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1

Identifying viruses from metagenomic data using deep learning

Ren, Jie, Song, Kai, Deng, Chao, Ahlgren, Nathan A., Fuhrman, Jed A., Li, Yi, Xie, Xiaohui, Poplin, Ryan, Sun, Fengzhu

Journal:

Quantitative Biology

Year:

2020

Language:

english

File:

PDF, 872 KB

english, 2020

2

Pressure-induced phase transition of tantalum mononitride

Fengzhu Ren, Yuanxu Wang

Journal:

Thin Solid Films

Year:

2011

Language:

english

File:

PDF, 577 KB

english, 2011

3

Pressure induced structural phase transition of OsB2: First-principles calculations

Fengzhu Ren, Yuanxu Wang, V.C. Lo

Journal:

Journal of Solid State Chemistry

Year:

2010

Language:

english

File:

PDF, 438 KB

english, 2010

4

Comparison of metagenomic samples using sequence signatures

Jiang, Bai, Song, Kai, Ren, Jie, Deng, Minghua, Sun, Fengzhu, Zhang, Xuegong

Journal:

Year:

2012

Language:

english

File:

PDF, 930 KB

english, 2012

5

Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

Song, Kai, Ren, Jie, Zhai, Zhiyuan, Liu, Xuemei, Deng, Minghua, Sun, Fengzhu

Journal:

Journal of Computational Biology

Year:

2013

Language:

english

File:

PDF, 629 KB

english, 2013

6

Stacking faults enriched silver nanowires: Facile synthesis, catalysis and SERS investigations

Xu, Minmin, Yang, Fengzhu, Yuan, Yaxian, Guo, Qinghua, Ren, Bin, Yao, Jianlin, Gu, Renao

Journal:

Journal of Colloid and Interface Science

Year:

2013

Language:

english

File:

PDF, 1.77 MB

english, 2013

7

Endowing single-electron-trapped oxygen vacancy self-modified titanium dioxide with visible-light photocatalytic activity by grafting Fe(III) nanocluster

Li, Haiyan, Ren, Fengzhu, Liu, Jinfeng, Wang, Qinglong, Li, Qiuye, Yang, Jianjun, Wang, Yuanxu

Journal:

Applied Catalysis B: Environmental

Year:

2015

Language:

english

File:

PDF, 1.59 MB

english, 2015

8

Enhanced photocatalytic activities of Bi 2 WO 6 by introducing Zn to replace Bi lattice sites: a first-principles study

Ren, Fengzhu, Zhang, Jihua, Wang, Yuanxu

Journal:

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

9

Enhanced photocatalytic oxidation of propylene over V-doped TiO2 photocatalyst: Reaction mechanism between V5+ and single-electron-trapped oxygen vacancy

Ren, Fengzhu, Li, Haiyan, Wang, Yuanxu, Yang, Jianjun

Journal:

Applied Catalysis B: Environmental

Year:

2015

Language:

english

File:

PDF, 3.99 MB

english, 2015

10

Enhanced visible-light photocatalytic activity of a g-C 3 N 4 /BiVO 4 nanocomposite: a first-principles study

Zhang, Jihua, Ren, Fengzhu, Deng, Mingsen, Wang, Yuanxu

Journal:

Physical Chemistry Chemical Physics

Year:

2015

Language:

english

File:

PDF, 2.93 MB

english, 2015

11

Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics

Ren, Jie, Song, Kai, Deng, Minghua, Reinert, Gesine, Cannon, Charles H., Sun, Fengzhu

Journal:

Year:

2015

Language:

english

File:

PDF, 332 KB

english, 2015

12

Effects of Mo/W codoping on the visible-light photocatalytic activity of monoclinic BiVO 4 within the GGA + U framework

Zhang, Jihua, Deng, Mingsen, Ren, Fengzhu, Wu, Yu, Wang, Yuanxu

Journal:

Year:

2016

Language:

english

File:

PDF, 1.15 MB

english, 2016

13

Graphene-coupled Bi2WO6 nanocomposite with Enhanced Photocatalytic Performance: first-principles study

Ren, Fengzhu, Zhang, Jihua, WANG, Yuanxu, Yao, Wen-Zhi

Journal:

