Dr. Patrick Zhao's Laboratory

The Zhao lab develops innovative bioinformatics methods, web servers, and biological databases to facilitate fundamental and applied life science research. The team applies computer and information science, statistical pattern recognition, artificial intelligence (AI), and machine learning (ML) technologies to study genome annotation, gene expression and regulation, sequence-structure-function relationship, and applications such as genomic prediction for plant breeding.

Research emphasis: Project areas:

List of published online tools, web servers, and digital resources:

Web Servers
psRNATarget A plant small RNA target analysis server PMID: 29718424, 21622958
pssRNAit A web server for designing effective and specific plant siRNAs with genome-wide off-target assessment PMID: 32651189
GWASPRO A high-performance genome-wide association analysis server PMID: 30508039
PIP_SNP Pipelines for Preprocessing Genotyped SNP Data Featured as LD Bin Mapping, Missing Genotype Imputing, and LD Bin Marker Synthesizing PMID: 34235432
KMC1D * A GPU-empowered parallel computing pipeline for main effect (1D) Kinship matrix calculation PMID: 33575561
KMC2D * A GPU-empowered parallel computing pipeline for epistatic effect (2D) Kinship matrix calculation PMID: 33575561
PATOWAS A pipeline for trait analysis in 'ome'-wide association studies PMID: 30272029
MAD-HiDTree Distinguishing HapMap accessions through recursive set partitioning in hierarchical decision trees PMID: 33613609
PlantTFcat An online plant transcription factor and transcriptional regulator categorization and analysis tools PMID: 24219505
PEPIS A pipeline for estimating epistatic effect in linkage mapping and genome-wide association studies PMID: 27224861
TrSSP Prediction of membrane transport proteins and their substrate specificities using primary sequence information PMID: 24968309
DeGNServer Deciphering genome-scale gene-gene interaction network through high performance reverse engineering analysis PMID: 24328032
GPLEXUS GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data PMID: 24178033
AtSubP The Arabidopsis subcellular localization prediction server PMID: 20647376
Online tools
AffyMap Affymetrix probe-set mapping tool  
GMEF Genotype marker extraction and filtering  
MPlot An Online Tool drawing Manhattan Plot  
QQPlot QQ-plot generator  
LegumeIP LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes PMID: 33166388, 26578557, 22110036
HRGRN A Graph search-empowered integrative database of Arabidopsis signaling transduction, metabolism and gene regulation networks PMID: 26657893
MtSSPdb The Medicago truncatula small secreted peptide database PMID: 32079733
Puccinia novopanici A genomic data resource for Puccinia novopanici PMID: 31050598
PvGEA Common Beam Gene Expression Atlas and Network Analysis PMID: 25283805
TrichOME A comparative 'omics' database for plant trichome PMID: 19939948
MPP Phenylpropanoids and plant defense -- an updated genomic perspective PMID: 21029326
Manuscript Resources
MPageRank Mining functional modules in heterogeneous biological networks using multiplex PageRank approach PMID: 27446133
MET-XAlign A metabolite cross-alignment tool for LC-MS based comparative metabolomics PMID: 26247233
MET-COFEA A liquid chromatography/mass spectrometry data processing platform for metabolite compound feature extraction and annotation PMID: 24856452
MET-COFEI A novel gas chromatography-mass spectrometry data Processing platform for metabolite compound feature extraction and identification  

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