| 1. |
2024
Do DT,Yang MR,Vo TNS,Le NQK,Wu YW.
Unitig-Centered Pan-Genome Machine Learning Approach for Predicting Antibiotic Resistance and Discovering Novel Resistance Genes in Bacterial Strains
. Computational and Structural Biotechnology Journal
.2024
;(23):1864-1876
|
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| 2. |
2023
Yang MR,Wu YW.
A Cross-Validated Feature Selection approach for extracting the most parsimonious feature sets and discovering potential antimicrobial resistance (AMR) biomarkers
. Computational and Structural Biotechnology Journal
.2023
;(21):769-779
|
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| 3. |
2023
Subburaj S,Yeh CH,Patel B,Huang TH,Hung WS,Chang CY, Wu YW, Lin PT.
K-mer-Based Human Gesture Recognition (KHGR) Using Curved Piezoelectric Sensor
. Electronics
.2023
;(12):210
|
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| 4. |
2023
Jian BS,Chiou SL,Hsu CC,Ho J,Wu YW,Chu J.
Bioinformatic Analysis Reveals both Oversampled and Underexplored Biosynthetic Diversity in Nonribosomal Peptides
. ACS Chemical Biology
.2023
;(18):476-483
|
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| 5. |
2023
Shao YH,Wu YW,Naufal M,Wu JH.
Genome-centered metagenomics illuminates adaptations of core members to a partial Nitritation–Anammox bioreactor under periodic microaeration
. Frontiers in Microbiology
.2023
;(14):1046769
|
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| 6. |
2023
Sufriyana H,Wu YW,Su ECY.
Human-guided deep learning with ante-hoc explainability by convolutional network from non-image data for pregnancy prognostication
. Neural Networks
.2023
;(162):99-116
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| 7. |
2023
Yang MR,Su SF,Wu YW.
Using bacterial pan-genome-based feature selection approach to improve the prediction of minimum inhibitory concentration (MIC)
. Frontiers in Genetics
.2023
;(14):1054032
|
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| 8. |
2023
Wang TY,Goh KS,Wang LJ,Wu LL,Wang FY,Wu YW.
Long-Read Genome Sequencing of Abscondita cerata (Coleoptera: Lampyridae), the Endemic Firefly of Taiwan
. Zoological Studies
.2023
;(62):e25
|
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| 9. |
2023
Huang ZJ,Patel B,Lu WH,Yang TY,Tung WC,Bučinskas V, Greitans M, Wu YW, Lin PT.
Yeast cell detection using fuzzy automatic contrast enhancement (FACE) and you only look once (YOLO)
. Scientific Reports
.2023
;(13):16222
|
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| 10. |
2023
Chen SJ,Wu YJ,Chen CC,Wu YW,Liou JM,Wu MS, Kuo CH, Lin CH.
Plasma metabolites of aromatic amino acids associate with clinical severity and gut microbiota of Parkinson’s disease
. npj Parkinson's disease
.2023
;(9):165
|
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| 11. |
2022
Chen SJ,Chen CC,Liao HY,Lin YT,Wu YW,Liou JM, Wu MS, Kuo CH, Lin CH.
Association of Fecal and Plasma Levels of Short-Chain Fatty Acids With Gut Microbiota and Clinical Severity in Parkinson Disease Patients
. Neurology
.2022
;(98):e848-e858
|
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| 12. |
2022
Wang PH,Chen YL,Wu TY,Wu YW,Wang TY,Shih CJ, Wei STS, Lai YL, Liu CX, Chiang YR.
Omics and mechanistic insights into di-(2-ethylhexyl) phthalate degradation in the O2-fluctuating estuarine sediments
. Chemosphere
.2022
;(299):134406
|
|
| 13. |
2022
Yang MR,Wu YW.
Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach
. BMC Bioinformatics
.2022
;(15):131
|
|
| 14. |
2022
Do DT,Yang MR,Lam LHT,Le NQK,Wu YW.
Improving MGMT methylation status prediction of glioblastoma through optimizing radiomics features using genetic algorithm-based machine learning approach
. Scientific Reports
.2022
;(12):13412
|
|
| 15. |
2022
Sufriyana H,Salim HM,Muhammad AR,Wu YW,Su ECY.
Blood biomarkers representing maternal-fetal interface tissues used to predict early-and late-onset preeclampsia but not COVID-19 infection
. Computational aand Structural Biotechnology Journal
.2022
;(20):4206-4224
|
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| 16. |
2022
Tom LM,Aulitto M,Wu YW,Deng K,Gao Y,Xiao N, Rodriguez BG, Louime C, Northen TR, Eudes A, Mortimer JC, Adams PD, Scheller HV, Simmons BA, Ceja-Navarro JA, Singer SW.
Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction
. Microbiome
.2022
;(10):183
|
|
| 17. |
2021
Gómez-Luciano LB,Wu YW,Chiang CM,Chang TS,Wu JY,Wang TY.
Complete Genome Sequence of the Soil-Isolated Psychrobacillus sp. Strain AK 1817, Capable of Biotransforming the Ergostane Triterpenoid Antcin K
. Microbiology Resource Annnouncements
.2021
;(10):e0124220
|
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| 18. |
2021
Chang TS,Chiang CM,Wang ZY,Tsai YL,Wu YW,Ting HJ, Wu JY.
One-Pot Bi-Enzymatic Cascade Synthesis of Novel Ganoderma Triterpenoid Saponins
. Catalysis
.2021
;(11):580
|
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| 19. |
2021
Wu YW,Singer SW.
Recovering Individual Genomes from Metagenomes Using MaxBin 2.0
. Current Protocols
.2021
;(1):e128
|
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| 20. |
2021
Characterization of the complete mitochondrial genome of Abscondita cerata (Olivier, 1911) (Coleoptera: Lampyridae) and its phylogenetic implications
. Mitochondrial DNA B Resource
.2021
;(6):2528-2530
|
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| 21. |
2021
Chang TS,Wang TY,Chiang CM,Lin YJ,Chen HL,Wu YW, Ting HJ, Wu JY.
Biotransformation of celastrol to a novel, well-soluble, low-toxic and anti-oxidative celastrol-29-O-β-glucoside by Bacillus glycosyltransferases
. Journal of bioscience and bioengineering
.2021
;(131):176-182
|
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| 22. |
2021
Chen CC,Lin CH,Hao WR,Yeh JS,Chiang KH,Fang YA, Chiu CC, Yang TY, Wu YW, Liu JC.
Influenza vaccination and the risk of ventricular arrhythmias in patients with chronic obstructive pulmonary disease: a population-based longitudinal study
. Frontiers in Cardiovascular Medicine
.2021
;(8):731844
|
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| 23. |
2021
Her HL,Lin PT,Wu YW.
PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains
. BMC Bioinformatics
.2021
;(22):548
|
|
| 24. |
2021
Wei STS,Chen YL,Wu YW,Wu TY,Lai YL,Wang PH, Ismail W, Lee TH, Chiang YR.
Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments
. mSystems
.2021
;(6):e0035821
|
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| 25. |
2020
Sufriyana H,Wu YW,Su ECY.
Prediction of Preeclampsia and Intrauterine Growth Restriction: Development of Machine Learning Models on a Prospective Cohort
. JMIR Medical Informatics
.2020
;(8):e15411
|
|
| 26. |
2020
Sufriyana H,Wu YW,Su ECY.
Artificial intelligence-assisted prediction of preeclampsia: Development and external validation of a nationwide health insurance dataset of the BPJS Kesehatan in Indonesia
. EBioMedicine
.2020
;(54):102710
|
|
| 27. |
2020
Huang YH,Wu YW,Chuang JY,Chang YC,Chang HF,Tao PL, Loh HH, Yeh SH.
Morphine produces potent antinociception, sedation, and hypothermia in humanized mice expressing human mu-opioid receptor splice variants
. Pain
.2020
;(161):1177-1190
|
|
| 28. |
2020
Chi NF,Chang TH,Lee CY,Wu YW,Shen TA,Chan L, Chen YR, Chiou HY, Hsu CY, Hu CJ.
Untargeted metabolomics predicts the functional outcome of ischemic stroke
. Journal of the Formosan Medical Association
.2020
;(120):234-241
|
|
| 29. |
2020
Sufriyana H,Husnayain A,Chen YL,Kuo CY,Singh O,Yeh TY, Wu YW, Su ECY.
Comparison of Multivariable Logistic Regression and Other Machine Learning Algorithms for Prognostic Prediction Studies in Pregnancy Care: Systematic Review and Meta-Analysis
. JMIR Medical Informatics
.2020
;(8):e16503
|
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| 30. |
2020
Wu WK,Panyod S,Liu PY,Chen CC,Kao HL,Chuang HL, Chen YH, Zou HB, Kuo HC, Kuo CH, Liao BY, Chiu THT, Chung CH, Lin AYC, Lee YC, Tang SL, Wang JT, Wu YW, Hsu CC, Sheen LY, Orekhov AN, Wu MS.
Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery
. Microbiome
.2020
;(8):162
|
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| 31. |
2019
Chaw SM,Liu YC,Wu YW,Wang HY,Lin CY,Wu CS, Ke HM, Chang LY, Hsu CY, Yang HT, Sudianto E, Hsu MH, Wu KP, WangLN, Leebens-Mack J, Tsai I.
Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution
. Nature Plants
.2019
;(5):63-73
|
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| 32. |
2019
Yang SH,Tandon K,Lu CY,Wada N,Shih CJ,Hsiao SSY, Jane WN, Lee TC, Yang CM, Liu CT, Denis V, Wu YT, Wang LT, Huang L, Lee DC, Wu YW, Yamashiro H, Tang SL.
Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera.
. Microbiome
.2019
;(7):3
|
|
| 33. |
2019
Kothari A,Wu YW,Chandonia JM,Charrier M,Rajeev L,Rocha A, Joyner D, Hazen T, Singer SW, Mukhopadhyay A.
Large circular plasmids from groundwater plasmidomes span multiple incompatibility groups and are enriched in multi-metal resistance genes
. mBio
.2019
;(10):e02899-18
|
|
| 34. |
2019
Wu YW,Yang SH,Hwangbo M,Chu KH.
Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system
. PLoS ONE
.2019
;(14):e0222143
|
|
| 35. |
2019
Chang TS,Chiang CM,Kao YH,Wu JY,Wu YW,Wang TY.
A New Triterpenoid Glucoside from a Novel Acidic Glycosylation of Ganoderic Acid A via Recombinant Glycosyltransferase of Bacillus subtilis
. Molecules
.2019
;(24):3457
|
|
| 36. |
2019
Chang TS,Wang TY,Heueh TY,Lee YW,Chuang HM,Cai WX, Wu JY, Chiang CM, and Wu YW.
A Genome-Centric Approach Reveals a Novel Glycosyltransferase from the GA A07 Strain of Bacillus thuringiensis Responsible for Catalyzing 15-O-Glycosylation of Ganoderic Acid A
. International Journal of Molecular Sciences
.2019
;(20):5192
|
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| 37. |
2018
Kolinko S,Wu YW,Tachea F,Denzel E,Hiras J,Gabriel R, Bäcker N, Chan LJ, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW.
A bacterial pioneer produces cellulase complexes that persist through community succession
. Nature Microbiology
.2018
;(3):99-107
|
|
| 38. |
2018
Wu YW.
ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes
. BMC Genomics
.2018
;(19):921
|
|
| 39. |
2018
Beller H,Rodrigues AV,Zargar K,Wu YW,Saini AK,Saville RM, Pereira JH, Adams PD, Tringe SG, Petzold CJ, and Keasling JD.
Enzyme discovery for toluene synthesis in anoxic microbial communities
. Nature Chemical Biology
.2018
;(14):451-457
|
|
| 40. |
2018
Her HL,Wu YW.
A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains
. Bioinformatics
.2018
;(34):i89-i95
|
|
| 41. |
2018
Kimbrel J,Ballor N,Wu YW,David M,Hazen T,Simmons B, Singer S, and Jansson J.
Microbial community structure and functional potential along a hypersaline gradient
. Frontiers in Microbiology
.2018
;(9):1492
|
|
| 42. |
2018
Wu YW,Li YJ.
Development and implementation of computational models provides solutions for biomedical community
. Computer Methods and Programs in Biomedicine
.2018
;(159):A1
|
|
| 43. |
2018
Liang X,Whitman J,Holwerda EK,Shao X,Tian L,Wu YW, Lombard V, Henrissat B, Klingeman DM, Yang ZK, Podar M, Richard TL, Elkins JG, Brown SD, Lynd LR.
Development and Characterization of Stable Anaerobic Thermophilic Methanogenic Microbiomes Fermenting Switchgrass at Decreasing Residence Times
. Biotechnology for Biofuels
.2018
;(11):243
|
|
| 44. |
2018
Wei S,Wu YW,Lee TH,Huang YS,Yang CY,Chen YL, Chiang YR.
Microbial functional responses to cholesterol catabolism in denitrifying sludge
. mSystems
.2018
;(3):e00113-18
|
|
| 45. |
2017
Sczyrba A,Hofmann P,Belmann P,Koslicki D,Janssen S,Dröge J; Gregor I; Majda S; Fiedler J; Dahms E; Bremges A; Fritz A; Garrido-Oter R; Jørgensen TS; Shapiro N; Blood PD; Gurevich A; Bai Y; Turaev D; DeMaere MZ; Chikhi R; Nagarajan N; Quince C; Meyer F.
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
. Nature Methods
.2017
;(14):1063-1071
|
|
| 46. |
2017
Wu YW,Shao Y,Khanipov K,Golovko G,Pimenova M,Fofanov Y, Chu KH.
