Balasubramanian, R, LaFramboise, T, Scholtens, D, and Gentleman, R (2004).
A graph theoretic approach to testing associations between disparate sources of functional genomics data.
Bioinformatics.

Carey, VJ, Gentry, J, Whalen, E, and Gentleman, R (2004).
Network structures and algorithms in Bioconductor.
Bioinformatics.

Chiaretti, S, Li, X, Gentleman, R, Vitale, A, Vignetti, M, Mandelli, F, Ritz, J, and Foa, R (2004).
Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival.
Blood 103(7):2771-8.

Gentleman, RC, Carey, VJ, Bates, DM, Bolstad, B, Dettling, M, Dudoit, S, Ellis, B, Gautier, L, Ge, Y, Gentry, J, Hornik, K, Hothorn, T, Huber, W, Iacus, S, Irizarry, R, Leisch, F, Li, C, Maechler, M, Rossini, AJ, Sawitzki, G, Smith, C, Smyth, G, Tierney, L, Yang, JY, and Zhang, J (2004).
Bioconductor: open software development for computational biology and bioinformatics.
Genome Biol 5(10):R80.

Huber, W, and Gentleman, R (2004).
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements.
Bioinformatics 20(10):1651-2.

Tengs, T, LaFramboise, T, Den, RB, Hayes, DN, Zhang, J, DebRoy, S, Gentleman, RC, O'Neill, K, Birren, B, and Meyerson, M (2004).
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments.
Nucleic Acids Res 32(15):e121.

Christopher, K, Mueller, TF, DeFina, R, Liang, Y, Zhang, J, Gentleman, R, and Perkins, DL (2003).
The graft response to transplantation: a gene expression profile analysis.
Physiol Genomics 15(1):52-64.

Dudoit, S, Gentleman, RC, and Quackenbush, J (2003).
Open source software for the analysis of microarray data.
Biotechniques Suppl:45-51.

Zhang, J, Carey, V, and Gentleman, R (2003).
An extensible application for assembling annotation for genomic data.
Bioinformatics 19(1):155-6.

Gentleman, RC, and Vandal, A (2001).
Computational Algorithms for Censored Data Problems Using
x.

Mutter, GL, Baak, JP, Fitzgerald, JT, Gray, R, Neuberg, D, Kust, GA, Gentleman, R, Gullans, SR, Wei, LJ, and Wilcox, M (2001).
Global expression changes of constitutive and hormonally regulated genes during endometrial neoplastic transformation.
Gynecol Oncol 83(2):177-85.

Gentleman, RC, Lawless, JF, Lindsey, JC, and Yan, P (1994).
Multi-state Markov models for analysing incomplete disease history data with illustrations for HIV disease.
Stat Med 13(8):805-21.

Gentleman, R, and Crowley, JJ (1992).
A graphical approach to the analysis of censored data.
Breast Cancer Res Treat 22(3):229-40.

Gentleman, R, and Crowley, J (1991).
Local full likelihood estimation for the proportional hazards model.
Biometrics 47(4):1283-96.