | BibTeX | 標籤: Cloud Computing; Computational Biology; Cost-Benefit Analysis; Deep Learning; Genetic Variation; Genome, Computer; Software; Whole Genome Sequencing, Human; High-Throughput Nucleotide Sequencing; Humans; Neural Networks


Huang, K. -Y.; Ong, S. -C.; Wu, C. -C.; Hsu, C. -W.; Lin, H. -C.; Fang, Y. -K.; Cheng, W. -H.; Huang, P. -J.; Chiu, C. -H.; Tang, P.

Metabolic reprogramming of hydrogenosomal amino acids in Trichomonas vaginalis under glucose restriction Journal Article

In: Journal of Microbiology, Immunology and Infection, 52 (4), pp. 630-637, 2019, ISSN: 16841182, (cited By 4).

Abstract | Links | BibTeX | 標籤: alanine; amino acid; arginine; arginine deiminase; branched chain amino acid; glucose; glutamic acid; isoleucine; lactate dehydrogenase; leucine; malate dehydrogenase (decarboxylating); methionine; phenylalanine; valine; amino acid; glucose; hydrolase; protozoal protein, Amino Acids; Biochemical Phenomena; Chromatography, Liquid; Energy Metabolism; Enzyme Assays; Glucose; Hydrolases; Mass Spectrometry; Metabolic Networks and Pathways; Protozoan Proteins; Sequence Analysis, RNA; Trichomonas vaginalis

Lee, C. -C.; Huang, P. -J.; Yeh, Y. -M.; Chen, S. -Y.; Chiu, C. -H.; Cheng, W. -H.; Tang, P.

Pathogenic Protist Transmembranome database (PPTdb): A web-based platform for searching and analysis of protist transmembrane proteins Journal Article

In: BMC Bioinformatics, 20 , 2019, ISSN: 14712105, (cited By 0).

Abstract | Links | BibTeX | 標籤: Ability evaluation; Functional annotation; Functional domains; Secondary structural elements; Trans-membrane proteins; Transporter proteins; Web based platform; WEB-BASED database, amino acid sequence; article; genome; human; infectious agent; membrane; mining; nonhuman; protein domain; protist; sequence alignment; structure activity relation; computer interface; factual database; fungus; genetics; metabolism; plant, carrier protein, Classification (of information); Database systems; Query processing; Websites, Databases, Factual; Fungi; Humans; Membrane Transport Proteins; Plants; User-Computer Interface, Proteins

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.

CoMutPlotter: A web tool for visual summary of mutations in cancer cohorts Journal Article

In: BMC Medical Genomics, 12 , 2019, ISSN: 17558794, (cited By 2).

Abstract | Links | BibTeX | 標籤: Cohort Studies; Computational Biology; Computer Graphics; Humans; Internet; Mutation; Neoplasms

Huang, K. -Y.; Chen, R. -M.; Lin, H. -C.; Cheng, W. -H.; Lin, H. -A.; Lin, W. -N.; Huang, P. -J.; Chiu, C. -H.; Tang, P.

Potential role of autophagy in proteolysis in Trichomonas vaginalis Journal Article

In: Journal of Microbiology, Immunology and Infection, 52 (2), pp. 336-344, 2019, ISSN: 16841182, (cited By 5).

Abstract | Links | BibTeX | 標籤: Autophagosomes; Autophagy; Autophagy-Related Protein 8 Family; Glucose; Humans; Leupeptins; Proteasome Endopeptidase Complex; Proteasome Inhibitors; Proteolysis; Proteostasis; Recombinant Proteins; Trichomonas vaginalis; Ubiquitination


Lu, C. -Y.; Huang, P. -J.; Hsu, C. -Y.

The cholesterol-hydroxyecdysone-vitellogenin pathway is involved in the longevity of trophocytes and oenocytes of queen honey bees (Apis mellifera) Journal Article

In: Apidologie, 49 (6), pp. 721-733, 2018, ISSN: 00448435, (cited By 3).

Abstract | Links | BibTeX | 標籤: Apis mellifera; Apoidea, cell; cytochrome; gene expression; honeybee; longevity; molecular analysis; protein; queen

Huang, P. -J.; Lee, C. -C.; Chiu, L. -Y.; Huang, K. -Y.; Yeh, Y. -M.; Yang, C. -Y.; Chiu, C. -H.; Tang, P.

