Gilchrist A, Au C, Hiding J, Bell A, Fernandez-Rodriguez J, Lesimple S, Nagaya H, Roy L, Calafell S, Hallett M, Paiement J, Kearney RE, Nilsson T, Bergeron J (2006) Quantitative proteomics yields insight into the secretory pathway of rat liver. Cell 127(6):1265-81.PMID:17174899.

Finak G, Sadekov S, Pepin F, Hallett M, Meterissian S, Halwan F, Khetani K, Souleimanova M, Zabolotny B, Omeroglu A, Park M (2006) Gene expression signatures of morphologically normal breast tissue identify basal-like tumors. Breast Cancer Research 8(5):R58. PMID: 17054791.

Scott M, Oomen R, Thomas D Y, Hallett M (2006) Predicting the sub cellular localization of viral proteins within a mammalian host cell. Virology Journal 3:24.PMID:16595001.

Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott M, Hallett M, Gromolini AO, Morris Q, Hughes T, Rossan J, Frey B, Emili A (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125(1):173-86. PMID: 16615898.

Haston C, Cory S, Lafontaine L, Dorion G, Hallett M (2006) Strain-dependent pulmonary gene expression profiles of a cystic fibrosis mouse model. Physiological Genomics 25(2):336-45. PMID: 16614460.

Lee P, Ge B, Greenwood C M T, Sinnett D, Fortin Y, Brunet, S, Fortin A, Takane M, Skamene E, Pastinen T, Hallett M, Hudson T J, Sladek R (2006) Mapping cis-acting regulatory variation in recombinant congenic strains. Physiological Genomics 25(2):294-302. PMID: 16449383.

Dujmovic V, Fellows MR, Hallett M, Kitching M, Liotta G, McCartin C, Nishimura N, Ragde P, Rosamond FA, Suderman M, Whitesides S, Wood DR (2006) A Fixed-Parameter Approach to 2-Layer Planarization. Algorithmica 45 (2): 159-182

Perkins T, Hallett M, Glass L (2006) Dynamical properties of model gene networks and implications for the inverse problem. BioSystems 84(2):115-23. PMID: 16386356. Scott M, Calafell S, Thomas D Y, Hallett M (2005) Refining subcellular localization. PLOS Computational Biology 1(6):e66.PMID:16322766.

Finak G, Godin N, Pepin F, Rajabi, Z, Srivastava V, Tang Z, Hallett M (2005) BIAS: Bioinformatics Integrated Application Software Bioinformatics 21(8):1745-6 PMID:15572471.

Haston C, Tomko T, Godin N, Kerckhoff L, Hallett M (2005) Murine candidate bleomycin-induced pulmonary fibrosis susceptibility genes identified by gene expression and sequence analysis of linkage regions. Journal of Medical Genetics 42(6):464-73. PMID: 15937080.

Scott, M, Perkins T, Bunnell  S, Pepin F, Thomas D, Hallett M (2005) Identifying regulatory subnetworks for a set of genes. Molecular and Cellular Proteomics 4(5):683-92. PMID: 15722371.

Scott M, Thomas D, Hallett M (2004) Predicting Subcellular Localization via Protein Motif Co-occurrence. Genome Research 14(10A):1957-66. PMID: 15466294.

Perkins T, Hallett M, Glass L (2004) Inferring logical models of gene expression dynamics. Journal of Theoretical Biology 230(3):289-99. PMID: 15302539.

Smith K, Hallett M (2004) Towards Quality Control in DNA Microarrays. Journal of Computational Biology 11(5):945-70. PMID: 15700411.

Scott M, Lu G, Hallett M, Thomas DY (2004) The Hera database and its use in the characterization of endoplasmic reticulum proteins. Bioinformatics 20(6):937-44. PMID: 14751973.

Hallett M, Lagergren L, Tofigh A (2004) Simulateous Identification of Gene Duplication and Horizontal Transfer Events. RECOMB, April, San Diego.

Addario-Berry L, Chor B, Hallett M, Lagergren J, Panconesi A, Wareham T (2004) Ancestral maximum likelihood of evolutionary trees is hard. Journal of Bioinformatics and Computational Biology 2(2):257-71. PMID: 15297981.