Author

Mehdi Joodaki

RWTH Aachen UniversityORCID 0000-0002-2184-7118Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Research Focus:differential expression· 3 Organism:human· 3 Assay:scRNA-seq· 3 Approach:statistical model· 3 Research Focus:clustering· 2 Research Focus:trajectory inference· 2 Research Focus:batch correction / integration· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

Christoph KuppeiD· 3 shared Ivan G. CostaiD· 3 shared James Shiniti NagaiiD· 2 shared Mina ShaiganiD· 2 shared Mingbo ChengiD· 2 shared Peter BööriD· 2 shared Rafael KramanniD· 2 shared Samaneh SamieiiD· 2 shared

Activity by Year

2019-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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3 shared papersBioinformatics

Christoph KuppeORCID

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Author profile →

4 papers

Recent·Most cited

Polyploid cardiomyocytes define disease-specific transcriptional states in the mammalian heart

Paul Kießling, Mehdi Joodaki, Daryna Pikulska, Emilia Scheidereit, Giulia Cesaro, Mayra Ruiz, Damin Kühn, Kai Peng, Osman Goni, Sebastian Foecking, Samaneh Samiei, Xian Liao, Kai Li, Zihao Feng, Delin Wang, , Christoph Kuppe

This study identifies polyploid cardiomyocytes as disease-specific transcriptional states in the mammalian heart and suggests targeting them for heart failure treatment.

bioRxiv · Feb 14, 2026 · PreprintGenomics

PILOT-GM-VAE: Patient-Level Analysis of single cell Disease Atlas with Optimal Transport of Gaussian Mixture Variational Autoencoders

Mehdi Joodaki, Mina Shaigan, Samaneh Samiei, James Shiniti Nagai, Tiago Maié, Christoph Kuppe, Ivan G. Costa

PILOT-GM-VAE analyzes single cell disease atlases to perform sample-level clustering, trajectory inference, and batch correction using Gaussian Mixture Variational Autoencoders with optimal transport.

Briefings in Bioinformatics · Aug 31, 2025Peer-reviewedBioinformatics

Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)

Mehdi Joodaki, Mina Shaigan, Victor Parra, Roman David Bülow, Christoph Kuppe, David Laurin Hölscher, Mingbo Cheng, James Shiniti Nagai, Michaël Goedertier, Nassim Bouteldja, Vladimı́r Tesař, Jonathan Barratt, Ian S D Roberts, Rosanna Coppo, Rafael Kramann, , Ivan G. Costa

PILOT uses optimal transport to analyze single-cell and pathomics data, detecting disease-associated samples and non-linear changes in cell populations and tissue structures.

Molecular Systems Biology · Dec 19, 2023Peer-reviewedBioinformatics

A scalable random walk with restart on heterogeneous networks with Apache Spark for ranking disease-causing genes using type-2 fuzzy data fusion

Mehdi Joodaki, Nasser Ghadiri, Zeinab Maleki, Maryam Lotfi Shahreza

This paper introduces RWRHN-FF, a method for ranking disease-causing genes using type-2 fuzzy data fusion on heterogeneous networks, showing improved performance over existing methods.

bioRxiv · Nov 16, 2019 · PreprintBioinformatics