Hidden Markov Chains and the Analysis of Genome Structure. - Gary A. Churchill (Comput. Chem., 1992)

Monte Carlo sequence alignment. - Gary A. Churchill (RECOMB, 1997)

Bayesian Restoration of a Hidden Markov Chain with Applications to DNA Sequencing. - Gary A. Churchill; Betty Lazareva (J. Comput. Biol., 1999)

Analysis of Variance for Gene Expression Microarray Data. - M. Kathleen Kerr; Mitchell Martin; Gary A. Churchill (J. Comput. Biol., 2000)

R/qtl: QTL Mapping in Experimental Crosses. - Karl W. Broman; Hao Wu 003; Saunak Sen; Gary A. Churchill (Bioinform., 2003)

A collaborative database of inbred mouse strain characteristics. - Stephen C. Grubb; Gary A. Churchill; Molly A. Bogue (Bioinform., 2004)

Experimental design for three-color and four-color gene expression microarrays. - Yong Woo; Winfried Krueger; Anupinder Kaur; Gary A. Churchill (ISMB (Supplement of Bioinformatics), 2005)

Estimating p-values in small microarray experiments. - Hyuna Yang; Gary A. Churchill (Bioinform., 2007)

CGDSNPdb: a database resource for error-checked and imputed mouse SNPs. - Lucie N. Hutchins; Yueming Ding; Jin P. Szatkiewicz; Randy von Smith; Hyuna Yang; Fernando Pardo-Manuel de Villena; Gary A. Churchill; Joel H. Graber (Database J. Biol. Databases Curation, 2010)

What Can Causal Networks Tell Us about Metabolic Pathways? - Rachael Hageman Blair; Daniel J. Kliebenstein; Gary A. Churchill (PLoS Comput. Biol., 2012)

Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression. - Narayanan Raghupathy; Kwangbom Choi; Matthew J. Vincent; Glen L. Beane; Keith S. Sheppard; Steven C. Munger; Ron Korstanje; Fernando Pardo-Manual de Villena; Gary A. Churchill (Bioinform., 2018)