VAReporter: Variant reporter for cancer research of massive parallel sequencing Journal Article

In: BMC Genomics, 19 , 2018, ISSN: 14712164, (cited By 1).

Abstract | Links | BibTeX | 標籤: Algorithms; Genetic Predisposition to Disease; High-Throughput Nucleotide Sequencing; Humans; Internet; Molecular Sequence Annotation; Mutation; Neoplasms; Precision Medicine; Whole Exome Sequencing; Workflow

Yang, C. -Y.; Yeh, Y. -M.; Yu, H. -Y.; Chin, C. -Y.; Hsu, C. -W.; Liu, H.; Huang, P. -J.; Hu, S. -N.; Liao, C. -T.; Chang, K. -P.; Chang, Y. -L.

Oral microbiota community dynamics associated with oral squamous cell carcinoma staging Journal Article

In: Frontiers in Microbiology, 9 (MAY), 2018, ISSN: 1664302X, (cited By 83).

Abstract | Links | BibTeX | 標籤: biological marker; phenylalanine; RNA 16S; tryptophan; tyrosine

Wu, S. -M.; Liu, H.; Huang, P. -J.; Chang, I. Y. -F.; Lee, C. -C.; Yang, C. -Y.; Tsai, W. -S.; Tan, B. C. -M.

circlncRNAnet: An integrated web-based resource for mapping functional networks of long or circular forms of noncoding RNAs Journal Article

In: GigaScience, 7 (1), pp. 1-10, 2018, ISSN: 2047217X, (cited By 41).

Abstract | Links | BibTeX | 標籤: circular, circular RNA; long untranslated RNA; RNA binding protein; unclassified drug; untranslated RNA; messenger RNA; microRNA; RNA; RNA, Computational Biology; Databases, Genetic; Gene Regulatory Networks; High-Throughput Nucleotide Sequencing; Humans; Internet; MicroRNAs; RNA; RNA Processing, Genetic; User-Computer Interface, Long Noncoding; RNA, Messenger; Sequence Analysis, Nucleic Acid; Epigenesis, Post-Transcriptional; RNA, RNA; Transcription

Huang, P. -J.; Chiu, L. -Y.; Lee, C. -C.; Yeh, Y. -M.; Huang, K. -Y.; Chiu, C. -H.; Tang, P.

MSignatureDB: A database for deciphering mutational signatures in human cancers Journal Article

In: Nucleic Acids Research, 46 (D1), pp. D964-D970, 2018, ISSN: 03051048, (cited By 26).

Abstract | Links | BibTeX | 標籤: Article; bioinformatics; cancer genetics; cancer research; gene sequence; genetic database; human; mutational analysis; priority journal; reference database; computer interface; genetics; mutation; neoplasm; nucleic acid database, Databases, Nucleic Acid; Humans; Mutation; Neoplasms; User-Computer Interface


Chen, T. -W.; Lee, C. -C.; Liu, H.; Wu, C. -S.; Pickering, C. R.; Huang, P. -J.; Wang, J.; Chang, I. Y. -F.; Yeh, Y. -M.; Chen, C. -D.; Li, H. -P.; Luo, J. -D.; Tan, B. C. -M.; Chan, T. E. H.; Hsueh, C.; Chu, L. J.; Chen, Y. -T.; Zhang, B.; Yang, C. -Y.; Wu, C. -C.; Hsu, C. -W.; See, L. -C.; Tang, P.; Yu, J. -S.; Liao, W. -C.; Chiang, W. -F.; Rodriguez, H.; Myers, J. N.; Chang, K. -P.; Chang, Y. -S.

APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism Journal Article

In: Nature Communications, 8 (1), 2017, ISSN: 20411723, (cited By 52).

