Publications
,CTFacTomo: Reconstructing 3D spatial structures of RNA tomography transcriptomes by collapsed tensor factorization
,Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs
,Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition
,A ventriculomegaly feature computational pipeline to improve the screening of normal pressure hydrocephalus on CT
,Structural neuroimaging markers of normal pressure hydrocephalus versus Alzheimer’s dementia and Parkinson’s disease, and hydrocephalus versus atrophy in chronic TBI—a narrative review
,Orchard: building large cancer phylogenies using stochastic combinatorial search
,GNTD: reconstructing spatial transcriptomes with graph-guided neural tensor decomposition informed by spatial and functional relations
,Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network
,Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion
,Scalable label propagation for multi-relational learning on the tensor product of graphs
,Efficient sequencing, assembly, and annotation of human KIR haplotypes
,Accurate and efficient KIR gene and haplotype inference from genome sequencing reads with novel K-mer signatures
,A large-scale comparative study of isoform expressions measured on four platforms
,Hierarchical canonical correlation analysis reveals phenotype, genotype, and geoclimate associations in plants
,A detailed view of KIR haplotype structures and gene families as provided by a new motif-based multiple sequence alignment
,Machine learning and statistical methods for clustering single-cell RNA-sequencing data
,Platform-integrated mRNA isoform quantification
,Path segmentation for movement trajectories with irregular sampling frequency using space-time interpolation and density-based spatial clustering
,mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control
,Scalable remote homology detection and fold recognition in massive protein networks
,Learning a low-rank tensor of pharmacogenomic multi-relations from biomedical networks
,Obesity-induced protein carbonylation in murine adipose tissue regulates the DNA-binding domain of nuclear zinc finger proteins
,An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response
,Vasodilator-stimulated phosphoprotein promotes liver metastasis of gastrointestinal cancer by activating a $\beta$1-integrin-FAK-YAP1/TAZ signaling pathway
,HRB2 and BBX21 interaction modulates Arabidopsis ABI5 locus and stomatal aperture
,A multitask clustering approach for single-cell RNA-seq analysis in recessive dystrophic epidermolysis bullosa
,DARPP-32 and t-DARPP promote non-small cell lung cancer growth through regulation of IKK$\alpha$-dependent cell migration
,Transfer learning across ontologies for phenome-genome association prediction
,Dropout prediction in home care training
,Revealing complete complex KIR haplotypes phased by long-read sequencing technology
,Detecting population-differentiation copy number variants in human population tree by sparse group selection
,Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development
,Network-based machine learning and graph theory algorithms for precision oncology
,Estimating KIR haplotype frequencies on a cohort of 10,000 individuals: a comprehensive study on population variations, typing resolutions, and reference haplotypes
,Meta-analysis of EMT datasets reveals different types of EMT
,Predicting small group accretion in social networks: A topology based incremental approach
,TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer
,Network-based phenome-genome association prediction by bi-random walk
,mRNA 3′-UTR shortening is a molecular signature of mTORC1 activation
,Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments
,Network-based isoform quantification with RNA-seq data for cancer transcriptome analysis
,SubPatCNV: approximate subspace pattern mining for mapping copy-number variations
,Platinum-sensitive recurrence in ovarian cancer: the role of tumor microenvironment
,Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers
,Network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment
,Transfer learning across cancers on DNA copy number variation analysis
,A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum
,Co-clustering phenome-genome for phenotype classification and disease gene discovery
,Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum
,Prediction of novel systems components in cell cycle regulation in malaria parasite by subnetwork alignments
,Global linear neighborhoods for efficient label propagation
,Prioritizing disease genes by bi-random walk
,Signed network propagation for detecting differential gene expressions and DNA copy number variations
,Approximate subspace pattern mining for mapping copy-number variations
,Sparse group selection on fused lasso components for identifying group-specific DNA copy number variations
,Inferring disease and gene set associations with rank coherence in networks
,Proteases in malaria parasites-a phylogenomic perspective
,A heterogeneous label propagation algorithm for disease gene discovery
,Network propagation models for gene selection
,Launching: university partnership for health informatics
,Subspace differential coexpression analysis: problem definition and a general approach
,Integrative classification and analysis of multiple arrayCGH datasets with probe alignment
,A hypergraph-based learning algorithm for classifying arraycgh data with spatial prior
,Learning random-walk kernels for protein remote homology identification and motif discovery
,Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel
,Partial profile alignment kernels for protein classification
,A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge
,Integrative biomarker discovery for breast cancer metastasis from gene expression and protein interaction data using error-tolerant pattern mining
,Robust and efficient identification of biomarkers by classifying features on graphs
,Learning on weighted hypergraphs to integrate protein interactions and gene expressions for cancer outcome prediction
,SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition
,Protein ranking by semi-supervised network propagation
,Identifying remote protein homologs by network propagation
,Profile-based string kernels for remote homology detection and motif extraction
,Motif-based protein ranking by network propagation
,Fast string kernels using inexact matching for protein sequences
,Inexact matching string kernels for protein classification
,Protein backbone angle prediction with machine learning approaches
,Fast kernels for inexact string matching