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)

The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer. - Rosa Aghdam; Taban Baghfalaki; Pegah Khosravi; Elnaz Saberi Ansari (Genom. Proteom. Bioinform., 2017)

Some node ordering methods for the K2 algorithm. - Rosa Aghdam; Vahid Rezaei Tabar; Hamid Pezeshk (Comput. Intell., 2019)

A neural network-based method for polypharmacy side effects prediction. - Raziyeh Masumshah; Rosa Aghdam; Changiz Eslahchi (BMC Bioinform., 2021)

Using informative features in machine learning based method for COVID-19 drug repurposing. - Rosa Aghdam; Mahnaz Habibi; Golnaz Taheri (J. Cheminformatics, 2021)

Human Limits in Machine Learning: Prediction of Plant Phenotypes Using Soil Microbiome Data. - Rosa Aghdam; Xudong Tang; Shan Shan; Richard Lankau; Claudia R. Solís-Lemus (CoRR, 2023)

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

GAEM: Genetic Algorithm based Expectation-Maximization for inferring Gene Regulatory Networks from incomplete data. - Parisa Niloofar; Rosa Aghdam; Changiz Eslahchi (Comput. Biol. Medicine, 2024)

MiNAA: Microbiome Network Alignment Algorithm. - Reed Nelson; Rosa Aghdam; Claudia R. Solís-Lemus (J. Open Source Softw., 2024)

Human limits in machine learning: prediction of potato yield and disease using soil microbiome data. - Rosa Aghdam; Xudong Tang; Shan Shan; Richard Lankau; Claudia R. Solís-Lemus (BMC Bioinform., 2024)

AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides. - Amin Darabi; Sayeh Sobhani; Rosa Aghdam; Changiz Eslahchi (BMC Bioinform., 2024)

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data. - Evan Gorstein; Rosa Aghdam; Claudia R. Solís-Lemus (PLoS Comput. Biol., 2025)