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Sun, Fengzhu

university of southern california

0H-index
0Paper Count
0Citation Count
Published Papers 80
Publication Date
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A Beginner's Guide to Using DeepVirFinder for Viral Sequence Identification From Metagenomic Datasets
errCurrent Protocols
IF2.2
err2026-01-29
err0
PREAI
errMo, Yuqian; Ahlgren, Nathan; Fuhrman, Jed A.; Sun, Fengzhu; Hou, Shengwei
errShare
errSave
ViTrace detects viral signatures in tumor transcriptomes using a hybrid language model
errCommunications Biology
IF5.1
err2025-12-13
err0
errOAAI
errFeng Zhou; Yushuang He; Fan Yang; Jin Gu; Fengzhu Sun; Shunzhi Zhu; Xiaobing Huang; Ying Wang
errShare
errSave
Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations
errPLOS COMPUTATIONAL BIOLOGY
IF3.6
err2025-11-01
err1
PREAI
errHuang, Yue; Tang, Tianqi; Dai, Xiaowu; Sun, Fengzhu
errShare
errSave
Estimated size of the total genome and protein space of viruses
errMSPHERE
IF3.1
err2025-02-25
err0
errOAAI
errLu, Congyu; Wu, Yifan; Zhang, Zheng; Mao, Longfei; Ge, Xingyi; Wu, Aiping; Sun, Fengzhu; Jiang, Yongqiang; Peng, Yousong
errShare
errSave
DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses
errgenomics proteomics bioinformatics
IF2.8
err2024-05-06
err2
errOAAI
errHou, Shengwei; Tang, Tianqi; Cheng, Siliangyu; Liu, Yuanhao; Xia, Tian; Chen, Ting; Fuhrman, Jed A.; Sun, Fengzhu
errShare
errSave
Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer (vol 13, 5566, 2022)
errNATURE COMMUNICATIONS
IF15.7
err2024-05-01
err0
errOAAI
errStackpole, Mary L.; Zeng, Weihua; Li, Shuo; Liu, Chun-Chi; Zhou, Yonggang; He, Shanshan; Yeh, Angela; Wang, Ziye; Sun, Fengzhu; Li, Qingjiao; Yuan, Zuyang; Yildirim, Asli; Chen, Pin-Jung; Winograd, Paul; Tran, Benjamin; Lee, Yi-Te; Li, Paul Shize; Noor, Zorawar; Yokomizo, Megumi; Ahuja, Preeti; Zhu, Yazhen; Tseng, Hsian-Rong; Tomlinson, James S.; Garon, Edward; French, Samuel; Magyar, Clara E.; Dry, Sarah; Lajonchere, Clara; Geschwind, Daniel; Choi, Gina; Saab, Sammy; Alber, Frank; Wong, Wing Hung; Dubinett, Steven M.; Aberle, Denise R.; Agopian, Vatche; Han, Steven-Huy B.; Ni, Xiaohui; Li, Wenyuan; Zhou, Xianghong Jasmine
errShare
errSave
DeepDecon accurately estimates cancer cell fractions in bulk RNA-seq data
errPATTERNS
IF7.4
err2024-05-01
err0
errOAAI
errHuang, Jiawei; Du, Yuxuan; Stucky, Andres; Kelly, Kevin R.; Zhong, Jiang F.; Sun, Fengzhu
errShare
errSave
Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity
errSCIENTIFIC REPORTS
IF3.9
err2024-03-25
err4
errOAAI
errWang, Beibei; Sun, Fengzhu; Luan, Yihui
errShare
errSave
Effective binning of metagenomic contigs using contrastive multi-view representation learning
errNATURE COMMUNICATIONS
IF15.7
err2024-01-17
err4
errOAAI
errWang, Ziye; You, Ronghui; Han, Haitao; Liu, Wei; Sun, Fengzhu; Zhu, Shanfeng
errShare
errSave
Identifying local associations in biological time series: algorithms, statistical significance, and applications
errBRIEFINGS IN BIOINFORMATICS
IF7.7
err2023-11-02
err0
PREAI
errAi, Dongmei; Chen, Lulu; Xie, Jiemin; Cheng, Longwei; Zhang, Fang; Luan, Yihui; Li, Yang; Hou, Shengwei; Sun, Fengzhu; Xia, Li Charlie
