PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information. - Rahul Siddharthan; Erik van Nimwegen; Eric D. Siggia (Regulatory Genomics, 2004)

PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny. - Rahul Siddharthan; Eric D. Siggia; Erik van Nimwegen (PLoS Comput. Biol., 2005)

Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. - Rahul Siddharthan (BMC Bioinform., 2006)

PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling. - Rahul Siddharthan (PLoS Comput. Biol., 2008)

Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model. - Gayathri Jayaraman; Rahul Siddharthan (BMC Bioinform., 2010)

ChIPulate: A comprehensive ChIP-seq simulation pipeline. - Vishaka Datta; Sridhar Hannenhalli; Rahul Siddharthan (PLoS Comput. Biol., 2019)

MMM and MMMSynth: Clustering of heterogeneous tabular data, and synthetic data generation. - Chandrani Kumari; Rahul Siddharthan (CoRR, 2023)