• Center Overview Members Analytical
  Capabilities Network
  Coordination

CDMC Analytical Capabilities

• Method
  Development
• Pipeline
  Development
• System
  Biology
• Metabolomics
   
• Infrastructure
  Development

 

Method Development

A comprehensive computational workflow for the integrative analyses of single-cell RNA-seq (scRNA-seq) and ATAC-seq (scATAC-seq) data from multiple platforms.

 

 

 

 

 

Integrative Analyses of Single-cell Transcriptome and Regulome using MAESTRO. Genome Biology 2020, 21: 198

 

Pipeline Development

Rcwl and RcwlPipelines: R and Bioconductor toolchain for bioinformatics tools and workflows.

 

 

 

Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines. Bioinformatics, 2021, 37(19), 3351
See also RCWL

 

System Biology

Pathway Topological and co-relation analyses.

 

 

 

 

 

 

 

BayesNetBP: An R Package for Probabilistic Reasoning in Bayesian Networks. Journal of Statistical Software 2020; 94(3)

Metabolic adaptation of ovarian tumors in patients treated with an IDO1 inhibitor constrains antitumor immune responses. Science Translational Medicine 2022;14(636).

 

Metabolomics

Metabolomics analysis and multi-omics integration.

 

 

 

 

 

 

 

Hypoxic activation of PFKFB4 in breast tumor microenvironment shapes metabolic and cellular plasticity to accentuate metastatic competence. Cell Rep 2022; 41(10).

Altered acetyl-CoA metabolism presents a new potential immunotherapy target in the obese lung microenvironment. Cancer Metab 2022; 10(1).

JAZF1: A Metabolic Regulator of Sensitivity to a Polyamine-Targeted Therapy. Mol Cancer Res 2023;21(1).

 

Infrastructure Development

The SingleCellExperiment class and data container stores multifaceted large-scale data and enables interoperability across Bioconductor packages.

 

 

 

 

Orchestrating Single-Cell Analysis with Bioconductor. Nature Methods, 2020, 17 (2): 137-145