CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. - Adam A. Margolin; Joel Greshock; Tara L. Naylor; Yael Mosse; John M. Maris; Graham Bignell; Alexander I. Saeed; John Quackenbush; Barbara L. Weber (Bioinform., 2005)

Validation of Decision Tree Methods in Predictive Analysis of Airborne Icing Incidents. - Tanya K. Gatlin; Daniel D. Kinn; John M. Maris; An-yuan Yu; Robert W. Maxson (J. Aerosp. Inf. Syst., 2017)

QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. - Paul Deveau; Leo Colmet Daage; Derek Oldridge; Virginie Bernard; Angela Bellini; Mathieu Chicard; Nathalie Clement; Eve Lapouble; Valerie Combaret; Anne Boland; Vincent Meyer; Jean-Francois Deleuze; et al. (Bioinform., 2018)

Pan-cancer genome and transcriptome analyses of 1, 699 paediatric leukaemias and solid tumours. - Xiaotu Ma; Yu Liu; Yanling Liu; Ludmil B. Alexandrov; Michael N. Edmonson; Charles Gawad; Xin Zhou; Yongjin Li; Michael Rusch; John Easton; Robert Huether; Veronica Gonzalez-Pena; et al. (Nat., 2018)

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. - Krutika S. Gaonkar; Federico Marini 002; Komal S. Rathi; Payal Jain; Yuankun Zhu; Nicholas A. Chimicles; Miguel A. Brown; Ammar S. Naqvi; Bo Zhang 062; Phillip B. Storm; John M. Maris; Pichai Raman; et al. (BMC Bioinform., 2020)

ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery. - Alvin Farrel; Peng Li; Sharon Veenbergen; Khushbu Patel; John M. Maris; Warren J. Leonard (BMC Bioinform., 2023)

ImmunoTar - integrative prioritization of cell surface targets for cancer immunotherapy. - Rawan Shraim; Brian Mooney; Karina L. Conkrite; Amber K. Hamilton; Gregg B. Morin; Poul H. Sorensen; John M. Maris; Sharon J. Diskin; Ahmet Sacan (Bioinform., 2025)