97 Publications (Page 1 of 4)
2019
A meta-proteogenomic approach to peptide identification incorporating assembly uncertainty and genomic variation.
Li, Sujun⋅Li, Sujun⋅Tang, Haixu⋅Tang, Haixu⋅Ye, Yuzhen and Ye, Yuzhen
Molecular & cellular proteomics : MCP, May 29, 2019. | Journal Article
 
A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data
Han, Wontack and Ye, Yuzhen
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, vol. 24, pp. 247, 2019-00-00. | Journal Article
 
CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis
Lam, Tony J and Ye, Yuzhen
The CRISPR Journal, vol. 2, (no. 1), pp. 50, 2019-02-01. | Journal Article
 
Effect of permafrost thaw on plant and soil fungal community in a boreal forest: Does fungal community change mediate plant productivity response?
Schütte, Ursel M. E⋅Schütte, Ursel M. E⋅Schütte, Ursel M. E⋅Henning, Jeremiah A⋅Henning, Jeremiah A⋅Henning, Jeremiah A⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Bowling, Annie⋅Bowling, Annie⋅Bowling, Annie⋅Ford, James⋅Ford, James⋅Ford, James⋅Genet, Hélène⋅Genet, Hélène⋅Genet, Hélène⋅Waldrop, Mark P⋅Waldrop, Mark P⋅Waldrop, Mark P⋅Turetsky, Merritt R⋅Turetsky, Merritt R⋅Turetsky, Merritt R⋅White, Jeffrey R⋅White, Jeffrey R⋅White, Jeffrey R⋅Bever, James D⋅Bever, James D⋅Bever, James D⋅Singh, Brajesh⋅Singh, Brajesh and Singh, Brajesh
Journal of Ecology, vol. 107, (no. 4), pp. 1752, July 2019. | Journal Article
 
Fe 2 O 3 Nanoparticles Modified 2D N‐Doped Porous Graphene‐like Carbon as an Efficient and Robust Electrocatalyst for Oxygen Reduction Reaction
Ye, Yuzhen⋅Wang, Bin⋅Liu, Gaopeng⋅Xu, Li⋅Xia, Jiexiang and Li, Huaming
ChemistrySelect, vol. 4, (no. 14), pp. 4139, 2019-04-16. | Journal Article
 
In-situ synthesis strategy for CoM (M = Fe, Ni, Cu) bimetallic nanoparticles decorated N-doped 1D carbon nanotubes/3D porous carbon for electrocatalytic oxygen evolution reaction
Liu, Gaopeng⋅Wang, Lin⋅Wang, Bin⋅Ding, Penghui⋅Wei, Wenxian⋅Ye, Yuzhen⋅Zhu, Wenshuai⋅Li, Huaming and Xia, Jiexiang
Journal of Alloys and Compounds, pp. 152470, 2019-10-00. | Journal Article
 
Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes.
Lam, Tony J and Ye, Yuzhen
BMC genomics, vol. 20, (no. 1), pp. 567, July 9, 2019. | Journal Article
 
MyDGR: a server for identification and characterization of diversity-generating retroelements.
Sharifi, Fatemeh and Ye, Yuzhen
Nucleic acids research, May 3, 2019. | Journal Article
 
Novel CNT/PbBiO2Br hybrid materials with enhanced broad spectrum photocatalytic activity toward ciprofloxacin (CIP) degradation
Wang, Bin⋅Liu, Gaopeng⋅Ye, Baisong⋅Ye, Yuzhen⋅Zhu, Wenshuai⋅Yin, Sheng⋅Xia, Jiexiang and Li, Huaming
Journal of Photochemistry & Photobiology, A: Chemistry, vol. 382, pp. 111901, 2019-09-01. | Journal Article
 
Reactable ionic liquid in situ-induced synthesis of Fe.sub.3O.sub.4 nanoparticles modified N-doped hollow porous carbon microtubes for boosting multifunctional electrocatalytic activity
Liu, Gaopeng⋅Wang, Bin⋅Ding, Penghui⋅Ye, Yuzhen⋅Wei, Wenxian⋅Zhu, Wenshuai⋅Xu, Li⋅Xia, Jiexiang and Li, Huaming
Journal of Alloys and Compounds, vol. 797, pp. 849, 20190815. | Journal Article
2017
A concurrent subtractive assembly approach for identification of disease associated sub-metagenomes.
Han, Wontack⋅Wang, Mingjie and Ye, Yuzhen
Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005-), vol. 2017, pp. 18-33, 2017. | Journal Article
 
