SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis. - Carlo Colantuoni; George Henry; Scott Zeger; Jonathan Pevsner (Bioinform., 2002)

Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. - Andrew E. Jaffe; Thomas Hyde; Joel Kleinman; Daniel Weinbergern; Joshua Chenoweth; Ronald McKay; Jeffrey T. Leek; Carlo Colantuoni (BMC Bioinform., 2015)

Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. - Andrew E. Jaffe; Thomas Hyde; Joel Kleinman; Daniel R. Weinberger; Joshua Chenoweth; Ronald McKay; Jeffrey T. Leek; Carlo Colantuoni (BMC Bioinform., 2016)

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. - Genevieve L. Stein-O'Brien; Jacob L. Carey; Waishing Lee; Michael Considine; Alexander V. Favorov; Emily Flam; Theresa Guo; Sijia Li; Luigi Marchionni; Thomas Sherman; Shawn Sivy; Daria A. Gaykalova; et al. (Bioinform., 2017)

projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering. - Gaurav Sharma; Carlo Colantuoni; Loyal A. Goff; Elana J. Fertig; Genevieve L. Stein-O'Brien (Bioinform., 2020)

Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics. - Eric W. Bridgeford; Shangsi Wang; Zeyi Wang; Ting Xu 001; R. Cameron Craddock; Jayanta Dey; Gregory Kiar; William R. Gray Roncal; Carlo Colantuoni; Christopher Douville; Stephanie Noble; Carey E. Priebe; et al. (PLoS Comput. Biol., 2021)

Identifying enhancer properties associated with genetic risk for complex traits using regulome-wide association studies. - Alex M. Casella; Carlo Colantuoni; Seth A. Ament (PLoS Comput. Biol., 2022)

The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain. - Seth A. Ament; Ricky S. Adkins; Robert Carter; Elena Chrysostomou; Carlo Colantuoni; Jonathan Crabtree; Heather Huot Creasy; Kylee Degatano; Victor Felix; Peter Gandt; Gwenn a Garden; Michelle G. Giglio; et al. (Nucleic Acids Res., 2023)