Abstract | Links | BibTeX | 標籤: Adult; Asian Continental Ancestry Group; Biomarkers, allele; biomarker; cancer; gene; gene expression; mutation; organic nitrogen compound; polymorphism; protein; survival, Genetic; Proteins; Sequence Deletion; Taiwan, human; cytidine deaminase; protein; tumor marker, Neoplastic; Germ-Line Mutation; Humans; Kaplan-Meier Estimate; Male; Middle Aged; Mouth Neoplasms; Polymorphism, Squamous Cell; Cohort Studies; Cytidine Deaminase; Female; Gene Expression Regulation, Taiwan, Tumor; Carcinoma

Chen, T. -W.; Gan, R. -C.; Fang, Y. -K.; Chien, K. -Y.; Liao, W. -C.; Chen, C. -C.; Wu, T. H.; Chang, I. Y. -F.; Yang, C.; Huang, P. -J.; Yeh, Y. -M.; Chiu, C. -H.; Huang, T. -W.; Tang, P.

FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation Journal Article

In: Scientific Reports, 7 (1), 2017, ISSN: 20452322, (cited By 20).

Abstract | Links | BibTeX | 標籤:

Lin, C. -C.; Lee, C. -C.; Lin, S. -H.; Huang, P. -J.; Li, H. -P.; Chang, Y. -S.; Tang, P.; Chao, M.

RNA recombination in Hepatitis delta virus: Identification of a novel naturally occurring recombinant Journal Article

In: Journal of Microbiology, Immunology and Infection, 50 (6), pp. 771-780, 2017, ISSN: 16841182, (cited By 10).

Abstract | Links | BibTeX | 標籤: Base Sequence; Genome, Genetic; RNA; RNA, genome; genotype; Hepatitis delta virus; Japan; RNA recombination; virus identification; virus strain; classification; delta agent hepatitis; genetic recombination; genetics; Hepatitis delta virus; human; nucleotide sequence; phylogeny; sequence analysis; Viet Nam; virology; virus genome, recombinant; virus RNA, RNA; RNA, RNA; Vietnam, Viral; Genotype; Hepatitis D; Hepatitis Delta Virus; Humans; Japan; Phylogeny; Recombination, Viral; Sequence Analysis

Cheng, W. -H.; Huang, K. -Y.; Huang, P. -J.; Lee, C. -C.; Yeh, Y. -M.; Ku, F. -M.; Lin, R.; Cheng, M. -L.; Chiu, C. -H.; Tang, P.

γ-Carboxymuconolactone decarboxylase: A novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis Journal Article

In: Parasites and Vectors, 10 (1), 2017, ISSN: 17563305, (cited By 2).

Abstract | Links | BibTeX | 標籤: Basal Bodies; Benzoates; Carboxy-Lyases; Cell Cycle; Iron; Protozoan Proteins; Trichomonas vaginalis, carboxylyase; gamma carboxymuconolactone decarboxylase; iron; nocodazole; unclassified drug; 4-carboxymuconolactone decarboxylase; benzoic acid derivative; carboxylyase; iron; protozoal protein

Bradic, M.; Warring, S. D.; Tooley, G. E.; Scheid, P.; Secor, W. E.; Land, K. M.; Huang, P. -J.; Chen, T. -W.; Lee, C. -C.; Tang, P.; Sullivan, S. A.; Carlton, J. M.

Genetic indicators of drug resistance in the highly repetitive genome of trichomonas vaginalis Journal Article

In: Genome Biology and Evolution, 9 (6), pp. 1658-1672, 2017, ISSN: 17596653, (cited By 25).

Abstract | Links | BibTeX | 標籤: antiprotozoal agent; protozoal protein, Antiprotozoal Agents; Drug Resistance; Female; Genome, classification; drug effects; drug resistance; female; gene linkage disequilibrium; genetic recombination; genetics; genome; human; parasitology; phylogeny; single nucleotide polymorphism; Trichomonas vaginalis; vaginal trichomoniasis, Genetic; Trichomonas vaginalis; Trichomonas Vaginitis, Protozoan; Humans; Linkage Disequilibrium; Phylogeny; Polymorphism, Single Nucleotide; Protozoan Proteins; Recombination

Sablok, G.; Chen, T. -W.; Lee, C. -C.; Yang, C.; Gan, R. -C.; Wegrzyn, J. L.; Porta, N. La; Nayak, K. C.; Huang, P. -J.; Varotto, C.; Tang, P.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications Journal Article

In: DNA Research, 24 (3), pp. 327-332, 2017, ISSN: 13402838, (cited By 1).