Physical Chemistry Chemical Physics

Year:

2016

Language:

english

File:

PDF, 1.66 MB

english, 2016

14

Origin of high thermoelectric performance of FeNb1−xZr/HfxSb1−ySny alloys: A first-principles study

Zhang, Xiwen, Wang, Yuanxu, Yan, Yuli, Wang, Chao, Zhang, Guangbiao, Cheng, Zhenxiang, Ren, Fengzhu, Deng, Hao, Zhang, Jihua

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 2.70 MB

english, 2016

15

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains

Liao, Weinan, Ren, Jie, Wang, Kun, Wang, Shun, Zeng, Feng, Wang, Ying, Sun, Fengzhu

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 2.40 MB

english, 2016

16

Novel (1 × 1)-reconstructions and native defects of TiO 2 anatase (101) surface

Wang, Qinggao, Ren, Fengzhu, Dong, Huafeng, Wang, Yuanxu

Journal:

Applied Surface Science

Year:

2017

Language:

english

File:

PDF, 418 KB

english, 2017

17

CAFE: aCcelerated Alignment-FrEe sequence analysis

Lu, Yang Young, Tang, Kujin, Ren, Jie, Fuhrman, Jed A., Waterman, Michael S., Sun, Fengzhu

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 2.10 MB

english, 2017

18

Ag-Mg antisite defect induced high thermoelectric performance of α-MgAgSb

Feng, Zhenzhen, Zhang, Jihua, Yan, Yuli, Zhang, Guangbiao, Wang, Chao, Peng, Chengxiao, Ren, Fengzhu, Wang, Yuanxu, Cheng, Zhenxiang

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 2.98 MB

english, 2017

19

Hybrid density functional study on the mechanism for the enhanced photocatalytic properties of the ultrathin hybrid layered nanocomposite g-C 3 N 4 /BiOCl

Yao, Wenzhi, Zhang, Jihua, Wang, Yuanxu, Ren, Fengzhu

Journal:

Applied Surface Science

Year:

2017

Language:

english

File:

PDF, 829 KB

english, 2017

20

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

Ahlgren, Nathan A., Ren, Jie, Lu, Yang Young, Fuhrman, Jed A., Sun, Fengzhu

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 507 KB

english, 2017

21

Alignment-Free Sequence Analysis and Applications

Ren, Jie, Bai, Xin, Lu, Yang Young, Tang, Kujin, Wang, Ying, Reinert, Gesine, Sun, Fengzhu

Journal:

Annual Review of Biomedical Data Science

Year:

2018

Language:

english

File:

PDF, 1.08 MB

english, 2018

22

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

Ren, Jie, Ahlgren, Nathan A., Lu, Yang Young, Fuhrman, Jed A., Sun, Fengzhu

Journal:

Year:

2017

Language:

english

File:

PDF, 1.24 MB

english, 2017

23

Spin-flip effect enhanced photocatalytic activity in Fe and single-electron-trapped oxygen vacancy co-doped TiO 2

Li, Haiyan, Ren, Fengzhu, Li, Qiuye, Yang, Jianjun, Wang, Yuanxu, Cheng, Zhenxiang

Journal:

Applied Surface Science

Year:

2018

Language:

english

File:

PDF, 2.46 MB

english, 2018

24

Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients

Nusbaum, David J, Sun, Fengzhu, Ren, Jie, Zhu, Zifan, Ramsy, Natalie, Pervolarakis, Nicholas, Kunde, Sachin, England, Whitney, Gao, Bei, Fiehn, Oliver, Michail, Sonia, Whiteson, Katrine

Journal:

FEMS Microbiology Ecology

Year:

2018

Language:

english

File:

PDF, 1.07 MB

english, 2018

25

Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures

Wang, Ying, Fu, Lei, Ren, Jie, Yu, Zhaoxia, Chen, Ting, Sun, Fengzhu

Journal:

Frontiers in Microbiology

Year:

2018

Language:

english

File:

PDF, 4.08 MB

english, 2018

26

Optimal choice of word length when comparing two Markov sequences using a χ 2-statistic

Bai, Xin, Tang, Kujin, Ren, Jie, Waterman, Michael, Sun, Fengzhu

Journal:

Year:

2017

Language:

english

File:

PDF, 1.30 MB

english, 2017

27

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA

Tang, Kujin, Ren, Jie, Cronn, Richard, Erickson, David L., Milligan, Brook G., Parker-Forney, Meaghan, Spouge, John L., Sun, Fengzhu

Journal:

Year:

2018

File:

PDF, 2.36 MB

2018

28

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA

Tang, Kujin, Ren, Jie, Cronn, Richard, Erickson, David L., Milligan, Brook G., Parker-Forney, Meaghan, Spouge, John L., Sun, Fengzhu

Journal:

Year:

2018

Language:

english

File:

PDF, 2.36 MB

english, 2018

29

Ab initio simulation studies on the room-temperature ferroelectricity in two-dimensional β -phase GeS

Yin, Huabing, Liu, Chang, Zheng, Guang-Ping, Wang, Yuanxu, Ren, Fengzhu

Journal:

Applied Physics Letters

Year:

2019

Language:

english

File:

PDF, 1.63 MB

english, 2019

30

An unexpected interaction between a H2O2 molecule and anatase TiO2(101) surface

Wang, Liming, Wang, Qinggao, Ren, Fengzhu, Wang, Yuanxu

Journal:

Applied Surface Science

Year:

2019

Language:

english

File:

PDF, 1.09 MB

english, 2019

31

MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

Zhu, Zifan, Ren, Jie, Michail, Sonia, Sun, Fengzhu

Journal:

Year:

2019

Language:

english

File:

PDF, 1.45 MB

english, 2019

32

Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression

Tang, Kujin, Ren, Jie, Sun, Fengzhu

Journal:

Year:

2019

File:

PDF, 2.95 MB

2019

33

Reads Binning Improves Alignment-Free Metagenome Comparison

Song, Kai, Ren, Jie, Sun, Fengzhu

Journal:

Frontiers in Genetics

Year:

2019

File:

PDF, 3.92 MB

2019

34

Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA

Chen, Pei, Li, Shuo, Li, Wenyuan, Ren, Jie, Sun, Fengzhu, Liu, Rui, Zhou, Xianghong Jasmine

Journal:

Journal of Translational Medicine

Year:

2020

Language:

english

File:

PDF, 2.03 MB

english, 2020

35

Ferroelectrically tunable magnetism in BiFeO3/BaTiO3 heterostructure revealed by the first-principles calculations

Wang, Wenxuan, Sun, Wei, Zhang, Guangbiao, Ren, Fengzhu, Wang, Yuanxu, You, Caiyin, Cheng, Zhenxiang

Journal:

Journal of Advanced Research

Year:

2020

File:

PDF, 1.98 MB

2020

36

Efficacy and safety of telbivudine treatment for the prevention of HBV perinatal transmission

Ren, Cuicui, Wang, Lili, Sun, Weihui, Ma, Lei, Dong, Zhi, Hao, Anhua, Zhou, Lin, Li, Fengzhu, Ma, Wenjie

Journal:

Medicine (Williams & Wilkins)

Year:

2020

File:

PDF, 186 KB

2020

37

Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data

Wan, Lin, Kang, Xin, Ren, Jie, Sun, Fengzhu

Journal:

Quantitative Biology

Year:

2020

File:

PDF, 1018 KB

2020

38

A network-based integrated framework for predicting virusâprokaryote interactions

Wang, Weili, Ren, Jie, Tang, Kujin, Dart, Emily, Ignacio-Espinoza, Julio Cesar, Fuhrman, JedÂ A, Braun, Jonathan, Sun, Fengzhu, Ahlgren, Nathan A

Journal:

NAR Genomics and Bioinformatics

Year:

2020

File:

PDF, 619 KB

2020

39

Monoanion-regulated high-voltage nitrile-based solid electrolyte with compatible lithium inertness

Hou, Qian, Wang, Hui, Zhao, Fengzhu, Zhang, Kun, Zhao, Hui, Qi, Yaqin, Ren, Zengying, Shen, Chao, Xie, Keyu

Journal:

Energy Storage Materials

Year:

2021

File:

PDF, 2.04 MB

2021

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