ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. - You Jung Kim; Nikhil Teletia; Victor Ruotti; Christopher A. Maher; Arul M. Chinnaiyan; Ron M. Stewart; James A. Thomson; Jignesh M. Patel (Bioinform., 2009)

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. - Zhaohui S. Qin; Jianjun Yu; Jincheng Shen; Christopher A. Maher; Ming Hu 001; Shanker Kalyana-Sundaram; Jindan Yu; Arul M. Chinnaiyan (BMC Bioinform., 2010)

ChimeraScan: a tool for identifying chimeric transcription in sequencing data. - Matthew K. Iyer; Arul M. Chinnaiyan; Christopher A. Maher (Bioinform., 2011)

Genome Modeling System: A Knowledge Management Platform for Genomics. - Malachi Griffith; Obi L. Griffith; Scott M. Smith; Avinash Ramu; Matthew B. Callaway; Anthony M. Brummett; Michael J. Kiwala; Adam C. Coffman; Allison A. Regier; Benjamin J. Oberkfell; Gabriel E. Sanderson; Thomas P. Mooney; et al. (PLoS Comput. Biol., 2015)

INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. - Jin Zhang; Elaine R. Mardis; Christopher A. Maher (Bioinform., 2017)

PACT: a pipeline for analysis of circulating tumor DNA. - Jace Webster; Ha X. Dang; Pradeep S. Chauhan; Wenjia Feng; Alex Shiang; Peter K. Harris; Russell K. Pachynski; Aadel A Chaudhuri; Christopher A. Maher (Bioinform., 2023)