Abstract | Links | BibTeX | 標籤: Chloroplast; Genome, Chloroplasts; Codon; Eukaryota; Evolution, codon, Mitochondrial; Genomics; Mitochondria; Software, Molecular; Genome


Gan, R. -C.; Chen, T. -W.; Wu, T. H.; Huang, P. -J.; Lee, C. -C.; Yeh, Y. -M.; Chiu, C. -H.; Huang, H. -D.; Tang, P.

PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms Journal Article

In: BMC Bioinformatics, 17 , 2016, ISSN: 14712105, (cited By 3).

Abstract | Links | BibTeX | 標籤: animal; biological model; Cnidaria; comparative study; gene expression profiling; genetics; genomics; high throughput sequencing; Internet; molecular genetics; procedures; sequence analysis; software, Animals; Cnidaria; Gene Expression Profiling; Genomics; High-Throughput Nucleotide Sequencing; Internet; Models, Biological; Molecular Sequence Annotation; Sequence Analysis, Birds; Gene expression; RNA; Websites, Functional annotation; Gene expression profiles; Next-generation sequencing; Quantification methods; Transcriptome assemblies; Transcriptome profiles; Transcriptome quantifications; Transcriptomes, RNA; Software; Transcriptome, transcriptome, Web services

Fang, Y. -K.; Chien, K. -Y.; Huang, K. -Y.; Cheng, W. -H.; Ku, F. -M.; Lin, R.; Chen, T. -W.; Huang, P. -J.; Chiu, C. -H.; Tang, P.

Responding to a Zoonotic Emergency with Multi-omics Research: Pentatrichomonas hominis Hydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics Journal Article

In: OMICS A Journal of Integrative Biology, 20 (11), pp. 662-669, 2016, ISSN: 15362310, (cited By 8).

Abstract | Links | BibTeX | 標籤: Animals; Cats; Dogs; Humans; Mass Spectrometry; Organelles; Proteome; Proteomics; Protozoan Infections; Protozoan Proteins; Sequence Analysis, proteome; protozoal protein; protozoal RNA; proteome; protozoal protein, RNA; Trichomonadida; Zoonoses


Fang, Y. -K.; Huang, K. -Y.; Huang, P. -J.; Lin, R.; Chao, M.; Tang, P.

Gene-expression analysis of cold-stress response in the sexually transmitted protist Trichomonas vaginalis Journal Article

In: Journal of Microbiology, Immunology and Infection, 48 (6), pp. 662-675, 2015, ISSN: 16841182, (cited By 13).

Abstract | Links | BibTeX | 標籤: Base Sequence; Cold-Shock Response; DNA, development and aging; human; metabolism; microbiology; nucleotide sequence; ubiquitination; vaginal trichomoniasis, DNA; Trichomonas vaginalis; Trichomonas Vaginitis; Ubiquitination, hydrogen peroxide; iron; messenger RNA; proteasome; sulfur; ubiquitin; hydrogen peroxide; protozoal DNA, Protozoan; Energy Metabolism; Expressed Sequence Tags; Female; Gene Library; Humans; Hydrogen Peroxide; Sequence Analysis

Huang, K. -Y.; Ku, F. -M.; Cheng, W. -H.; Lee, C. -C.; Huang, P. -J.; Chu, L. J.; Cheng, C. -C.; Fang, Y. -K.; Wu, H. -H.; Tang, P.

Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis Journal Article

In: Antimicrobial Agents and Chemotherapy, 59 (11), pp. 6891-6903, 2015, ISSN: 00664804, (cited By 5).

Abstract | Links | BibTeX | 標籤: amino acid transfer RNA ligase; carbohydrate; reactive oxygen metabolite; reduced nicotinamide adenine dinucleotide dehydrogenase; tetracycline; transcriptome; antitrichomonal agent; tetracycline, Antitrichomonal Agents; Cell Death; Glycolysis; High-Throughput Nucleotide Sequencing; Tetracycline; Trichomonas vaginalis

Chen, T. -W.; Gan, R. -C.; Chang, Y. -F.; Liao, W. -C.; Wu, T. H.; Lee, C. -C.; Huang, P. -J.; Lee, C. -Y.; Chen, Y. -Y. M.; Chiu, C. -H.; Tang, P.

Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing Journal Article

In: BMC Genomics, 16 (1), 2015, ISSN: 14712164, (cited By 4).

Abstract | Links | BibTeX | 標籤: Bacteria (microorganisms); Escherichia coli; Streptococcus parasanguinis, Bacterial; Genome, Bacterial; High-Throughput Nucleotide Sequencing; INDEL Mutation; Reference Standards; Streptococcus, Base Pair Mismatch; Base Pairing; Contig Mapping; Escherichia coli; Gene Library; Genes, genomic DNA

Cheng, W. -H.; Huang, K. -Y.; Huang, P. -J.; Hsu, J. -H.; Fang, Y. -K.; Chiu, C. -H.; Tang, P.

Nitric oxide maintains cell survival of Trichomonas vaginalis upon iron depletion Journal Article

In: Parasites and Vectors, 8 (1), 2015, ISSN: 17563305, (cited By 10).

Abstract | Links | BibTeX | 標籤: 1', 3, 3'-tetraethylbenzimidazolocarbocyanine; benzimidazole derivative; benzyloxycarbonylleucyl-leucyl-leucine aldehyde; carbocyanine; enzyme inhibitor; iron; leupeptin; n(g) methylarginine; nitric oxide; nitric oxide synthase; protozoal protein; reactive oxygen metabolite; transcriptome, 5', 6, 6'-tetrachloro-1, Adaptation, arginine; benzyloxycarbonylleucylleucylleucinal; iron; n(g) methylarginine; nitric oxide; proteasome; reactive nitrogen species; reactive oxygen metabolite; transcriptome; 5, Biological; Nitric Oxide; Nitric Oxide Synthase; omega-N-Methylarginine; Protozoan Proteins; Reactive Oxygen Species; Sequence Analysis, Physiological; Animals; Base Sequence; Benzimidazoles; Carbocyanines; Cell Survival; Enzyme Inhibitors; High-Throughput Nucleotide Sequencing; Humans; Iron; Leupeptins; Models, RNA; Transcriptome; Trichomonas Infections; Trichomonas vaginalis

Huang, P. -J.; Lee, C. -C.; Tan, B. C. -M.; Yeh, Y. -M.; Chu, L. J.; Chen, T. -W.; Chang, K. -P.; Lee, C. -Y.; Gan, R. -C.; Liu, H.; Tang, P.

CMPD: Cancer mutant proteome database Journal Article

In: Nucleic Acids Research, 43 (D1), pp. D849-D855, 2015, ISSN: 03051048, (cited By 7).

Abstract | Links | BibTeX | 標籤: Cell Line, mutant protein; proteome; tumor protein, Protein; Humans; Internet; Mutant Proteins; Mutation; Neoplasm Proteins; Neoplasms; Proteome, Tumor; Databases

Chen, S. -J.; Liu, H.; Liao, C. -T.; Huang, P. -J.; Huang, Y.; Hsu, A.; Tang, P.; Chang, Y. -S.; Chenx, H. -C.; Yen, T. -C.

Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature Journal Article

In: Oncotarget, 6 (20), pp. 18066-18080, 2015, ISSN: 19492553, (cited By 37).

Abstract | Links | BibTeX | 標籤: 4, 5 trisphosphate 3 phosphatase; protein p53; protein tyrosine phosphatase SHP 2; Smad4 protein; tumor marker, Adult; Aged; Biomarkers, B Raf kinase; cyclin dependent kinase inhibitor 2A; fibroblast growth factor receptor 3; Notch1 receptor; phosphatidylinositol 3, Tumor; Carcinoma

Huang, P. -J.; Lee, C. -C.; Tan, B. C. -M.; Yeh, Y. -M.; Huang, K. -Y.; Gan, R. -C.; Chen, T. -W.; Lee, C. -Y.; Yang, S. -T.; Liao, C. -S.; Liu, H.; Tang, P.

Vanno: A visualization-aided variant annotation tool Journal Article

In: Human Mutation, 36 (2), pp. 167-174, 2015, ISSN: 10597794, (cited By 4).

