Author

A. Ercument Cicek

Bilkent University

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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Bioinformatics· 2 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Organism:human· 2 Research Focus:protein structure prediction· 2 Approach:benchmark study· 1 Assay:bulk RNA-seq· 1 Assay:CUT&Tag· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Helyasadat Hashemi Aghdam· 2 shared Sobhan Shukueian Tabrizi· 2 shared Aaron Topol· 1 shared Andrew Browne· 1 shared Andrew Chess· 1 shared Ben ReadheadiD· 1 shared Benjamin A Logsdon· 1 shared Bin Zhang· 1 shared

Activity by Year

2016-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersBioinformatics

Helyasadat Hashemi Aghdam

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3 papers

Recent·Most cited

RPFace: From biased structural benchmarks to generalizable RNA-protein interface prediction

Helyasadat Hashemi Aghdam, Sobhan Shukueian Tabrizi, A. Ercument Cicek

RPFace predicts RNA-protein interfaces directly from sequence, outperforming existing methods on RNA interfaces and generalizing to in vivo data without pretraining.

bioRxiv · Nov 6, 2026 · PreprintBioinformatics

RPI-Zero: Zero-shot RNA-Protein Interaction Prediction

Kerim Eren, E. Irem Esendemir, Sobhan Shukueian Tabrizi, Helyasadat Hashemi Aghdam, A. Ercument Cicek

RPI-Zero predicts RNA-protein interactions without prior data by using a sequence-only model trained on a large benchmark of CLIP experiments.

bioRxiv · Nov 5, 2026 · PreprintBioinformatics

Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia

Menachem Fromer, Panos Roussos, Solveig K Sieberts, Jessica S Johnson, David H Kavanagh, Thanneer M Perumal, Douglas M Ruderfer, Edwin C Oh, Aaron Topol, Hardik R Shah, Lambertus L Klei, Robin Kramer, Dalila Pinto, Zeynep H Gumus, A. Ercument Cicek, , Lara M Mangravit

The paper uses gene expression data from schizophrenia cases and controls to show that common variants at 20% of schizophrenia risk loci regulate brain gene expression, with functional impacts on neural progenitor cells and zebrafish neuroanatomy.

bioRxiv · May 9, 2016Genomics