Author

Doruk Cakmakci

McGill UniversityORCID 0000-0002-7626-7647Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Assay:ATAC-seq· 1 Research Focus:cell type annotation· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Assay:metabolomics· 1

Frequent Co-Authors

A. Ercüment ÇiçekiD· 1 shared Anjali ChawlaiD· 1 shared Caroline BundiD· 1 shared Corina NagyiD· 1 shared Dariusz ŻurawekiD· 1 shared Deborah C. MashiD· 1 shared Gabriella FrosiiD· 1 shared Gary Gang Chen· 1 shared

Activity by Year

2023-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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1 shared paperBioinformatics

A. Ercüment ÇiçekORCID

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2 papers

Recent·Most cited

Differential Chromatin Architecture and Risk Variants in Deep Layer Excitatory Neurons and Grey Matter Microglia Contribute to Major Depressive Disorder

Anjali Chawla, Doruk Cakmakci, Laura M. Fiori, Wenmin Zang, Malosree Maitra, Jennie Yang, Dariusz Żurawek, Gabriella Frosi, Reza Rahimian, Haruka Mitsuhashi, Maria Antonietta Davoli, Ryan Denniston, Gary Gang Chen, Volodymyr Yerko, Deborah C. Mash, , Gustavo Turecki

This study identifies differential chromatin architecture and risk variants in specific brain cell types associated with major depressive disorder.

Nature Genetics · Aug 1, 2025Peer-reviewedGenomics

PiDeel: Pathway-informed deep learning model for survivalanalysis and pathological classification of gliomas

Gün Kaynar, Doruk Cakmakci, Caroline Bund, Julien Todeschi, Izzie Jacques Namer, A. Ercüment Çiçek

PiDeeL improves survival analysis and pathological classification of gliomas by integrating pathway information into a deep learning model, achieving better performance metrics than existing methods.

Bioinformatics · Nov 1, 2023Peer-reviewedBioinformatics