Draft Genome Sequence of Zobellella denitrificans ZD1 (JCM 13380), a salt-tolerant denitrifying bacterium capable of producing poly(3-hydroxybutyrate)
. Genome Announcements
.2017
;(5):00948-17
|
|
| 47. |
2016
Wu YW,Higgins B,Yu C,Reddy AP,Ceballos S,Joh LD, Simmons BA, Singer SW, VanderGheynst JS.
Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis
. mSystems
.2016
;(1):e00120-16
|
|
| 48. |
2016
Wu YW,Simmons BA,Singer SW.
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
. Bioinformatics
.2016
;(32):605-607
|
|
| 49. |
2016
Kothari A,Charrier M,Wu YW,Malfatti S,Zhou CE,Singer SW, Dugan L, Mukhopadhyay A.
Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization
. FEMS Microbiology Letters
.2016
;(363):fnw224
|
|
| 50. |
2016
Hiras J,Wu YW,Deng K,Nicora CD,Aldrich JT,Frey D, Kolinko S, Robinson ER, Jacobs JM, Adams P, Northen T, Simmons BA, Singer SW.
Comparative community proteomics demonstrates the unexpected importance of an actinobacterial glycoside hydrolase family 12 for crystalline cellulose hydrolysis
. mBIO
.2016
;(7):e01106-e01116
|
|
| 51. |
2016
Hiras J,Wu YW,Eichorst SA,Simmons BA,Singer SW.
Refining the Phylum Chlorobi by Resolving the Phylogeny and Metabolic Potential of the Representative of a Deeply Branching, Uncultivated Lineage
. ISME
.2016
;(10):833-845
|
|
| 52. |
2015
Nelson W,Maezato Y,Wu YW,Romine M,Lindemann S.
Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia
. Applied and Environmental Microbiology
.2015
;(82):255-267
|
|
| 53. |
2015
Lin KH,Liao BY,Chang HW,Huang SW,Chang TY,Yang CY, Wang YB, Lin YTK, Wu YW, Tang SL, Yu HT.
Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
. BMC Genomics
.2015
;(16):1029
|
|
| 54. |
2015
Wu YW,Joshua CJ,Eichorst SA,Gladden JM,Simmons BA,Singer SW.
Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia
. BioEnergy Research
.2015
;(8):1031-1035
|
|
| 55. |
2014
Wu YW,Tang YH,Tringe SG,Simmons SA,Singer SW.
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
. Microbiome
.2014
;(2):26
|
|
| 56. |
2013
Wu YW,Doak TG,Ye Y.
The gain and loss of chromosomal integron systems in the Treponema species
. BMC Evolutionary Biology
.2013
;(13):16
|
|
| 57. |
2012
Wu YW,Rho M,Doak TG,Ye Y.
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics
. Bioinformatics
.2012
;(28):i363-i369
|
|
| 58. |
2012
Wu YW,Rho M,Doak TG,Ye Y.
Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes
. Applied and Environmental Microbiology
.2012
;(78):5288-5296
|
|
| 59. |
2012
Rho M,Wu YW,Tang H,Doak TG,Ye Y.
Diverse CRISPRs evolving in human microbiomes
. PLoS Genetics
.2012
;(8):e10024
|
|
| 60. |
2011
Wu YW,Ye Y.
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
. Journal of Computational Biology
.2011
;(18):523-534
|
|
| 61. |
2010
Salmans ML,Chaw SM,Lin CP,Shih ACC,Wu YW,Mulligan MR.
Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes
. Current Genetics
.2010
;(56):439-446
|
|
| 62. |
2008
Chaw SM,Shih ACC,Wang D,Wu YW,Liu SM,Chou TY.
The Mitochondrial Genome of the Gymnosperm Cycas taitungensis Contains a Novel Family of Short Interspersed Elements, Bpu sequences, and Abundant RNA Editing Sites
. Molecular Biology and Evolution
.2008
;(25):603-615
|
|
| 63. |
2007
Wang D,Wu Y,Shih ACC,Wu CS,Wang YN,Chaw SM.
Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 million years ago
. Molecular Biology and Evolution
.2007
;(24):2040-2048
|
|
| 64. |
2007
Shih ACC,Lee DT,Peng CL,Wu YW.
Phylo-mLogo: An interactive multiple-logo visualization tool for large-number sequence alignments
. BMC Bioinformatics
.2007
;(8):63
|
|
| 65. |
2006
Shih ACC,Lee DT,Lin L,Peng CL,Chen SH,Wu YW, Wong CY, Chou MY, Shiao TC, Hsieh MF.
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools
. BMC Bioinformatics
.2006
;(7):103
|
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