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Research Output 2006 2019

  • 823 Citations
  • 12 h-Index
  • 32 Article
2019

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
Groundwater
Plasmids
Genes
Microbiota
Metals
1 Citation (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

Chlorobi
Metagenomics
Anthozoa
Skeleton
Oxygen

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

Laurales
camphor
Cinnamomum
Angiospermae
Magnoliales
2018
7 Citations (Scopus)

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

Cellulase
Glycoside Hydrolases
Cellulosomes
Microbial Consortia
Metagenomics
2 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

Escherichia coli
Escherichia Coli
Learning systems
Machine Learning
Genome
2 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

Panicum
Microbiota
Carbohydrates
residence time
solubilization
11 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

Toluene
Enzymes
Aromatic Hydrocarbons
Metagenomics
S-Adenosylmethionine
7 Citations (Scopus)
Genome
Genes
Metagenome
16S Ribosomal RNA
Bacterial Genomes
1 Citation (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

Salinity
Enzymes
Carbohydrates
Metagenome
Metagenomics

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

Cholesterol
catabolism
Functional Response
functional response
steroid
2017
89 Citations (Scopus)

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

Metagenome
Benchmarking
Metagenomics
Software
Genes

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

Biopolymers
Base Composition
Taiwan
Ecosystem
Salts
2016
8 Citations (Scopus)

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

Glycoside Hydrolases
Cellulose
Proteomics
Hydrolysis
Proteins
18 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

Metagenomics
genome
Halomonas
Genome
Population
3 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

Ionic Liquid
Ionic Liquids
Polysaccharides
Microbiota
bioenergy
20 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

Chlorobi
Bacteroidetes
refining
Phylogeny
branching
2 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

RAG-1 Genes
Acinetobacter
Oils
Bacteria
Alkanes
2015
3 Citations (Scopus)

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

Thermus thermophilus
Thermus
Xylose
xylose
Metabolism
130 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

Metagenomics
Binning
Metagenome
Genome
Genes
6 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

Hot Springs
Metagenomics
Taiwan
Carbon
Microbial Interactions
2014
152 Citations (Scopus)

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

Metagenome
Metagenomics
Genome
Myxococcales
Microbial Consortia
2013
4 Citations (Scopus)

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

Treponema
Treponema phagedenis
pathogen
sexually transmitted disease
phylogenetics
2012
74 Citations (Scopus)

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

Clustered Regularly Interspaced Short Palindromic Repeats
Microbiota
mouth
loci
immune system
11 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

Integrons
Stomatognathic Diseases
Spirochaetales
Treponema
mouth
9 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

Metagenomics
Stitching
Network Algorithms
Matching Algorithm
Fragment
2011
76 Citations (Scopus)

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

Metagenomics
Binning
Bins
Genome
Genes
2010
16 Citations (Scopus)

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

Gymnosperms
Angiosperms
Mitochondrial Genome
Cycas
Nucleotides
2008
89 Citations (Scopus)

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

Cycas
Gymnosperms
RNA Editing
RNA editing
Mitochondrial Genome
2007
19 Citations (Scopus)

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

Sequence Alignment
Alignment
Visualization
Position-Specific Scoring Matrices
Viruses
49 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

Chloroplast DNA
Mitochondrial Genome
Gymnosperms
gymnosperm
Mitochondrial DNA
2006
14 Citations (Scopus)

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

Sequence Alignment
Nucleotides
Sequence Analysis
Alignment
Visualization