Abstract | Links | BibTeX | 標籤: Data Curation; Exome; Genome, DNA; Software, Human; Genomics; High-Throughput Nucleotide Sequencing; Humans; Molecular Sequence Annotation; Sequence Analysis


Chen, T. -W.; Li, H. -P.; Lee, C. -C.; Gan, R. -C.; Huang, P. -J.; Wu, T. H.; Lee, C. -Y.; Chang, Y. -F.; Tang, P.

ChIPseek, a web-based analysis tool for ChIP data Journal Article

In: BMC Genomics, 15 (1), 2014, ISSN: 14712164, (cited By 45).

Abstract | Links | BibTeX | 標籤: activating transcription factor 2; activating transcription factor 3; transcription factor Ets 1; transcription factor GATA 1, Animals; Chromatin Immunoprecipitation; Computational Biology; Genomics; High-Throughput Nucleotide Sequencing; Humans; Software; Web Browser, Arabidopsis; Danio rerio; Rattus; Rhacophorus; Schizosaccharomycetaceae


Huang, P. -J.; Yeh, Y. -M.; Gan, R. -C.; Lee, C. -C.; Chen, T. -W.; Lee, C. -Y.; Liu, H.; Chen, S. -J.; Tang, P.

CPAP: Cancer panel analysis pipeline Journal Article

In: Human Mutation, 34 (10), pp. 1340-1346, 2013, ISSN: 10597794, (cited By 3).

Abstract | Links | BibTeX | 標籤: Biological; Web Browser, cancer panel; Circos; ion torrent; target sequencing, Computational Biology; Databases, Genetic; Humans; Neoplasms; Software; Tumor Markers

Hackenberg, M.; Huang, P. -J.; Huang, C. -Y.; Shi, B. -J.; Gustafson, P.; Langridge, P.

A Comprehensive expression profile of micrornas and other classes of non-coding small RNAs in barley under phosphorous-deficient and-sufficient conditions Journal Article

In: DNA Research, 20 (2), pp. 109-125, 2013, ISSN: 13402838, (cited By 67).

Abstract | Links | BibTeX | 標籤: Base Sequence; Gene Expression Regulation, Chloroplast; Hordeum; MicroRNAs; Phosphorus; RNA, Hordeum; Hordeum vulgare subsp. vulgare, microRNA; phosphorus; RNA induced silencing complex; small interfering RNA; transfer RNA, Plant; Genome, Plant; RNA, RNA; Transcriptome, Small Untranslated; Sequence Analysis

Huang, K. -Y.; Shin, J. -W.; Huang, P. -J.; Ku, F. -M.; Lin, W. -C.; Lin, R.; Hsu, W. -M.; Tang, P.

Functional profiling of the Tritrichomonas foetus transcriptome and proteome Journal Article

In: Molecular and Biochemical Parasitology, 187 (1), pp. 60-71, 2013, ISSN: 01666851, (cited By 12).

Abstract | Links | BibTeX | 標籤: article; expressed sequence tag; matrix assisted laser desorption ionization time of flight mass spectrometry; nonhuman; priority journal; protein domain; protein expression; protein motif; ribosome; Tritrichomonas foetus; two dimensional electrophoresis, complementary DNA; proteome; transcriptome, Electrophoresis, Gel, Mass, Matrix-Assisted Laser Desorption-Ionization; Transcriptome; Tritrichomonas foetus, Two-Dimensional; Expressed Sequence Tags; Proteome; Protozoan Proteins; Spectrometry


Huang, K-Y.; Huang, P. -J.; Ku, F. -M.; Lin, R.; Alderete, J. F.; Tanga, P.

Comparative transcriptomic and proteomic analyses of Trichomonas vaginalis following adherence to fibronectin Journal Article

In: Infection and Immunity, 80 (11), pp. 3900-3911, 2012, ISSN: 00199567, (cited By 27).

Abstract | Links | BibTeX | 標籤: article; cell adhesion; gene expression profiling; gene library; nonhuman; priority journal; protein binding; protein expression; proteomics; sequence analysis; transcriptomics; Trichomonas vaginalis; trophozoite; upregulation, Cell Adhesion; Electrophoresis, complementary DNA; cysteine proteinase; fibronectin; glyceraldehyde 3 phosphate; glyceraldehyde 3 phosphate dehydrogenase; heat shock protein, Gel, Messenger; Signal Transduction; Transcriptome; Trichomonas vaginalis, Two-Dimensional; Fibronectins; Gene Expression Profiling; Mass Spectrometry; Proteome; Proteomics; Protozoan Proteins; Real-Time Polymerase Chain Reaction; RNA

Huang, P. -J.; Lin, W. -C.; Chen, S. -C.; Lin, Y. -H.; Sun, C. -H.; Lyu, P. -C.; Tang, P.

