- Wang, Z., K. Kin, F. López-Giráldez, H. Johannesson, and J. P. Townsend, 2012. Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics and Biology 49: 533-543.
- Wang, Z., N. Lehr, F. Trail, and J. P. Townsend, 2012. Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. Fungal Genetics and Biology 49(5): 405-413.
- Zhang, Z., and J.P. Townsend, 2009. Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS Computational Biology 5(6): e1000421.
- Landry, C.R., J.P. Townsend, D.L. Hartl and D. Cavalieri, 2006. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 15: 575-591.
- Kasuga, T., J.P. Townsend, C. Tian, L.B. Gilbert, G. Mannhaupt, J.W. Taylor, and L.N. Glass, 2005. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research 33(20): 6469-6485.
- Townsend, J.P., 2004. Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. BMC Bioinformatics 5: 54. Simulated ratios:
- Townsend, J.P., D. Cavalieri, and D.L. Hartl. 2003. Population genetic variation in genome-wide gene expression in wine yeasts. Molecular Biology and Evolution 20 (6): 955-963.
- Townsend, J.P., and D.L. Hartl. 2002. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biology 3 (12): research0071.1-0071.16.
- Cavalieri, D., J.P. Townsend, and D.L. Hartl, 2000. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proceedings of the National Academy of Sciences 97: 12369-12374.