Skip to main content

Fridley Lab

About the Lab

The Fridley lab is focused on the development of novel statistical and bioinformatic methods to answer questions that arise in cancer and pediatric research. Recently, the lab has been working on analytical methods and software for understanding the spatial architecture of the tumor immune microenvironment and how this is related to clinical outcomes by leveraging the information in single-cell protein (funded by a NIH/NCI R01 CA279065) and spatial transcriptomic (funded by a NIH/NCI U01 CA274489) experiments. 

In addition to analytical methods and software development, the Fridley Lab (in collaboration with other labs) are working on projects studying the Tumor Microenvironment of ovarian cancer and pediatric cancers, including Ewing Sarcoma (Masonic Cancer Alliance Grant).  

A list of recent software developed by the Fridley Lab is provided below in addition to the Lab’s GitHub page. 

  • BTIME (Bayesian Hierachical Models for Single-Cell Protein Data): an R package to fit Bayesian Hierachical beta-binomial models for modeling immune cell population with predictors/exposures. Options for different covariances/relationship structures between cell population are able to be modeled. Lead Developer: Dr. Chase Sakitis. 
  • iTIME (interactive Tumor Immune MicroEnvironment): a shiny application that creates interactive figures for examining spatial organization of individual tumors and provides basic spatial and summary information. Lead Developer: Dr. Alex Soupir    
  • spatialTIME: R package for visualizing and analyzing single-cell protein data for studying the tumor immune microenvironment (TIME).  Lead Developer: Dr. Alex Soupir  
  • spatialGE: R package that provides visualizations and quantification of the tumor microenvironment heterogeneity through gene expression surfaces, spatial heterogeneity statistics that can be compared against clinical information, spot-level cell deconvolution and spatially informed clustering, all using a new data object to store data and resulting analyses simultaneously. Lead Developer: Dr. Oscar Ospina  
  • spatialGE web application: Using the spatialGE R package, a web application was developed to enable non-computational investigators to explore their spatial transcriptomic data. Lead Developers: Dr. Oscar Ospina, Roberto Manjarres-Betancur
  • NB.Mclust: R package for Negative binomial model-based clustering of RNA-seq data. Lead Developer: Dr. Qian Li 
  • IntNMF: R package for Integrative clustering of multiple genomic datasets with non-negative matrix factorization (NMF). Lead Developer: Dr. Prabhakar Chalise  
  • InterSIM: R package for Simulation of Inter-Related Genomic/Molecular Datasets. Lead Developer: Dr. Prabhakar Chalise  

Leader

Brooke Fridley, PhD, is the Division Director for Health Services & Outcomes Research in the Department of Pediatrics. She is also the Associate Chair for Research for the Department of Pediatrics and Director of the Biostatistics & Computational Biology Core. She holds the Stanley H. Durwood Endowed Chair for Health Outcomes and is Professor of Pediatrics at University of Missouri-Kansas City.  

Dr. Fridley's career is distinguished by her expertise in biostatistical and statistical genomics. Her laboratory is dedicated to developing innovative analytical methods to address complex challenges encountered in biomedical research, particularly in oncology. Currently, her lab is developing new computational methods and software for the analysis of data from spatial transcriptomic and proteomic technologies. She also has significant experience as a collaborative biostatistician, particularly in cancer epidemiology, cancer genomics, statistical genetics, pharmacogenomics and oncology-based clinical trials.

With more than 300 publications, Dr. Fridley has served as Principal Investigator or Multiple Principal Investigator on five NIH research grants and has co-led an NIH/NCI T32 training grant in cancer biology and data science. She has also contributed as Co-Investigator to numerous NIH research grants, program project grants and center grants. Throughout her career, Dr. Fridley has provided mentorship to graduate students, postdoctoral fellows, staff members and faculty, reflecting her commitment to advancing the field through research and education.

Before joining Children’s Mercy, Dr. Fridley was the Chair of the Department of Biostatistics and Bioinformatics and the Scientific Director of Biostatistics and Bioinformatics Shared Resource at the Moffitt Cancer Center. Prior to that, she was the Director of Biostatistics and Informatics Shared Resource at University of Kansas Cancer Center and the Site Director for K-INBRE (Kansas Idea Network of Biomedical Research Excellence) Bioinformatics Core at the University of Kansas Medical Center. She also has served as faculty at the Mayo Clinic in Rochester, MN. Dr. Fridley received her MS and PhD in Statistics from Iowa State University.

Labs and Research Teams menu
Headshot of Brooke Fridley, PhD
Brooke Fridley, PhD

Stanley H. Durwood Foundation Endowed Chair in Health Outcomes; Division Director, Health Services & Outcomes Research (HSOR); Director, Biostatistics and Computational Biology Core (BCB); Associate Chair for Research, Department of Pediatrics; Professor of Pediatrics, University of Missouri-Kansas City School of Medicine

Children's Mercy
Children’s Mercy Research Institute
Research Areas
Labs and Research Teams
Fridley Lab