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Research Output

  • 1065 Citations
  • 13 h-Index
  • 37 Article
2020
Open Access

Morphine produces potent antinociception, sedation, and hypothermia in humanized mice expressing human mu-opioid receptor splice variants

Huang, Y-H., Wu, Y-W., Chuang, J-Y., Chang, Y-C., Chang, H-F., Tao, P-L., Loh, H. H. & Yeh, S-H., Feb 6 2020, In : Pain.

Research output: Contribution to journalArticle

2019

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

Chang, T. S., Wang, T. Y., Hsueh, T. Y., Lee, Y. W., Chuang, H. M., Cai, W. X., Wu, J. Y., Chiang, C. M. & Wu, Y. W., Oct 2 2019, In : International Journal of Molecular Sciences. 20, 20, 5192.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)
Open Access
1 Citation (Scopus)

A new triterpenoid glucoside from a novel acidic glycosylation of ganoderic acid a via recombinant glycosyltransferase of bacillus subtilis

Chang, T. S., Chiang, C. M., Kao, Y. H., Wu, J. Y., Wu, Y. W. & Wang, T. Y., Sep 24 2019, In : Molecules. 24, 19, 3457.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Large circular plasmids from groundwater plasmidomes span multiple incompatibility groups and are enriched in multimetal resistance genes

Kothari, A., Wu, Y. W., Chandonia, J. M., Charrier, M., Rajeev, L., Rocha, A. M., Joyner, D. C., Hazen, T. C., Singer, S. W. & Mukhopadhyay, A., Jan 1 2019, In : mBio. 10, 1, e02899-18.

Research output: Contribution to journalArticle

Open Access
4 Citations (Scopus)

Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera

Yang, S. H., Tandon, K., Lu, C. Y., Wada, N., Shih, C. J., Hsiao, S. S. Y., Jane, W. N., Lee, T. C., Yang, C. M., Liu, C. T., Denis, V., Wu, Y. T., Wang, L. T., Huang, L., Lee, D. C., Wu, Y. W., Yamashiro, H. & Tang, S. L., Jan 4 2019, In : Microbiome. 7, 1, 3.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution

Chaw, S. M., Liu, Y. C., Wu, Y. W., Wang, H. Y., Lin, C. Y. I., Wu, C. S., Ke, H. M., Chang, L. Y., Hsu, C. Y., Yang, H. T., Sudianto, E., Hsu, M. H., Wu, K. P., Wang, L. N., Leebens-Mack, J. H. & Tsai, I. J., Jan 1 2019, In : Nature Plants. 5, 1, p. 63-73 11 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)
2018

A bacterial pioneer produces cellulase complexes that persist through community succession

Kolinko, S., Wu, Y. W., Tachea, F., Denzel, E., Hiras, J., Gabriel, R., Bäcker, N., Chan, L. J. G., Eichorst, S. A., Frey, D., Chen, Q., Azadi, P., Adams, P. D., Pray, T. R., Tanjore, D., Petzold, C. J., Gladden, J. M., Simmons, B. A. & Singer, S. W., Jan 1 2018, In : Nature Microbiology. 3, 1, p. 99-107 9 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains

Her, H. L. & Wu, Y. W., Jul 1 2018, In : Bioinformatics. 34, 13, p. i89-i95

Research output: Contribution to journalArticle

7 Citations (Scopus)

Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times

Liang, X., Whitham, J. M., Holwerda, E. K., Shao, X., Tian, L., Wu, Y-W., Lombard, V., Henrissat, B., Klingeman, D. M., Yang, Z. K., Podar, M., Richard, T. L., Elkins, J. G., Brown, S. D. & Lynd, L. R., 2018, In : Biotechnology for Biofuels. 11, 1

Research output: Contribution to journalArticle

9 Citations (Scopus)

Discovery of enzymes for toluene synthesis from anoxic microbial communities

Beller, H. R., Rodrigues, A. V., Zargar, K., Wu, Y. W., Saini, A. K., Saville, R. M., Pereira, J. H., Adams, P. D., Tringe, S. G., Petzold, C. J. & Keasling, J. D., May 1 2018, In : Nature Chemical Biology. 14, 5, p. 451-457 7 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)
12 Citations (Scopus)