From Gene Annotation to Function Prediction for Metagenomics.
Sharifi, Fatemeh and Ye, Yuzhen
Methods in molecular biology (Clifton, N.J.), vol. 1611, pp. 27-34, 2017. | Journal Article
 
Functional association prediction by community profiling.
Jiao, Dazhi⋅Han, Wontack and Ye, Yuzhen
Methods (San Diego, Calif.), April 26, 2017. | Journal Article
 
Improving de novo metatranscriptome assembly via machine learning algorithms
Mohsen, Hussein⋅Mohsen, Hussein⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Tang, Haixu and Tang, Haixu
International Journal of Computational Biology and Drug Design, vol. 10, (no. 2), pp. 91, 2017-00-00. | Journal Article
 
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements.
Zhang, Quan and Ye, Yuzhen
BMC bioinformatics, vol. 18, (no. 1), pp. 92, February 6, 2017. | Journal Article
2016
A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics
Tang, Haixu⋅Tang, Haixu⋅Li, Sujun⋅Li, Sujun⋅Ye, Yuzhen and Ye, Yuzhen
PLoS Computational Biology, vol. 12, (no. 12), Dec 2016. | Journal Article
 
Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data.
Ye, Yuzhen and Zhang, Quan
RNA (New York, N.Y.), vol. 22, (no. 7), pp. 945-956, July 2016. | Journal Article
 
Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola
Nimkulrat, Sutichot⋅Nimkulrat, Sutichot⋅Lee, Heewook⋅Lee, Heewook⋅Doak, Thomas G⋅Doak, Thomas G⋅Ye, Yuzhen and Ye, Yuzhen
Frontiers in microbiology, vol. 7, pp. 852, 2016-00-00. | Journal Article
 
Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering.
House, Geoffrey L⋅House, Geoffrey L⋅House, Geoffrey L⋅Ekanayake, Saliya⋅Ekanayake, Saliya⋅Ekanayake, Saliya⋅Ruan, Yang⋅Ruan, Yang⋅Ruan, Yang⋅Schütte, Ursel M E⋅Schütte, Ursel M E⋅Schütte, Ursel M E⋅Kaonongbua, Wittaya⋅Kaonongbua, Wittaya⋅Kaonongbua, Wittaya⋅Fox, Geoffrey⋅Fox, Geoffrey⋅Fox, Geoffrey⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Ye, Yuzhen⋅Bever, James D⋅Bever, James D and Bever, James D
Applied and environmental microbiology, vol. 82, (no. 16), pp. 4921-4930, August 15, 2016. | Journal Article
 
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.
Ye, Yuzhen⋅Ye, Yuzhen⋅Tang, Haixu and Tang, Haixu
Bioinformatics (Oxford, England), vol. 32, (no. 7), pp. 1001-1008, April 1, 2016. | Journal Article
2015
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota.
Bao, Guanhui⋅Bao, Guanhui⋅Wang, Mingjie⋅Wang, Mingjie⋅Doak, Thomas G⋅Doak, Thomas G⋅Ye, Yuzhen and Ye, Yuzhen
Frontiers in microbiology, vol. 6, pp. 896, 2015. | Journal Article
 
Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes.
Wang, Mingjie⋅Doak, Thomas G and Ye, Yuzhen
Genome biology, vol. 16, pp. 243, 2015. | Journal Article
 
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
Ye, Yuzhen⋅Ye, Yuzhen⋅Tang, Haixu and Tang, Haixu
2015-04-06. | Journal Article
2014
Expanding the catalog of cas genes with metagenomes.
Zhang, Quan⋅Doak, Thomas and Ye, Yuzhen
Nucleic acids research, vol. 42, (no. 4), pp. 2448-59, 2014/Feb. | Journal Article
 
Gene finding in metatranscriptomic sequences
Ismail, Wazim⋅Ye, Yuzhen and Tang, Haixu
BMC Bioinformatics , vol. 15, pp. S8, 2014. | Journal Article