A clustering approach for estimating parameters of a profile hidden Markov model. - Rosa Aghdam; Hamid Pezeshk; Seyed Amir Malekpour; Soudabeh Shemehsavar; Changiz Eslahchi (Int. J. Data Min. Bioinform., 2013)

PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities. - Seyed Amir Malekpour; Hamid Pezeshk; Mehdi Sadeghi (BMC Bioinform., 2017)

Modeling the probability distribution of the bacterial burst size via a game-theoretic approach. - Seyed Amir Malekpour; Parsa Pakzad; Mohammad-Hadi Foroughmand-Araabi; Sama Goliaei; Ruzbeh Tusserkani; Bahram Goliaei; Mehdi Sadeghi (J. Bioinform. Comput. Biol., 2018)

LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks. - Seyed Amir Malekpour; Amir Reza Alizad-Rahvar; Mehdi Sadeghi (BMC Bioinform., 2020)

wpLogicNet: logic gate and structure inference in gene regulatory networks. - Seyed Amir Malekpour; Maryam Shahdoust; Rosa Aghdam; Mehdi Sadeghi (Bioinform., 2023)

Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms. - Seyed Amir Malekpour; Laleh Haghverdi; Mehdi Sadeghi (Briefings Bioinform., 2024)