Author

Hatice Yücel

The Netherlands Cancer Institute

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genetics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Assay:ATAC-seq· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Bas van SteenseliD· 2 shared Vinícius H. Franceschini-SantosiD· 2 shared Carlos G. Urzúa-TraslaviñaiD· 1 shared Celia Hermana-Garcia-Agullo· 1 shared Emile E. VoestiD· 1 shared Jérémie BredaiD· 1 shared Jeroen de RidderiD· 1 shared Lucía Barbadilla-Martínez· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 38 mutual co-author links

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2 shared papersGenomics

Bas van SteenselORCID

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2 papers

Recent·Most cited

Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays

Max Trauernicht, Vinícius H. Franceschini-Santos, Hatice Yücel, Teodora Filipovska, Bas van Steensel

This study compares ATAC-seq-based estimates of transcription factor activity with multiplexed reporter assays across perturbations, finding overlap but also discrepancies in their sensitivity to different TF types.

Molecular Systems Biology · Aug 17, 2026Peer-reviewedGenomics

The regulatory grammar of human promoters uncovered by MPRA-trained deep learning

Lucía Barbadilla-Martínez, Noud H.M. Klaassen, Vinícius H. Franceschini-Santos, Jérémie Breda, Miguel Hernández-Quiles, Tijs van Lieshout, Carlos G. Urzúa-Traslaviña, Hatice Yücel, Minh Chau Luong Boi, Celia Hermana-Garcia-Agullo, Sebastian Gregoricchio, Wilbert T. Zwart, Emile E. Voest, Lude Franke, Michiel Vermeulen, , Bas van Steensel

This paper introduces PARM, a deep learning model trained on MPRA data to predict human promoter activity and identify TF binding preferences, revealing positional and functional differences in regulatory grammar.

bioRxiv · Jul 9, 2024 · PreprintGenetics