A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data. - Yang Xie; Wei Pan 011; Arkady B. Khodursky (Bioinform., 2005)

Modeling regulatory sites with higher order position-dependent weight matrices. - Hossein Zare; Mostafa Kaveh; Arkady B. Khodursky (ICASSP, 2008)

A Parametric Joint Model of DNA-Protein Binding, Gene Expression and DNA Sequence Data to Detect Target Genes of a Transcription Factor. - Wei Pan 011; Peng Wei 005; Arkady B. Khodursky (Pacific Symposium on Biocomputing, 2008)

Entropy-based analysis of ChIP-Sequencing data. - Hossein Zare; Mostafa Kaveh; Arkady B. Khodursky (GENSiPS, 2009)

Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations. - Hossein Zare; Dipen Sangurdekar; Poonam Srivastava; Mostafa Kaveh; Arkady B. Khodursky (BMC Syst. Biol., 2009)