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A catalog of small proteins from the global microbiome

Y Duan CD Santos-Júnior TS Schmidt A Fullam BLS de Almeida C Zhu M Kuhn XM Zhao P Bork LP Coelho

Nature Communications2024
Long-read sequencing reveals extensive gut phagenome structural variations driven by genetic exchange with bacterial hosts

S Lai H Wang P Bork WH Chen Zhao XM

Science Advances2024
Efficient Recovery of Complete Gut Viral Genomes by Combined Short‐and Long‐Read Sequencing

J Chen C Sun Y Dong M Jin S Lai L Jia X Zhao H Wang NL Gao P Bork P Z Liu WH Chen XM Zhao

Advanced Science2024
Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial

J Zhu C Sun M Li G Hu XM Zhao Chen WH

Gut2024
STAB2: an updated spatio-temporal cell atlas of the human and mouse brain

YT Yang Z Gan J Zhang X Zhao Y Yang S Han W Wu XM Zhao

Nucleic Acids Research2024
Engineering of cytosine base editors with DNA damage minimization and editing scope diversification

B Yuan S Zhang L Song J Chen J Cao J Qiu Z Qiu J Chen Zhao XM Cheng TL

Nucleic Acids Research2023
Enterotypes of the human gut mycobiome

S Lai Y Yan Y Pu S Lun JG Qiu BH Jiang MI Keller M Wang P Bork WH Chen Y Zheng XM Zhao

Microbiome2023
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues

X Zhao L Song A Yang Z Zhang J Zhang YT Yang XM Zhao

Genome Medicine2023
Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases

C Sun J Chen M Jin X Zhao Y Li Y Dong N Gao Z Liu P Bork XM Zhao WH Chen

Advanced Science2023
Performance of Gut Microbiome as an Independent Diagnostic Tool for 20 Diseases: Cross-Cohort Validation of Machine-Learning Classifiers

M Li J Liu J Zhu H Wang C Sun NL Gao XM Zhao WH Chen

Gut Microbes2023
TadA reprogramming to generate potent miniature base editors with high precision

S Zhang L Song B Yuan C Zhang J Cao J Chen J Qiu Y Tai J Chen Z Qiu XM Zhao TL Cheng

Nature Communications2023
Co-VAE: Drug-target binding affinity prediction by co-regularized variational autoencoders

T Li XM Zhao L Li

IEEE Pattern Analysis and Machine Intelligence2022
metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies

S Lai S Pan C Sun L.P Coelho WH Chen XM Zhao

Genome Biology2022
Cellular transcriptional alterations of peripheral blood in Alzheimer’s disease

L Song YT Yang Q Guo XM Zhao

BMC Medicine2022
Longer screen time utilization is associated with the polygenic risk for Attention-deficit/hyperactivity disorder with mediation by brain white matter microstructure

A Yang ET Rolls G Dong J Du Y Li J Feng W Cheng XM Zhao

EBioMedicine2022
Impaired type I interferon signaling activity implicated in the peripheral blood transcriptome of preclinical Alzheimer's disease

L Song J Chen C-Y Lo Q Guo J Feng XM Zhao

EBioMedicine2022
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments

S Pan C Zhu XM Zhao Coelho LP

Nature Communications2022
Disrupted long-range gene regulations elucidate shared tissue-specific mechanisms of neuropsychiatric disorders

J Chen L Song A Yang G Dong XM Zhao

Molecular psychiatry2022
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison

D Dai J Zhu C Sun M Li J Liu S Wu K Ning LJ He XM Zhao WH Chen

Nucleic Acids Research2022
mBodyMap: a curated database for microbes across human body and their associations with health and diseases

H Jin G Hu C Sun Y Duan Z Zhang Z Liu XM Zhao WH Chen

Nucleic Acids Research2022
Towards the biogeography of prokaryotic genes

L.P Coelho R Alves Río, Á. R Del P. N Myers C. P Cantalapiedra J Giner-Lamia T. S Schmidt D. R Mende A Orakov I Letunic F Hildebrand T Van Rossum S. K Forslund S Khedkar O.M Maistrenko S Pan L Jia P Ferretti S Sunagawa XM Zhao H.B Nielsen J Huerta-Cepas P Bork

Nature2021
Identifying age-specific gene signatures of the human cerebral cortex with joint analysis of transcriptomes and functional connectomes

X Zhao J Chen P Xiao J Feng Q Nie XM Zhao

Briefings in Bioinformatics2021
A Global Overview of Genetically Interpretable Multimobidities among Common Diseases in the UK Biobank

G Dong J Feng F Sun J Chen XM Zhao

Genome Medicine2021
Treatment regimens may compromise gut-microbiome-derived signatures for liver cirrhosis

S Wu P Jiang XM Zhao WH Chen

Cell metabolism2021
A 12-genus bacterial signature identifies a group of severe autistic children with differential sensory behavior and brain structures

K Shi L Zhang J Yu Z Chen S Lai X Zhao WG Li Q Luo W Lin J Feng J P Bork XM Zhao F Li

Clinical and translational medicine2021
STAB: a spatio-temporal cell atlas of the human brain

L Song S Pan Z Zhang L Jia WH Chen XM Zhao

Nucleic Acids Research2021
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements

S Lai L Jia B Subramanian S Pan J Zhang Y Dong WH Chen XM Zhao

Nucleic Acids Research2021
OGEE v3: Online GEne essentiality database with increased coverage of organisms and human cell lines

S Gurumayum P Jiang X Hao TL Campos ND Young PK Korhonen RB Gasser P Bork XM Zhao L He WH Chen

Nucleic Acids Research2021
HISP: a hybrid intelligent approach for identifying directed signaling pathways

XM Zhao S Li

Journal of Molecular Cell Biology2017
Integrative analysis of mutational and transcriptional profiles reveals driver mutations of metastatic breast cancers

JH Lee XM Zhao I Yoon JY Lee NH Kwon YY Wang KM Lee MJ Lee J Kim HG Moon Y In JK Hao KM Park DY Noh W Han S Kim

Cell Discovery2016
PPIM: A protein-protein interaction database for maize

G Zhu A Wu XJ Xu PP Xiao L Lu J Liu Y Cao L Chen J Wu XM Zhao

Plant Physiology2016
The drug cocktail network

KJ Xu J Song XM Zhao

BMC Systems Biology2012
Prediction of drug combinations by integrating molecular and pharmacological data

XM Zhao M Iskar G Zeller M Kuhn V van Noort P Bork

PLoS Computational Biology2011
A systems biology approach to identify effective cocktail drugs

Z Wu XM Zhao L Chen

BMC Systems Biology2010
A discriminative approach for identifying domain-domain interactions from protein-protein interactions

XM Zhao L Chen K Aihara

Proteins2010
Uncovering signal transduction networks from high-throughput data by integer linear programming

XM Zhao RS Wang L Chen K Aihara

Nucleic Acids Research2008
Gene function prediction using labeled and unlabeled data

XM Zhao Y Wang LN Chen K Aihara

BMC Bioinformatics2008

友情链接： Aihara Group Kim Group Bork Group Chen Lab Gerstein Lab