Identification of putative miRNAs from the deep-branching unicellular flagellates Journal Article

In: Genomics, 99 (2), pp. 101-107, 2012, ISSN: 08887543, (cited By 29).

Abstract | Links | BibTeX | 標籤: Animalia; Eukaryota; Giardia intestinalis; Mastigophora (flagellates); Pentatrichomonas hominis; Protista; Trichomonas vaginalis; Tritrichomonas foetus, article; bioinformatics; controlled study; flagellate; gene control; gene expression profiling; Giardia lamblia; high throughput sequencing; nonhuman; priority journal; reverse transcription polymerase chain reaction; trichomonas hominis; Trichomonas vaginalis; Tritrichomonas foetus; trophozoite, Chromosome Mapping; Gene Expression Profiling; Giardia lamblia; High-Throughput Nucleotide Sequencing; MicroRNAs; Real-Time Polymerase Chain Reaction; RNA, DNA; Trichomonadida, microRNA, Protozoan; Sequence Analysis

Chen, T. W.; Gan, R. C.; Wu, T. H.; Huang, P. J.; Lee, C. Y.; Chen, Y. Y.; Chen, C. C.; Tang, P.

FastAnnotator--an efficient transcript annotation web tool. Journal Article

In: BMC genomics, 13 Suppl 7 , 2012, ISSN: 14712164, (cited By 48).

Abstract | Links | BibTeX | 標籤: animal; article; bacterial genome; Caenorhabditis elegans; computer interface; computer program; genetic database; genetics; genome; Internet; nucleotide sequence; Streptococcus, Animals; Base Sequence; Caenorhabditis elegans; Databases, Bacterial; Internet; Software; Streptococcus; Transcriptome; User-Computer Interface, Genetic; Genome; Genome, transcriptome

Horváthová, L.; Šafaříková, L.; Basler, M.; Hrdý, I.; Campo, N. B.; Shin, J. -W.; Huang, K. -Y.; Huang, P. -J.; Lin, R.; Tang, P.; Tachezy, J.

Transcriptomic identification of iron-regulated and iron-independent gene copies within the heavily duplicated trichomonas vaginalis genome Journal Article

In: Genome Biology and Evolution, 4 (10), pp. 1017-1029, 2012, ISSN: 17596653, (cited By 45).

Abstract | Links | BibTeX | 標籤: article; DNA microarray; expressed sequence tag; gene; gene dosage; gene duplication; gene expression regulation; gene library; genetics; genome; glycolysis; metabolism; molecular evolution; Trichomonas vaginalis, Cysteine Proteases; Evolution, cysteine proteinase; iron; iron sulfur protein; transcriptome, Eukaryota; Protista; Trichomonadida; Trichomonas; Trichomonas vaginalis, Molecular; Expressed Sequence Tags; Gene Dosage; Gene Duplication; Gene Expression Regulation; Gene Library; Genes, Protozoan; Genome, Protozoan; Glycolysis; Iron; Iron-Sulfur Proteins; Oligonucleotide Array Sequence Analysis; Transcriptome; Trichomonas vaginalis


Huang, P. -J.; Liu, Y. -C.; Lee, C. -C.; Lin, W. -C.; Gan, R. R. -C.; Lyu, P. -C.; Tang, P.

DSAP: Deep-sequencing small RNA analysis pipeline Journal Article

In: Nucleic Acids Research, 38 (SUPPL. 2), pp. W385-W391, 2010, ISSN: 03051048, (cited By 77).

Abstract | Links | BibTeX | 標籤: article; automation; bioinformatics; chicken; client server application; gene expression; nonhuman; nucleotide sequence; priority journal; RNA analysis; RNA sequence; sequence database; sequence homology; species comparison; chemistry; computer program; Internet; metabolism; sequence analysis, Internet; MicroRNAs; RNA, microRNA; RNA; untranslated RNA, RNA; Software, Untranslated; Sequence Analysis


Lin, W. -C.; Huang, K. -Y.; Chen, S. -C.; Huang, T. -Y.; Chen, S. -J.; Huang, P. -J.; Tang, P.

