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:- Advancing bioinformatics, computational biology for basic and applied plant science research.
- Advancing and deploying data science, statistical genetics, and AI/ML in prediction-based plant breeding.
- Artificial intelligence (AI)/machine learning (ML) in genomic prediction
- Genotype-phenotype (G2P) association discovery via integrative genome-scale biological network & genome-wide association analysis
- Gene expression, regulation, and network biology
- Novel gene discovery and gene function annotation
- Comparative ‘omics’ and biological database development
- Applications in systems biology of small regulatory RNAs, signaling peptides, membrane transport proteins, and enzymes involved in various aspects of plant biology
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 | |
Databases | ||
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 |