Reproducibility of genotypes as measured by the affymetrix GeneChip® 100K Human Mapping Array set. - Brooke L. Fridley; Stephen T. Turner; Arlene B. Chapman; Andrei S. Rodin; Eric Boerwinkle; Kent R. Bailey (Comput. Stat. Data Anal., 2008)

Comparison of Methods for Meta-dimensional Data Analysis Using in Silico and Biological Data Sets. - Emily Rose Holzinger; Scott M. Dudek; Alex T. Frase; Brooke L. Fridley; Prabhakar Chalise; Marylyn D. Ritchie (EvoBIO, 2012)

Comparison of penalty functions for sparse canonical correlation analysis. - Prabhakar Chalise; Brooke L. Fridley (Comput. Stat. Data Anal., 2012)

PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data. - Nicholas B. Larson; Brooke L. Fridley (Bioinform., 2013)

InterSIM: Simulation tool for multiple integrative 'omic datasets'. - Prabhakar Chalise; Rama Raghavan 002; Brooke L. Fridley (Comput. Methods Programs Biomed., 2016)

An ensemble-based Cox proportional hazards regression framework for predicting survival in metastatic castration-resistant prostate cancer (mCRPC) patients. - Richard Meier; Stefan Graw; Joseph Usset; Rama Raghavan 002; Junqiang Dai; Prabhakar Chalise; Shellie Ellis; Brooke L. Fridley; Devin C. Koestler (F1000Research, 2016)

Subject level clustering using a negative binomial model for small transcriptomic studies. - Qian Li 023; Janelle R. Noel-MacDonnell; Devin C. Koestler; Ellen L. Goode; Brooke L. Fridley (BMC Bioinform., 2018)

GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. - Qian Li 023; Kate Fisher; Wenjun Meng; Bin Fang; Eric A. Welsh; Eric B. Haura; John M. Koomen; Steven A. Eschrich; Brooke L. Fridley; Yian Ann Chen (Bioinform., 2020)

Network-based integrative clustering of multiple types of genomic data using non-negative matrix factorization. - Prabhakar Chalise; Yonghui Ni; Brooke L. Fridley (Comput. Biol. Medicine, 2020)

spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data. - Jordan H. Creed; Christopher M. Wilson; Alex C. Soupir; Christelle M. Colin-Leitzinger; Gregory J. Kimmel; Oscar E. Ospina; Nicholas H. Chakiryan; Joseph Markowitz; Lauren C. Peres; Anna Coghill; Brooke L. Fridley (Bioinform., 2021)

spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics. - Oscar E. Ospina; Christopher M. Wilson; Alex C. Soupir; Anders Berglund; Inna Smalley; Kenneth Y. Tsai; Brooke L. Fridley (Bioinform., 2022)

Tumor immune cell clustering and its association with survival in African American women with ovarian cancer. - Christopher M. Wilson; Alex C. Soupir; Ram Thapa; Jordan H. Creed; Jonathan Nguyen; Carlos Moran Segura; Travis A. Gerke; Joellen M. Schildkraut; Lauren C. Peres; Brooke L. Fridley (PLoS Comput. Biol., 2022)

scSpatialSIM: a simulator of spatial single-cell molecular data. - Alex C. Soupir; Julia Wrobel; Jordan H. Creed; Oscar E. Ospina; Christopher M. Wilson; Brandon J. Manley; Lauren C. Peres; Brooke L. Fridley (SoftwareX, 2025)