Microbial community structure and functional potential along a hypersaline gradient

Kimbrel, J. A., Ballor, N., Wu, Y-W., David, M. M., Hazen, T. C., Simmons, B. A., Singer, S. W. & Jansson, J. K., 2018, In : Frontiers in Microbiology. 9, JUL

Research output: Contribution to journalArticle

4 Citations (Scopus)

Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge

Wei, S. T-S., Wu, Y-W., Lee, T-H., Huang, Y-S., Yang, C-Y., Chen, Y-L. & Chiang, Y-R., Nov 13 2018, In : mSystems. 3, 5

Research output: Contribution to journalArticle

2017

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software

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, T. S., Shapiro, N., Blood, P. D., Gurevich, A., Bai, Y., Turaev, D., DeMaere, M. Z. & 47 others, Chikhi, R., Nagarajan, N., Quince, C., Meyer, F., Balvočiūtė, M., Hansen, L. H., Sørensen, S. J., Chia, B. K. H., Denis, B., Froula, J. L., Wang, Z., Egan, R., Don Kang, D., Cook, J. J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y-W., Singer, S. W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M. D., Lingner, T., Lin, H-H., Liao, Y-C., Silva, G. G. Z., Cuevas, D. A., Edwards, R. A., Saha, S., Piro, V. C., Renard, B. Y., Pop, M., Klenk, H-P., Göker, M., Kyrpides, N. C., Woyke, T., Vorholt, J. A., Schulze-Lefert, P., Rubin, E. M., Darling, A. E., Rattei, T. & McHardy, A. C., Nov 2017, In : Nature Methods. 14, 11, p. 1063-1071 9 p.

Research output: Contribution to journalArticle

141 Citations (Scopus)

Draft genome sequence of Zobellella denitrificans ZD1 (JCM 13380), a salt-tolerant denitrifying bacterium capable of producing poly(3-hydroxybutyrate)

Wu, Y. W., Shao, Y., Khanipov, K., Golovko, G., Pimenova, M., Fofanov, Y. & Chu, K. H., Jan 1 2017, In : Genome Announcements. 5, 36

Research output: Contribution to journalArticle

3 Citations (Scopus)
2016

Comparative community proteomics demonstrates the unexpected importance of actinobacterial glycoside hydrolase family 12 protein for crystalline cellulose hydrolysis

Hiras, J., Wu, Y. W., Deng, K., Nicora, C. D., Aldrich, J. T., Frey, D., Kolinko, S., Robinson, E. W., Jacobs, J. M., Adams, P. D., Northen, T. R., Simmons, B. A. & Singer, S. W., Jul 1 2016, In : mBio. 7, 4, e01106-16.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia

Nelson, W. C., Maezato, Y., Wu, Y. W., Romine, M. F. & Lindemann, S. R., 2016, In : Applied and Environmental Microbiology. 82, 1, p. 255-267 13 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis

Wu, Y-W., Higgins, B., Yu, C., Reddy, A. P., Ceballos, S., Joh, L. D., Simmons, B. A., Singer, S. W. & VanderGheynst, J. S., Dec 17 2016, In : mSystems. 1, 6

Research output: Contribution to journalArticle

5 Citations (Scopus)

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage

Hiras, J., Wu, Y. W., Eichorst, S. A., Simmons, B. A. & Singer, S. W., Apr 1 2016, In : ISME Journal. 10, 4, p. 833-845 13 p.

Research output: Contribution to journalArticle

26 Citations (Scopus)

Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization

Kothari, A., Charrier, M., Wu, Y. W., Malfatti, S., Zhou, C. E., Singer, S. W., Dugan, L. & Mukhopadhyay, A., 2016, In : FEMS Microbiology Letters. 363, 20, fnw224.