errShare
errSave
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
errNATURE COMMUNICATIONS
IF15.7
err2023-10-06
err6
errOAAI
errDu, Yuxuan; Sun, Fengzhu
errShare
errSave
ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data
errNATURE COMMUNICATIONS
IF15.7
err2023-01-31
err14
errOAAI
errDu, Yuxuan; Fuhrman, Jed A.; Sun, Fengzhu
errShare
errSave
MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities
errGENOME BIOLOGY
IF9.4
err2023-01-06
err20
errOAAI
errWang, Ziye; Huang, Pingqin; You, Ronghui; Sun, Fengzhu; Zhu, Shanfeng
errShare
errSave
Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer
errNATURE COMMUNICATIONS
IF15.7
err2022-09-29
err45
errOAAI
errStackpole, Mary L.; Zeng, Weihua; Li, Shuo; Liu, Chun-Chi; Zhou, Yonggang; He, Shanshan; Yeh, Angela; Wang, Ziye; Sun, Fengzhu; Li, Qingjiao; Yuan, Zuyang; Yildirim, Asli; Chen, Pin-Jung; Winograd, Paul; Tran, Benjamin; Lee, Yi-Te; Li, Paul Shize; Noor, Zorawar; Yokomizo, Megumi; Ahuja, Preeti; Zhu, Yazhen; Tseng, Hsian-Rong; Tomlinson, James S.; Garon, Edward; French, Samuel; Magyar, Clara E.; Dry, Sarah; Lajonchere, Clara; Geschwind, Daniel; Choi, Gina; Saab, Sammy; Alber, Frank; Wong, Wing Hung; Dubinett, Steven M.; Aberle, Denise R.; Agopian, Vatche; Han, Steven-Huy B.; Ni, Xiaohui; Li, Wenyuan; Zhou, Xianghong Jasmine
errShare
errSave
Sparse logistic regression revealed the associations between HBV PreS quasispecies and hepatocellular carcinoma
errVIROLOGY JOURNAL
IF3.8
err2022-06-28
err2
errOAAI
errJia, Jian-an; Zhang, Shuqin; Bai, Xin; Fang, Meng; Chen, Shipeng; Liang, Xiaotao; Zhu, Shanfeng; Wong, Danny Ka-Ho; Zhang, Anye; Feng, Jianfeng; Sun, Fengzhu; Gao, Chunfang
errShare
errSave
16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis
errSCIENTIFIC REPORTS
IF3.9
err2022-04-19
err32
errOAAI
errZuo, Wenxuan; Wang, Beibei; Bai, Xin; Luan, Yihui; Fan, Yingying; Michail, Sonia; Sun, Fengzhu
errShare
errSave
HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
errGENOME BIOLOGY
IF9.4
err2022-02-28
err25
errOAAI
errDu, Yuxuan; Sun, Fengzhu
errShare
errSave
DeepLINK: Deep learning inference using knockoffs with applications to genomics
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2021-09-07
err16
PREAI
errZhu, Zifan; Fan, Yingying; Kong, Yinfei; Lv, Jinchi; Sun, Fengzhu
errShare
errSave
Improving brain age estimates with deep learning leads to identification of novel genetic factors associated with brain aging
errNEUROBIOLOGY OF AGING
IF3.5
err2021-09-01
err18
errOAAI
errNing, Kaida; Duffy, Ben A.; Franklin, Meredith; Matloff, Will; Zhao, Lu; Arzouni, Nibal; Sun, Fengzhu; Toga, Arthur W.
errShare
errSave
ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network
errgenomics proteomics bioinformatics
IF2.8
err2021-08-05
err7
errOAAI
errWang, Ziye; Li, Shuo; You, Ronghui; Zhu, Shanfeng; Zhou, Xianghong Jasmine; Sun, Fengzhu
errShare
errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
R
Rob Knight
H-index: 255 · Papers: 1.8K
D
Daniel Levy
H-index: 230 · Papers: 1.6K
R
Ramachandran S. Vasan
H-index: 204 · Papers: 1.9K
D
Daniel H. Geschwind
H-index: 188 · Papers: 966
M
Martin G. Larson
H-index: 184 · Papers: 839
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