Malate dehydrogenase is negatively regulated by miR-1 in Trichomonas vaginalis Journal Article

In: Parasitology Research, 105 (6), pp. 1683-1689, 2009, ISSN: 09320113, (cited By 16).

Abstract | Links | BibTeX | 標籤: Animals; Base Sequence; Down-Regulation; Gene Expression Profiling; Gene Expression Regulation; Malate Dehydrogenase; MicroRNAs; Molecular Sequence Data; Proteome; Trichomonas vaginalis, article; bioinformatics; controlled study; enzyme regulation; gene; gene control; genetic transfection; miR 1 gene; nonhuman; nucleotide sequence; priority journal; protein targeting; proteomics; protozoal genetics; transcriptomics; Trichomonas vaginalis; trophozoite; tv mdh gene, malate dehydrogenase; microRNA, Protista; Trichomonas vaginalis

Lin, W. -C.; Li, S. -C.; Lin, W. -C.; Shin, J. -W.; Hu, S. -N.; Yu, X. -M.; Huang, T. -Y.; Chen, S. -C.; Chen, H. -C.; Chen, S. -J.; Huang, P. -J.; Gan, R. Ruei-Chi; Chiu, C. -H.; Tang, P.

Identification of microRNA in the protist Trichomonas vaginalis Journal Article

In: Genomics, 93 (5), pp. 487-493, 2009, ISSN: 08887543, (cited By 59).

Abstract | Links | BibTeX | 標籤: Amino Acid Sequence; Animals; Base Sequence; Chromosome Mapping; Cloning, article; bioinformatics; gene expression; gene identification; molecular cloning; nonhuman; nucleotide sequence; parasite cultivation; priority journal; protist life cycle stage; real time polymerase chain reaction; sequence homology; serial analysis of gene expression; Trichomonas vaginalis, microRNA, Molecular; Gene Expression Regulation; Genome, Protista; Trichomonas vaginalis, Protozoan; MicroRNAs; Molecular Sequence Data; Nucleic Acid Conformation; Trichomonas vaginalis

Huang, K. -Y.; Chien, K. -Y.; Lin, Y. -C.; Hsu, W. -M.; Fong, I. -K.; Huang, P. -J.; Yueh, Y. -M.; Gan, R. R. -C.; Tang, P.

A proteome reference map of Trichomonas vaginalis Journal Article

In: Parasitology Research, 104 (4), pp. 927-933, 2009, ISSN: 09320113, (cited By 32).

Abstract | Links | BibTeX | 標籤: Animals; Databases, Computer-Assisted; Proteome; Proteomics; Protozoan Proteins; Reference Standards; Spectrometry, cysteine proteinase; cytoskeleton protein; proteome; proteome; protozoal protein, development and aging; human; image processing; mass spectrometry; metabolism; protein database; proteomics; standard; trophozoite; two dimensional gel electrophoresis, Gel, Mass, Matrix-Assisted Laser Desorption-Ionization; Trichomonas vaginalis; Trophozoites, Protein; Electrophoresis, Protozoa; Trichomonas vaginalis, Two-Dimensional; Female; Gene Expression Profiling; Humans; Image Processing


Lo, W. -C.; Huang, P. -J.; Chang, C. -H.; Lyu, P. -C.

Protein structural similarity search by Ramachandran codes Journal Article

In: BMC Bioinformatics, 8 , 2007, ISSN: 14712105, (cited By 42).

Abstract | Links | BibTeX | 標籤: Algorithms; Amino Acid Sequence; Database Management Systems; Databases, Amino Acid, Database searches; Expectation values; Functional annotation; Homologous structures; Protein structures; Sequence Alignment Methods; Sequence similarity; Structural similarity, Java programming language; Search engines; Tools; Web services, protein, Protein; Information Storage and Retrieval; Molecular Sequence Data; Proteins; Sequence Alignment; Sequence Analysis, Protein; Sequence Homology, Proteins