Research output: Contribution to journalArticle

2 Citations (Scopus)
2015

Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia

Wu, Y. W., Joshua, C., Eichorst, S. A., Gladden, J. M., Simmons, B. A. & Singer, S. W., Mar 12 2015, In : Bioenergy Research. 8, 3, p. 1031-1038 8 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets

Wu, Y. W., Simmons, B. A. & Singer, S. W., Sep 15 2015, In : Bioinformatics. 32, 4, p. 605-607 3 p.

Research output: Contribution to journalArticle

196 Citations (Scopus)

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

Lin, K. H., Liao, B. Y., Chang, H. W., Huang, S. W., Chang, T. Y., Yang, C. Y., Wang, Y. B., Lin, Y. T. K., Wu, Y. W., Tang, S. L. & Yu, H. T., Dec 3 2015, In : BMC Genomics. 16, 1, 1029.

Research output: Contribution to journalArticle

8 Citations (Scopus)
2014

MaxBin: An automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

Wu, Y. W., Tang, Y. H., Tringe, S. G., Simmons, B. A. & Singer, S. W., Mar 4 2014, In : Microbiome. 2, 1, 26.

Research output: Contribution to journalArticle

190 Citations (Scopus)
2013

The gain and loss of chromosomal integron systems in the Treponema species

Wu, Y. W., Doak, T. G. & Ye, Y., 2013, In : BMC Evolutionary Biology. 13, 1, 16.

Research output: Contribution to journalArticle

5 Citations (Scopus)
2012

Diverse CRISPRs evolving in human microbiomes

Rho, M., Wu, Y. W., Tang, H., Doak, T. G. & Ye, Y., Jun 2012, In : PLoS Genetics. 8, 6, e1002441.

Research output: Contribution to journalArticle

75 Citations (Scopus)

Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes

Wu, Y. W., Rho, M., Doak, T. G. & Ye, Y., Aug 2012, In : Applied and Environmental Microbiology. 78, 15, p. 5288-5296 9 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics

Wu, Y. W., Rho, M., Doak, T. G. & Ye, Y., Sep 2012, In : Bioinformatics. 28, 18, bts388.

Research output: Contribution to journalArticle

9 Citations (Scopus)
2011

A novel abundance-based algorithm for binning metagenomic sequences using l-tuples

Wu, Y. W. & Ye, Y., Mar 1 2011, In : Journal of Computational Biology. 18, 3, p. 523-534 12 p.

Research output: Contribution to journalArticle

83 Citations (Scopus)
2010

Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes

Salmans, M. L., Chaw, S. M., Lin, C. P., Shih, A. C. C., Wu, Y. W. & Mulligan, R. M., Oct 2010, In : Current Genetics. 56, 5, p. 439-446 8 p.

Research output: Contribution to journalArticle

17 Citations (Scopus)
2008

The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites

Chaw, S. M., Chun-Chieh Shih, A., Wang, D., Wu, Y. W., Liu, S. M. & Chou, T. Y., Mar 2008, In : Molecular Biology and Evolution. 25, 3, p. 603-615 13 p.

Research output: Contribution to journalArticle

93 Citations (Scopus)
2007

Phylo-mLogo: An interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

Shih, A. C. C., Lee, D. T., Peng, C. L. & Wu, Y. W., 2007, In : BMC Bioinformatics. 8, 63.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA

Wang, D., Wu, Y. W., Shih, A. C. C., Wu, C. S., Wang, Y. N. & Chaw, S. M., Sep 2007, In : Molecular Biology and Evolution. 24, 9, p. 2040-2048 9 p.

Research output: Contribution to journalArticle

52 Citations (Scopus)
2006

SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools

Shih, A. C. C., Lee, D. T., Lin, L., Peng, C. L., Chen, S. H., Wu, Y. W., Wong, C. Y., Chou, M. Y., Shiao, T. C. & Hsieh, M. F., Mar 2 2006, In : BMC Bioinformatics. 7, 103.

Research output: Contribution to journalArticle

14 Citations (Scopus)