吳育瑋(Wu, Yu-Wei) 助理教授

Email
yuwei.wu@tmu.edu.tw
現   職
醫學資訊研究所 助理教授

學經歷

畢業學校與學位[修業時間]
Indiana UniversitySchool of Informatics 博士
2007/08~2012/08
清華大學資訊工程系 碩士
1998/09~2000/06
東海大學資訊科學系 學士
1994/09~1997/06

本校學術經歷

任職單位與職稱[起迄時間]
醫學資訊研究所助理教授
2016/10/24~
醫學資訊研究所專案助理研究員
2016/09/20~2016/10/23

本校行政經歷

服務單位與職稱[起迄時間]
無資料!

其它經歷

任職單位與職稱[起迄時間]
中央研究院博士後研究員
2016/08/16~2016/09/19
Lawrence Berkeley National Lab,USAPostdoc
2012/09/04~2016/07/15
中央研究院研究助理
2005/03/04~2007/06/30
資訊工業策進會工程師
2000/10/01~2005/03/03

專長與研究領域

學門領域
生物資訊與醫療資訊
生物資訊與醫療資訊
學術專長

論文著作

清冊下載

論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
2012 Rho M,Wu YW,Tang H,Doak TG,Ye Y. Diverse CRISPRs evolving in human microbiomes . PLoS Genetics .2012 ;(8):e10024


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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


論文 Journal Paper
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

研究計畫

計畫名稱
108 運用機器學習演算法透過基因體資訊挖掘未知基因的功能與預測細菌抗藥性(1/3)
補助單位
科技部

計畫名稱
107 使用Kmer 與神經網路進行智慧影像辨識與分類
補助單位
臺北醫學大學

計畫名稱
106 利用基因網絡分析尋找假定蛋白質 (hypothetical protein)與抗藥性的關係
補助單位
科技部

計畫名稱
106 運用機器學習的方法辨識與發掘微生物基因體中的隱藏資訊
補助單位
臺北醫學大學

計畫名稱
106 藉由整合多重組學的資料解析與判定人體中未知細菌的基因表現及該細菌在環境中伴演的角色(2/2)
補助單位
科技部

計畫名稱
105 新聘教師研究補助
補助單位
臺北醫學大學

計畫名稱
105 尋找藥物結構、菌種特性與MIC distribution的關聯與預測模型
補助單位
科技部

計畫名稱
105 藉由整合多重組學的資料解析與判定人體中未知細菌的基因表現及該細菌在環境中伴演的角色(1/2)
補助單位
科技部