Fengzhu Sun

Latest

• DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses
• Identifying group-specific sequences for microbial communities using long k-mer sequence signatures
• COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
• Comparison of metatranscriptomic samples based on k-tuple frequencies
• Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks
• Computational methods for the analysis of tag sequences in metagenomics studies
• Modeling RNA degradation for RNA-Seq with applications
• Accurate genome relative abundance estimation based on shotgun metagenomic reads
• Bayesian models and Gibbs sampling strategies for local graph alignment and motif identification in stochastic biological networks
• Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy
• Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations
• An integrated approach to the prediction of domain-domain interactions
• An integrative approach for causal gene identification and gene regulatory pathway inference
• Diffusion kernel-based logistic regression models for protein function prediction
• Further understanding human disease genes by comparing with housekeeping genes and other genes
• Network motif identification in stochastic networks
• Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy
• Assessment of the reliability of protein-protein interactions using protein localization and gene expression data
• HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms
• Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies
• Mapping gene ontology to proteins based on protein--protein interaction data
• Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data
• A dynamic programming algorithm for haplotype block partitioning
• Inferring domain-domain interactions from protein-protein interactions
• Prediction of protein function using protein-protein interaction data