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Tissue heterogeneity and clonal evolution

• Single Cell
  • : sample size estimation to powerfully detect cell abundance changes in a case-control study using single-cell assays
  • Single-Cell Multiomics Analysis
    • : integrating datasets obtained from different technologies including scRNA-seq, scATAC-seq, spatial omics and CyTOF
    • : SNV detection/imputation from scRNA-seq, snATAC-seq data.
    • : selecting most informative features/genes/proteins in a single-cell dataset.
  • Single-Cell Pathway Analysis: : probe the coordinated expression of a geneset in a single cell-population
    
  • Single-Cell DNA Analysis
    • : Variant detection from single-cell DNA sequencing data
    • Single cell lineage inference
      • , phylogenetic tree from somatic mutations detected in single cell DNA
      • , phylogenetic tree from somatic copy number alterations detected in single cell DNA
  • Single-Cell RNA Analysis
    • Cell-type/signature characterization
      • , cell-type specific marker
    • Developmental/temporal inference
      • , latent periodic process (e.g., cell cycle, EMT, circadian rhythm) inference
  • Single-Cell Proteomics
    • : reduce spillover noise in CyTOF data
• Tissue deconvolution
  • , joint autologous bulk tumor DNA/RNA-seq allelic expression profiling, designated as a tool

Human Genomics

• Genomic Structural Variation
  • Identification of structural variants from the next generation sequencing (NGS) data
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  • Identification of structural variants from the single molecule (PacBio) sequencing data
  • Detection of somatic single nucleotide variants and small indels in NGS cancer genomes
    • Detection of somatic SNVs and Indels from PCR targeted Sanger sequencing data

Transcriptomics

• Detection of gene fusions from paired end whole-transcriptome RNA-seq data
• Integrative fusion/genomic breakpoint identification from DNA and RNA sequencing data

Functional Genomics

• Cancer driver mutation annotation
• Multi-level Variant annotation
  • , , forward/reverse genomic/transcriptome/proteome